US20210207130A1

US20210207130A1 - Methods and compositions for the making and using of guide nucleic acids

Info

Publication number: US20210207130A1
Application number: US16/995,761
Authority: US
Inventors: Stephane B. GOURGUECHON
Original assignee: ARC Bio LLC
Current assignee: ARC Bio LLC
Priority date: 2015-12-07
Filing date: 2020-08-17
Publication date: 2021-07-08
Also published as: JP2024051149A; CA3006781A1; JP2021141904A; US10787662B2; WO2017100343A1; CN109310784B; EP3386550A1; EP3386550B1; CN109310784A; AU2016365720A1; EP3386550A4; JP2018535689A; US20190270984A1; AU2016365720B2; EP3871695A1; DK3386550T3; JP6995751B2

Abstract

Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.

Description

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No. 15/742,862, filed Jan. 8, 2018, which is a U.S. National Stage Application under 35 U.S.C. § 371 of International Application No. PCT/US2016/065420, filed Dec. 7, 2016, which claims the benefit of U.S. Provisional Application No. 62/264,262, filed Dec. 7, 2015, and of U.S. Provisional Application No. 62/298,963, filed Feb. 23, 2016, each of which is hereby incorporated by reference in its entirety.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The present application is being filed with a Sequence Listing in electronic format. The content of the ASCII text file of the sequence listing named “155949-00086_Sequence_Listing.TXT” which is 797 kb in size was created on Aug. 17, 2020, and electronically submitted via EFS-Web herewith the application is incorporated herein by reference in its entirety.

BACKGROUND

Human clinical DNA samples and sample libraries such as cDNA libraries derived from RNA contain highly abundant sequences that have little informative value and increase the cost of sequencing. While methods have been developed to deplete these unwanted sequences (e.g., via hybridization capture), these methods are often time-consuming and can be inefficient.
Although a guide nucleic acid (gNA) mediated nuclease systems (such as guide RNA (gRNA)-mediated Cas systems) can efficiently deplete any target DNA, targeted depletion of very high numbers of unique DNA molecules is not feasible. For example, a sequencing library derived from human blood may contain >99% human genomic DNA. Using a gRNA-mediated Cas9 system-based method to deplete this genomic DNA to detect an infectious agent circulating in the human blood would require extremely high numbers of gRNAs (about 10-100 million gRNAs), in order to ensure that a gRNA will be present every 30-50 base pairs (bp), and that no target DNA will be missed. Very large numbers of gRNAs can be predicted computationally and then synthesized chemically, but at a prohibitively expensive cost.
Therefore, there is a need in the art to provide a cost-effective method of converting any DNA into a gNA (e.g., gRNA) library to enable, for example, genome-wide depletion of unwanted DNA sequences from those of interest, without prior knowledge about their sequences. Provided herein are methods and compositions that address this need.

SUMMARY

Provided herein are compositions and methods to generate gNAs and collections of gNAs from any source nucleic acid. For example, gRNAs and collections of gRNAs can be generated from source DNA, such as genomic DNA. Such gNAs and collections of the same are useful for a variety of applications, including depletion, partitioning, capture, or enrichment of target sequences of interest, genome-wide labeling, genome-wide editing, genome-wide functional screens, and genome-wide regulation.
In one aspect, the invention described herein provides a collection of nucleic acids, a plurality of the nucleic acids in the collection comprising: a first segment comprising a regulatory region; a second segment encoding a targeting sequence; and a third segment encoding a nucleic acid-guided nuclease system protein-binding sequence, wherein at least 10% of the nucleic acids in the collection vary in size. In another aspect, the invention described herein provides a collection of nucleic acids, a plurality of the nucleic acids in the collection comprising: a first segment comprising a regulatory region; a second segment encoding a targeting sequence, wherein the size of the second segment is greater than 21 bp; and a third segment encoding a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein. In some embodiments, the size of the second segment varies from 15-250 bp across the collection of nucleic acids. In some embodiments, at least 10% of the second segments in the collection are greater than 21 bp. In some embodiments, the size of the second segment is not 20 bp. In some embodiments, the size of the second segment is not 21 bp. In some embodiments, the collection of nucleic acids is a collection of DNA. In some embodiments, the second segment is single stranded DNA. In some embodiments, the third segment is single stranded DNA. In some embodiments, the second segment is double stranded DNA. In some embodiments, the third segment is double stranded DNA. In some embodiments, the regulatory region is a region capable of binding a transcription factor. In some embodiments, the regulatory region comprises a promoter. In some embodiments, the promoter is selected from the group consisting of T7, SP6, and T3. In some embodiments, the targeting sequence is directed at a mammalian genome, eukaryotic genome, prokaryotic genome, or a viral genome. In some embodiments, the targeting sequence is directed at repetitive or abundant DNA. In some embodiments, the targeting sequence is directed at mitochondrial DNA, ribosomal DNA, Alu DNA, centromeric DNA, SINE DNA, LINE DNA, or STR DNA. In some embodiments, the sequence of the second segments is selected from Table 3 and/or Table 4. In some embodiments, the collection comprises at least 10²unique nucleic acid molecules. In some embodiments, the targeting sequence is at least 80% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the collection comprises targeting sequences directed to sequences of interest spaced about every 10,000 bp or less across the genome of an organism. In some embodiments, the PAM sequence is AGG, CGG, or TGG. In some embodiments, the PAM sequence is specific for a CRISPR/Cas system protein selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. In some embodiments, the third segment comprises DNA encoding a gRNA stem-loop sequence. In some embodiments, the third segment encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the sequence of the third segment encodes for a crRNA and a tracrRNA. In some embodiments, the nucleic acid-guided nuclease system protein is from a bacterial species. In some embodiments, the nucleic acid-guided nuclease system protein is from an archaea species. In some embodiments, the CRISPR/Cas system protein is a Type I, Type II, or Type III protein. In some embodiments, the CRISPR/Cas system protein is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, dCas9 and cas9 nickase. In some embodiments, the third segment comprises DNA encoding a Cas9-binding sequence. In some embodiments, a plurality of third segments of the collection encode for a first nucleic acid-guided nuclease system protein binding sequence, and a plurality of the third segments of the collection encode for a second nucleic acid-guided nuclease system protein binding sequence. In some embodiments, the third segments of the collection encode for a plurality of different binding sequences of a plurality of different binding sequences of a plurality of different nucleic acid-guided nuclease system proteins.
In another aspect, the invention described herein provides for a collection of guide RNAs (gRNAs), comprising: a first RNA segment a targeting sequence; and a second RNA segment comprising a nucleic acid-guided nuclease system protein-binding sequence, wherein at least 10% of the gRNAs in the collection vary in size. In some embodiments, the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein. In some embodiments, the size of the first segment varies from 15-250 bp across the collection of gRNAs. In some embodiments, the at least 10% of the first segments in the collection are greater than 21 bp. In some embodiments, the size of the first segment is not 20 bp. In some embodiments, the size of the first segment is not 21 bp. In some embodiments, the targeting sequence is directed at a mammalian genome, eukaryotic genome, prokaryotic genome, or viral genome. In some embodiments, the targeting sequence is directed at repetitive or abundant DNA. In some embodiments, the targeting sequence is directed at mitochondrial DNA, ribosomal DNA, Alu DNA, centromeric DNA, SINE DNA, LINE DNA, or STR DNA. In some embodiments, the sequence of the first segments is RNA encoded by sequences selected from Table 3 and/or Table 4. In some embodiments, the collection comprises at least (unique gRNAs. In some embodiments, the gRNAs comprise cytosine, guanine, and adenine. In some embodiments, a subset of the gRNAs further comprises thymine. In some embodiments, a subset of the gRNAs further comprises uracil. In some embodiments, the first segment is at least 80% complementary to a target genomic sequence of interest. In some embodiments, the targeting sequence is at least 80% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments the PAM sequence is AGG, CGG, or TGG. In some embodiments, the PAM sequence is specific for a CRISPR/Cas system protein selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. In some embodiments, the second segment comprises a gRNA stem-loop sequence. In some embodiments, the third segment comprises DNA encoding a gRNA stem-loop sequence. In some embodiments, the third segment comprises the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or comprises the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the second segment comprises a crRNA and a tracrRNA. In some embodiments, the nucleic acid-guided nuclease system protein is from a bacterial species. In some embodiments, the nucleic acid-guided nuclease system protein is from an archaea species. In some embodiments, the CRISPR/Cas system protein is a Type I, Type II, or Type III protein. In some embodiments, the CRISPR/Cas system protein is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, dCas9 and cas9 nickase. In some embodiments, the second segment comprises a Cas9-binding sequence. In some embodiments, at least 10% of the gRNAs in the collection vary in their 5′ terminal-end sequence. In some embodiments, the collection comprises targeting sequences directed to sequences of interest spaced every 10,000 bp or less across the genome of an organism. In some embodiments, a plurality of second segments of the collection comprise a first nucleic acid-guided nuclease system protein binding sequence, and a plurality of the second segments of the collection comprise a second nucleic acid-guided nuclease system protein binding sequence. In some embodiments, the second segments of the collection comprise a plurality of different binding sequences of a plurality of different nucleic acid-guided nuclease system proteins. In some embodiments, a plurality of the gRNAs of the collection are attached to a substrate. In some embodiments, a plurality of the gRNAs of the collection comprise a label. In some particular embodiments, a plurality of the gRNAs of the collection comprise different labels.
In another aspect, the invention described herein provides nucleic acid comprising: a first segment comprising a regulatory region; a second segment encoding a targeting sequence, wherein the targeting sequence is greater than 30 bp; and a third segment encoding a nucleic acid encoding a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease is a CRISPR/Cas system protein. In some embodiments, the nucleic acid is DNA. In some embodiments, the second segment is single stranded DNA. In some embodiments, the third segment is single stranded DNA. In some embodiments, the second segment is double stranded DNA. In some embodiments, the third segment is double stranded DNA. In some embodiments, the regulatory region is a region capable of binding a transcription factor. In some embodiments, the regulatory region comprises a promoter. In some embodiments, the promoter is selected from the group consisting of T7, SP6, and T3. In some embodiments, the targeting sequence is directed at a mammalian genome, eukaryotic genome, prokaryotic genome, or a viral genome. In some embodiments, the targeting sequence is directed at abundant or repetitive DNA. In some embodiments, the targeting sequence is directed at mitochondrial DNA, ribosomal DNA, Alu DNA, centromeric DNA, SINE DNA, LINE DNA, or STR DNA. In some embodiments, the sequence of the second segments is selected from Table 3 and/or Table 4. In some embodiments, the targeting sequence is at least 80% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the target genomic sequence of interest is 5′ upstream of a PAM sequence. In some embodiments, the PAM sequence is specific for a CRISPR/Cas system protein selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. In some embodiments, the third segment comprises DNA encoding a gRNA stem-loop sequence. In some embodiments, the third segment comprises DNA encoding a gRNA stem-loop sequence. In some embodiments, the third segment encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the nucleic acid-guided nuclease system protein is from a bacterial species. In some embodiments, the nucleic acid-guided nuclease system protein is from an archaea species. In some embodiments, the CRISPR/Cas system protein is a Type I, Type II, or Type III protein. In some embodiments, the CRISPR/Cas system protein is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, dCas9 and cas9 nickase. In some embodiments, the third segment comprises DNA encoding a Cas9-binding sequence.
In another aspect, the invention described herein provides a guide RNA comprising a first segment comprising a targeting sequence, wherein the size of the first segment is greater than 30 bp; and a second segment comprising a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease is a CRISPR/Cas system protein. In some embodiments, the gRNA comprises an adenine, a guanine, and a cytosine. In some embodiments, the gRNA further comprises a thymine. In some embodiments, the gRNA further comprises a uracil. In some embodiments, the size of the first RNA segment is between 30 and 250 bp. In some embodiments, the targeting sequence is directed at a mammalian genome, eukaryotic genome, prokaryotic genome, or viral genome. In some embodiments, the targeting sequence is directed at repetitive or abundant DNA. In some embodiments, the targeting sequence is directed at mitochondrial DNA, ribosomal DNA, Alu DNA, centromeric DNA, SINE DNA, LINE DNA, or STR DNA. In some embodiments, the first segment is at least 80% complementary to the target genomic sequence of interest. In some embodiments, the targeting sequence is at least 80% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the second segment comprises a gRNA stem-loop sequence. In some embodiments, the sequence of the second segment comprises GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or comprises the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the sequence of the third segment comprises a crRNA and a tracrRNA. In some embodiments, the nucleic acid-guided nuclease system protein is from a bacterial species. In some embodiments, the nucleic acid-guided nuclease system protein is from an archaea species. In some embodiments, the CRISPR/Cas system protein is a Type I, Type II, or Type III protein. In some embodiments, the CRISPR/Cas system protein is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, dCas9 and cas9 nickase. In some embodiments, the second segment is a Cas9-binding sequence.
In another aspect, the invention provides a complex comprising a nucleic acid-guided nuclease system protein and a comprising a first segment comprising a targeting sequence, wherein the size of the first segment is greater than 30 bp; and a second segment comprising a nucleic acid-guided nuclease system protein-binding sequence.
In another aspect, the invention described herein provides a method for depleting and partitioning of targeted sequences in a sample, enriching a sample for non-host nucleic acids, or serially depleting targeted nucleic acids in a sample comprising: providing nucleic acids extracted from a sample; and contacting the sample with a plurality of complexes comprising (i) any one of the collection of gRNAs provided herein; and (ii) nucleic acid-guided nuclease system proteins. In some embodiments, the nucleic acid-guided nuclease system proteins are CRISPR/Cas system proteins. In some embodiments, the CRISPR/Cas system proteins are Cas9 proteins.
In another aspect, the invention provides a method of making a collection of nucleic acids, each comprising a DNA encoding a targeting sequence ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, comprising: (a) providing double-stranded DNA molecules, each comprising a sequence of interest 5′ to a PAM sequence, and its reverse complementary sequence on the opposite strand; (b) performing an enzymatic digestion reaction on the double stranded DNA molecules, wherein cleavages are generated at the PAM sequence and/or its reverse complementary sequence on the opposite strand, but never completely remove the PAM sequence and/or its reverse complementary sequence on the opposite strand from the double stranded DNA; (c) ligating adapters comprising a recognition sequence to the resulting DNA molecules of step b; (d) contacting the DNA molecules of step c with an restriction enzyme that recognizes the recognition sequence of step c, whereby generating DNA fragments comprising blunt-ended double strand breaks immediately 5′ to the PAM sequence, whereby removing the PAM sequence and the adapter containing the enzyme recognition site; and (e) ligating the resulting double stranded DNA fragments of step d with a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, whereby generating a plurality of DNA fragments, each comprising a DNA encoding a targeting sequence ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease is a CRISPR/Cas nucleic acid-guided nuclease system protein. In some embodiments, the starting DNA molecules of the collection further comprise a regulatory sequence upstream of the sequence of interest 5′ to the PAM sequence. In some embodiments, the regulatory sequence comprises a promoter. In some embodiments, the promoter comprises a T7, Sp6, or T3 sequence. In some embodiments, the double stranded DNA molecules are genomic DNA, intact DNA, or sheared DNA. In some embodiments, the genomic DNA is human, mouse, avian, fish, plant, insect, bacterial, or viral. In some embodiments, the DNA segments encoding a targeting sequence are at least 22 bp. In some embodiments, the DNA segments encoding a targeting sequence are 15-250 bp in size range. In some embodiments, the PAM sequence is AGG, CGG, or TGG. In some embodiments, the PAM sequence is specific for a CRISPR/Cas system protein selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. In some embodiments, step (b) further comprises (1) contacting the DNA molecules with an enzyme capable of creating a nick in a single strand at a CCD site, whereby generating a plurality of nicked double stranded DNA molecules, each comprising a sequence of interest followed by an HGG sequence, wherein the DNA molecules are nicked at the CCD sites; and (2) contacting the nicked double stranded DNA molecules with an endonuclease, whereby generating a plurality of double stranded DNA fragments, each comprising a sequence of interest followed by an HGG sequence wherein residual nucleotides from HGG and/or CCD sequences is (are) left behind. In some embodiments, step (d) further comprises PCR amplification of the adaptor-ligated DNA fragments from step (c) before cutting with the restriction enzyme recognizing the recognition sequence of step (c), wherein after PCR, the recognition sequence is positioned 3′ of the PAM sequence, and a regulatory sequence is positioned at the 5′ distal end of the PAM sequence. In some embodiments, the enzymatic reaction of step (b) comprises the use of a Nt.CviPII enzyme, and a T7 Endonuclease I enzyme. In some embodiments, step (c) further comprises a blunt-end reaction with a T4 DNA Polymerase, if the adapter to be ligated does not comprise an overhang. In some embodiments, the adapter of step (c) is either (1) double stranded, comprising a restriction enzyme recognition sequence in one strand, and a regulatory sequence in the other strand, if the adapter is Y-shaped and comprises an overhang; or (2) has a palindromic enzyme recognition sequence in both strands, if the adapter is not Y-shaped. In some embodiments, the restriction enzyme of step (d) is MlyI. In some embodiments, the restriction enzyme of step (d) is BaeI. In some embodiments, step (d) further comprises contacting the DNA molecules with an XhoI enzyme. In some embodiments, in step (e) the DNA encoding a nucleic acid-guided nuclease system-protein binding sequence encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the targeted sequences of interest are spaced every 10,000 bp or less across the genome of an organism.
In another aspect, the invention provides a method of making a collection of nucleic acids, each comprising a DNA encoding a targeting sequence ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, comprising: (a) providing a plurality of double stranded DNA molecules, each comprising a sequence of interest, an NGG site, and its complement CCN site; (b) contacting the molecules with an enzyme capable of creating a nick in a single strand at a CCN site, whereby generating a plurality of nicked double stranded DNA molecules, each comprising a sequence of interest 5′ to the NGG site, wherein the DNA molecules are nicked at the CCD sites; (c) contacting the nicked double stranded DNA molecules with an endonuclease, whereby generating a plurality of double stranded DNA fragments, each comprising a sequence of interest, wherein the fragments comprise an terminal overhang; (d) contacting the double stranded DNA fragments with an enzyme without 5′ to 3′ exonuclease activity to blunt end the double stranded DNA fragments, whereby generating a plurality of blunt ended double stranded fragments, each comprising a sequence of interest; (e) contacting the blunt ended double stranded fragments of step d with an enzyme that cleaves the terminal NGG site; and (f) ligating the resulting double stranded DNA fragments of step e with a DNA encoding a nucleic acid-guided nuclease system-protein binding sequence, whereby generating a plurality of DNA fragments, each comprising a targeting sequence ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease is a CRISPR/Cas system protein. In some embodiments, the plurality of double stranded DNA molecules have a regulatory sequence 5′ upstream of the NGG sites. In some embodiments, the regulatory sequence comprises a T7, SP6, or T3 sequence. In some embodiments, the NGG site comprises AGG, CGG, or TGG, and the CCN site comprises CCT, CCG, or CCA. In some embodiments, the plurality of double stranded DNA molecules, each comprising a sequence of interest comprise sheared fragments of genomic DNA. In some embodiments, the genomic DNA is mammalian, prokaryotic, eukaryotic, avian, bacterial or viral. In some embodiments, the plurality of double stranded DNA molecules in step (a) are at least 500 bp. In some embodiments, the enzyme in step b is a Nt.CviPII enzyme. In some embodiments, the enzyme in step c is a T7 Endonuclease I. In some embodiments, the enzyme in step d is a T4 DNA Polymerase. In some embodiments, in step f the DNA encoding a nucleic acid-guided nuclease system-protein binding sequence encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the step e additionally comprises ligating adaptors carrying a MlyI recognition site and digesting with MlyI enzyme. In some embodiments, the sequence of interest is spaced every 10,000 bp or less across the genome.
In another aspect, the invention provides a method of making a collection of nucleic acids, each comprising a DNA encoding a targeting sequence and a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, comprising: (a) providing genomic DNA comprising a plurality of sequences of interest, comprising NGG and CCN sites; (b) contacting the genomic DNA with an enzyme capable of creating nicks in the genomic DNA, whereby generating nicked genomic DNA, nicked at CCN sites; (c) contacting the nicked genomic DNA with an endonuclease, whereby generating double stranded DNA fragments, with an overhang; (d) ligating the DNA with overhangs from step c to a Y-shaped adapter, thereby introducing a restriction enzyme recognition sequence only at 3′ of the NGG site and a regulatory sequence 5′ of the sequence of interest; (e) contacting the product from step d with an enzyme that cleaves away the NGG site together with the adaptor carrying the enzyme recognition sequence; and (f) ligating the resulting double stranded DNA fragments of step e with a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, whereby generating a plurality of DNA fragments, each comprising a sequence of interest ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence. In some embodiments, the nucleic acid-guided nuclease is a CRISPR/Cas system protein. In some embodiments, the NGG site comprises AGG, CGG, or TGG, and CCN site comprises CCT, CCG, or CCA. In some embodiments, the regulatory sequence comprises a promoter sequence. In some embodiments, the promoter sequence comprises a T7, SP6, or T3 sequence. In some embodiments, the DNA fragments are sheared fragments of genomic DNA.
In some embodiments, the genomic DNA is mammalian, prokaryotic, eukaryotic, or viral. In some embodiments, the fragments are at least 200 bp. In some embodiments, the enzyme in step b is a Nt.CviPII enzyme. In some embodiments, the enzyme in step c is a T7 Endonuclease I. In some embodiments, step d further comprises PCR amplification of the adaptor-ligated DNA. In some embodiments, in step f, the DNA encoding nucleic acid-guided nuclease system protein-binding sequence encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2). In some embodiments, the enzyme removing NGG site in step e is MlyI. In some embodiments, the target of interest of the collection is spaced every 10,000 bp or less across the genome.
In another aspect, the invention provides kits and/or reagents useful for performing a method of making a collection of nucleic acids, each comprising a DNA encoding a targeting sequence ligated to a DNA encoding a nucleic acid-guided nuclease system protein-binding sequence, as described in the embodiments herein.
In another aspect, the invention described herein provides kit comprising a collection of nucleic acids, a plurality of the nucleic acids in the collection comprising: a first segment comprising a regulatory region; a second segment encoding a targeting sequence; and a third segment encoding a CRISPR/Cas system protein-binding sequence, wherein at least 10% of the nucleic acids in the collection vary in size.
In another aspect, the invention described herein provides a kit comprising a collection of nucleic acids, a plurality of the nucleic acids in the collection comprising: a first segment comprising a regulatory region; a second segment encoding a targeting sequence, wherein the size of the second segment is greater than 21 bp; and a third segment encoding a CRISPR/Cas system protein-binding sequence.
In another aspect, the invention described herein provides a kit comprising a collection of guide RNAs comprising a first RNA segment a targeting sequence; and a second RNA segment comprising a CRISPR/Cas system protein-binding sequence, wherein at least 10% of the gRNAs in the collection vary in size.
In another aspect, the invention described herein provides a method of making a collection of guide nucleic acids, comprising: a. obtaining abundant cells in a source sample; b. collecting nucleic acids from said abundant cells; and c. preparing a collection of guide nucleic acids (gNAs) from said nucleic acids. In some embodiments, said abundant cells comprise cells from one or more most abundant bacterial species in said source sample. In some embodiments, said abundant cells comprise cells from more than one species. In some embodiments, said abundant cells comprise human cells. In some embodiments, said abundant cells comprise animal cells. In some embodiments, said abundant cells comprise plant cells. In some embodiments, said abundant cells comprise bacterial cells. In some embodiments, the method further comprises contacting nucleic acid-guided nucleases with said library of gNAs to form nucleic acid-guided nuclease-gNA complexes. In some embodiments, the method further comprises using said nucleic acid-guided nuclease-gNA complexes to cleave target nucleic acids at target sites, wherein said gNAs are complementary to said target sites. In some embodiments, said target nucleic acids are from said source sample. In some embodiments, a species of said target nucleic acids is the same as a species of said source sample. In some embodiments, said species of said target nucleic acids and said species of said source sample is human. In some embodiments, said species of said target nucleic acids and said species of said source sample is animal. In some embodiments, said species of said target nucleic acids and said species of said source sample is plant.
In another aspect, the invention described herein provides a method of making a collection of nucleic acids, each comprising a targeting sequence, comprising: a. obtaining source DNA; b. nicking said source DNA with a nicking enzyme at nicking enzyme recognition sites, thereby producing double-stranded breaks at proximal nicks; and c. repairing overhangs of said double-stranded breaks, thereby producing a double-stranded fragment comprising (i) a targeting sequence and (ii) said nicking enzyme recognition site. In another aspect, the invention described herein provides a method of making a collection of nucleic acids, each comprising a targeting sequence, comprising: a. obtaining source DNA; b. nicking said source DNA with a nicking enzyme at nicking enzyme recognition sites, thereby producing a nick; and c. synthesizing a new strand from said nick, thereby producing a single-stranded fragment of said source DNA comprising a targeting sequence. In some embodiments, the method further comprises producing a double-stranded fragment comprising said targeting sequence from said single-stranded fragment. In some embodiments, said producing said double-stranded fragment comprises random priming and extension. In some embodiments, said random priming is conducted with a primer comprising a random n-mer region and a promoter region. In some embodiments, said random n-mer region is a random hexamer region. In some embodiments, said random n-mer region is a random octamer region. In some embodiments, said promoter region is a T7 promoter region. In some embodiments, the method further comprises ligating a nuclease recognition site nucleic acid comprising a nuclease recognition site to said double-stranded fragment. In some embodiments, said nuclease recognition site corresponds to a nuclease that cuts at a distance from said nuclease recognition site equal to the length of said nicking enzyme recognition sites. In some embodiments, said nuclease recognition site is a MlyI recognition site. In some embodiments, said nuclease recognition site is a BaeI recognition site. In some embodiments, the method further comprises digesting said double-stranded fragment with said nuclease, thereby removing said nicking enzyme recognition site from said double-stranded fragment. In some embodiments, the method further comprises ligating said double-stranded fragment to a nucleic acid-guided nuclease system protein recognition site nucleic acid comprising a nucleic acid-guided nuclease system protein recognition site. In some embodiments, said nucleic acid-guided nuclease system protein recognition site comprises a guide RNA stem-loop sequence. In some embodiments, said nuclease recognition site corresponds to a nuclease that cuts at a distance from said nuclease recognition site equal to a length of said targeting sequence. In some embodiments, said length of said targeting sequence is 20 base pairs. In some embodiments, said nuclease recognition site is a MmeI recognition site. In some embodiments, the method further comprises digesting said double-stranded fragment with said nuclease. In some embodiments, said nuclease recognition site corresponds to a nuclease that cuts at a distance from said nuclease recognition site equal to a length of said targeting sequence plus a length of said nicking enzyme recognition sites. In some embodiments, said length of said targeting sequence plus a length of said nicking enzyme recognition sites is 23 base pairs. In some embodiments, said nuclease recognition site is a EcoP15I recognition site. In some embodiments, the method further comprises digesting said double-stranded fragment with said nuclease. In some embodiments, the method further comprises ligating said double-stranded fragment to a nucleic acid-guided nuclease system protein recognition site nucleic acid comprising a nucleic acid-guided nuclease system protein recognition site. In some embodiments, said nucleic acid-guided nuclease system protein recognition site comprises a guide RNA stem-loop sequence.
In another aspect, the invention described herein provides a kit comprising all essential reagents and instructions for carrying out the methods of aspects of the invention described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates an exemplary scheme for producing a collection of gRNAs (a gRNA library) from genomic DNA.

FIG. 2 illustrates another exemplary scheme for producing a collection of gRNAs (a gRNA library) from genomic DNA.

FIG. 3 illustrates an exemplary scheme for nicking of DNA and subsequent treatment with polymerase to generate blunt ends.

FIG. 4 illustrates an exemplary scheme for sequential production of a library of gNAs using three adapters.

FIG. 5 illustrates an exemplary scheme for sequential production of a library of gNAs using one adapter and one oligo.

FIG. 6 illustrates an exemplary scheme for generation of a large pool of DNA fragments with blunt ends using Nicking Enzyme Mediated DNA Amplification (NEMDA).

FIG. 7 illustrates an exemplary scheme for generation of a large pool of gNAs using Nicking Enzyme Mediated DNA Amplification (NEMDA).

DETAILED DESCRIPTION OF THE INVENTION

There is a need in the art for a scalable, low-cost approach to generate large numbers of diverse guide nucleic acids (gNAs) (e.g., gRNAs, gDNAs) for a variety of downstream applications.
Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described.
Numeric ranges are inclusive of the numbers defining the range.
For purposes of interpreting this specification, the following definitions will apply and whenever appropriate, terms used in the singular will also include the plural and vice versa. In the event that any definition set forth below conflicts with any document incorporated herein by reference, the definition set forth shall control.
As used herein, the singular form “a”, “an”, and “the” includes plural references unless indicated otherwise.
It is understood that aspects and embodiments of the invention described herein include “comprising,” “consisting,” and “consisting essentially of” aspects and embodiments.
The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se.
The term “nucleic acid,” as used herein, refers to a molecule comprising one or more nucleic acid subunits. A nucleic acid can include one or more subunits selected from adenosine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), and modified versions of the same. A nucleic acid comprises deoxyribonucleic acid (DNA), ribonucleic acid (RNA), combinations, or derivatives thereof. A nucleic acid may be single-stranded and/or double-stranded.
The nucleic acids comprise “nucleotides”, which, as used herein, is intended to include those moieties that contain purine and pyrimidine bases, and modified versions of the same. Such modifications include methylated purines or pyrimidines, acylated purines or pyrimidines, alkylated riboses or other heterocycles. In addition, the term “nucleotide” or “polynucleotide” includes those moieties that contain hapten or fluorescent labels and may contain not only conventional ribose and deoxyribose sugars, but other sugars as well. Modified nucleosides, nucleotides or polynucleotides also include modifications on the sugar moiety, e.g., wherein one or more of the hydroxyl groups are replaced with halogen atoms or aliphatic groups, or are functionalized as ethers, amines, or the like.
The term “nucleic acids” and “polynucleotides” are used interchangeably herein. Polynucleotide is used to describe a nucleic acid polymer of any length, e.g., greater than about 2 bases, greater than about 10 bases, greater than about 100 bases, greater than about 500 bases, greater than 1000 bases, up to about 10,000 or more bases composed of nucleotides, e.g., deoxyribonucleotides or ribonucleotides, and may be produced enzymatically or synthetically (e.g., PNA as described in U.S. Pat. No. 5,948,902 and the references cited therein) which can hybridize with naturally occurring nucleic acids in a sequence specific manner analogous to that of two naturally occurring nucleic acids, e.g., can participate in Watson-Crick base pairing interactions. Naturally-occurring nucleotides include guanine, cytosine, adenine and thymine (G, C, A and T, respectively). DNA and RNA have a deoxyribose and ribose sugar backbones, respectively, whereas PNA's backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. In PNA various purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. A locked nucleic acid (LNA), often referred to as inaccessible RNA, is a modified RNA nucleotide. The ribose moiety of an LNA nucleotide is modified with an extra bridge connecting the 2′ oxygen and 4′ carbon. The bridge “locks” the ribose in the 3′-endo (North) conformation, which is often found in the A-form duplexes. LNA nucleotides can be mixed with DNA or RNA residues in the oligonucleotide whenever desired. The term “unstructured nucleic acid,” or “UNA” is a nucleic acid containing non-natural nucleotides that bind to each other with reduced stability. For example, an unstructured nucleic acid may contain a G′ residue and a C′ residue, where these residues correspond to non-naturally occurring forms, i.e., analogs, of G and C that base pair with each other with reduced stability, but retain an ability to base pair with naturally occurring C and G residues, respectively. Unstructured nucleic acid is described in US20050233340, which is incorporated by reference herein for disclosure of UNA.
The term “oligonucleotide” as used herein denotes a single-stranded multimer of nucleotides.
Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
The term “cleaving,” as used herein, refers to a reaction that breaks the phosphodiester bonds between two adjacent nucleotides in both strands of a double-stranded DNA molecule, thereby resulting in a double-stranded break in the DNA molecule.
The term “nicking” as used herein, refers to a reaction that breaks the phosphodiester bond between two adjacent nucleotides in only one strand of a double-stranded DNA molecule, thereby resulting in a break in one strand of the DNA molecule.
The term “cleavage site, as used herein, refers to the site at which a double-stranded DNA molecule has been cleaved.
The “nucleic acid-guided nuclease-gNA complex” refers to a complex comprising a nucleic acid-guided nuclease protein and a guide nucleic acid (gNA, for example a gRNA or a gDNA). For example the “Cas9-gRNA complex” refers to a complex comprising a Cas9 protein and a guide RNA (gRNA). The nucleic acid-guided nuclease may be any type of nucleic acid-guided nuclease, including but not limited to wild type nucleic acid-guided nuclease, a catalytically dead nucleic acid-guided nuclease, or a nucleic acid-guided nuclease-nickase.
The term “nucleic acid-guided nuclease-associated guide NA” refers to a guide nucleic acid (guide NA). The nucleic acid-guided nuclease-associated guide NA may exist as an isolated nucleic acid, or as part of a nucleic acid-guided nuclease-gNA complex, for example a Cas9-gRNA complex.
The terms “capture” and “enrichment” are used interchangeably herein, and refer to the process of selectively isolating a nucleic acid region containing: sequences of interest, targeted sites of interest, sequences not of interest, or targeted sites not of interest.
The term “hybridization” refers to the process by which a strand of nucleic acid joins with a complementary strand through base pairing as known in the art. A nucleic acid is considered to be “selectively hybridizable” to a reference nucleic acid sequence if the two sequences specifically hybridize to one another under moderate to high stringency hybridization and wash conditions. Moderate and high stringency hybridization conditions are known (see, e.g., Ausubel, et al., Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons 1995 and Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Edition, 2001 Cold Spring Harbor, N.Y.). One example of high stringency conditions includes hybridization at about 42° C. in 50% formamide, 5×SSC, 5×Denhardt's solution, 0.5% SDS and 100 μg/ml denatured carrier DNA followed by washing two times in 2×SSC and 0.5% SDS at room temperature and two additional times in 0.1×SSC and 0.5% SDS at 42° C.
The term “duplex,” or “duplexed,” as used herein, describes two complementary polynucleotides that are base-paired, i.e., hybridized together.
The term “amplifying” as used herein refers to generating one or more copies of a target nucleic acid, using the target nucleic acid as a template.
The term “genomic region,” as used herein, refers to a region of a genome, e.g., an animal or plant genome such as the genome of a human, monkey, rat, fish or insect or plant. In certain cases, an oligonucleotide used in the method described herein may be designed using a reference genomic region, i.e., a genomic region of known nucleotide sequence, e.g., a chromosomal region whose sequence is deposited at NCBI's Genbank database or other databases, for example.
The term “genomic sequence,” as used herein, refers to a sequence that occurs in a genome. Because RNAs are transcribed from a genome, this term encompasses sequence that exist in the nuclear genome of an organism, as well as sequences that are present in a cDNA copy of an RNA (e.g., an mRNA) transcribed from such a genome.
The term “genomic fragment,” as used herein, refers to a region of a genome, e.g., an animal or plant genome such as the genome of a human, monkey, rat, fish or insect or plant. A genomic fragment may be an entire chromosome, or a fragment of a chromosome. A genomic fragment may be adapter ligated (in which case it has an adapter ligated to one or both ends of the fragment, or to at least the 5 end of a molecule), or may not be adapter ligated.
In certain cases, an oligonucleotide used in the method described herein may be designed using a reference genomic region, i.e., a genomic region of known nucleotide sequence, e.g., a chromosomal region whose sequence is deposited at NCBI's Genbank database or other databases, for example. Such an oligonucleotide may be employed in an assay that uses a sample containing a test genome, where the test genome contains a binding site for the oligonucleotide.
The term “ligating,” as used herein, refers to the enzymatically catalyzed joining of the terminal nucleotide at the 5′ end of a first DNA molecule to the terminal nucleotide at the 3′ end of a second DNA molecule.
If two nucleic acids are “complementary,” each base of one of the nucleic acids base pairs with corresponding nucleotides in the other nucleic acid. The term “complementary” and “perfectly complementary” are used synonymously herein.
The term “separating,” as used herein, refers to physical separation of two elements (e.g., by size or affinity, etc.) as well as degradation of one element, leaving the other intact. For example, size exclusion can be employed to separate nucleic acids, including cleaved targeted sequences.
In a cell, DNA usually exists in a double-stranded form, and as such, has two complementary strands of nucleic acid referred to herein as the “top” and “bottom” strands. In certain cases, complementary strands of a chromosomal region may be referred to as “plus” and “minus” strands, the “first” and “second” strands, the “coding” and “noncoding” strands, the “Watson” and “Crick” strands or the “sense” and “antisense” strands. The assignment of a strand as being a top or bottom strand is arbitrary and does not imply any particular orientation, function or structure. Until they become covalently linked, the first and second strands are distinct molecules. For ease of description, the “top” and “bottom” strands of a double-stranded nucleic acid in which the top and bottom strands have been covalently linked will still be described as the “top” and “bottom” strands. In other words, for the purposes of this disclosure, the top and bottom strands of a double-stranded DNA do not need to be separated molecules. The nucleotide sequences of the first strand of several exemplary mammalian chromosomal regions (e.g., BACs, assemblies, chromosomes, etc.) is known, and may be found in NCBI's Genbank database, for example.
The term “top strand,” as used herein, refers to either strand of a nucleic acid but not both strands of a nucleic acid. When an oligonucleotide or a primer binds or anneals “only to a top strand,” it binds to only one strand but not the other. The term “bottom strand,” as used herein, refers to the strand that is complementary to the “top strand.” When an oligonucleotide binds or anneals “only to one strand,” it binds to only one strand, e.g., the first or second strand, but not the other strand. If an oligonucleotide binds or anneals to both strands of a double-stranded DNA, the oligonucleotide may have two regions, a first region that hybridizes with the top strand of the double-stranded DNA, and a second region that hybridizes with the bottom strand of the double-stranded DNA.
The term “double-stranded DNA molecule” refers to both double-stranded DNA molecules in which the top and bottom strands are not covalently linked, as well as double-stranded DNA molecules in which the top and bottom stands are covalently linked. The top and bottom strands of a double-stranded DNA are base paired with one other by Watson-Crick interactions.
The term “denaturing,” as used herein, refers to the separation of at least a portion of the base pairs of a nucleic acid duplex by placing the duplex in suitable denaturing conditions. Denaturing conditions are well known in the art. In one embodiment, in order to denature a nucleic acid duplex, the duplex may be exposed to a temperature that is above the T_mof the duplex, thereby releasing one strand of the duplex from the other. In certain embodiments, a nucleic acid may be denatured by exposing it to a temperature of at least 90° C. for a suitable amount of time (e.g., at least 30 seconds, up to 30 mins). In certain embodiments, fully denaturing conditions may be used to completely separate the base pairs of the duplex. In other embodiments, partially denaturing conditions (e.g., with a lower temperature than fully denaturing conditions) may be used to separate the base pairs of certain parts of the duplex (e.g., regions enriched for A-T base pairs may separate while regions enriched for G-C base pairs may remain paired). Nucleic acid may also be denatured chemically (e.g., using urea or NaOH).
The term “genotyping” as used herein, refers to any type of analysis of a nucleic acid sequence, and includes sequencing, polymorphism (SNP) analysis, and analysis to identify rearrangements.
The term “sequencing,” as used herein, refers to a method by which the identity of consecutive nucleotides of a polynucleotide are obtained.
The term “next-generation sequencing” refers to the so-called parallelized sequencing-by-synthesis or sequencing-by-ligation platforms, for example, those currently employed by Illumina, Life Technologies, and Roche, etc. Next-generation sequencing methods may also include nanopore sequencing methods or electronic-detection based methods such as Ion Torrent technology commercialized by Life Technologies.
The term “complementary DNA” or cDNA refers to a double-stranded DNA sample that was produced from an RNA sample by reverse transcription of RNA (using primers such as random hexamers or oligo-dT primers) followed by second-strand synthesis by digestion of the RNA with RNaseH and synthesis by DNA polymerase.
The term “RNA promoter adapter” is an adapter that contains a promoter for a bacteriophage RNA polymerase, e.g., the RNA polymerase from bacteriophage T3, T7, SP6 or the like.
Other definitions of terms may appear throughout the specification.
For any of the structural and functional characteristics described herein, methods of determining these characteristics are known in the art.
Guide Nucleic Acids (gNAs)
Provided herein are guide nucleic acids (gNAs) derivable from any nucleic acid source. The gNAs can be guide RNAs (gRNAs) or guide DNAs (gDNAs). The nucleic acid source can be DNA or RNA. Provided herein are methods to generate gNAs from any source nucleic acid, including DNA from a single organism, or mixtures of DNA from multiple organisms, or mixtures of DNA from multiple species, or DNA from clinical samples, or DNA from forensic samples, or DNA from environmental samples, or DNA from metagenomic DNA samples (for example a sample that contains more than one species of organism). Examples of any source DNA include, but are not limited to any genome, any genome fragment, cDNA, synthetic DNA, or a DNA collection (e.g. a SNP collection, DNA libraries). The gNAs provided herein can be used for genome-wide applications.
In some embodiments, the gNAs are derived from genomic sequences (e.g., genomic DNA). In some embodiments, the gNAs are derived from mammalian genomic sequences. In some embodiments, the gNAs are derived from eukaryotic genomic sequences. In some embodiments, the gNAs are derived from prokaryotic genomic sequences. In some embodiments, the gNAs are derived from viral genomic sequences. In some embodiments, the gNAs are derived from bacterial genomic sequences. In some embodiments, the gNAs are derived from plant genomic sequences. In some embodiments, the gNAs are derived from microbial genomic sequences. In some embodiments, the gNAs are derived from genomic sequences from a parasite, for example a eukaryotic parasite.
In some embodiments, the gNAs are derived from repetitive DNA. In some embodiments, the gNAs are derived from abundant DNA. In some embodiments, the gNAs are derived from mitochondrial DNA. In some embodiments, the gNAs are derived from ribosomal DNA. In some embodiments, the gNAs are derived from centromeric DNA. In some embodiments, the gNAs are derived from DNA comprising Alu elements (Alu DNA). In some embodiments, the gNAs are derived from DNA comprising long interspersed nuclear elements (LINE DNA). In some embodiments, the gNAs are derived from DNA comprising short interspersed nuclear elements (SINE DNA). In some embodiments the abundant DNA comprises ribosomal DNA. In some embodiments, the abundant DNA comprises host DNA (e.g., host genomic DNA or all host DNA). In an example, the gNAs can be derived from host DNA (e.g., human, animal, plant) for the depletion of host DNA to allow for easier analysis of other DNA that is present (e.g., bacterial, viral, or other metagenomic DNA). In another example, the gNAs can be derived from the one or more most abundant types (e.g., species) in a mixed sample, such as the one or more most abundant bacteria species in a metagenomic sample. The one or more most abundant types (e.g., species) can comprise the two, three, four, five, six, seven, eight, nine, ten, or more than ten most abundant types (e.g., species). The most abundant types can be the most abundant kingdoms, phyla or divisions, classes, orders, families, genuses, species, or other classifications. The most abundant types can be the most abundant cell types, such as epithelial cells, bone cells, muscle cells, blood cells, adipose cells, or other cell types. The most abundant types can be non-cancerous cells. The most abundant types can be cancerous cells. The most abundant types can be animal, human, plant, fungal, bacterial, or viral. gNAs can be derived from both a host and the one or more most abundant non-host types (e.g., species) in a sample, such as from both human DNA and the DNA of the one or more most abundant bacterial species. In some embodiments, the abundant DNA comprises DNA from the more abundant or most abundant cells in a sample. For example, for a specific sample, the highly abundant cells can be extracted and their DNA can be used to produce gNAs; these gNAs can be used to produce depletion library and applied to original sample to enable or enhance sequencing or detection of low abundance targets.
In some embodiments, the gNAs are derived from DNA comprising short terminal repeats (STRs).
In some embodiments, the gNAs are derived from a genomic fragment, comprising a region of the genome, or the whole genome itself. In one embodiment, the genome is a DNA genome. In another embodiment, the genome is a RNA genome.
In some embodiments, the gNAs are derived from a eukaryotic or prokaryotic organism; from a mammalian organism or a non-mammalian organism; from an animal or a plant; from a bacteria or virus; from an animal parasite; from a pathogen.
In some embodiments, the gNAs are derived from any mammalian organism. In one embodiment the mammal is a human. In another embodiment the mammal is a livestock animal, for example a horse, a sheep, a cow, a pig, or a donkey. In another embodiment, a mammalian organism is a domestic pet, for example a cat, a dog, a gerbil, a mouse, a rat. In another embodiment the mammal is a type of a monkey.
In some embodiments, the gNAs are derived from any bird or avian organism. An avian organism includes but is not limited to chicken, turkey, duck and goose.
In some embodiments, the gNAs are derived from a plant. In one embodiment, the plant is rice, maize, wheat, rose, grape, coffee, fruit, tomato, potato, or cotton.
In some embodiments, the gNAs are derived from a species of bacteria. In one embodiment, the bacteria are tuberculosis-causing bacteria.
In some embodiments, the gNAs are derived from a virus.
In some embodiments, the gNAs are derived from a species of fungi.
In some embodiments, the gNAs are derived from a species of algae.
In some embodiments, the gNAs are derived from any mammalian parasite.
In some embodiments, the gNAs are derived from any mammalian parasite. In one embodiment, the parasite is a worm. In another embodiment, the parasite is a malaria-causing parasite. In another embodiment, the parasite is a Leishmaniasis-causing parasite. In another embodiment, the parasite is an amoeba.
In some embodiments, the gNAs are derived from a nucleic acid target. Contemplated targets include, but are not limited to, pathogens; single nucleotide polymorphisms (SNPs), insertions, deletions, tandem repeats, or translocations; human SNPs or STRs; potential toxins; or animals, fungi, and plants. In some embodiments, the gRNAs are derived from pathogens, and are pathogen-specific gNAs.
In some embodiments, a guide NA of the invention comprises a first NA segment comprising a targeting sequence, wherein the targeting sequence is 15-250 bp; and a second NA segment comprising a nucleic acid guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence. In some embodiments, the targeting sequence is greater than 21 bp, greater than 22 bp, greater than 23 bp, greater than 24 bp, greater than 25 bp, greater than 26 bp, greater than 27 bp, greater than 28 bp, greater than 29 bp, greater than 30 bp, greater than 40 bp, greater than 50 bp, greater than 60 bp, greater than 70 bp, greater than 80 bp, greater than 90 bp, greater than 100 bp, greater than 110 bp, greater than 120 bp, greater than 130 bp, greater than 140 bp, or even greater than 150 bp. In an exemplary embodiment, the targeting sequence is greater than 30 bp. In some embodiments, the targeting sequences of the present invention range in size from 30-50 bp. In some embodiments, targeting sequences of the present invention range in size from 30-75 bp. In some embodiments, targeting sequences of the present invention range in size from 30-100 bp. For example, a targeting sequence can be at least 15 bp, 20 bp, 25 bp, 30 bp, 35 bp, 40 bp, 45 bp, 50 bp, 55 bp, 60 bp, 65 bp, 70 bp, 75 bp, 80 bp, 85 bp, 90 bp, 95 bp, 100 bp, 110 bp, 120 bp, 130 bp, 140 bp, 150 bp, 160 bp, 170 bp, 180 bp, 190 bp, 200 bp, 210 bp, 220 bp, 230 bp, 240 bp, or 250 bp. In specific embodiments, the targeting sequence is at least 22 bp. In specific embodiments, the targeting sequence is at least 30 bp.
In some embodiments, target-specific gNAs can comprise a nucleic acid sequence that is complementary to a region on the opposite strand of the targeted nucleic acid sequence 5′ to a PAM sequence, which can be recognized by a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein. In some embodiments the targeted nucleic acid sequence is immediately 5′ to a PAM sequence. In specific embodiments, the nucleic acid sequence of the gNA that is complementary to a region in a target nucleic acid is 15-250 bp. In specific embodiments, the nucleic acid sequence of the gNA that is complementary to a region in a target nucleic acid is 22, 23, 24, 25, 30, 35, 40, 45, 50, 60, 70, 75, 80, 90, or 100 bp.
In some particular embodiments, the targeting sequence is not 20 bp. In some particular embodiments, the targeting sequence is not 21 bp.
In some embodiments, the gNAs comprise any purines or pyrimidines (and/or modified versions of the same). In some embodiments, the gNAs comprise adenine, uracil, guanine, and cytosine (and/or modified versions of the same). In some embodiments, the gNAs comprise adenine, thymine, guanine, and cytosine (and/or modified versions of the same). In some embodiments, the gNAs comprise adenine, thymine, guanine, cytosine and uracil (and/or modified versions of the same).
In some embodiments, the gNAs comprise a label, are attached to a label, or are capable of being labeled. In some embodiments, the gNA comprises is a moiety that is further capable of being attached to a label. A label includes, but is not limited to, enzyme, an enzyme substrate, an antibody, an antigen binding fragment, a peptide, a chromophore, a lumiphore, a fluorophore, a chromogen, a hapten, an antigen, a radioactive isotope, a magnetic particle, a metal nanoparticle, a redox active marker group (capable of undergoing a redox reaction), an aptamer, one member of a binding pair, a member of a FRET pair (either a donor or acceptor fluorophore), and combinations thereof.
In some embodiments, the gNAs are attached to a substrate. The substrate can be made of glass, plastic, silicon, silica-based materials, functionalized polystyrene, functionalized polyethyleneglycol, functionalized organic polymers, nitrocellulose or nylon membranes, paper, cotton, and materials suitable for synthesis. Substrates need not be flat. In some embodiments, the substrate is a 2-dimensional array. In some embodiments, the 2-dimensional array is flat. In some embodiments, the 2-dimensional array is not flat, for example, the array is a wave-like array. Substrates include any type of shape including spherical shapes (e.g., beads). Materials attached to substrates may be attached to any portion of the substrates (e.g., may be attached to an interior portion of a porous substrates material). In some embodiments, the substrate is a 3-dimensional array, for example, a microsphere. In some embodiments, the microsphere is magnetic. In some embodiments, the microsphere is glass. In some embodiments, the microsphere is made of polystyrene. In some embodiments, the microsphere is silica-based. In some embodiments, the substrate is an array with interior surface, for example, is a straw, tube, capillary, cylindrical, or microfluidic chamber array. In some embodiments, the substrate comprises multiple straws, capillaries, tubes, cylinders, or chambers.
Nucleic Acids Encoding gNAs
Also provided herein are nucleic acids encoding for gNAs (e.g., gRNAs or gDNAs). In some embodiments, by encoding it is meant that a gNA results from the transcription of a nucleic acid encoding for a gNA (e.g., gRNA). In some embodiments, by encoding, it is meant that the nucleic acid is a template for the transcription of a gNA (e.g., gRNA). In some embodiments, by encoding, it is meant that a gNA results from the reverse transcription of a nucleic acid encoding for a gNA. In some embodiments, by encoding, it is meant that the nucleic acid is a template for the reverse transcription of a gNA. In some embodiments, by encoding, it is meant that a gNA results from the amplification of a nucleic acid encoding for a gNA. In some embodiments, by encoding, it is meant that the nucleic acid is a template for the amplification of a gNA.
In some embodiments the nucleic acid encoding for a gNA comprises a first segment comprising a regulatory region; a second segment comprising targeting sequence, wherein the second segment can range from 15 bp-250 bp; and a third segment comprising a nucleic acid encoding a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence.
In some embodiments, the nucleic acids encoding for gNAs comprise DNA. In some embodiments, the first segment is double stranded DNA. In some embodiments, the first segment is single stranded DNA. In some embodiments, the second segment is single stranded DNA. In some embodiments, the third segment is single stranded DNA. In some embodiments, the second segment is double stranded DNA. In some embodiments, the third segment is double stranded DNA.
In some embodiments, the nucleic acids encoding for gNAs comprise RNA.
In some embodiments the nucleic acids encoding for gNAs comprise DNA and RNA.
In some embodiments, the regulatory region is a region capable of binding a transcription factor. In some embodiments, the regulatory region comprises a promoter. In some embodiments, the promoter is selected from the group consisting of T7, SP6, and T3.
Collections of gNAs
Provided herein are collections (interchangeably referred to as libraries) of gNAs.
As used herein, a collection of gNAs denotes a mixture of gNAs containing at least 102 unique gNAs. In some embodiments a collection of gNAs contains at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰unique gNAs. In some embodiments a collection of gNAs contains a total of at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰gNAs.
In some embodiments, a collection of gNAs comprises a first NA segment comprising a targeting sequence; and a second NA segment comprising a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence, wherein at least 10% of the gNAs in the collection vary in size. In some embodiments, the first and second segments are in 5′- to 3-order′.
In some embodiments, the size of the first segment varies from 15-250 bp, or 30-100 bp, or 22-30 bp, or 15-50 bp, or 15-75 bp, or 15-100 bp, or 15-125 bp, or 15-150 bp, or 15-175 bp, or 15-200 bp, or 15-225 bp, or 15-250 bp, or 22-50 bp, or 22-75 bp, or 22-100 bp, or 22-125 bp, or 22-150 bp, or 22-175 bp, or 22-200 bp, or 22-225 bp, or 22-250 bp across the collection of gNAs.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the first segments in the collection are greater than 21 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the first segments in the collection are greater than 25 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the first segments in the collection are greater than 30 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the first segments in the collection are 15-50 bp.
In some embodiments, at least 0%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the first segments in the collection are 30-100 bp.
In some particular embodiments, the size of the first segment is not 20 bp.
In some particular embodiments, the size of the first segment is not 21 bp.
In some embodiments, the gNAs and/or the targeting sequence of the gNAs in the collection of gRNAs comprise unique 5′ ends. In some embodiments, the collection of gNAs exhibit variability in sequence of the 5′ end of the targeting sequence, across the members of the collection. In some embodiments, the collection of gNAs exhibit variability at least 5%, or at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75% variability in the sequence of the 5′ end of the targeting sequence, across the members of the collection.
In some embodiments, the 3′ end of the gNA targeting sequence can be any purine or pyrimidine (and/or modified versions of the same). In some embodiments, the 3′ end of the gNA targeting sequence is an adenine. In some embodiments, the 3′ end of the gNA targeting sequence is a guanine. In some embodiments, the 3′ end of the gNA targeting sequence is a cytosine. In some embodiments, the 3′ end of the gNA targeting sequence is a uracil. In some embodiments, the 3′ end of the gNA targeting sequence is a thymine. In some embodiments, the 3′ end of the gNA targeting sequence is not cytosine.
In some embodiments, the collection of gNAs comprises targeting sequences which can base-pair with the targeted DNA, wherein the target of interest is spaced at least every 1 bp, at least every 2 bp, at least every 3 bp, at least every 4 bp, at least every 5 bp, at least every 6 bp, at least every 7 bp, at least every 8 bp, at least every 9 bp, at least every 10 bp, at least every 11 bp, at least every 12 bp, at least every 13 bp, at least every 14 bp, at least every 15 bp, at least every 16 bp, at least every 17 bp, at least every 18 bp, at least every 19 bp, 20 bp, at least every 25 bp, at least every 30 bp, at least every 40 bp, at least every 50 bp, at least every 100 bp, at least every 200 bp, at least every 300 bp, at least every 400 bp, at least every 500 bp, at least every 600 bp, at least every 700 bp, at least every 800 bp, at least every 900 bp, at least every 1000 bp, at least every 2500 bp, at least every 5000 bp, at least every 10,000 bp, at least every 15,000 bp, at least every 20,000 bp, at least every 25,000 bp, at least every 50,000 bp, at least every 100,000 bp, at least every 250,000 bp, at least every 500,000 bp, at least every 750,000 bp, or even at least every 1,000,000 bp across a genome of interest.
In some embodiments, the collection of gNAs comprises a first NA segment comprising a targeting sequence; and a second NA segment comprising a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence, wherein the gNAs in the collection can have a variety of second NA segments with various specificities for protein members of the nucleic acid-guided nuclease system (e.g., CRISPR/Cas system). For example a collection of gNAs as provided herein, can comprise members whose second segment comprises a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence specific for a first nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein; and also comprises members whose second segment comprises a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence specific for a second nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein, wherein the first and second nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins are not the same. In some embodiments a collection of gNAs as provided herein comprises members that exhibit specificity to at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or even at least 20 nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins. In one specific embodiment, a collection of gNAs as provided herein comprises members that exhibit specificity for a Cas9 protein and another protein selected from the group consisting of Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.
In some embodiments, a plurality of the gNA members of the collection are attached to a label, comprise a label or are capable of being labeled. In some embodiments, the gNA comprises is a moiety that is further capable of being attached to a label. A label includes, but is not limited to, enzyme, an enzyme substrate, an antibody, an antigen binding fragment, a peptide, a chromophore, a lumiphore, a fluorophore, a chromogen, a hapten, an antigen, a radioactive isotope, a magnetic particle, a metal nanoparticle, a redox active marker group (capable of undergoing a redox reaction), an aptamer, one member of a binding pair, a member of a FRET pair (either a donor or acceptor fluorophore), and combinations thereof.
In some embodiments, a plurality of the gNA members of the collection are attached to a substrate. The substrate can be made of glass, plastic, silicon, silica-based materials, functionalized polystyrene, functionalized polyethyleneglycol, functionalized organic polymers, nitrocellulose or nylon membranes, paper, cotton, and materials suitable for synthesis. Substrates need not be flat. In some embodiments, the substrate is a 2-dimensional array. In some embodiments, the 2-dimensional array is flat. In some embodiments, the 2-dimensional array is not flat, for example, the array is a wave-like array. Substrates include any type of shape including spherical shapes (e.g., beads). Materials attached to substrates may be attached to any portion of the substrates (e.g., may be attached to an interior portion of a porous substrates material). In some embodiments, the substrate is a 3-dimensional array, for example, a microsphere. In some embodiments, the microsphere is magnetic. In some embodiments, the microsphere is glass. In some embodiments, the microsphere is made of polystyrene. In some embodiments, the microsphere is silica-based. In some embodiments, the substrate is an array with interior surface, for example, is a straw, tube, capillary, cylindrical, or microfluidic chamber array. In some embodiments, the substrate comprises multiple straws, capillaries, tubes, cylinders, or chambers.

Collections of Nucleic Acids Encoding % NAs

Provided herein are collections (interchangeably referred to as libraries) of nucleic acids encoding for gNAs (e.g., gRNAs or gDNAs). In some embodiments, by encoding it is meant that a gNA results from the transcription of a nucleic acid encoding for a gNA. In some embodiments, by encoding, it is meant that the nucleic acid is a template for the transcription of a gNA.
As used herein, a collection of nucleic acids encoding for gNAs denotes a mixture of nucleic acids containing at least 10²unique nucleic acids. In some embodiments a collection of nucleic acids encoding for gNAs contains at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰unique nucleic acids encoding for gNAs. In some embodiments a collection of nucleic acids encoding for gNAs contains a total of at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰nucleic acids encoding for gNAs.
In some embodiments, a collection of nucleic acids encoding for gNAs comprises a first segment comprising a regulatory region; a second segment comprising a targeting sequence; and a third segment comprising a nucleic acid encoding a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence, wherein at least 10% of the nucleic acids in the collection vary in size.
In some embodiments, the first, second, and third segments are in 5′- to 3′-order′.
In some embodiments, the nucleic acids encoding for gNAs comprise DNA. In some embodiments, the first segment is single stranded DNA. In some embodiments, the first segment is double stranded DNA. In some embodiments, the second segment is single stranded DNA. In some embodiments, the third segment is single stranded DNA. In some embodiments, the second segment is double stranded DNA. In some embodiments, the third segment is double stranded DNA.
In some embodiments, the nucleic acids encoding for gNAs comprise RNA.
In some embodiments the nucleic acids encoding for gNAs comprise DNA and RNA.
In some embodiments, the regulatory region is a region capable of binding a transcription factor. In some embodiments, the regulatory region comprises a promoter. In some embodiments, the promoter is selected from the group consisting of T7, SP6, and T3.
In some embodiments, the size of the second segments (targeting sequence) in the collection varies from 15-250 bp, or 30-100 bp, or 22-30 bp, or 15-50 bp, or 15-75 bp, or 15-100 bp, or 15-125 bp, or 15-150 bp, or 15-175 bp, or 15-200 bp, or 15-225 bp, or 15-250 bp, or 22-50 bp, or 22-75 bp, or 22-100 bp, or 22-125 bp, or 22-150 bp, or 22-175 bp, or 22-200 bp, or 22-225 bp, or 22-250 bp across the collection of gNAs.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the second segments in the collection are greater than 21 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the second segments in the collection are greater than 25 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the second segments in the collection are greater than 30 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the second segments in the collection are 15-50 bp.
In some embodiments, at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or 100% of the second segments in the collection are 30-100 bp.
In some particular embodiments, the size of the second segment is not 20 bp.
In some particular embodiments, the size of the second segment is not 21 bp.
In some embodiments, the gNAs and/or the targeting sequence of the gNAs in the collection of gNAs comprise unique 5′ ends. In some embodiments, the collection of gNAs exhibit variability in sequence of the 5′ end of the targeting sequence, across the members of the collection. In some embodiments, the collection of gNAs exhibit variability at least 5%, or at least 10%, or at least 15%, or at last 20%, or at least 25%, or at least 30%, or at least 35%, or at least 40%, or at least 45%, or at least 50%, or at least 55%, or at least 60%, or at least 65%, or at least 70%, or at least 75% variability in the sequence of the 5′ end of the targeting sequence, across the members of the collection.
In some embodiments, the collection of nucleic acids comprises targeting sequences, wherein the target of interest is spaced at least every 1 bp, at least every 2 bp, at least every 3 bp, at least every 4 bp, at least every 5 bp, at least every 6 bp, at least every 7 bp, at least every 8 bp, at least every 9 bp, at least every 10 bp, at least every 11 bp, at least every 12 bp, at least every 13 bp, at least every 14 bp, at least every 15 bp, at least every 16 bp, at least every 17 bp, at least every 18 bp, at least every 19 bp, 20 bp, at least every 25 bp, at least every 30 bp, at least every 40 bp, at least every 50 bp, at least every 100 bp, at least every 200 bp, at least every 300 bp, at least every 400 bp, at least every 500 bp, at least every 600 bp, at least every 700 bp, at least every 800 bp, at least every 900 bp, at least every 1000 bp, at least every 2500 bp, at least every 5000 bp, at least every 10,000 bp, at least every 15,000 bp, at least every 20,000 bp, at least every 25,000 bp, at least every 50,000 bp, at least every 100,000 bp, at least every 250,000 bp, at least every 500,000 bp, at least every 750,000 bp, or even at least every 1,000,000 bp across a genome of interest.
In some embodiments, the collection of nucleic acids encoding for gNAs comprise a third segment encoding for a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence, wherein the segments in the collection vary in their specificity for protein members of the nucleic acid-guided nuclease system (e.g., CRISPR/Cas system). For example, a collection of nucleic acids encoding for gNAs as provided herein, can comprise members whose third segment encode for a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence specific for a first nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein; and also comprises members whose third segment encodes for a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence specific for a second nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein, wherein the first and second nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins are not the same. In some embodiments, a collection of nucleic acids encoding for gNAs as provided herein comprises members that exhibit specificity to at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or even at least 20 nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins. In one specific embodiment, a collection of nucleic acids encoding for gNAs as provided herein comprises members that exhibit specificity for a Cas9 protein and another protein selected from the group consisting of Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.

Sequences of Interest

Provided herein are gNAs and collections of gNAs, derived from any source DNA (for example from genomic DNA, cDNA, artificial DNA, DNA libraries), that can be used to target sequences of interest in a sample for a variety of applications including, but not limited to, enrichment, depletion, capture, partitioning, labeling, regulation, and editing. The gNAs comprise a targeting sequence, directed at sequences of interest.
In some embodiments, the sequences of interest are genomic sequences (genomic DNA). In some embodiments, the sequences of interest are mammalian genomic sequences. In some embodiments, the sequences of interest are eukaryotic genomic sequences. In some embodiments, the sequences of interest are prokaryotic genomic sequences. In some embodiments, the sequences of interest are viral genomic sequences. In some embodiments, the sequences of interest are bacterial genomic sequences. In some embodiments, the sequences of interest are plant genomic sequences. In some embodiments, the sequences of interest are microbial genomic sequences. In some embodiments, the sequences of interest are genomic sequences from a parasite, for example a eukaryotic parasite. In some embodiments, the sequences of interest are host genomic sequences (e.g., the host organism of a microbiome, a parasite, or a pathogen). In some embodiments, the sequences of interest are abundant genomic sequences, such as sequences from the genome or genomes of the most abundant species in a sample.
In some embodiments, the sequences of interest comprise repetitive DNA. In some embodiments, the sequences of interest comprise abundant DNA. In some embodiments, the sequences of interest comprise mitochondrial DNA. In some embodiments, the sequences of interest comprise ribosomal DNA. In some embodiments, the sequences of interest comprise centromeric DNA. In some embodiments, the sequences of interest comprise DNA comprising Alu elements (Alu DNA). In some embodiments, the sequences of interest comprise long interspersed nuclear elements (LINE DNA). In some embodiments, the sequences of interest comprise short interspersed nuclear elements (SINE DNA). In some embodiments, the abundant DNA comprises ribosomal DNA.
In some embodiments, the sequences of interest comprise single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), cancer genes, inserts, deletions, structural variations, exons, genetic mutations, or regulatory regions.
In some embodiments, the sequences of interest can be a genomic fragment, comprising a region of the genome, or the whole genome itself. In one embodiment, the genome is a DNA genome. In another embodiment, the genome is a RNA genome.
In some embodiments, the sequences of interest are from a eukaryotic or prokaryotic organism; from a mammalian organism or a non-mammalian organism; from an animal or a plant; from a bacteria or virus from an animal parasite; from a pathogen.
In some embodiments, the sequences of interest are from any mammalian organism. In one embodiment the mammal is a human. In another embodiment the mammal is a livestock animal, for example a horse, a sheep, a cow, a pig, or a donkey. In another embodiment, a mammalian organism is a domestic pet, for example a cat, a dog, a gerbil, a mouse, a rat. In another embodiment the mammal is a type of a monkey.
In some embodiments, the sequences of interest are from any bird or avian organism. An avian organism includes but is not limited to chicken, turkey, duck and goose.
In some embodiments, the sequences of interest are from a plant. In one embodiment, the plant is rice, maize, wheat, rose, grape, coffee, fruit, tomato, potato, or cotton.
In some embodiments, the sequences of interest are from a species of bacteria. In one embodiment, the bacteria are tuberculosis-causing bacteria.
In some embodiments, the sequences of interest are from a virus.
In some embodiments, the sequences of interest are from a species of fungi.
In some embodiments, the sequences of interest are from a species of algae.
In some embodiments, the sequences of interest are from any mammalian parasite.
In some embodiments, the sequences of interest are obtained from any mammalian parasite. In one embodiment, the parasite is a worm. In another embodiment, the parasite is a malaria-causing parasite. In another embodiment, the parasite is a Leishmaniasis-causing parasite. In another embodiment, the parasite is an amoeba.
In some embodiments, the sequences of interest are from a pathogen.

Targeting Sequences

As used herein, a targeting sequence is one that directs the gNA to the sequences of interest in a sample. For example, a targeting sequence targets a particular sequence of interest, for example the targeting sequence targets a genomic sequence of interest.
Provided herein are gNAs and collections of gNAs that comprise a segment that comprises a targeting sequence. Also provided herein, are nucleic acids encoding for gNAs, and collections of nucleic acids encoding for gNAs that comprise a segment encoding for a targeting sequence.
In some embodiments, the targeting sequence comprises DNA.
In some embodiments, the targeting sequence comprises RNA.
In some embodiments, the targeting sequence comprises RNA, and shares at least 70% sequence identity, at least 75% sequence identity, at least 80% sequence identity, at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or shares 100% sequence identity to a sequence 5′ to a PAM sequence on a sequence of interest, except that the RNA comprises uracils instead of thymines. In some embodiments, the PAM sequence is AGG, CGG, or TGG.
In some embodiments, the targeting sequence comprises DNA, and shares at least 70% sequence identity, at least 75% sequence identity, at least 80% sequence identity, at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or shares 100% sequence identity to a sequence 5′ to a PAM sequence on a sequence of interest.
In some embodiments, the targeting sequence comprises RNA and is complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the targeting sequence is at least 70% complementary, at least 75% complementary, at least 80% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, or is 100% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the PAM sequence is AGG, CGG, or TGG.
In some embodiments, the targeting sequence comprises DNA and is complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the targeting sequence is at least 70% complementary, at least 75% complementary, at least 80% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, or is 100% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the PAM sequence is AGG, CGG, or TGG.
In some embodiments, a DNA encoding for a targeting sequence of a gRNA shares at least 70% sequence identity, at least 75% sequence identity, at least 80% sequence identity, at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or shares 100 sequence identity to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence. In some embodiments, the PAM sequence is AGG, CGG, or TGG.
In some embodiments, a DNA encoding for a targeting sequence of a gRNA is complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence and is at least 70% complementary, at least 75% complementary, at least 80% complementary, at least 85% complementary, at least 90% complementary, at least 95% complementary, or is 100% complementary to a sequence 5′ to a PAM sequence on a sequence of interest. In some embodiments, the PAM sequence is AGG, CGG, or TGG.

Nucleic Acid-Guided Nuclease System Proteins

Provided herein are gNAs and collections of gNAs comprising a segment that comprises a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence. Also provided herein, are nucleic acids encoding for gNAs, and collections of nucleic acids encoding for gNAs that comprise a segment encoding a nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) protein-binding sequence. A nucleic acid-guided nuclease system can be an RNA-guided nuclease system. A nucleic acid-guided nuclease system can be a DNA-guided nuclease system.
Methods of the present disclosure can utilize nucleic acid-guided nucleases. As used herein, a “nucleic acid-guided nuclease” is any nuclease that cleaves DNA, RNA or DNA/RNA hybrids, and which uses one or more nucleic acid guide nucleic acids (gNAs) to confer specificity. Nucleic acid-guided nucleases include CRISPR/Cas system proteins as well as non-CRISPR/Cas system proteins.
The nucleic acid-guided nucleases provided herein can be DNA guided DNA nucleases; DNA guided RNA nucleases; RNA guided DNA nucleases; or RNA guided RNA nucleases. The nucleases can be endonucleases. The nucleases can be exonucleases. In one embodiment, the nucleic acid-guided nuclease is a nucleic acid-guided-DNA endonuclease. In one embodiment, the nucleic acid-guided nuclease is a nucleic acid-guided-RNA endonuclease.
A nucleic acid-guided nuclease system protein-binding sequence is a nucleic acid sequence that binds any protein member of a nucleic acid-guided nuclease system. For example, a CRISPR/Cas system protein-binding sequence is a nucleic acid sequence that binds any protein member of a CRISPR/Cas system.
In some embodiments, the nucleic acid-guided nuclease is selected from the group consisting of CAS Class I Type 1, CAS Class I Type III, CAS Class 1 Type IV, CAS Class II Type 11, and CAS Class 11 Type V. In some embodiments, CRISPR/Cas system proteins include proteins from CRISPR Type I systems, CRISPR Type II systems, and CRISPR Type III systems. In some embodiments, the nucleic acid-guided nuclease is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, Csf1, C2c2, and NgAgo.
In some embodiments, nucleic acid-guided nuclease system proteins (e.g., CRISPR/Cas system proteins) can be from any bacterial or archaeal species.
In some embodiments, the nucleic acid-guided nuclease system proteins (e.g., CRISPR/Cas system proteins) are from, or are derived from nucleic acid-guided nuclease system proteins (e.g., CRISPR/Cas system proteins) from Streptococcus pyogenes, Staphylococcus aureus, Neisseria meningitidis, Streptococcus thermophiles, Treponema denticola, Francisella tularensis, Pasteurella multocida, Campylobacter jejuni, Campylobacter lari, Mycoplasma gallisepticum, Nitratifractor salsuginis, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, Gluconacetobacter diazotrophicus, Azospirillum, Sphaerochaeta globus, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Legionella pneumophila, Suterella wadsworthensis, or Corynebacter diphtheria.
In some embodiments, examples of nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins can be naturally occurring or engineered versions.
In some embodiments, naturally occurring nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins include Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. Engineered versions of such proteins can also be employed.
In some embodiments, engineered examples of nucleic acid-guided nuclease system (e.g., CRISPR/Cas system) proteins include catalytically dead nucleic acid-guided nuclease system proteins. The term “catalytically dead” generally refers to a nucleic acid-guided nuclease system protein that has inactivated nucleases (e.g., HNH and RuvC nucleases). Such a protein can bind to a target site in any nucleic acid (where the target site is determined by the guide NA), but the protein is unable to cleave or nick the target nucleic acid (e.g., double-stranded DNA). In some embodiments, the nucleic acid-guided nuclease system catalytically dead protein is a catalytically dead CRISPR/Cas system protein, such as catalytically dead Cas9 (dCas9). Accordingly, the dCas9 allows separation of the mixture into unbound nucleic acids and dCas9-bound fragments. In one embodiment, a dCas9/gRNA complex binds to targets determined by the gRNA sequence. The dCas9 bound can prevent cutting by Cas9 while other manipulations proceed. In another embodiment, the dCas9 can be fused to another enzyme, such as a transposase, to target that enzyme's activity to a specific site. Naturally occurring catalytically dead nucleic acid-guided nuclease system proteins can also be employed.
In some embodiments, engineered examples of nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins also include nucleic acid-guided nickases (e.g., Cas nickases). A nucleic acid-guided nickase refers to a modified version of a nucleic acid-guided nuclease system protein, containing a single inactive catalytic domain. In one embodiment, the nucleic acid-guided nickase is a Cas nickase, such as Cas9 nickase. A Cas9 nickase may contain a single inactive catalytic domain, for example, either the RuvC- or the HNH-domain. With only one active nuclease domain, the Cas9 nickase cuts only one strand of the target DNA, creating a single-strand break or “nick”. Depending on which mutant is used, the guide NA-hybridized strand or the non-hybridized strand may be cleaved. Nucleic acid-guided nickases bound to 2 gNAs that target opposite strands will create a double-strand break in a target double-stranded DNA. This “dual nickase” strategy can increase the specificity of cutting because it requires that both nucleic acid-guided nuclease/gNA (e.g., Cas9/gRNA) complexes be specifically bound at a site before a double-strand break is formed. Naturally occurring nickase nucleic acid-guided nuclease system proteins can also be employed.
In some embodiments, engineered examples of nucleic acid-guided nuclease system proteins also include nucleic acid-guided nuclease system fusion proteins. For example, a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein may be fused to another protein, for example an activator, a repressor, a nuclease, a fluorescent molecule, a radioactive tag, or a transposase.
In some embodiments, the nucleic acid-guided nuclease system protein-binding sequence comprises a gNA (e.g., gRNA) stem-loop sequence.
In some embodiments, a double-stranded DNA sequence encoding the gNA (e.g., gRNA) stem-loop sequence comprises the following DNA sequence on one strand (5′>3′, GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCG AGTCGGTGCTTTTTTT) (SEQ ID NO: 3), and its reverse-complementary DNA on the other strand (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4).
In some embodiments, a single-stranded DNA sequence encoding the gNA (e.g., gRNA) stem-loop sequence comprises the following DNA sequence: (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4), wherein the single-stranded DNA serves as a transcription template.
In some embodiments, the gNA (e.g., gRNA) stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU) (SEQ ID NO: 1)
In some embodiments, a double-stranded DNA sequence encoding the gNA (e.g., gRNA) stem-loop sequence comprises the following DNA sequence on one strand (5′>3′, GTTTTAGAGCTATGCTGGAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGGCACCGAGTCGGTGCTTTTTTTC) (SEQ ID NO: 5), and its reverse-complementary DNA on the other strand (5′>3′, GAAAAAAAGCACCGACTCGGTGCCAITTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6).
In some embodiments, a single-stranded DNA sequence encoding the gNA (e.g., gRNA) stem-loop sequence comprises the following DNA sequence: (5′>3′, GAAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6), wherein the single-stranded DNA serves as a transcription template.
In some embodiments, the gNA (e.g., gRNA) stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC) (SEQ ID NO: 2).
In some embodiments, provided herein is a nucleic acid encoding for a gNA (e.g., gRNA) comprising a first segment comprising a regulatory region; a second segment encoding a targeting sequence; and a third segment comprising a nucleic acid encoding a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein-binding sequence. In some embodiments, the third segment comprises a single transcribed component, which upon transcription yields a NA (e.g., RNA) stem-loop sequence. In some embodiments, the third segment comprising a single transcribed component that encodes for the gNA (e.g., gRNA) stem-loop sequence is double-stranded, comprises the following DNA sequence on one strand (5′>3′, GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCG AGTCGGTGCTTTTTTTTT) (SEQ ID NO: 3), and its reverse-complementary DNA on the other strand (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4). In some embodiments, the third segment comprising a single transcribed component that encodes for the gNA (e.g., gRNA) stem-loop sequence is single-stranded, and comprises the following DNA sequence: (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATITTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4), wherein the single-stranded DNA serves as a transcription template. In some embodiments, upon transcription from the single transcribed component, the resulting gNA (e.g., gRNA) stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU) (SEQ ID NO: 1). In some embodiments, the third segment comprising a single transcribed component that encodes for the gNA (e.g., gRNA) stem-loop sequence is double-stranded, comprises the following DNA sequence on one strand (5′>3′, GTTTTAGAGCTATGCTGGAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGGCACCGAGTCGGTGCTTTTTTTC) (SEQ ID NO: 5), and its reverse-complementary DNA on the other strand (5′>3′, GAAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6). In some embodiments, the third segment comprising a single transcribed component that encodes for the gNA (e.g., gRNA) stem-loop sequence is single-stranded, and comprises the following DNA sequence: (5′>3′, GAAAAAAAGCACCGACTCGGTGCCACUITITrCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6), wherein the single-stranded DNA serves as a transcription template. In some embodiments, upon transcription from the single transcribed component, the yielded gRNA stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC) (SEQ ID NO: 2). In some embodiments, the third segment comprises two sub-segments, which encode for a crRNA and a tracrRNA upon transcription. In some embodiment, the crRNA does not comprise the N20 plus the extra sequence which can hybridize with tracrRNA. In some embodiments, the crRNA comprises the extra sequence which can hybridize with tracrRNA. In some embodiments, the two sub-segments are independently transcribed. In some embodiments, the two sub-segments are transcribed as a single unit. In some embodiments, the DNA encoding the crRNA comprises N_targetGTTTTAGAGCTATGCTGTTTTG (SEQ ID NO: 7), where N_targetrepresents the targeting sequence. In some embodiments, the DNA encoding the tracrRNA comprises the sequence GGAACCATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGC ACCGAGTCGGTGCTTTTTTT (SEQ ID NO: 8).
In some embodiments, provided herein is a nucleic acid encoding for a gNA (e.g., gRNA) comprising a first segment comprising a regulatory region; a second segment encoding a targeting sequence; and a third segment comprising a nucleic acid encoding a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein-binding sequence. In some embodiments, the third segment comprises a DNA sequence, which upon transcription yields a gRNA stem-loop sequence capable of binding a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein. In one embodiment, the DNA sequence can be double-stranded. In some embodiments, the third segment double stranded DNA comprises the following DNA sequence on one strand (5′>3′, GTITAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCG AGTCGGTGCTTTTTTT) (SEQ ID NO: 3), and its reverse-complementary DNA on the other strand (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4). In some embodiments, the third segment double stranded DNA comprises the following DNA sequence on one strand (5′>3′, GTTITAGAGCTATGCTGGAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGGCACCGAGTCGGTGCTTTTTTTC) (SEQ ID NO: 5), and its reverse-complementary DNA on the other strand (5′>3′, GAAAAAAAGCACCGACTCGGTGCCACTrFITCAAGTTGATAACGGACTAGCCTTATTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6). In one embodiment, the DNA sequence can be single-stranded. In some embodiments, the third segment single stranded DNA comprises the following DNA sequence (5′>3′, AAAAAAAGCACCGACTCGGTGCCACTITrrICAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTAT TTCTAGCTCTAAAAC) (SEQ ID NO: 4), wherein the single-stranded DNA serves as a transcription template. In some embodiments, the third segment single stranded DNA comprises the following DNA sequence (5′>3′, GAAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAACTTGCT ATGCTGTTTCCAGCATAGCTCTAAAAC) (SEQ ID NO: 6), wherein the single-stranded DNA serves as a transcription template. In some embodiments, the third segment comprises a DNA sequence which, upon transcription, yields a first RNA sequence that is capable of forming a hybrid with a second RNA sequence, and which hybrid is capable of CRISPR/Cas system protein binding. In some embodiments, the third segment is double-stranded DNA comprising the DNA sequence on one strand: (5′>3′, GTTTTAGAGCTATGCTGTTTTG) (SEQ ID NO: 9) and its reverse complementary DNA sequence on the other strand: (5′>3′, CAAAACAGCATAGCTCTAAAAC) (SEQ ID NO: 10). In some embodiments, the third segment is single-stranded DNA comprising the DNA sequence of (5′>3′, CAAAACAGCATAGCTCTAAAAC) (SEQ ID NO: 10). In some embodiments, the second segment and the third segment together encode for a crRNA sequence. In some embodiments, the second RNA sequence that is capable of forming a hybrid with the first RNA sequence encoded by the third segment of the nucleic acid encoding a gRNA is a tracrRNA. In some embodiments, the tracrRNA comprises the sequence (5′>3′, GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUUUUU) (SEQ ID NO: 11). In some embodiments, the tracrRNA is encoded by a double-stranded DNA comprising sequence of (5′>3′, GGAACCATTCAAAACAGCATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGC ACCGAGTCGGTGCTTTTTTT) (SEQ ID NO: 8), and optionally fused with a regulatory sequence at its 5′ end. In some embodiments, the regulatory sequence can be bound by a transcription factor. In some embodiments, the regulatory sequence is a promoter. In some embodiments, the regulatory sequence is a T7 promoter, comprising the sequence of (5′>3′, GCCTCGAGCTAATACGACTCACTATAGAG) (SEQ ID NO: 12).
In some embodiments, provided herein is a nucleic acid encoding for a gNA comprising a first segment comprising a regulatory region; a second segment encoding a targeting sequence; and a third segment comprising a nucleic acid encoding a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein-binding sequence. In some embodiments, the third segment encodes for a RNA sequence that, upon post-transcriptional cleavage, yields a first RNA segment and a second RNA segment. In some embodiments, the first RNA segment comprises a crRNA and the second RNA segment comprises a tracrRNA, which can form a hybrid and together, provide for nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein binding. In some embodiments, the third segment further comprises a spacer in between the transcriptional unit for the first RNA segment and the second RNA segment, which spacer comprises an enzyme cleavage site.
In some embodiments, provided herein is a gNA (e.g., gRNA) comprising a first NA segment comprising a targeting sequence and a second NA segment comprising a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein-binding sequence. In some embodiments, the size of the first segment is greater than 30 bp. In some embodiments, the second segment comprises a single segment, which comprises the gRNA stem-loop sequence. In some embodiments, the gRNA stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGCUUUUUUU) (SEQ ID NO: 1). In some embodiments, the gRNA stem-loop sequence comprises the following RNA sequence: (5′>3′, GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGA AAAAGUGGCACCGAGUCGGUGCUUUUUUUC) (SEQ ID NO: 2). In some embodiments, the second segment comprises two sub-segments: a first RNA sub-segment (crRNA) that forms a hybrid with a second RNA sub-segment (tracrRNA), which together act to direct nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein binding. In some embodiments, the sequence of the second sub-segment comprises GUUUUAGAGCUAUGCUGUUUUG. In some embodiments, the first RNA segment and the second RNA segment together forms a crRNA sequence. In some embodiments, the other RNA that will form a hybrid with the second RNA segment is a tracrRNA. In some embodiments the tracrRNA comprises the sequence of 5′>3′, GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 11).

CRISPR/Cas System Nucleic Acid-Guided Nucleases

In some embodiments, CRISPR/Cas system proteins are used in the embodiments provided herein. In some embodiments, CRISPR/Cas system proteins include proteins from CRISPR Type I systems, CRISPR Type II systems, and CRISPR Type III systems.
In some embodiments, CRISPR/Cas system proteins can be from any bacterial or archaeal species.
In some embodiments, the CRISPR/Cas system protein is isolated, recombinantly produced, or synthetic.
In some embodiments, the CRISPR/Cas system proteins are from, or are derived from CRISPR/Cas system proteins from Streptococcus pyogenes, Staphylococcus aureus, Neisseria meningitidis, Streptococcus thermophiles, Treponema denticola, Francisella tularensis, Pasteurella multocida, Campylobacter jejuni, Campylobacter lari, Mycoplasma gallisepticum, Nitratifractor salsuginis, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, Gluconacetobacter diazotrophicus, Azospirillum, Sphaerochaeta globus, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Legionella pneumophila, Suterella wadsworthensis, or Corynebacter diphtheria.
In some embodiments, examples of CRISPR/Cas system proteins can be naturally occurring or engineered versions.
In some embodiments, naturally occurring CRISPR/Cas system proteins can belong to CAS Class I Type I, III, or IV, or CAS Class II Type II or V, and can include Cas9, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cmr5, Csf1, C2c2, and Cpf1.
In an exemplary embodiment, the CRISPR/Cas system protein comprises Cas9.
A “CRISPR/Cas system protein-gNA complex” refers to a complex comprising a CRISPR/Cas system protein and a guide NA (e.g. a gRNA or a gDNA). Where the gNA is a gRNA, the gRNA may be composed of two molecules, i.e., one RNA (“crRNA”) which hybridizes to a target and provides sequence specificity, and one RNA, the “tracrRNA”, which is capable of hybridizing to the crRNA. Alternatively, the guide RNA may be a single molecule (i.e., a gRNA) that contains crRNA and tracrRNA sequences.
A CRISPR/Cas system protein may be at least 60% identical (e.g., at least 70%, at least 80%, or 90% identical, at least 95% identical or at least 98% identical or at least 99% identical) to a wild type CRISPR/Cas system protein. The CRISPR/Cas system protein may have all the functions of a wild type CRISPR/Cas system protein, or only one or some of the functions, including binding activity, nuclease activity, and nuclease activity.
The term “CRISPR/Cas system protein-associated guide NA” refers to a guide NA. The CRISPR/Cas system protein-associated guide NA may exist as isolated NA, or as part of a CRISPR/Cas system protein-gNA complex.

Cas9

In some embodiments, the CRISPR/Cas System protein nucleic acid-guided nuclease is or comprises Cas9. The Cas9 of the present invention can be isolated, recombinantly produced, or synthetic.
Examples of Cas9 proteins that can be used in the embodiments herin can be found in F. A. Ran, L. Cong, W. X. Yan, D. A. Scott, J. S. Gootenberg, A. J. Kriz, B. Zetsche, O. Shalem, X. Wu, K. S. Makarova, E. V. Koonin, P. A. Sharp, and F. Zhang; “In vivo genome editing using Staphylococcus aureus Cas9” Nature 520, 186-191 (9 Apr. 2015) doi:10.1038/nature14299, which is incorporated herein by reference.
In some embodiments, the Cas9 is a Type II CRISPR system derived from Streptococcus pyogenes, Staphylococcus aureus, Neisseria meningitidis, Streptococcus thermophiles, Treponema denticola, Francisella tularensis, Pasteurella multocida, Campylobacter jejuni, Campylobacter lar, Mycoplasma gallisepticum, Nitratifractor salsuginis, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, Gluconacetobacter diazotrophicus, Azospirillum, Sphaerochaeta globus, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Legionella pneumophila, Suterella wadsworthensis, or Corynebacter diphtheria.
In some embodiments, the Cas9 is a Type II CRISPR system derived from S. pyogenes and the PAM sequence is NGG located on the immediate 3′ end of the target specific guide sequence. The PAM sequences of Type II CRISPR systems from exemplary bacterial species can also include: Streptococcus pyogenes (NGG), Staph aureus (NNGRRT), Neisseria meningitidis (NNNNGA TT), Streptococcus thermophilus (NNAGAA) and Treponema denticola (NAAAAC) which are all usable without deviating from the present invention.
In one exemplary embodiment, Cas9 sequence can be obtained, for example, from the pX330 plasmid (available from Addgene), re-amplified by PCR then cloned into pET30 (from EMD biosciences) to express in bacteria and purify the recombinant 6His tagged protein.
A “Cas9-gNA complex” refers to a complex comprising a Cas9 protein and a guide NA. A Cas9 protein may be at least 60% identical (e.g., at least 70%, at least 80%, or 90% identical, at least 95% identical or at least 98% identical or at least 99% identical) to a wild type Cas9 protein, e.g., to the Streptococcus pyogenes Cas9 protein. The Cas9 protein may have all the functions of a wild type Cas9 protein, or only one or some of the functions, including binding activity, nuclease activity, and nuclease activity.
The term “Cas9-associated guide NA” refers to a guide NA as described above. The Cas9-associated guide NA may exist isolated, or as part of a Cas9-gNA complex.

Non-CRISPR/Cas System Nucleic Acid-Guided Nucleases

In some embodiments, non-CRISPR/Cas system proteins are used in the embodiments provided herein.
In some embodiments, the non-CRISPR/Cas system proteins can be from any bacterial or archaeal species.
In some embodiments, the non-CRISPR/Cas system protein is isolated, recombinantly produced, or synthetic.
In some embodiments, the non-CRISPR/Cas system proteins are from, or are derived from Aquifex aeolicus, Thermus thermophilus, Streptococcus pyogenes, Staphylococcus aureus, Neisseria meningitidis, Streptococcus thermophiles, Treponema denticola, Francisella tularensis, Pasteurella multocida, Campylobacter jejuni, Campylobacter lari, Mycoplasma gallisepticum, Nitratifractor salsuginis, Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, Gluconacetobacter diazotrophicus, Azospirillum, Sphaerochaeta globus, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus, Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Legionella pneumophila, Suterella wadsworthensis, Natronobacterium gregoryi, or Corynebacter diphtheria.
In some embodiments, the non-CRISPR/Cas system proteins can be naturally occurring or engineered versions.
In some embodiments, a naturally occurring non-CRISPR/Cas system protein is NgAgo (Argonaute from Natronobacterium gregoryi).
A “non-CRISPR/Cas system protein-gNA complex” refers to a complex comprising a non-CRISPR/Cas system protein and a guide NA (e.g. a gRNA or a gDNA). Where the gNA is a gRNA, the gRNA may be composed of two molecules, i.e., one RNA (“crRNA”) which hybridizes to a target and provides sequence specificity, and one RNA, the “tracrRNA”, which is capable of hybridizing to the crRNA. Alternatively, the guide RNA may be a single molecule (i.e., a gRNA) that contains crRNA and tracrRNA sequences.
A non-CRISPR/Cas system protein may be at least 60% identical (e.g., at least 70%, at least 80%, or 90% identical, at least 95% identical or at least 98% identical or at least 99% identical) to a wild type non-CRISPR/Cas system protein. The non-CRISPR/Cas system protein may have all the functions of a wild type non-CRISPR/Cas system protein, or only one or some of the functions, including binding activity, nuclease activity, and nuclease activity.
The term “non-CRISPR/Cas system protein-associated guide NA” refers to a guide NA. The non-CRISPR/Cas system protein-associated guide NA may exist as isolated NA, or as part of a non-CRISPR/Cas system protein-gNA complex.

Catalytically Dead Nucleic Acid-Guided Nucleases

In some embodiments, engineered examples of nucleic acid-guided nucleases include catalytically dead nucleic acid-guided nucleases (CRISPR/Cas system nucleic acid-guided nucleases or non-CRISPR/Cas system nucleic acid-guided nucleases). The term “catalytically dead” generally refers to a nucleic acid-guided nuclease that has inactivated nucleases, for example inactivated HNH and RuvC nucleases. Such a protein can bind to a target site in any nucleic acid (where the target site is determined by the guide NA), but the protein is unable to cleave or nick the nucleic acid.
Accordingly, the catalytically dead nucleic acid-guided nuclease allows separation of the mixture into unbound nucleic acids and catalytically dead nucleic acid-guided nuclease-bound fragments. In one exemplary embodiment, a dCas9/gRNA complex binds to the targets determined by the gRNA sequence. The dCas9 bound can prevent cutting by Cas9 while other manipulations proceed.
In another embodiment, the catalytically dead nucleic acid-guided nuclease can be fused to another enzyme, such as a transposase, to target that enzyme's activity to a specific site.
In some embodiments, the catalytically dead nucleic acid-guided nuclease is dCas9, dCpf1, dCas3, dCas8a-c, dCas10, dCse1, dCsy1, dCsn2, dCas4, dCsm2, dCm5, dCsf1, dC2C2, or dNgAgo.
In one exemplary embodiment the catalytically dead nucleic acid-guided nuclease protein is a dCas9.

Nucleic Acid-Guided Nuclease Nickases

In some embodiments, engineered examples of nucleic acid-guided nucleases include nucleic acid-guided nuclease nickases (referred to interchangeably as nickase nucleic acid-guided nucleases).
In some embodiments, engineered examples of nucleic acid-guided nucleases include CRISPR/Cas system nickases or non-CRISPR/Cas system nickases, containing a single inactive catalytic domain.
In some embodiments, the nucleic acid-guided nuclease nickase is a Cas9 nickase, Cpf1 nickase, Cas3 nickase, Cas8a-c nickase, Cas10 nickase, Cse1 nickase, Csy1 nickase, Csn2 nickase, Cas4 nickase, Csm2 nickase, Cm5 nickase, Csf1 nickase, C2C2 nickase, or a NgAgo nickase.
In one embodiment, the nucleic acid-guided nuclease nickase is a Cas9 nickase.
In some embodiments, a nucleic acid-guided nuclease nickase can be used to bind to target sequence. With only one active nuclease domain, the nucleic acid-guided nuclease nickase cuts only one strand of a target DNA, creating a single-strand break or “nick”. Depending on which mutant is used, the guide NA-hybridized strand or the non-hybridized strand may be cleaved. nucleic acid-guided nuclease nickases bound to 2 gNAs that target opposite strands can create a double-strand break in the nucleic acid. This “dual nickase” strategy increases the specificity of cutting because it requires that both nucleic acid-guided nuclease/gNA complexes be specifically bound at a site before a double-strand break is formed.
In exemplary embodiments, a Cas9 nickase can be used to bind to target sequence. The term “Cas9 nickase” refers to a modified version of the Cas9 protein, containing a single inactive catalytic domain, i.e., either the RuvC- or the HNH-domain. With only one active nuclease domain, the Cas9 nickase cuts only one strand of the target DNA, creating a single-strand break or “nick”. Depending on which mutant is used, the guide RNA-hybridized strand or the non-hybridized strand may be cleaved. Cas9 nickases bound to 2 gRNAs that target opposite strands will create a double-strand break in the DNA. This “dual nickase” strategy can increase the specificity of cutting because it requires that both Cas9/gRNA complexes be specifically bound at a site before a double-strand break is formed.
Capture of DNA can be carried out using a nucleic acid-guided nuclease nickase. In one exemplary embodiment, a nucleic acid-guided nuclease nickase cuts a single strand of double stranded nucleic acid, wherein the double stranded region comprises methylated nucleotides.

Dissociable and Thermostable Nucleic Acid-Guided Nucleases

In some embodiments, thermostable nucleic acid-guided nucleases are used in the methods provided herein (thermostable CRISPR/Cas system nucleic acid-guided nucleases or thermostable non-CRISPR/Cas system nucleic acid-guided nucleases). In such embodiments, the reaction temperature is elevated, inducing dissociation of the protein; the reaction temperature is lowered, allowing for the generation of additional cleaved target sequences. In some embodiments, thermostable nucleic acid-guided nucleases maintain at least 50% activity, at least 55% activity, at least 60% activity, at least 65% activity, at least 70% activity, at least 75% activity, at least 80% activity, at least 85% activity, at least 90% activity, at least 95% activity, at least 96% activity, at least 97% activity, at least 98% activity, at least 99% activity, or 100% activity, when maintained for at least 75° C. for at least 1 minute. In some embodiments, thermostable nucleic acid-guided nucleases maintain at least 50% activity, when maintained for at least 1 minute at least at 75° C., at least at 80° C., at least at 85° C., at least at 90° C., at least at 91° C., at least at 92° C., at least at 93° C., at least at 94° C., at least at 95° C., 96° C., at least at 97° C., at least at 98° C., at least at 99° C., or at least at 100° C. In some embodiments, thermostable nucleic acid-guided nucleases maintain at least 50% activity, when maintained at least at 75° C. for at least 1 minute, 2 minutes, 3 minutes, 4 minutes, or 5 minutes. In some embodiments, a thermostable nucleic acid-guided nuclease maintains at least 50% activity when the temperature is elevated, lowered to 25° C.-50° C. In some embodiments, the temperature is lowered to 25° C., to 30° C., to 35° C. to 40° C., to 45° C., or to 50° C. In one exemplary embodiment, a thermostable enzyme retains at least 90% activity after 1 min at 95° C.
In some embodiments, the thermostable nucleic acid-guided nuclease is thermostable Cas9, thermostable Cpf1, thermostable Cas3, thermostable Cas8a-c, thermostable Cas10, thermostable Cse1, thermostable Csy1, thermostable Csn2, thermostable Cas4, thermostable Csm2, thermostable Cm5, thermostable Csf1, thermostable C2C2, or thermostable NgAgo.
In some embodiments, the thermostable CRISPR/Cas system protein is thermostable Cas9.
Thermostable nucleic acid-guided nucleases can be isolated, for example, identified by sequence homology in the genome of thermophilic bacteria Streptococcus thermophilus and Pyrococcus furiosus. Nucleic acid-guided nuclease genes can then be cloned into an expression vector. In one exemplary embodiment, a thermostable Cas9 protein is isolated.
In another embodiment, a thermostable nucleic acid-guided nuclease can be obtained by in vitro evolution of a non-thermostable nucleic acid-guided nuclease. The sequence of a nucleic acid-guided nuclease can be mutagenized to improve its thermostability.
Methods of Making Collections of gNAs
Provided herein are methods that enable the generation of a large number of diverse gRNAs, collections of gNAs, from any source nucleic acid (e.g., DNA). Methods provided herein can employ enzymatic methods including but not limited to digestion, ligation, extension, overhang filling, transcription, reverse transcription, amplification.
Generally, the method can comprise providing a nucleic acid (e.g., DNA); employing a first enzyme (or combinations of first enzymes) that cuts at a part of the PAM sequence in the nucleic acid, in a way that a residual nucleotide sequence from the PAM sequence is left; ligating an adapter that positions a restriction enzyme typeIIS site (an enzyme that cuts outside yet near its recognition motif) at a distance to eliminate the PAM sequence; employing a second typeIIS enzyme (or combination of second enzymes) to eliminate the PAM sequence together with the adapter; and fusing a sequence that can be recognized by protein members of the nucleic acid-guided nuclease (e.g., CRISPR/Cas) system, for example, a gRNA stem-loop sequence. In some embodiments, the first enzymatic reactions cuts part of the PAM sequence in a way that residual nucleotide sequence from the PAM sequence is left, and that the nucleotide sequence immediately 5′ to the PAM sequence can be any purine or pyrimidine, not just those with a cytosine 5′ to the PAM sequence, for example, not just those that are C/NGG or C/TAG, etc.
Table 1 shows exemplary strategies/protocols to convert any source nucleic acid (e.g., DNA) into a collection of gNAs (e.g., gRNAs) using different restriction enzymes.

TABLE 1

Exemplary strategies for preparing a collection of guide nucleic acids.

		First		3′ Adapter sequence with
CRISPR/Cas	PAM	Enzyme/		typeIIS enzyme site
System	Se-	Compo-		(provided with only one
Species	quence	nents	Strategy	strand sequence 5′→3′)

Streptococcus	NGG	CviPII	Nicks immediately 5′ of CCD sequence,	ggGACTCggatccctatagtc
pyogenes			nicks the other strand with T7 endonuclease	(SEQ ID NO: 4421)
(SP); SpCas9			I, blunt with T4 DNA polymerase; ligate to
			adapter; cut with MlyI to remove PAM and
			adapter; ligate gRNA stem-loop sequence at
			3′ end

Staphylococcus	NNGRRT	AlwI	Cut, blunt with T4 DNA polymerase; ligate to	ttttagcggccgcctgctgCTCtacaa
aureus	or		adapter SA; cut with EcoP15I to remove	agacgatgacgacaagcgt
(SA); SaCas9	NNGRR		PAM and adapter; blunt end; ligate gRNA	(SEQ ID NO: 4422)
	(N)		stem-loop sequence at 3′ end

Neisseria	NNNNGA	TfiI	Cut, blunt with T4 DNA polymerase; ligate to	TCgcggccgcttttattctgctgCTCt
meningitidis	TT		adapter NM; cut with EcoRI to eliminate	acaaagacgatgacgacaagcgt
(NM)			unwanted DNA and EcoP15I to remove PAM	(SEQ ID NO: 4428)
			and adapter; blunt end; ligate gRNA stem-
			loop sequence at 3′ end

Streptococcus	NNAGAA	BsmI	Cut, blunt with T4 DNA polymerase; ligate to	ttacggccgcttttattctgctgCTCt
thermophilus	W		adapter ST; cut with EcoP15I to remove PAM	acaaagacgatgacgacaagcgt
(ST)			and adapter; blunt end; ligate gRNA stem-	(SEQ ID NO: 4429)
			loop sequence at 3′ end

Treponema	NAAAAC	Cly7489I	Cut, blunt with T4 DNA polymerase; ligate to	tttagcggccgcctgecgCTCtacaaa
denticola		I	adapter TD; cut with EcoP15I to remove	gacgatgacgacaagcgt
(TD)			PAM and adapter	(SEQ ID NO: 4430)

Table 2 shows additional exemplary strategies/protocols to convert any source nucleic acid (e.g., DNA) into a collection of gNAs (e.g., gRNAs) using different restriction enzymes.

TABLE 2

Additional exemplary strategies for preparing a collection of guide nucleic acids.

CRISPR/		First		Adapter oligo sequence (with
Cas System	PAM	Enzyme/		Inosine overhangs, all in 5′→3′
Species	Sequence	Component	Exemplary Strategy	direction)

Streptococcus	NGG	CviPII	Nicks immediately 5′ of CCD	Adapter oligo I:
pyogenes (SP);			sequence, nicks the other strand	ggggGACTCggatccctatagtgatac
SpCas9			with T7 endonuclease I; ligate to	aaagacgatgacgacaagcg
			adapter; cut with MlyI to remove	(SEQ ID NO: 4404)
			PAM and 3′ adapter; ligate gRNA	Adapter oligo 2:
			stem-loop sequence at 3′ end	gcctcgagcta*atacgactcactatag
				ggatccaagtccc
				(* denotes a phosphorothioate
				backbone linkage)
				(SEQ ID NO: 4405)

Staphylococcus	NNGRRT or	AlwI	Cut; ligate to adapter SA; cut	Adapter oligo 1:
aureus (SA),	NNGRR(N)		with EcoP15I to remove PAM and 3′	IttttagcggccgcctgctgCTCtacaaa
SaCas9			adapter; blunt end; ligate gRNA	gacgatgacgacaagcgt
			stem-loop sequence at 3′ end	(SEQ ID NO: 4422)
				Adapter oligo 2:
				gagatcagcttctgcattgatgcGAGcag
				caggcggccgctaaaa
				(SEQ ID NO: 4423)

Neisseria	NNNNGATT	TfiI	Cut; ligate to adapter NM; cut	Adapter oligo 1:
meningitidis			with EcoP15I to remove PAM and	attTCgcggccgcttttattctgctgCTCt
(NM)			3′ adapter; blunt end; ligate	acaaagacgatgacgacaagcgt
			gRNA stem-loop sequence at 3′	(SEQ ID NO: 4424)
			end	Adapter oligo 2:
				gagatcagcttctgcattgatgcGAGcag
				cagaataaaagcggccgcGA
				(SEQ ID NO: 4425)

Streptococcus	NNAGAAW	BsmI	Cut; ligate to adapter ST; cut	Adapter oligo 1:
thermophilus			with EcoP15I to remove PAM and 3′	gcggccgcttttattctgctgCTCtacaaa
(ST)			adapter; blunt end; ligate gRNA	gacgatgacgacaagcgt
			stem-loop sequence at 3′ end	(SEQ ID NO: 4426)
				Adapter oligo 2:
				gagatcagcttctgcattgatgcGAGcag
				cagaataaaagcggccgcIG
				SEQ ID NO: 4427)

Exemplary applications of the compositions and methods described herein are provided in FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG. 6, and FIG. 7. The figures depict non-limiting exemplary embodiments of the present invention that includes a method of constructing a gNA library (e.g., gRNA library) from input nucleic acids (e.g., DNA), such as genomic DNA (e.g., human genomic DNA).
In FIG. 1, the starting material can be fragmented genomic DNA (e.g., human) or other source DNA. These fragments are blunt-ended before constructing the library 101. T7 promoter adapters are ligated to the blunt-ended DNA fragments 102, which is then PCR amplified. Nt.CviPII is then used to generate a nick on one strand of the PCR product immediately 5′ to the CCD sequence 103. T7 Endonuclease I cleaves on the opposite strand 1, 2, or 3 bp 5′ of the nick 104. The resulting DNA fragments are blunt-ended with T4 DNA Polymerase, leaving HGG sequence at the end of the DNA fragment 105. The resulting DNA is cleaned and recovered on beads. An adapter carrying MlyI recognition site is ligated to the blunt-ended DNA fragment immediately 3′ of HGG sequence 106. MlyI generates a blunt-end cleavage immediately 5′ to the HGG sequence, removing HGG together with the adapter sequence 107. The resulting DNA fragments are cleaned and recovered again on beads. A gRNA stem-loop sequence is then ligated to the blunt-end cleaved by MlyI, forming a gRNA library covering the human genome 108. This library of DNA is then PCR amplified and cleaned on beads, ready for in vitro transcription.
In FIG. 2, the starting material can intact genomic DNA (e.g., human) or other source DNA 201. Nt.CviPII and T7 Endonuclease I are used to generate nicks on each strand of the human genomic DNA, resulting in smaller DNA fragments 202. DNA fragments of 200-600 bp are size selected on beads, then ligated with Y-shaped adapters carrying a GG overhang on the 5′. One strand of the Y-shaped adapter contains a MlyI recognition site, wherein the other strand contains a mutated MlyI site and a T7 promoter sequence 203. Because of these features, after PCR amplification, the T7 promoter sequence is at the distal end of the HGG sequence, and the MlyI sequence is at the rear end of HGG 204. Digestion with MlyI generates a cleavage immediately 5′ of HGG sequence 205. MlyI generates a blunt-end cleavage immediately 5′ to the HGG sequence, removing HGG together with the adapter sequence 206. A gRNA stem-loop sequence is then ligated to the blunt-end cleaved by MlyI, forming a gRNA library covering the human genome. This library of DNA is then PCR amplified and cleaned on beads, ready for in vitro transcription.
In FIG. 3, the source DNA (e.g., genomic DNA) can be nicked 301, for example with a nicking enzyme. In some cases, the nicking enzyme can have a recognition site that is three or fewer bases in length. In some cases, CviPII is used, which can recognize and nick at a sequence of CCD (where D represents a base other than C). Nicks can be proximal, surrounding a region containing the sequence (represented by the thicker line) which will be used to yield the guide RNA N20 sequence. When nicks are proximal, a double stranded break can occur and lead to 5′ or 3′ overhangs 302. These overhangs can be repaired, for example with a polymerase (e.g., T4 polymerase). In some cases, such as with 5′ strands, repair can comprise synthesizing a complementary strand. In some case, such as with 3′ strands, repair can comprise removing overhangs. Repair can result in a blunt end including the N20 guide sequence and a sequence complementary to the nick recognition sequence (e.g., HGG, where H represents a base other than G).
In FIG. 4, continuing for example from the end of FIG. 3, different combinations of adapters can be ligated to the DNA to allow for the desired cleaving. Adapters with a recognition site for a nuclease enzyme that cuts 3 base pairs from the site (e.g., MlyI) can be ligated 401, and digestion at that site can be used to remove a left over sequence, such as an HGG sequence 402. Adapters with a recognition site for a nuclease that cuts 20 base pairs from the site (e.g., MmeI) 403. These adapters can also include a second recognition site for a nuclease that cuts the proper number of nucleotides from the site to later remove the first recognition site (e.g., BsaXI). The first enzyme can be used to cut 20 nucleotides down, thereby keeping the N20 sequence 404. Then, a promoter adapter (e.g., T7) can be ligated next to the N20 sequence 405. Then, the nuclease corresponding to the second recognition site (e.g., BsaXI) can be used to remove the adapter for the site that cuts 20 nucleotides away (e.g., MmeI) 406. Finally, the guide RNA stem-loop sequence adapter can be ligated to the N20 sequence 407 to prepare for guide RNA production.
Alternatively, the protocol shown in FIG. 5 can follow the end of a protocol such as that shown in FIG. 3. Adapters with a recognition site for a nuclease enzyme that cleaves 25 nucleotides from the site (e.g., EcoP151) can be ligated to the DNA 501. These adapters can also include a second recognition site for a nuclease that cuts the proper number of nucleotides from the site to later remove the first recognition site (e.g., Bac) and any other left-over sequence, such as HGG. The enzyme corresponding to the first recognition site (e.g., EcoP15I) can then be used to cleave after the N20 sequence 502. Then, a promoter adapter (e.g., T7) can be ligated next to the N20 sequence 503. The enzyme corresponding to the second recognition site (e.g., BaeI) can then be used to remove the recognition sites and any residual sequence (e.g., HGG) 504. Finally, the guide RNA stem-loop sequence adapter can be ligated (e.g., by single strand ligation) to the N20 sequence 505.
As an alternative to protocols such as that shown in FIG. 3, the protocol shown in FIG. 6 can be used in preparation for protocols such as those shown in FIG. 4 or FIG. 5. A nick can be introduced by a nicking enzyme (e.g., CviPII) 601. In some cases, the nick recognition site is three or fewer bases in length. In some cases, CviPII is used, which can recognize and nick at a sequence of CCD. A polymerase (e.g., Bst large fragment DNA polymerase) can then be used to synthesize a new DNA strand starting from the nick while displacing the old strand 602. Because of the DNA synthesis, the nick can be sealed and made available to be nicked again 603. Subsequent cycles of nicking and synthesis can be used to yield large amounts of target sequences 604. These single stranded copies of target sequences can be made double stranded, for example by random priming and extension. These double stranded nucleic acids comprising N20 sequences can then be further processed by methods disclosed herein, such as those shown in FIG. 4 or FIG. 5.
As another alternative to protocols such as that shown in FIG. 3 or FIG. 6, the protocol shown in FIG. 7 can be used in preparation for protocols such as those shown in FIG. 4 or FIG. 5. A nick can be introduced by a nicking enzyme (e.g., CviPII) 701. In some cases, the nicking enzyme recognition site is three or fewer bases in length. In some cases, CviPII is used, which can recognize and nick at a sequence of CCD. A polymeras (e.g., Bst large fragment DNA polymerase) can then be used to synthesize a new DNA strand starting from the nick while displacing the old strand (e.g., nicking endonuclease-mediated strand-displacement DNA amplification (NEMDA)). The reaction parameters can be adjusted to control the size of the single stranded DNA produced. For example, the nickase:polymerase ratio (e.g., CviPII:Bts large fragment polymerase ratio) can be adjusted. Reaction temperature can also be adjusted. Next, an oligonucleotide can be added 704 which has (in the 5′>3′ direction) a promoter (e.g., T7 promoter) 702 followed by a random n-mer (e.g., random 6-mer, random 8-mer) 703. The random n-mer region can bind to a region of the single stranded DNA generated previously. For example, binding can be conducted by denaturing at high temperature followed by rapid cool down, which can allow the random n-mer region to bind to the single stranded DNA generated by NEMDA. In some cases, the DNA is denatured at 98° C. for 7 minutes then cooled down rapidly to 10° C. Extension and/or amplification can be used to produce double-stranded DNA. Blunt ends can be produced, for example enzymatically (e.g., by treatment with DNA polymerase I at 20° C.). This can result in one end ending at the promoter (e.g., T7 promoter) and the other end ending at any nicking enzyme recognition sites (e.g., any CCD sites). These fragments can then be purified, for example by size selection (e.g., by gel purification, capillary electrophoresis, or other fragment separation techniques). In some cases, the target fragments are about 50 base pairs in length (adapter sequence (e.g., T7 adapter)+target N20 sequence+nicking enzyme recognition site or complement (e.g., HGG)). Fragments can then be ligated to an adapter comprising a nuclease recognition site for a nuclease that cuts an appropriate distance away to remove the nicking enzyme recognition site 705. For example, for a three-nucleotide long nicking enzyme recognition site (e.g., CCD for CviPII). BaeI can be used. The appropriate nuclease (e.g., BaeI) can then be used to remove the nuclease recognition site and the nicking enzyme recognition site 706. The remaining nucleic acid sequence (e.g., the N20 site) can then be ligated to the final stem-loop sequence for the guide RNA 707. Amplification (e.g., PCR) can be conducted. Guide RNAs can be produced.
In some embodiments, a collection of gNAs (e.g., gRNAs) targeting human mitochondrial DNA (mtDNA) is created, that can be used for directing nucleic acid-guided nuclease (e.g., Cas9) proteins, comprising the nucleic acid-guided nuclease (e.g., Cas9) target sequence. In some embodiments, the targeting sequence of this collection of gNAs (e.g., gRNAs) are encoded by DNA sequences comprising at least the 20 nt sequence provided in the second column from the right of Table 3 (if the NGG sequence is on positive strand) and Table 4 (if the NGG sequence is on negative strand). In some embodiments, a collection of gRNA nucleic acids, as provided herein, with specificity for human mitochondrial DNA, comprise a plurality of members, wherein the members comprise a plurality of targeting sequences provided in the second column from the right column of Table 3 and/or the second column from the right of Table 4.

TABLE 3

gRNA target sequence for human mtDNA carrying NGG sequence on the (+) strand.

	Chr end	nt sequence on the (+)		20 nt gRNA target
Chr start	position	strand containing gRNA		sequence
position	(+	target sequence followed	SEQ	(will encode the gRNA	SEQ
(+ strand)	strand)	by NGG	ID NO:	targeting sequence)	ID NO:

13	35	ATCACCCTATTAACCAC	13	ATCACCCTATTAACCA	436
		TCACGG		CTCA

14	36	TCACCCTATTAACCACT	14	TCACCCTATTAACCAC	437
		CACGGG		TCAC

32	54	ACGGGAGCTCTCCATGC	15	ACGGGAGCTCTCCATG	438
		ATTTGG		CATT

45	67	ATGCATTTGGTATTTTC	16	ATGCATTTGGTATTTT	439
		GTCTGG		CGTC

46	68	TGCATTTGGTATTTTCGT	17	TGCATTTGGTATTTTC	440
		CTGGG		GTCT

47	69	GCATTTGGTATTTTCGT	18	GCATTTGGTATTTTCG	441
		CTGGGG		TCTG

48	70	CATTTGGTATTTTCGTCT	19	CATTTGGTATTTTCGTC	442
		GGGGG		TGG

49	71	ATTTGGTATTTTCGTCTG	20	ATTTGGTATTTTCGTCT	443
		GGGGG		GGG

79	101	GCGATAGCATTGCGAGA	21	GCGATAGCATTGCGAG	444
		CGCTGG		ACGC

85	107	GCATTGCGAGACGCTGG	22	GCATTGCGAGACGCTG	445
		AGCCGG		GAGC

163	185	GCACCTACGTTCAATAT	23	GCACCTACGTTCAATA	446
		TACAGG		TTAC

207	229	GTTAATTAATTAATGCT	24	GTTAATTAATTAATGC	447
		TGTAGG		TTGT

301	323	AACCCCCCCTCCCCCGC	25	AACCCCCCCTCCCCCG	448
		TTCTGG		CTTC

388	410	AGATTTCAAATTTTATC	26	AGATTTCAAATTTTAT	449
		TTTTGG		CTTT

391	413	TTTCAAATTTTATCTTTT	27	TTTCAAATTTTATCTTT	450
		GGCGG		TGG

604	626	ATACACTGAAAATGTTT	28	ATACACTGAAAATGTT	451
		AGACGG		TAGA

605	627	TACACTGAAAATGTTTA	29	TACACTGAAAATGTTT	452
		GACGGG		AGAC

631	653	ACATCACCCCATAAACA	30	ACATCACCCCATAAAC	453
		AATAGG		AAAT

636	658	ACCCCATAAACAAATAG	31	ACCCCATAAACAAATA	454
		GTTTGG		GGTT

727	749	TCTAAATCACCACGATC	32	TCTAAATCACCACGAT	455
		AAAAGG		CAAA

788	810	TTAGCCTAGCCACACCC	33	TTAGCCTAGCCACACC	456
		CCACGG		CCCA

789	811	TAGCCTAGCCACACCCC	34	TAGCCTAGCCACACCC	457
		CACGGG		CCAC

851	873	AACTAAGCTATACTAAC	35	AACTAAGCTATACTAA	458
		CCCAGG		CCCC

852	874	ACTAAGCTATACTAACC	36	ACTAAGCTATACTAAC	459
		CCAGGG		CCCA

856	878	AGCTATACTAACCCCAG	37	AGCTATACTAACCCCA	460
		GGTTGG		GGGT

880	902	CAATTTCGTGCCAGCCA	38	CAATTTCGTGCCAGCC	461
		CCGCGG		ACCG

912	934	TAACCCAAGTCAATAGA	39	TAACCCAAGTCAATAG	462
		AGCCGG		AAGC

1009	1031	CACAAAATAGACTACG	40	ACACAAATAGACTACG	463
		AAAGTGG		AAAG

1051	1073	ACAATAGCTAAGACCCA	41	ACAATAGCTAAGACCC	464
		AACTGG		AAAC

1052	1074	CAATAGCTAAGACCCAA	42	CAATAGCTAAGACCCA	465
		ACTGGG		AACT

1148	1170	AGCCACAGCTTAAAACT	43	AGCCACAGCTTAAAAC	466
		CAAAGG		TCAA

1154	1176	AGCTTAAAACTCAAAGG	44	AGCTTAAAACTCAAAG	467
		ACCTGG		GACC

1157	1179	TTAAAACTCAAAGGACC	45	TTAAAACTCAAAGGAC	468
		TGGCGG		CTGG

1178	1200	GGTGCTTCATATCCCTC	46	GGTGCTTCATATCCCT	469
		TAGAGG		CTAG

1267	1289	TCTTCAGCAAACCCTGA	47	TCTTCAGCAAACCCTG	470
		TGAAGG		ATGA

1306	1328	AGTACCCACGTAAAGAC	48	AGTACCCACGTAAAGA	471
		GTTAGG		CGTT

1312	1334	CACGTAAAGACGTTAGG	49	CACGTAAAGACGTTAG	472
		TCAAGG		GTCA

1326	1348	AGGTCAAGGTGTAGCCC	50	AGGTCAAGGTGTAGCC	473
		ATGAGG		CATG

1329	1351	TCAAGGTGTAGCCCATG	51	TCAAGGTGTAGCCCAT	474
		AGGTGG		GAGG

1339	1361	GCCCATGAGGTGGCAA	52	GCCCATGAGGTGGCAA	475
		GAAATGG		GAAA

1340	1362	CCCATGAGGTGGCAAG	53	CCCATGAGGTGGCAAG	476
		AAATGGG		AAAT

1389	1411	GATAGCCCTTATGAAAC	54	GATAGCCCTTATGAAA	477
		TTAAGG		CTTA

1390	1412	ATAGCCCTTATGAAACT	55	ATAGCCCTTATGAAAC	478
		TAAGGG		TTAA

1397	1419	TTATGAAACTTAAGGGT	56	TTATGAAACTTAAGGG	479
		CGAAGG		TCGA

1400	1422	TGAAACTTAAGGGTCGA	57	TGAAACTTAAGGGTCG	480
		AGGTGG		AAGG

1441	1463	AGTAGAGTGCTTAGTTG	58	AGTAGAGTGCTTAGTT	481
		AACAGG		GAAC

1442	1464	GTAGAGTGCTTAGTTGA	59	GTAGAGTGCTTAGTTG	482
		ACAGGG		AACA

1494	1516	CCTCCTCAAGTATACTT	60	CCTCCTCAAGTATACT	483
		CAAAGG		TCAA

1530	1552	ACCCCTACGCATTTATA	61	ACCCCTACGCATTTAT	484
		TAGAGG		ATAG

1548	1570	AGAGGAGACAAGTCGT	62	AGAGGAGACAAGTCG	485
		AACATGG		TAACA

1560	1582	TCGTAACATGGTAAGTG	63	TCGTAACATGGTAAGT	486
		TACTGG		GTAC

1573	1595	AGTGTACTGGAAAGTGC	64	AGTGTACTGGAAAGTG	487
		ACTTGG		CACT

1620	1642	AAAGCACCCAACTTACA	65	AAAGCACCCAACTTAC	488
		CTTAGG		ACTT

1726	1748	CATTTACCCAAATAAAG	66	CATTTACCCAAATAAA	489
		TATAGG		GTAT

1746	1768	AGGCGATAGAAATTGA	67	AGGCGATAGAAATTG	490
		AACCTGG		AAACC

1770	1792	GCAATAGATATAGTACC	68	GCAATAGATATAGTAC	491
		GCAAGG		CGCA

1771	1793	CAATAGATATAGTACCG	69	CAATAGATATAGTACC	492
		CAAGGG		GCAA

1809	1831	TAACCAAGCATAATATA	70	TAACCAAGCATAATAT	493
		GCAAGG		AGCA

1862	1884	TAACTAGAAATAACTTT	71	TAACTAGAAATAACTT	494
		GCAAGG		TGCA

1947	1969	CCGTCTATGTAGCAAAA	72	CCGTCTATGTAGCAAA	495
		TAGTGG		ATAG

1948	1970	CGTCTATGTAGCAAAAT	73	CGTCTATGTAGCAAAA	496
		AGTGGG		TAGT

1960	1982	AAAATAGTGGGAAGAT	74	AAAATAGTGGGAAGA	497
		TTATAGG		TTTAT

1966	1988	GTGGGAAGATTTATAGG	75	GTGGGAAGATTTATAG	498
		TAGAGG		GTAG

1987	2009	GGCGACAAACCTACCG	76	GGCGACAAACCTACCG	499
		AGCCTGG		AGCC

1997	2019	CTACCGAGCCTGGTGAT	77	CTACCGAGCCTGGTGA	500
		AGCTGG		TAGC

2086	2108	ATTTAACTGTTAGTCCA	78	ATTTAACTGTTAGTCC	501
		AAGAGG		AAAG

2099	2121	TCCAAAGAGGAACAGC	79	TCCAAAGAGGAACAG	502
		TCTTTGG		CTCTT

2107	2129	GGAACAGCTCTTTGGAC	80	GGAACAGCTCTTTGGA	503
		ACTAGG		CACT

2152	2174	AAAAATTTAACACCCAT	81	AAAAATTTAACACCCA	504
		AGTAGG		TACT

2247	2269	CTGAACTCCTCACACCC	82	CTGAACTCCTCACACC	505
		AATTGG		CAAT

2414	2436	CCTCACTGTCAACCCAA	83	CCTCACTGTCAACCCA	506
		CACAGG		ACAC

2427	2449	CCAACACAGGCATGCTC	84	CCAACACAGGCATGCT	507
		ATAAGG		CATA

2432	2454	ACAGGCATGCTCATAAG	85	ACAGGCATGCTCATAA	508
		GAAAGG		GGAA

2449	2471	GAAAGGTTAAAAAAAG	86	GAAAGGTTAAAAAAA	509
		TAAAAGG		GTAAA

2456	2478	TAAAAAAAGTAAAAGG	87	TAAAAAAAGTAAAAG	510
		AACTCGG		GAACT

2515	2537	TCTAGCATCACCAGTAT	88	TCTAGCATCACCAGTA	511
		TAGAGG		TTAG

2546	2568	GCCCAGTGACACATGTT	89	GCCCAGTGACACATGT	512
		TAACGG		TTAA

2552	2574	TGACACATGTTTAACGG	90	TGACACATGTTTAACG	513
		CCGCGG		GCCG

2571	2593	GCGGTACCCTAACCGTG	91	GCGGTACCCTAACCGT	514
		CAAAGG		GCAA

2599	2621	TAATCACTTGTTCCTTA	92	TAATCACTTGTTCCTT	515
		AATAGG		AAAT

2600	2622	AATCACTTGTTCCTTAA	93	AATCACTTGTTCCTTA	516
		ATAGGG		AATA

2614	2636	TAAATAGGGACCTGTAT	94	TAAATAGGGACCTGTA	517
		GAATGG		TGAA

2624	2646	CCTGTATGAATGGCTCC	95	CCTGTATGAATGGCTC	518
		ACGAGG		CACG

2625	2647	CTGTATGAATGGCTCCA	96	CTGTATGAATGGCTCC	519
		CGAGGG		ACGA

2676	2698	AAATTGACCTGCCCGTG	97	AAATTGACCTGCCCGT	520
		AAGAGG		GAAG

2679	2701	TTGACCTGCCCGTGAAG	98	TTGACCTGCCCGTGAA	521
		AGGCGG		GAGG

2680	2702	TGACCTGCCCGTGAAGA	99	TGACCTGCCCGTGAAG	522
		GGCGGG		AGGC

2711	2733	AGCAAGACGAGAAGAC	100	AGCAAGACGAGAAGA	523
		CCTATGG		CCCTA

2755	2777	ACAGTACCTAACAAACC	101	ACAGTACCTAACAAAC	524
		CACAGG		CCAC

2789	2811	CAAACCTGCATTAAAAA	102	CAAACCTGCATTAAAA	525
		TTTCGG		ATTT

2793	2815	CCTGCATTAAAAATTTC	103	CCTGCATTAAAAATTT	526
		GGTTGG		CGGT

2794	2816	CTGCATTAAAAATTTCG	104	CTGCATTAAAAATTTC	527
		GTTGGG		GGTT

2795	2817	TGCATTAAAAATTTCGG	105	TGCATTAAAAATTTCG	528
		TTGGGG		GTTG

2804	2826	AATTTCGGTTGGGGCGA	106	AATTTCGGTTGGGGCG	529
		CCTCGG		ACCT

2895	2917	TGATCCAATAACTTGAC	107	TGATCCAATAACTTGA	530
		CAACGG		CCAA

2911	2933	CCAACGGAACAAGTTAC	108	CCAACGGAACAAGTTA	531
		CCTAGG		CCCT

2912	2934	CAACGGAACAAGTTACC	109	CAACGGAACAAGTTAC	532
		CTAGGG		CCTA

2954	2976	CTAGAGTCCATATCAAC	110	CTAGAGTCCATATCAA	533
		AATAGG		CAAT

2955	7977	TAGAGTCCATATCAACA	111	TAGAGTCCATATCAAC	534
		ATAGGG		AATA

2974	2996	AGGGTTTACGACCTCGA	112	AGGGTTTACGACCTCG	535
		TGTTGG		ATGT

2980	3002	TACGACCTCGATGTTGG	113	TACGACCTCGATGTTG	536
		ATCAGG		GATC

2992	3014	GTTGGATCAGGACATCC	114	GTTGGATCAGGACATC	537
		CGATGG		CCGA

3010	3032	GATGGTGCAGCCGCTAT	115	GATGGTGCAGCCGCTA	538
		TAAAGG		TTAA

3058	3080	TACGTGATCTGAGTTCA	116	TACGTGATCTGAGTTC	539
		GACCGG		AGAC

3069	3091	AGTTCAGACCGGAGTAA	117	AGTTCAGACCGGAGTA	540
		TCCAGG		ATCC

3073	3095	CAGACCGGAGTAATCCA	118	CAGACCGGAGTAATCC	541
		GGTCGG		AGGT

3110	3132	CAAATTCCTCCCTGTAC	119	CAAATTCCTCCCTGTA	542
		GAAAGG		CGAA

3125	3147	ACGAAAGGACAAGAGA	120	ACGAAAGGACAAGAG	543
		AATAAGG		AAATA

3203	3225	ACCCACACCCACCCAAG	121	ACCCACACCCACCCAA	544
		AACAGG		GAAC

3204	3226	CCCACACCCACCCAAGA	122	CCCACACCCACCCAAG	545
		ACAGGG		AACA

3217	3239	AAGAACAGGGTTTGTTA	123	AAGAACAGGGTTTGTT	546
		AGATGG		AAGA

3227	3249	TTTGTTAAGATGGCAGA	124	TTTGTTAAGATGGCAG	547
		GCCCGG		AGCC

3262	3284	ACTTAAAACTTTACAGT	125	ACTTAAAACTTTACAG	548
		CAGAGG		TCAG

3294	3316	TCTTCTTAACAACATAC	126	TCTTCTTAACAACATA	549
		CCATGG		CCCA

3336	3358	TGTACCCATTCTAATCG	127	TGTACCCATTCTAATC	550
		CAATGG		GCAA

3370	3392	CTTACCGAACGAAAAAT	128	CTTACCGAACGAAAAA	551
		TCTAGG		TTCT

3391	3413	GGCTATATACAACTACG	129	GGCTATATACAACTAC	552
		CAAAGG		GCAA

3406	3428	CGCAAAGGCCCCAACGT	130	CGCAAAGGCCCCAAC	553
		TGTAGG		GTTGT

3415	3437	CCCAACGTTGTAGGCCC	131	CCCAACGTTGTAGGCC	554
		CTACGG		CCTA

3416	3438	CCAACGTTGTAGGCCCC	132	CCAACGTTGTAGGCCC	555
		TACGGG		CTAC

3570	3592	CCTCCCCATACCCAACC	133	CCTCCCCATACCCAAC	556
		CCCTGG		CCCC

3586	3608	CCCCTGGTCAACCTCAA	134	CCCCTGGTCAACCTCA	557
		CCTAGG		ACCT

3643	3665	GTTTACTCAATCCTCTG	135	GTTTACTCAATCCTCT	558
		ATCAGG		GATC

3644	3666	TTTACTCAATCCTCTGA	136	TTTACTCAATCCTCTG	559
		TCAGGG		ATCA

3676	3698	AACTCAAACTACGCCCT	137	AACTCAAACTACGCCC	560
		GATCGG		TGAT

3757	3779	CTATCAACATTACTAAT	138	CTATCAACATTACTAA	561
		AAGTGG		TAAG

3828	3850	ACTCCTGCCATCATGAC	139	ACTCCTGCCATCATGA	562
		CCTTGG		CCCT

3892	3914	ACCCCCTTCGACCTTGC	140	ACCCCCTTCGACCTTG	563
		CGAAGG		CCGA

3893	3915	CCCCCTTCGACCTTGCC	141	CCCCCTTCGACCTTGC	564
		GAAGGG		CGAA

3894	3916	CCCCTTCGACCTTGCCG	142	CCCCTTCGACCTTGCC	565
		AAGGGG		GAAG

3913	3935	GGGGAGTCCGAACTAGT	143	GGGGAGTCCGAACTA	566
		CTCAGG		GTCTC

3937	3959	TTCAACATCGAATACGC	144	TTCAACATCGAATACG	567
		CGCAGG		CCGC

4015	4037	CTCACCACTACAATCTT	145	CTCACCACTACAATCT	568
		CCTAGG		TCCT

4287	4309	ACTTTGATAGAGTAAAT	146	ACTTTGATAGAGTAAA	569
		AATAGG		TAAT

4311	4333	GCTTAAACCCCCTTATT	147	GCTTAAACCCCCTTAT	570
		TCTAGG		TTCT

4386	4408	TCACACCCCATCCTAAA	148	TCACACCCCATCCTAA	571
		GTAAGG		AGTA

4406	4428	AGGTCAGCTAAATAAGC	149	AGGTCAGCTAAATAAG	572
		TATCGG		CTAT

4407	4429	GGTCAGCTAAATAAGCT	150	GGTCAGCTAAATAAGC	573
		ATCGGG		TATC

4428	4450	GGCCCATACCCCGAAAA	151	GGCCCATACCCCGAAA	574
		TGTTGG		ATGT

4460	4482	TCCCGTACTAATTAATC	152	TCCCGTACTAATTAAT	575
		CCCTGG		CCCC

4494	4516	ATCTACTCTACCATCTTT	153	ATCTACTCTACCATCT	576
		GCAGG		TTGC

4542	4564	CACTGATTTTTTACCTG	154	CACTGATTTTTTACCT	577
		AGTAGG		GAGT

4692	4714	CTCTTCAACAATATACT	155	CTCTTCAACAATATAC	578
		CTCCGG		TCTC

4767	4789	ATAGCTATAGCAATAAA	156	ATAGCTATAGCAATAA	579
		ACTAGG		AACT

4799	4821	CTTTCACTTCTGAGTCC	157	CTTTCACTTCTGAGTC	580
		CAGAGG		CCAG

4809	4831	TGAGTCCCAGAGGTTAC	158	TGAGTCCCAGAGGTTA	581
		CCAAGG		CCCA

4827	4849	CAAGGCACCCCTCTGAC	159	CAAGGCACCCCTCTGA	582
		ATCCGG		CATC

4941	4963	TCAATCTTATCCATCAT	160	TCAATCTTATCCATCA	583
		AGCAGG		TAGC

4950	4972	TCCATCATAGCAGGCAG	161	TCCATCATAGCAGGCA	584
		TTGAGG		GTTG

4953	4975	ATCATAGCAGGCAGTTG	162	ATCATAGCAGGCAGTT	585
		AGGTGG		GAGG

5010	5032	TACTCCTCAATTACCCA	163	TACTCCTCAATTACCC	586
		CATAGG		ACAT

5202	5274	CCATCCACCCTCCTCTC	164	CCATCCACCCTCCTCT	587
		CCTAGG		CCCT

5205	5227	TCCACCCTCCTCTCCCT	165	TCCACCCTCCTCTCCCT	588
		AGGAGG		AGG

5223	5245	GGAGGCCTGCCCCCGCT	166	GGAGGCCTGCCCCCGC	589
		AACCGG		TAAC

539	5261	TAACCGGCTTTTTGCCC	167	TAACCGGCTTTTTGCC	590
		AAATGG		CAAA

5240	5262	AACCGGCTTTTTGCCCA	168	AACCGGCTTTTTGCCC	591
		AATGGG		AAAT

5500	5522	TAATAATCTTATAGAAA	169	TAATAATCTTATAGAA	592
		TTTAGG		ATTT

5569	5591	CTTAATTTCTGTAACAG	170	CTTAATTTCTGTAACA	593
		CTAAGG		GCTA

5646	5668	CTAAGCCCTTACTAGAC	171	CTAAGCCCTTACTAGA	594
		CAATGG		CCAA

5647	5669	TAAGCCCTTACTAGACC	172	TAAGCCCTTACTAGAC	595
		AATGGG		CAAT

5697	5719	AGCTAAGCACCCTAATC	173	AGCTAAGCACCCTAAT	596
		AACTGG		CAAC

5723	5745	CAATCTACTTCTCCCGC	174	CAATCTACTTCTCCCG	597
		CGCCGG		CCGC

5724	5746	AATCTACTTCTCCCGCC	175	AATCTACTTCTCCCGC	598
		GCCGGG		CGCC

5732	5754	TCTCCCGCCGCCGGGAA	176	TCTCCCGCCGCCGGGA	599
		AAAAGG		AAAA

5735	5757	CCCGCCGCCGGGAAAA	177	CCCGCCGCCGGGAAA	600
		AAGGCGG		AAAGG

5736	5758	CCGCCGCCGGGAAAAA	178	CCGCCGCCGGGAAAA	601
		AGGCGGG		AAGGC

5747	5769	AAAAAAGGCGGGAGAA	179	AAAAAAGGCGGGAGA	602
		GCCCCGG		AGCCC

5751	5773	AAGGCGGGAGAAGCCC	180	AAGGCGGGAGAAGCC	603
		CGGCAGG		CCGGC

5800	5822	ATTCAATATGAAAATCA	181	ATTCAATATGAAAATC	604
		CCTCGG		ACCT

5806	5828	TATGAAAATCACCTCGG	182	TATGAAAATCACCTCG	605
		ACTCTGG		GAGC

5816	5838	ACCTCGGAGCTGGTAAA	183	ACCTCGGAGCTGGTAA	606
		AAGAGG		AAAG

5928	5950	TCTACAAACCACAAAGA	184	TCTACAAACCACAAAG	607
		CATTGG		ACAT

5949	5971	GGAACACTATACCTATT	185	GGAACACTATACCTAT	608
		ATTCGG		TATT

5961	5983	CTATTATTCGGCGCATG	186	CTATTATTCGGCGCAT	609
		AGCTGG		GAGC

5970	5992	GGCGCATGAGCTGGAGT	187	GGCGCATGAGCTGGA	610
		CCTAGG		GTCCT

6005	6027	CCTCCTTATTCGAGCCG	188	CCTCCTTATTCGAGCC	611
		AGCTGG		GAGC

6006	6028	CTCCTTATTCGAGCCGA	189	CTCCTTATTCGAGCCG	612
		GCTGGG		AGCT

6027	6049	GGCCAGCCAGGCAACCT	190	GGCCAGCCAGGCAAC	613
		TCTAGG		CTTCT

6108	3130	ATAGTAATACCCATCAT	191	ATAGTAATACCCATCA	614
		AATCGG		TAAT

6111	6133	GTAATACCCATCATAAT	192	GTAATACCCATCATAA	615
		CGGAGG		TCGG

6117	6139	CCCATCATAATCGGAGG	193	CCCATCATAATCGGAG	616
		CTTTGG		GCTT

6144	6166	TGACTAGTTCCCCTAAT	194	TGACTAGTTCCCCTAA	617
		AATCGG		TAAT

6158	6180	AATAATCGGTGCCCCCG	195	AATAATCGGTGCCCCC	618
		ATATGG		GATA

6236	6258	CCTGCTCGCATCTGCTA	196	CCTGCTCGCATCTGCT	619
		TAGTGG		ATAG

6239	6261	GCTCGCATCTGCTATAG	197	GCTCGCATCTGCTATA	620
		TGGAGG		GTGG

6243	6265	GCATCTGCTATAGTGGA	198	GCATCTGCTATAGTGG	621
		GGCCGG		AGGC

6249	6271	GCTATAGTGGAGGCCGG	199	GCTATAGTGGAGGCCG	622
		AGCAGG		GAGC

6255	6277	GTGGAGGCCGGAGCAG	200	GTGGAGGCCGGAGCA	623
		GAACAGG		GGAAC

6282	6304	ACAGTCTACCCTCCCTT	201	ACAGTCTACCCTCCC	624
		AGCAGG		TAGC

6283	6305	CAGTCTACCCTCCCTTA	202	CAGTCTACCCTCCCTT	625
		GCAGGG		AGCA

6300	6322	GCAGGGAACTACTCCCA	203	GCAGGGAACTACTCCC	626
		CCCTGG		ACCC

6342	6364	ATCTTCTCCTTACACCT	204	ATCTTCTCCTTACACCT	627
		AGCAGG		AGC

6360	6382	GCAGGTGTCTCCTCTAT	205	GCAGGTGTCTCCTCTA	628
		CTTAGG		TCTT

6361	6383	CAGGTGTCTCCTCTATC	206	CAGGTGTCTCCTCTAT	629
		TTAGGG		CTTA

6362	6384	AGGTGTCTCCTCTATCT	207	AGGTGTCTCCTCTATC	630
		TAGGGG		TTAG

6495	6517	TCTCTCCCAGTCCTAGC	208	TCTCTCCCAGTCCTAG	631
		TGCTGG		CTGC

6552	6574	ACCACCTTCTTCGACCC	209	ACCACCTTCTTCGACC	632
		CGCCGG		CCGC

6555	6577	ACCTTCTTCGACCCCGC	210	ACCTTCTTCGACCCCG	633
		CGGAGG		CCGG

6558	6580	TTCTTCGACCCCGCCGG	211	TTCTTCGACCCCGCCG	634
		AGGAGG		GAGG

6597	6619	CAACACCTATTCTGATT	212	CAACACCTATTCTGAT	635
		TTTCGG		TTTT

6630	6652	GTTTATATTCTTATCCTA	213	GTTTATATTCTTATCCT	636
		CCAGG		ACC

6636	6658	ATTCTTATCCTACCAGG	214	ATTCTTATCCTACCAG	637
		CTTCGG		GCTT

6669	6691	CATATTGTAACTTACTA	215	CATATTGTAACTTACT	638
		CTCCGG		ACTC

6687	6709	TCCGGAAAAAAAGAAC	216	TCCGGAAAAAAAGAA	639
		CATTTGG		CCATT

6696	6718	AAAGAACCATTTGGATA	217	AAAGAACCATTTGGAT	640
		CATAGG		ACAT

6701	6723	ACCATTTGGATACATAG	218	ACCATTTGGATACATA	641
		GTATGG		GGTA

6723	6745	GTCTGAGCTATGATATC	219	GTCTGAGCTATGATAT	642
		AATTGG		CAAT

6732	6754	ATGATATCAATTGGCTT	220	ATGATATCAATTGGCT	643
		CCTAGG		TCCT

6713	6755	TGATATCAATTGGCTTC	221	TGATATCAATTGGCTT	644
		CTAGGG		CCTA

6768	6790	GCACACCATATATTTAC	222	GCACACCATATATTTrA	645
		AGTAGG		CAGT

6831	6853	ATAATCATCGCTATCCC	223	ATAATCATCGCTATCC	646
		CACCGG		CCAC

6867	6889	AGCTGACTCGCCACACT	224	AGCTGACTCGCCACAC	647
		CCACGG		TCCA

6909	6931	GCTGCAGTGCTCTGAGC	225	GCTGCAGTGCTCTGAG	648
		CCTAGG		CCCT

6933	6955	TTCATCTTTCTTTTCACC	226	TTCATCTTTCTTTTCAC	649
		GTAGG		CGT

6936	6958	ATCTTTCTTTTCACCGTA	227	ATCTTTCTTTTCACCGT	650
		GGTGG		AGG

6945	6967	TTCACCGTAGGTGGCCT	228	TTCACCGTAGGTGGCC	651
		GACTGG		TGAC

7032	7054	TTCCACTATGTCCTATC	229	TTCCACTATGTCCTAT	652
		AATAGG		CAAT

7053	7075	GGAGCTGTATTTGCCAT	230	GGAGCTGTATTTGCCA	653
		CATAGG		TCAT

7056	7078	GCTGTATTTGCCATCAT	231	GCTGTATTTGCCATCA	654
		AGGAGG		TAGG

7086	7108	CACTGATTTCCCCTATT	232	CACTGATTTCCCCTAT	655
		CTCAGG		TCTC

7140	7162	CATTTCACTATCATATT	233	CATTTCACTATCATAT	656
		CATCGG		TCAT

7176	7198	TTCTTCCCACAACACTT	234	TTCTTCCCACAACACT	657
		TCTCGG		TTCT

7185	7207	CAACACTTTCTCGGCCT	235	CAACACTTTCTCGGCC	658
		ATCCGG		TATC

7205	7227	CGGAATGCCCCGACGTT	236	CGGAATGCCCCGACGT	659
		ACTCGG		TACT

7251	7273	TGAAACATCCTATCATC	237	TGAAACATCCTATCAT	660
		TGTAGG		CTGT

7358	7380	AGAAGAACCCTCCATAA	238	AGAAGAACCCTCCATA	661
		ACCTGG		AACC

7371	7393	ATAAACCTGGAGTGACT	239	ATAAACCTGGAGTGAC	662
		ATATGG		TATA

7432	7454	ACATAAAATCTAGACAA	240	ACATAAAATCTAGACA	663
		AAAAGG		AAAA

7436	7458	AAAATCTAGACAAAAA	241	AAAATCTAGACAAAA	664
		AGGAAGG		AAGGA

7457	7479	GGAATCGAACCCCCCAA	242	GGAATCGAACCCCCCA	665
		AGCTGG		AAGC

7476	7498	CTGGTTTCAAGCCAACC	243	CTGGTTTCAAGCCAAC	666
		CCATGG		CCCA

7499	7521	CCTCCATGACTTTTTCA	244	CCTCCATGACTTTTTC	667
		AAAAGG		AAAA

7544	7566	CTTTGTCAAAGTTAAAT	245	CTTTGTCAAAGTTAAA	668
		TATAGG		TTAT

7567	7589	CTAAATCCTATATATCT	246	CTAAATCCTATATATC	669
		TAATGG		TTAA

7586	7608	ATGGCACATGCAGCGCA	247	ATGGCACATGCAGCGC	670
		AGTAGG		AAGT

7741	7763	TACTAACATCTCAGACG	248	TACTAACATCTCAGAC	671
		CTCAGG		GCTC

7831	7853	CATCCTTTACATAACAG	249	CATCCTTTACATAACA	672
		ACGAGG		GACG

7865	7887	TCCCTTACCATCAAATC	250	TCCCTTACCATCAAAT	673
		AATTGG		CAAT

7875	7897	TCAAATCAATTGGCCAC	251	TCAAATCAATTGGCCA	674
		CAATGG		CCAA

7904	7926	ACCTACGAGTACACCGA	252	ACCTACGAGTACACCG	675
		CTACGG		ACTA

7907	7929	TACGAGTACACCGACTA	253	TACGAGTACACCGACT	676
		CGGCGG		ACGG

7955	7977	CCCCCATTATTCCTAGA	254	CCCCCATTTTCCTAG	677
		ACCAGG		AACC

8069	8091	TCATGAGCTGTCCCCAC	255	TCATGAGCTGTCCCCA	678
		ATTAGG		CATT

8093	8115	TTAAAAACAGATGCAAT	256	TTAAAAACAGATGCAA	679
		TCCCGG		TTCC

8131	8153	CACTTTCACCGCTACAC	257	CACTTTCACCGCTACA	680
		GACCGG		CGAC

8132	8154	ACTTTCACCGCTACACG	258	ACTTTCACCGCTACAC	681
		ACCGGG		GACC

8133	8155	CTTTCACCGCTACACGA	259	CTTTCACCGCTACACG	682
		CCGGGG		ACCG

8134	8156	TTTCACCGCTACACGAC	260	TTTCACCGCTACACGA	683
		CGGGGG		CCGG

8144	8166	ACACGACCGGGGGTAT	261	ACACGACCGGGGGTAT	684
		ACTACGG		ACTA

8165	8187	GGTCAATGCTCTGAAAT	262	GGTCAATGCTCTGAAA	685
		CTGTGG		TCTG

8228	8250	CCCCTAAAAATCTTTGA	263	CCCCTAAAAATCTTTG	686
		AATAGG		AAAT

8229	8251	CCCTAAAAATCTTTGAA	264	CCCTAAAAATCTTTGA	687
		ATAGGG		AATA

8370	8392	CCCAACTAAATACTACC	265	CCCAACTAAATACTAC	688
		GTATGG		CGTA

8551	8573	TTCATTGCCCCCACAAT	266	TTCATTTGCCCCCACAA	689
		CCTAGG		TCCT

8698	8720	ATAACCATACACAACAC	267	ATAACCATACACAACA	690
		TAAAGG		CTAA

8761	8783	ATTGCCACAACTAACCT	268	ATTGCCACAACTAACC	691
		CCTCGG		TCCT

8817	8839	ACTATCTATAAACCTAG	269	ACTATCTATAAACCTA	692
		CCATGG		GCCA

8835	8857	CATGGCCATCCCCTTAT	270	CATGGCCATCCCCTTA	693
		GAGCGG		TGAG

8836	8858	ATGGCCATCCCCTTATG	271	ATGGCCATCCCCTTAT	694
		AGCGGG		GAGC

8851	8873	TGAGCGGGCACAGTGAT	272	TGAGCGGGCACAGTG	695
		TATAGG		ATTAT

8899	8921	CTAGCCCACTTCTTACC	273	CTAGCCCACTTCTTAC	696
		ACAAGG		CACA

8973	8995	ACTCATTCAACCAATAG	274	ACTCATTCAACCAATA	697
		CCCTGG		GCCC

9004	9026	CTAACCGCTAACATTACC	275	CTAACCGCTAACATTA	698
		TGCAGG		CTGC

9028	9050	CACCTACTCATGCACCT	276	CACCTACTCATGCACC	699
		AATTGG		TAAT

9243	9265	CCCAGCCCATGACCCCT	277	CCCAGCCCATGACCCC	700
		AACAGG		TAAC

9244	9266	CCAGCCCATGACCCCTA	278	CCAGCCCATGACCCCT	701
		ACAGGG		AACA

9245	9267	CAGCCCATGACCCCTAA	279	CAGCCCATGACCCCTA	702
		CAGGGG		ACAG

9273	9295	TCAGCCCTCCTAATGAC	280	TCAGCCCTCCTAATGA	703
		CTCCGG		CCTC

9321	9343	TCCATAACGCTCCTCAT	281	TCCATAACGCTCCTCA	704
		ACTAGG		TACT

9358	9380	CACTAACCATATACCAA	282	CACTAACCATATACCA	705
		TGATGG		ATGA

9390	9412	ACACGAGAAAGCACAT	283	ACACGAGAAAGCACA	706
		ACCAAGG		TACCA

9417	9439	CACACACCACCTGTCCA	284	CACACACCACCTGTCC	707
		AAAAGG		AAAA

9429	9451	GTCCAAAAAGGCCTTCG	285	GTCCAAAAAGGCCTTC	708
		ATACGG		GATA

9430	9452	TCCAAAAAGGCCTTCGA	286	TCCAAAAAGGCCTTCG	709
		TACGGG		ATAC

9471	9493	TCAGAAGTTTTTTTCTTC	287	TCAGAAGTTTTTTTCTT	710
		GCAGG		CGC

9522	9544	CTAGCCCCTACCCCCCA	288	CTAGCCCCTACCCCCC	711
		ATTAGG		AATT

9525	9547	GCCCCTACCCCCCAATT	289	GCCCCTACCCCCCAAT	712
		AGGAGG		TAGG

9526	9548	CCCCTACCCCCCAATTA	290	CCCCTACCCCCCAATT	713
		GGAGGG		AGGA

9532	9554	CCCCCCAATTAGGAGGG	291	CCCCCCAATTAGGAGG	714
		CACTGG		GCAC

9543	9565	GGAGGGCACTGGCCCCC	292	GGAGGGCCACTGGCCCC	715
		AACAGG		CAAC

9606	9628	ACATCCGTATTACTCGC	293	ACATCCGTATTACTCG	716
		ATCAGG		CATC

9692	9714	ACTGCTTATTACAATTT	294	ACTGCTTATTACAATT	717
		TACTGG		TTAC

9693	9715	CTGCTTATTACAATTTT	295	CTGCTTATTACAATTTT	718
		ACTGGG		ACT

9756	9778	TCTCCCTTCACCATTTCC	296	TCTCCCTTCACCATTTC	719
		GACGG		CGA

9765	9787	ACCATTTCCGACGGCAT	297	ACCATTTCCGACGGCA	720
		CTACGG		TCTA

9789	9811	TCAACATTTTTTGTAGC	298	TCAACATTTTTTGTAG	721
		CACAGG		CCAC

9798	9820	TTTGTAGCCACAGGCTT	299	TTTGTAGCCACAGGCT	722
		CCACGG		TCCA

9816	9838	CACGGACTTCACGTCAT	300	CACGGACTTCACGTCA	723
		TATTGG		TTAT

9885	9907	TTTACATCCAAACATCA	301	TTTACATCCAAACATC	724
		CTTTGG		ACTT

9910	9932	TCGAAGCCGCCGCCTGA	302	TCGAAGCCGCCGCCTG	725
		TACTGG		ATAC

9926	9948	ATACTGGCATTTTGTAG	303	ATACTGGCATTTTGTA	726
		ATGTGG		GATG

9963	9985	TATGTCTCCATCTATTG	304	TATGTCTCCATCTATT	727
		ATGAGG		GATG

9964	9986	ATGTCTCCATCTATTGA	305	ATGTCTCCATCTATTG	728
		TGAGGG		ATGA

10122	10144	TTTTGACTACCACAACT	306	TTTTGACTACCACAAC	729
		CAACGG		TCAA

10155	10177	AAATCCACCCCTTACGA	307	AAATCCACCCCTTACG	730
		GTGCGG		AGTG

10343	10365	CATCATCCTAGCCCTAA	308	CATCATCCTAGCCCTA	731
		GTCTGG		AGTC

10365	10387	GCCTATGAGTGACTACA	309	GCCTATGAGTGACTAC	732
		AAAAGG		AAAA

10385	10407	AGGATTAGACTGAACCG	310	AGGATTAGACTGAACC	733
		AATTGG		GAAT

10500	10522	GCATTTACCATCTCACT	311	GCATTTACCATCTCAC	734
		TCTAGG		TTCT

10551	10573	TCCTCCCTACTATGCCT	312	TCCTCCCTACTATGCC	735
		AGAAGG		TAGA

10664	10686	CTTTGCCGCCTGCGAAG	313	CTTTGCCGCCTGCGAA	736
		CAGCGG		GCAG

10667	10689	TGCCGCCTGCGAAGCAG	314	TGCCGCCTGCGAAGCA	737
		CGGTGG		GCGG

10668	10690	GCCGCCTGCGAAGCAGC	315	GCCGCCTGCGAAGCAG	738
		GGTGGG		CGGT

10704	10726	GTCTCAATCTCCAACAC	316	GTCTCAATCTCCAACA	739
		ATATGG		CATA

10972	10994	ACTCCTACCCCTCACAA	317	ACTCCTACCCCTCACA	740
		TCATGG		ATCA

11128	11150	AACCACACTTATCCCCA	318	AACCACACTTATCCCC	741
		CCTTGG		ACCT

11147	11169	TTGGCTATCATCACCCG	319	TTGGCTATCATCACCC	742
		ATGAGG		GATG

11174	11196	CAGCCAGAACGCCTGA	320	CAGCCAGAACGCCTGA	743
		ACGCAGG		ACGC

11204	11226	TTCCTATTCTACACCCT	321	TTCCTATTCTACACCCT	744
		AGTAGG		AGT

11252	11274	ATTTACACTCACAACAC	322	ATTTACACTCACAACA	745
		CCTAGG		CCCT

11369	11391	ATAGTAAAGATACCTCT	323	ATAGTAAAGATACCTC	746
		TTACGG		TTTA

11417	11439	CATGTCGAAGCCCCCAT	324	CATGTCGAAGCCCCCA	747
		CGCTGG		TCGC

11418	11440	ATGTCGAAGCCCCCATC	325	ATGTCGAAGCCCCCAT	748
		GCTGGG		CGCT

11453	11475	GCCGCAGTACTCTTAAA	326	GCCGCAGTACTCTTAA	749
		ACTAGG		AACT

11456	11478	GCAGTACTCTTAAAACT	327	GCAGTACTCTTAAAAC	750
		AGGCGG		TAGG

11462	11484	CTCTTAAAACTAGGCGG	328	CTCTTAAAACTAGGCG	751
		CTATGG		GCTA

11540	11562	TTCCTTGTACTATCCCTA	329	TTCCTTGTACTATCCCT	752
		TGAGG		ATG

11669	11691	CAAACCCCCTGAAGCTT	330	CAAACCCCCTGAAGCT	753
		CACCGG		TCAC

11696	11718	GTCATTCTCATAATCGC	331	GTCATTCTCATAATCG	754
		CCACGG		CCCA

11697	11719	TCATTCTCATAATCGCC	332	TCATTCTCATAATCGC	755
		CACGGG		CCAC

11777	11799	CGCATCATAATCCTCTC	333	CGCATCATAATCCTCT	756
		TCAAGG		CTCA

11866	11888	ACCCCCCACTATTAACC	334	ACCCCCACTATTAAC	757
		TACTGG		CTAC

11867	11889	CCCCCCACTATTAACCT	335	CCCCCCACTATTAACC	758
		ACTGGG		TACT

11927	11949	AATATCACTCTCCTACT	336	AATATCACTCTCCTAC	759
		TACAGG		TTAC

11985	12007	ACATATTTACCACAACA	337	ACATATTTACCACAAC	760
		CAATGG		ACAA

11986	12008	CATATTTACCACAACAC	338	CATATTTACCACAACA	761
		AATGGG		CAAT

11987	12009	ATATTTACCACAACACA	339	ATATTTACCACAACAC	762
		ATGGGG		AATG

12104	12126	CTCAACCCCGACATCAT	340	CTCAACCCCGACATCA	763
		TACCGG		TTAC

12105	12127	TCAACCCCGACATCATT	341	TCAACCCCGACATCAT	764
		ACCGGG		TACC

12164	12186	GATTGTGAATCTGACAA	342	GATTGTGAATCTGACA	765
		CAGAGG		ACAG

12235	12257	TGCCCCCATGTCTAACA	343	TGCCCCCATGTCTAAC	766
		ACATGG		AACA

12254	12276	ATGGCTTTCTCAACTTTT	344	ATGGCTTTCTCAACTT	767
		AAAGG		TTAA

12272	12294	AAAGGATAACAGCTATC	345	AAAGGATAACAGCTAT	768
		CATTGG		CCAT

12279	12301	AACAGCTATCCATTGGT	346	AACAGCTATCCATTGG	769
		CTTAGG		TCTT

12294	12316	GTCTTAGGCCCCAAAAA	347	GTCTTAGGCCCCAAAA	770
		TTTTGG		ATTT

12608	12630	CTGTAGCATTGTTCGTT	348	CTGTAGCATTGTTCGT	771
		ACATGG		TACA

12742	12764	AACCTATTCCAACTGTT	349	AACCTATTCCAACTGT	772
		CATCGG		TCAT

12750	12772	CCAACTGTTCATCGGCT	350	CCAACTGTTCATCGGC	773
		GAGAGG		TGAG

12751	12773	CAACTGTTCATCGGCTG	351	CAACTGTTCATCGGCT	774
		AGAGGG		GAGA

12757	12779	TTCATCGGCTGAGAGGG	352	TTCATCGGCTGAGAGG	775
		CGTAGG		GCGT

12847	12869	GCAATCCTATACAACCG	353	GCAATCCTATACAACC	776
		TATCGG		GTAT

12856	12878	TACAACCGTATCGGCGA	354	TACAACCGTATCGGCG	777
		TATCGG		ATAT

12958	12980	CCAAGCCTCACCCCACT	355	CCAAGCCTCACCCCAC	778
		ACTAGG		TACT

12979	13001	GGCCTCCTCCTAGCAGC	356	GGCCTCCTCCTAGCAG	779
		AGCAGG		CAGC

12997	13019	GCAGGCAAATCAGCCC	357	GCAGGCAAATCAGCCC	780
		AATTAGG		AATT

13030	13052	TGACTCCCCTCAGCCAT	358	TGACTCCCCTCAGCCA	781
		AGAAGG		TAGA

13081	13103	TCAAGCACTATAGTTGT	359	TCAAGCACTATAGTTG	782
		AGCAGG		TAGC

13156	13178	CAAACTCTAACACTATG	360	CAAACTCTAACACTAT	783
		CTTAGG		GCTT

13246	13268	TTCTCCACTTCAAGTCA	361	TTCTCCACTTCAAGTC	784
		ACTAGG		AACT

13267	13289	GGACTCATAATAGTTAC	362	GGACTCATAATAGTTA	785
		AATCGG		CAAT

13345	13367	GCCATACTATTTATGTG	363	GCCATACTATTTATGT	786
		CTCCGG		GCTC

13346	13368	CCATACTATTTATGTGC	364	CCATACTATTTATGTG	787
		TCCGGG		CTCC

13393	13415	GAACAAGATATTCGAA	365	GAACAAGATATTCGAA	788
		AAATAGG		AAAT

13396	13418	CAAGATATTCGAAAAAT	366	CAAGATATTCGAAAAA	789
		AGGAGG		TAGG

13441	13463	ACTTCAACCTCCCTCAC	367	ACTTCAACCTCCCTCA	790
		CATTGG		CCAT

13459	13481	ATTGGCAGCCTAGCATT	368	ATTGGCAGCCTAGCAT	791
		AGCAGG		TAGC

13477	13499	GCAGGAATACCTTTCCT	369	GCAGGAATACCTTTCC	792
		CACAGG		TCAC

13612	13634	ATAATTCTTCTCACCCT	370	ATAATTCTTCTCACCC	793
		AACAGG		TAAC

13686	13708	ACTAAACCCCATTAAAC	371	ACTAAACCCCATTAAA	794
		GCCTGG		CGCC

13693	13715	CCCATTAAACGCCTGGC	372	CCCATTAAACGCCTGG	795
		AGCCGG		CAGC

13708	13730	GCAGCCGGAAGCCTATT	373	GCAGCCGGAAGCCTAT	796
		CGCAGG		TCGC

13804	13826	GCCCTCGCTGTCACTTT	374	GCCCTCGCTGTCACTT	797
		CCTAGG		TCCT

13894	13916	TTTTATTTCTCCAACATA	375	TTTTATTTCTCCAACAT	798
		CTCGG		ACT

13936	13958	CACCGCACAATCCCCTA	376	CACCGCACAATCCCCT	799
		TCTAGG		ATCT

14059	14081	ATCATCACCTCAACCCA	377	ATCATCACCTCAACCC	800
		AAAAGG		AAAA

14237	14259	TACAAAGCCCCCGCACC	378	TACAAAGCCCCCGCAC	801
		AATAGG		CAAT

14417	14439	ACCCCTGACCCCCATGC	379	ACCCCTGACCCCCATG	802
		CTCAGG		CCTC

14579	14601	AATACTAAACCCCCATA	380	AATACTAAACCCCCAT	803
		AATAGG		AAAT

14585	14607	AAACCCCCATAAATAGG	381	AAACCCCCATAAATAG	804
		AGAAGG		GAGA

14664	14686	CATACATCATTATTCTC	382	CATACATCATTATTCT	805
		GCACGG		CGCA

14825	14847	ATCTCCGCATGATGAAA	383	ATCTCCGCATGATGAA	806
		CTTCGG		ACTT

14837	14859	TGAAACTTCGGCTCACT	384	TGAAACTTCGGCTCAC	807
		CCTTGG		TCCT

14867	14889	CTGATCCTCCAAATCAC	385	CTGATCCTCCAAATCA	808
		CACAGG		CCAC

14951	14973	ATCACTCGAGACGTAAA	386	ATCACTCGAGACGTAA	809
		TTATGG		ATTA

14981	15003	ATCCGCTACCTTCACGC	387	ATCCGCTACCTTCACG	810
		CAATGG		CCAA

15020	15042	ATCTGCCTCTTCCTACA	388	ATCTGCCTCTTCCTAC	811
		CATCGG		ACAT

15021	15043	TCTGCCTCTTCCTCACA	389	TCTGCCTCTTCCTACA	812
		ATCGGG		CATC

15026	15048	CTCTTCCTACACATCGG	390	CTCTTCCTACACATCG	813
		GCGAGG		GGCG

15038	15060	ATCGGGCGAGGCCTATA	391	ATCGGGCGAGGCCTAT	814
		TTACGG		ATTA

15071	15093	TACTCAGAAACCTGAAA	392	TACTCAGAAACCTGAA	815
		CATCGG		ACAT

15113	15135	ACTATAGCAACAGCCTT	393	ACTATAGCAACAGCCT	816
		CATAGG		TCAT

15131	15153	ATAGGCTATGTCCTCCC	394	ATAGGCTATGTCCTCC	817
		GTGAGG		CGTG

15149	15171	TGAGGCCAAATATCATT	395	TGAGGCCAAATATCAT	818
		CTGAGG		TCTG

15150	15172	GAGGCCAAATATCATTC	396	GAGGCCAAATATCATT	819
		TGAGGG		CTGA

15151	15173	AGGCCAAATATCATTCT	397	AGGCCAAATATCATTC	820
		GAGGGG		TGAG

15194	15216	CTATCCGCCATCCCATA	398	CTATCCGCCATCCCAT	821
		CATTGG		ACAT

15195	15217	TATCCGCCATCCCATAC	399	TATCCGCCATCCCATA	822
		ATTGGG		CATT

15221	15243	GACCTAGTTCAATGAAT	400	GACCTAGTTCAATGAA	823
		CTGAGG		TCTG

15224	15246	CTAGTTCAATGAATCTG	401	CTAGTTCAATGAATCT	824
		AGGAGG		GAGG

15334	15356	CCTCCTATTCTTGCACG	402	CCTCCTATTCTTGCAC	825
		AAACGG		GAAA

15335	15357	CTCCTATTCTTGCACGA	403	CTCCTATTCTTGCACG	826
		AACGGG		AAAC

15353	15375	ACGGGATCAAACAACC	404	ACGGGATCAAACAAC	827
		CCCTAGG		CCCCT

15416	15438	TACACAATCAAAGACGC	405	TACACAATCAAAGACG	828
		CCTCGG		CCCT

15476	15498	CTATTCTCACCAGACCT	406	CTATTCTCACCAGACC	829
		CCTAGG		TCCT

15590	15612	CGATCCGTCCCTAACAA	407	CGATCCGTCCCTAACA	830
		ACTAGG		AACT

15593	15615	TCCGTCCCTAACAAACT	408	TCCGTCCCTAACAAAC	831
		AGGAGG		TAGG

15740	15762	CTCCTCATTCTAACCTG	409	CTCCTCATTCTAACCT	832
		AATCGG		GAAT

15743	15765	CTCATTCTAACCTGAAT	410	CTCATTCTAACCTGAA	833
		CGGAGG		TCGG

15776	15798	AGCTACCCTTTTACCAT	411	AGCTACCCTTTTACCA	834
		CATTGG		TCAT

15861	15883	TTGAAAACAAAATACTC	412	TTGAAAACAAAATACT	835
		AAATGG		CAAA

15862	15884	TGAAAACAAAATACTCA	413	TGAAAACAAAATACTC	836
		AATGGG		AAAT

15906	15928	AATACACCAGTCTTGTA	414	AATACACCAGTCTTGT	837
		AACCGG		AAAC

15928	15950	GAGATGAAAACCTTTTT	415	GAGATGAAAACCTTTT	838
		CCAAGG		TCCA

16012	16034	AACTATTCTCTGTTCTTT	416	AACTTTCTCTGTTCTT	839
		CATGG		TCA

16013	16035	ACTATTCTCTGTTCTTTC	417	ACTATTCTCTGTTCTTT	840
		ATGGG		CAT

16014	16036	CTATTCTCTGTTCTTTCA	418	CTATTCTCTGTTCTTTC	841
		TGGGG		ATG

16026	16048	CTTTCATGGGGAAGCAG	419	CTTTCATGGGGAAGCA	842
		ATTTGG		GATT

16027	16049	TTTCATGGGGAAGCAGA	420	TTTCATGGGGAAGCAG	843
		TTTGGG		ATTT

16108	16130	CAGCCACCATGAATATT	421	CAGCCACCATGAATAT	844
		GTACGG		TGTA

16252	16274	AAAGCCACCCCTCACCC	422	AAAGCCACCCCTCACC	845
		ACTAGG		CACT

16348	16370	CAAATCCCTTCTCGTCC	423	CAAATCCCTTCTCGTC	846
		CCATGG		CCCA

16367	16389	ATGGATGACCCCCCTCA	424	ATGGATGACCCCCCTC	847
		GATAGG		AGAT

16368	16390	TGGATGACCCCCCTCAG	425	TGGATGACCCCCCTCA	848
		ATAGGG		GATA

16369	16391	GGATGACCCCCCTCAGA	426	GGATGACCCCCCTCAG	849
		TAGGGG		ATAG

16434	16456	GAGTGCTACTCTCCTCG	427	GAGTGCTACTCTCCTC	850
		CTCCGG		GCTC

16435	16457	AGTGCTACTCTCCTCGC	428	AGTGCTACTCTCCTCG	851
		TCCGGG		CTCC

16449	16471	CGCTCCGGGCCCATAAC	429	CGCTCCGGGCCCATAA	852
		ACTTGG		CACT

16450	16472	GCTCCGGGCCCATAACA	430	GCTCCGGGCCCATAAC	853
		CTTGGG		ACTT

16451	16473	CTCCGGGCCCATAACAC	431	CTCCGGGCCCATAACA	854
		TTGGGG		CTTG

16452	16474	TCCGGGCCCATAACACT	432	TCCGGGCCCATAACAC	855
		TGGGGG		TTGG

16482	16504	AGTGAACTGTATCCGAC	433	AGTGAACTGTATCCGA	856
		ATCTGG		CATC

16495	16517	CGACATCTGGTTCCTAC	434	CGACATCTGGTTCCTA	857
		TTCAGG		CTTC

16496	16518	GACATCTGGTTCCTACT	435	GACATCTGGTTCCTAC	858
		TCAGGG		TTCA

TABLE 4

gRNA target sequence for human mtDNA carrying NGG sequence on the (−) strand.

		nt sequence on the (+)
		strand containing CCN
	Chr end	sequence followed by the		20 nt gRNA target
Chr start	position	reverse complementary		sequence
position	(+	sequence of gRNA target	SEQ	(will encode the gRNA	SEQ
(+ strand)	strand)	sequence	ID NO:	targeting sequence)	ID NO:

17	39	CCCTATTAACCACTCAC	859	GCTCCCGTGAGTGGTT	2628
		GGGAGC		AATA

18	40	CCTATTAACCACTCACG	860	AGCTCCCGTGAGTGGT	2629
		GGAGCT		TAAT

26	48	CCACTCACGGGAGCTCT	861	GCATGGAGAGCTCCCG	2630
		CCATGC		TGAG

43	65	CCATGCATTTGGTATTT	862	AGACGAAAATACCAA	2631
		TCGTCT		ATGCA

104	126	CCGGAGCACCCTATGTC	863	TACTGCGACATAGGGT	2632
		GCAGTA		GCTC

112	134	CCCTATGTCGCAGTATC	864	AAGACAGATACTGCG	2633
		TGTCTT		ACATA

113	135	CCTATGTCGCAGTATCT	865	AAAGACAGATACTGC	2634
		GTCTTT		GACAT

140	162	CCTGCCTCATCCTATTA	866	GATAAATAATAGGATG	2635
		TTTATC		AGGC

144	166	CCTCATCCTATTATTTAT	867	GTGCGATAAATAATAG	2636
		CGCAC		GATG

150	172	CCTATTATTTATCGCAC	868	ACGTAGGTGCGATAAA	2637
		CTACGT		TAAT

166	188	CCTACGTTCAATATTAC	869	TCGCCTGTAATATTGA	2638
		AGGCGA		ACGT

261	283	CCACTTTCCACACAGAC	870	TATGATGTCTGTGTGG	2639
		ATCATA		AAAG

268	290	CCACACAGACATCATAA	871	TTTTTGTTATGATGTCT	2640
		CAAAAA		GTG

298	320	CCAAACCCCCCCTCCCC	872	GAAGCGGGGGAGGGG	2641
		CGCTTC		GGGTT

304	326	CCCCCCTCCCCCGCTTC	873	TGGCCAGAAGCGGGG	2642
		TGGCCA		GAGGG

305	327	CCCCCTCCCCCGCTTCT	874	GTGGCCAGAAGCGGG	2643
		GGCCAC		GGAGG

306	328	CCCCTCCCCCGCTTCTG	875	TGTGGCCAGAAGCGG	2644
		GCCACA		GGGAG

107	329	CCCTCCCCCGCTTCTGG	876	CTGTGGCCAGAAGCGG	2645
		CCACAG		GGGA

308	330	CCTCCCCCGCTTCTGGC	877	GCTGTGGCCAGAAGCG	2646
		CACAGC		GGGG

311	333	CCCCCGCTTCTGGCCAC	878	AGTGCTGTGGCCAGAA	2647
		AGCACT		GCGG

312	334	CCCCGCTTCTGGCCACA	879	AAGTGCTGTGGCCAGA	2648
		GCACTT		AGCG

313	335	CCCGCTTCTGGCCACAG	880	TAAGTGCTGTGGCCAG	2649
		CACTTA		AAGC

314	336	CCGCTTCTGGCCACAGC	881	TTAAGTGCTGTGGCCA	2650
		ACTTAA		GAAG

324	346	CCACAGCACTTAAACAC	882	AGAGATGTGTTTAAGT	2651
		ATCTCT		GCTG

348	370	CCAAACCCCAAAAACA	883	GGTTCTTTGTTTTTGGG	2652
		AAGAACC		GTT

353	375	CCCCAAAAACAAAGAA	884	GTTAGGGTTCTTTGTTT	2653
		CCCTAAC		TTG

354	376	CCCAAAAACAAAGAAC	885	TGTTAGGGTTCTTTGTT	2654
		CCTAACA		TTT

355	377	CCAAAAACAAAGAACC	886	GTGTTAGGGTTCTTTG	2655
		CTAACAC		TTTT

369	391	CCCTAACACCAGCCTAA	887	ATCTGGTTAGGCTGGT	2656
		CCAGAT		GTTA

370	392	CCTAACACCAGCCTAAC	888	AATCTGGTTAGGCTGG	2657
		CAGATT		TGTT

377	399	CCAGCCTAACCAGATTT	889	AATTTGAAATCTGGTT	2658
		CAAATT		AGGC

381	403	CCTAACCAGATTTCAAA	890	ATAAAATTTGAAATCT	2659
		TTTTAT		GGTT

386	408	CCAGATTTCAAATTTTA	891	AAAAGATAAAATTTGA	2660
		TCTTTT		AATC

433	455	CCCCCCAACTAACACAT	892	AAAATAATGTGTTAGT	2661
		TATTTT		TGGG

434	456	CCCCCAACTAACACATT	893	GAAAATAATGTGTTAG	2662
		ATTTTC		TTGG

435	457	CCCCAACTAACACATTA	894	GGAAAATAATGTGTTA	2663
		TTTTCC		GTTG

436	458	CCCAACTAACACATTAT	895	GGGAAAATAATGTGTT	2664
		TTTCCC		AGTT

437	459	CCAACTAACACATTATT	896	GGGGAAAATAATGTGT	7665
		TTCCCC		TAGT

456	478	CCCCTCCCACTCCCATA	897	TAGTAGTATGGGAGTG	2666
		CTACTA		GGAG

457	479	CCCTCCCACTCCCATAC	898	TTAGTAGTATGGGAGT	2667
		TACTAA		GGGA

458	480	CCTCCCACTCCCATACT	899	ATTAGTAGTATGGGAG	2668
		ACTAAT		TGGG

461	483	CCCACTCCCATACTACT	900	GAGATTAGTAGTATGG	2669
		AATCTC		GAGT

462	484	CCACTCCCATACTACTA	901	TGAGATTAGTAGTATG	2670
		ATCTCA		GGAG

467	489	CCCATACTACTAATCTC	902	ATTGATGAGATTAGTA	2671
		ATCAAT		GTAT

468	490	CCATACTACTAATCTCA	903	TATTGATGAGATTAGT	2672
		TCAATA		AGTA

494	516	CCCCCGCCCATCCTACC	904	GTGCTGGGTAGGATGG	2673
		CAGCAC		GCGG

495	517	CCCCGCCCATCCTACCC	905	TGTGCTGGGTAGGATG	2674
		AGCACA		GGCG

496	518	CCCGCCCATCCTACCCA	906	GTGTGCTGGGTAGGAT	2675
		GCACAC		GGGC

497	519	CCGCCCATCCTACCCAG	907	TGTGTGCTGGGTAGGA	2676
		CACACA		TGGG

500	522	CCCATCCTACCCAGCAC	908	GTGTGTGTGCTGGGTA	2677
		ACACAC		GGAT

501	523	CCATCCTACCCAGCACA	909	TGTGTGTGTGCTGGTA	2678
		CACACA		AGGA

505	527	CCTACCCAGCACACACA	910	GCGGTGTGTGTGTGCT	2679
		CACCGC		GGGT

509	531	CCCAGCACACACACACC	911	AGCAGCGGTGTGTGTG	2680
		GCTGCT		TGCT

510	532	CCAGCACACACACACCG	912	TAGCAGCGGTGTGTGT	2681
		CTGCTA		GTGC

524	546	CCGCTGCTAACCCCATA	913	TCGGGGTATGGGGTTA	2682
		CCCCGA		GCAG

534	556	CCCCATACCCCGAACCA	914	TTTGGTTGGTTCGGGG	2683
		ACCAAA		TATG

535	557	CCCATACCCCGAACCAA	915	GTTTGGTTGGTTCGGG	2684
		CCAAAC		GTAT

536	558	CCATACCCCGAACCAAC	916	GGTTTGGTTGGTTCGG	2685
		CAAACC		GGTA
541	563	CCCCGAACCAACCAAAC	917	TTTGGGGTTTGGTTGG	2686

		CCCAAA		TTCG
542	564	CCCGAACCAACCAAACC	918	CTTTGGGGTTTGGTTG	2687
		CCAAAG		GTTC

543	565	CCGAACCAACCAAACCC	919	TCTTTGGGGTTTGGTT	2688
		CAAAGA		GGTT

548	570	CCAACCAAACCCCAAA	920	GGGTGTCTTTGGGGTT	2689
		GACACCC		TGGT

552	574	CCAAACCCCAAAGACA	921	TGGGGGGTGTCTTTGG	2690
		CCCCCCA		GGTT

557	579	CCCCAAAGACACCCCCC	922	AACTGTGGGGGGTGTC	2691
		ACAGTT		TTTG

558	580	CCCAAAGACACCCCCCA	923	AAACTGTGGGGGGTGT	2692
		CAGTTT		CTTT

559	581	CCAAAGACACCCCCCAC	924	TAAACTGTGGGGGGTG	2693
		AGTTTA		TCTT

568	590	CCCCCCACAGTTTATGT	925	TAAGCTACATAAACTG	2694
		AGCTTA		TGGG

569	591	CCCCCACAGTTTATGTA	926	GTAAGCTACATAAACT	2695
		GCTTAC		GTGG

570	592	CCCCACAGTTTATGTAG	927	GGTAAGCTACATAAAC	2696
		CTTACC		TGTG

571	593	CCCACAGTTTATGTAGC	928	AGGTAAGCTACATAAA	2697
		TTACCT		CTGT

572	594	CCACAGTTTATGTAGCT	929	GAGGTAAGCTACATAA	2698
		TACCTC		ACTG

591	613	CCTCCTCAAAGCAATAC	930	TTCAGTGTATTGCTTT	2699
		ACTGAA		GAGG

594	616	CCTCAAAGCAATACACT	931	ATTTTCAGTGTATTGC	2700
		GAAAAT		TTTG

637	659	CCCCATAAACAAATAGG	932	ACCAAACCTATTTGTT	2701
		TTTGGT		TATG

638	660	CCCATAAACAAATAGGT	933	GACCAAACCTATTTGT	2702
		TTGGTC		TTAT

639	661	CCATAAACAAATAGGTT	934	GGACCAAACCTATTTG	2703
		TGGTCC		TTTA

660	682	CCTAGCCTTTCTATTAG	935	TAAGAGCTAATAGAA	2704
		CTCTTA		AGGCT

665	687	CCTTTCTATTAGCTCTTA	936	CTTACTAAGAGCTAAT	2705
		GTAAG		AGAA

705	727	CCCCGTTCCAGTGAGTT	937	AGGGTGAACTCACTGG	2706
		CACCCT		AACG

706	728	CCCGTTCCAGTGAGTTC	938	GAGGGTGAACTCACTG	2707
		ACCCTC		GAAC

707	729	CCGTTCCAGTGAGTTCA	939	AGAGGGTGAACTCACT	2708
		CCCTCT		GGAA

712	734	CCAGTGAGTTCACCCTC	940	GATTTAGAGGGTGAAC	2709
		TAAATC		TCAC

724	746	CCCTCTAAATCACCACG	941	TTTGATCGTGGTGATT	2710
		ATCAAA		TAGA

725	747	CCTCTAAATCACCACGA	942	TTTTGATCGTGGTGAT	2711
		TCAAAA		TTAG

736	758	CCACGATCAAAAGGAA	943	ATGCTTGTTCCTTTTGA	2712
		CAAGCAT		TCG

792	814	CCTAGCCACACCCCCAC	944	TTTCCCGTGGGGGTGT	2713
		GGGAAA		GGCT

797	819	CCACACCCCCACGGGAA	945	TGCTGTTTCCCGTGGG	2714
		ACAGCA		GGTG

802	824	CCCCCACGGGAAACAG	946	ATCACTGCTGTTTCCC	2715
		CAGTGAT		GTGG

803	825	CCCCACGGGAAACAGC	947	AATCACTGCTGTTTCC	2716
		AGTGATT		CGTG

804	826	CCCACGGGAAACAGCA	948	TAATCACTGCTGTTTC	2717
		GTGATTA		CCGT

805	827	CCACGGGAAACAGCAG	949	TTAATCACTGCTGTTT	2718
		TGATTAA		CCCG

828	850	CCTTTAGCAATAAACGA	950	AAACTTTCGTTTATTG	2719
		AAGTTT		CTAA

867	889	CCCCAGGGTTGGTCAAT	951	CACGAAATTGACCAAC	2720
		TTCGTG		CCTG

868	890	CCCAGGGTTGGTCAATT	952	GCACGAAATTGACCAA	2721
		TCGTGC		CCCT

869	891	CCAGGGTTGGTCAATTT	953	GGCACGAAATTGACCA	2722
		CGTGCC		ACCC

890	912	CCAGCCACCGCGGTCAC	954	AATCGTGTGACCGCGG	2723
		ACGATT		TGGC

894	916	CCACCGCGGTCACACGA	955	GGTTAATCGTGTGACC	2724
		TTAACC		GCGG

897	919	CCGCGGTCACACGATTA	956	TTGGGTTAATCGTGTG	2725
		ACCCAA		ACCG

915	937	CCCAAGTCAATAGAAGC	957	ACGCCGGCTTCTATTG	2726
		CGGCGT		ACTT

916	938	CCAAGTCAATAGAAGCC	958	TACGCCGGCTTCTATT	2727
		GGCGTA		GACT

931	953	CCGGCGTAAAGAGTGTT	959	ATCTAAAACACTCTTT	2728
		TTAGAT		ACGC

956	978	CCCCCTCCCCAATAAAG	960	TTTTAGCTTTTTGGG	2729
		CTAAAA		GAGG

957	979	CCCCTCCCCAATAAAGC	961	GTTTTAGCTTTATTGG	2730
		TAAAAC		GGAG

958	980	CCCTCCCCAATAAAGCT	962	AGTTTTAGCTTTATTG	2731
		AAAACT		GGGA

959	981	CCTCCCCAATAAAGCTA	963	GAGTTTTAGCTTTATT	2732
		AAACTC		GGGG

962	984	CCCCAATAAAGCTAAAA	964	GGTGAGTTTTAGCTTT	2733
		CTCACC		ATTG

963	985	CCCAATAAAGCTAAAAC	965	AGGTGAGTTTTAGCTT	2734
		TCACCT		TATT

964	986	CCAATAAAGCTAAAACT	966	CAGGTGAGTTTTAGCT	2735
		CACCTG		TTAT

983	1005	CCTGAGTTGTAAAAAAC	967	ACTGGAGTTTTTTACA	2736
		TCCAGT		ACTC

1001	1023	CCAGTTGACACAAAATA	968	GTAGTCTATTTTGTGT	2737
		GACTAC		CAAC

1064	1086	CCCAAACTGGGATTAGA	969	GGGGTATCTAATCCCA	2738
		TACCCC		GTTT

1065	1087	CCAAACTGGGATTAGAT	970	TGGGGTATCTAATCCC	2739
		ACCCCA		AGTT

1083	1105	CCCCACTATGCTTAGCC	971	GTTTAGGGCTAAGCAT	2740
		CTAAAC		AGTG

1084	1106	CCCACTATGCTTAGCCC	972	GGTTTAGGGCTAAGCA	2741
		TAAACC		TAGT

1085	1107	CCACTATGCTTAGCCCT	973	AGGTTTAGGGCTAAGC	2742
		AAACCT		ATAG

1098	1120	CCCTAAACCTCAACAGT	974	GATTTAACTGTTGAGG	2743
		TAAATC		TTTA

1099	1121	CCTAAACCTCAACAGTT	975	TGATTTAACTGTTGAG	2744
		AAATCA		GTTT

1105	1127	CCTCAACAGTTAAATCA	976	TTTTGTTGATTTAACTG	2745
		ACAAAA		TTG

1135	1157	CCAGAACACTACGAGCC	977	AGCTGTGGCTCGTAGT	2746
		ACAGCT		GTTC

1150	1172	CCACAGCTTAAAACTCA	978	GTCCTTTGAGTTTTAA	2747
		AAGGAC		GCTG

1172	1194	CCTGGCGGTGCTTCATA	979	GAGGGATATGAAGCA	2748
		TCCCTC		CCGCC

1190	1212	CCCTCTAGAGGAGCCTG	980	ACAGAACAGGCTCCT	2749
		TTCTGT		TAGA

1191	1213	CCTCTAGAGGAGCCTGT	981	TACAGAACAGGCTCCT	2750
		TCTGTA		CTAG

1203	1225	CCTGTTCTGTAATCGAT	982	GGGTTTATCGATTACA	2751
		AAACCC		GAAC

1223	1245	CCCCGATCAACCTCAC	983	AGAGGTGGTGAGGTTG	2752
		ACCTCT		ATCG

1224	1246	CCCGATCAACCTCACCA	984	AAGAGGTGGTGAGGTT	2753
		CCTCTT		GATC

1225	1247	CCGATCAACCTCACCAC	985	CAAGAGGTGGTGAGG	2754
		CTCTTG		TTGAT

1233	1255	CCTCACCACCTCTTGCT	986	AGGCTGAGCAAGAGG	2755
		CAGCCT		TGGTG

1238	1260	CCACCTCTTGCTCAGCC	987	TATATAGGCTGAGCAA	2756
		TATATA		GAGG

1241	1263	CCTCTTGCTCAGCCTAT	988	CGGTATATAGGCTGAG	2757
		ATACCG		CAAG

1253	1275	CCTATATACCGCCATCT	989	TGCTGAAGATGGCGGT	2758
		TCAGCA		ATAT

1261	1283	CCGCCATCTTCAGCAAA	990	TCAGGGTTTGCTGAAG	2759
		CCCTGA		ATGG

1264	1286	CCATCTTCAGCAAACCC	991	TCATCAGGGTTTGCTG	2760
		TGATGA		AAGA

1278	1300	CCCTGATGAAGGCTACA	992	TTACTTTGTAGCCTTC	2761
		AAGTAA		ATCA

1279	1301	CCTGATGAAGGCTACAA	993	CTTACTTTGTAGCCTTC	2762
		AGTAAG		ATC

1310	1332	CCCACGTAAAGACGTTA	994	TTGACCTAACGTCTTT	2763
		GGTCAA		ACGT

1311	1333	CCACGTAAAGACGTTAG	995	CTTGACCTAACGTCTT	2764
		GTCAAG		TACG

1340	1362	CCCATGAGGTGGCAAG	996	CCCATTTGTTGCCACC	2765
		AAATGGG		TCAT

1341	1363	CCATGAGGTGGCAAGA	997	GCCCATTTCTTGCCAC	2766
		AATGGGC		CTCA

1375	1397	CCCCAGAAAACTACGAT	998	AGGGCTATCGTAGTTT	2767
		AGCCCT		TCTG

1376	1398	CCCAGAAAACTACGATA	999	AAGGGCTATCGTAGTT	2768
		GCCCTT		TTCT

1377	1399	CCAGAAAACTACGATA	1000	TAAGGGCTATCGTAGT	2769
		GCCCTTA		TTTC

1394	1416	CCCTTATGAAACTTAAG	1001	TCGACCCTTAAGTTTC	2770
		GGTCGA		ATAA

1395	1417	CCTTATGAAACTTAAGG	1002	TTCGACCCTTAAGTTT	2771
		GTCGAA		CATA

1465	1487	CCCTGAAGCGCGTACAC	1003	GGCGGTGTGTACGCGC	2772
		ACCGCC		TTCA

1466	1488	CCTGAAGCGCGTACACA	1004	GGGCGGTGTGTACGCG	2773
		CCGCCC		CTTC

1483	1505	CCGCCCTCACCCTCCT	1005	TACTTGAGGAGGGTGA	2774
		CAAGTA		CGGG

1486	1508	CCCGTCACCCTCCTCAA	1006	GTATACTTGAGGAGGG	2775
		GTATAC		TGAC

1487	1509	CCGTCACCCTCCTCAAG	1007	AGTATACTTGAGGAGG	7776
		TATACT		GTGA

1493	1515	CCCTCCTCAAGTATACT	1008	CTTTGAAGTATACTTG	2777
		TCAAAG		AGGA

1494	1516	CCTCCTCAAGTATACTT	1009	CCTTTGAAGTATACTT	2778
		CAAAGG		GAGG

1497	1519	CCTCAAGTATACTTCAA	1010	TGTCCTTTGAAGTATA	2779
		AGGACA		CTTG

1531	1553	CCCCTACGCATTTATAT	1011	TCCTCTATATAAATGC	2780
		AGAGGA		GTAG

1532	1554	CCCTACGCATTTATATA	1012	CTCCTCTATATAAATG	2781
		GAGGAG		CGTA

1533	1555	CCTACGCATTTATATAG	1013	TCTCCTCTATATAAAT	2782
		AGGAGA		GCGT

1601	1623	CCAGAGTGTAGCTTAAC	1014	CTTTGTGTTAAGCTAC	2783
		ACAAAG		ACTC

1626	1648	CCCAACTTACACTTAGG	1015	AAATCTCCTAAGTGTA	2784
		AGATTT		AGTTT

162	1649	CCAACTTACACTTAGGA	1016	GAAATCTCCTAAGTGT	2785
		GATTTC		AAGT

1662	1684	CCGCTCTGAGCTAAACC	1017	GGGCTAGGTTTAGCTC	2786
		TAGCCC		AGAG

1677	1699	CCTAGCCCCAAACCCAC	1018	GGTGGAGTGGGTTTGG	2787
		TCCACC		GGCT

1682	1704	CCCCAAACCCACTCCAC	1019	AGTAAGGTGGAGTGG	2788
		CTTACT		GTTTG

1683	1705	CCCAAACCCACTCCACC	1020	TAGTAAGGTGGAGTGG	2789
		TTACTA		GTTT

1684	1706	CCAAACCCACTCCACCT	1021	GTAGTAAGGTGGAGTG	2790
		TACTAC		GGTT

1689	1711	CCCACTCCACCTTACTA	1022	GTCTGGTAGTAAGGTG	2791
		CCAGAC		GAGT

1690	1712	CCACTCCACCTTACTAC	1023	TGTCTGGTAGTAAGGT	2792
		CAGACA		GGAG

1695	1717	CCACCTTACTACCAGAC	1024	AAGGTTGTCTGGTAGT	2793
		AACCTT		AAGG

1698	1720	CCTTACTACCAGACAAC	1025	GCTAAGGTTGTCTGGT	2794
		CTTAGC		AGTA

1706	1728	CCAGACAACCTTAGCC	1026	ATGGTTTGGCTAAGGT	2795
		AACCAT		TGTC

1714	1736	CCTTAGCCAAACCATTT	1027	TTGGGTAAATGGTTTG	2796
		ACCCAA		GCTA

1720	1742	CCAAACCATTTACCCAA	1028	CTTTATTTGGGTAAAT	2797
		ATAAAG		GGTT

1725	1747	CCATTTACCCAAATAAA	1029	CTATACTTTATTTGGG	2798
		GTATAG		TAAA

1732	1754	CCCAAATAAAGTATAGG	1030	CTATCGCCTATACTTT	2799
		CGATAG		ATTT

1733	1755	CCAAATAAAGTATAGGC	1031	TCTATCGCCTATACTTT	2800
		GATAGA		ATT

1764	1786	CCTGGCGCAATAGATAT	1032	GGTACTATATCTATTG	2801
		AGTACC		CGCC

1785	1807	CCGCAAGGGAAAGATG	1033	AATTTTTCATCTTTCCC	2802
		AAAAATT		TTG

1812	1834	CCAAGCATAATATAGCA	1034	AGTCCTTGCTATATTA	2803
		AGGACT		TGCT

1837	1859	CCCCTATACCTTCTGCA	1035	TCATTATGCAGAAGGT	2804
		TAATGA		ATAG

1838	1860	CCCTATACCTTCTGCAT	1036	TTCATTATGCAGAAGG	2805
		AATGAA		TATA

1839	1861	CCTATACCTTCTGCATA	1037	ATTCATTATGCAGAAG	2806
		ATGAAT		GTAT

1845	1867	CCTTCTGCATAATGAAT	1038	TAGTTAATTCATTATG	2807
		TAACTA		CAGA

1889	1911	CCAAAGCTAAGACCCCC	1039	GGTTTCGGGGGTCTTA	2808
		GAAACC		GCTT

1901	1923	CCCCCGAAACCAGACG	1040	GGTAGCTCGTCTGGTT	2809
		AGCTACC		TCGG

1902	1924	CCCCGAAACCAGACGA	1041	AGGTAGCTCGTCTGGT	2810
		GCTAC		TTCG

1903	1925	CCCGAAACCAGACGAG	1042	TAGGTAGCTCGTCTGG	2811
		CTACCTA		TTTC

1904	1926	CCGAAACCAGACGAGC	1043	TTAGGTAGCTCGTCTG	2812
		TACCTAA		GTTT

1910	1932	CCAGACGAGCTACCTAA	1044	CTGTTCTTTTGGTAGCT	2813
		GAACAG		CGTC

1922	1944	CCTAAGAACAGCTAAA	1045	GTGCTCTTTTAGCTGTT	2814
		AGAGCAC		CTT

1946	1968	CCCGTCTATGTAGCAAA	1046	CACTATTTTGCTACAT	2815
		ATAGTG		AGAC

1947	1969	CCGTCTATGTAGCAAAA	1047	CCACTATTTTGCTACA	2816
		TAGTGG		TAGA

1996	2018	CCTACCGAGCCTGGTGA	1048	CAGCTATCACCAGGCT	2817
		TAGCTG		CGGT

2000	2022	CCGAGCCTGGTGATAGC	1049	CAACCAGCTATCACCA	2818
		TGGTTG		GGCT

2005	2027	CCTGGTGATAGCTGGTT	1050	TTGGACAACCAGCTAT	2819
		GTCCAA		CACC

2024	2046	CCAAGATAGAATCTTAG	1051	GTTGAACTAAGATTCT	2820
		TTCAAC		ATCT

2057	2079	CCCACAGAACCCTCTAA	1052	GGGGATTTAGAGGGTT	2821
		ATCCCC		CTGT

2058	2080	CCACAGAACCCTCTAAA	1053	AGGGGATTTAGAGGGT	2822
		TCCCCT		TCTG

2066	7088	CCCTCTAAATCCCCTTG	1054	AATTTACAAGGGGATT	2823
		TAAATT		TAGA

2067	2089	CCTCTAAATCCCCTTGT	1055	AAATTTACAAGGGGAT	2824
		AAATTT		TTAG

2076	2098	CCCCTTGTAAATTTAAC	1056	CTAACAGTTAAATTTA	2825
		TGTTAG		CAAG

2077	2099	CCCTTGTAAATTTAACT	1057	ACTAACAGTTAAATTT	2826
		GTTAGT		ACAA

2078	2100	CCTTGTAAATTTAACTG	1058	GACTAACAGTTAAATT	2827
		TTAGTC		TACA

2100	2122	CCAAAGAGGAACAGCT	1059	TCCAAAGAGCTGTTCC	2828
		CTTTGGA		TCTT

2136	2158	CCTTGTAGAGAGAGTAA	1060	AATTTTTTACTCTCTCT	2829
		AAAATT		ACA

2164	2186	CCCATAGTAGGCCTAAA	1061	GCTGCTTTTAGGCCTA	2830
		AGCAGC		CTAT

2165	2187	CCATAGTAGGCCTAAAA	1062	GGCTGCTTTTAGGCCT	2831
		GCAGCC		ACTA

2175	2197	CCTAAAAGCAGCCACCA	1063	CTTAATTGGTGGCTGC	2832
		ATTAAG		TTTT

2186	2208	CCACCAATTAAGAAAGC	1064	TTGAACGCTTTCTTAA	2833
		GTTCAA		TTGG

2189	2211	CCAATTAAGAAAGCGTT	1065	AGCTTGAACGCTTTCT	2834
		CAAGCT		AAT

2217	2239	CCCACTACCTAAAAAAT	1066	TTTGGGATTTTTTAGG	2835
		CCCAAA		TAGT

2218	2240	CCACTACCTAAAAAATC	1067	GTTTGGGATTTTTTAG	2836
		CCAAAC		GTAG

2224	2246	CCTAAAAAATCCCAAAC	1068	TTATATGTTTGGGATT	2837
		ATATAA		TTTT

2234	2256	CCCAAACATATAACTGA	1069	AGGAGTTCAGTTATAT	2838
		ACTCCT		GTTT

2235	2257	CCAAACATATAACTGAA	1070	GAGGAGTTCAGTTATA	2839
		CTCCTC		TGTT

2254	2276	CCTCACACCCAATTGGA	1071	GATTGGTCCAATTGGG	2840
		CCAATC		TGTG

2261	2283	CCCAATTGGACCAATCT	1072	GGTGATAGATTGGTCC	2841
		ATCACC		AATT

2262	2284	CCAATTGGACCAATCTA	1073	GGGTGATAGATTGGTC	2842
		TCACCC		CAAT

2271	2293	CCAATCTATCACCCTAT	1074	TCTTCTATAGGGTGAT	2843
		AGAAGA		AGAT

2282	2304	CCCTATAGAAGAACTAA	1075	CTAACATTAGTTCTTC	2844
		TGTTAG		TATA

2283	2305	CCTATAGAAGAACTAAT	1076	ACTAACATTAGTTCTT	7845
		GTTAGT		CTAT

2328	2350	CCTCCGCATAAGCCTGC	1077	TCTGACGCAGGCTTAT	2846
		GTCAGA		GCGG

2331	2353	CCGCATAAGCCTGCGTC	1078	TAATCTGACGCAGGCT	2847
		AGATTA		TATG

2340	2362	CCTGCGTCAGATTAAAA	1079	TCAGTGTTTTAATCTG	2848
		CACTGA		ACGC

2378	2400	CCCAATATCTACAATCA	1080	GTTGGTTGATTGTAGA	2849
		ACCAAC		TATT

2379	2401	CCAATATCTACAATCAA	1081	TGTTGGTTGATTGTAG	2850
		CCAACA		ATAT

2396	2418	CCAACAAGTCATTATTA	1082	TGAGGGTAATAATGAC	2851
		CCCTCA		TTGT

2413	2435	CCCTCACTGTCAACCCA	1083	CTGTGTTGGGTTGACA	2852
		ACACAG		GTGA

2414	2436	CCTCACTGTCAACCCAA	1084	CCTGTGTTGGGTTGAC	2853
		CACAGG		AGTG

2426	2448	CCCAACACGGCATGCT	1085	CTTATGAGCATGCCTG	2854
		CATAAG		TGTT

2427	2449	CCAACACAGGCATGCTC	1086	CCTTATGAGCATGCCT	2855
		ATAAGG		GTGT

2488	2510	CCCCGCCTGTTTACCAA	1087	ATGTTTTTGGTAAACA	2856
		AAACAT		GGCG

2489	2511	CCCGCCTGTTTACCAAA	1088	GATGTTTTTGGTAAAC	2857
		AACATC		AGGC

2490	2512	CCGCCTGTTTACCAAAA	1089	TGATGTTTTTGGTAAA	2858
		ACATCA		CAGG

2493	2515	CCTGTTTACCAAAAACA	1090	AGGTGATGTTTTTGGT	2859
		TCACCT		AAAC

2501	2523	CCAAAAACATCACCTCT	1091	GATGCTAGAGGTGATG	2860
		AGCATC		TTTT

2513	2535	CCTCTAGCATCACCAGT	1092	TCTAATACTGGTGATG	2861
		ATTAGA		CTAG

2525	2547	CCAGTATTAGAGGCACC	1093	GCAGGCGGTGCCTCTA	2862
		GCCTGC		ATAC

2540	2562	CCGCCTGCCCAGTGACA	1094	AACATGTGTCACTGGG	2863
		CATGTT		CAGG

2543	2565	CCTGCCCAGTGACACAT	1095	TTAAACATGTGTCACT	2864
		GTTTAA		GGGC

2547	2569	CCCAGTGACACATGTTT	1096	GCCGTTAAACATGTGT	2865
		AACGGC		CACT

2548	2570	CCAGTGACACATGTTTA	1097	GGCCGTTAAACATGTG	2866
		ACGGCC		TCAC

2569	2591	CCGCGGTACCCTAACCG	1098	TTTGCACGGTTAGGGT	2867
		TGCAAA		ACCG

2577	2599	CCCTAACCGTGCAAAGG	1099	ATGCTACCTTTGCACG	2868
		TAGCAT		GTTA

2578	2600	CCTAACCGTGCAAAGGT	1100	TATGCTACCTTTGCAC	2869
		AGCATA		GGTT

2583	2605	CCGTGCAAAGGTAGCAT	1101	GTGATTATGTACCT	2870
		AATCAC		TGCA

2611	2633	CCTTAAATAGGGACCTG	1101	TTCATACAGGTCCCTA	2871
		TATGAA		TTTA

2624	2646	CCTGTATGAATGGCTCC	1103	CCTCGTGGAGCCATTC	2872
		ACGAGG		ATAC

2639	2661	CCACGAGGGTTCAGCTG	1104	AAGAGACAGCTGAAC	2873
		TCTCTT		CCTCG

2670	2692	CCAGTGAAATTGACCTG	1105	CACGGGCAGGTCAATT	2874
		CCCGTG		TCAC

2683	2705	CCTGCCCGTGAAGAGGC	1106	ATGCCCGCCTCTTCAC	7875
		GGGCAT		GGGC

2687	2709	CCCGTGAAGAGGCGGG	1107	TGTTATGCCCGCCTCT	2876
		CATAACA		TCAC

2688	2710	CCGTGAAGAGGCGGGC	1108	GTGTTATGCCCGCCTC	2877
		ATAACAC		TTCA

2726	2748	CCCTATGGAGCTTTAAT	1109	TAATAAATTAAAGC	2878
		TTATTA		CATA

2727	2749	CCTATGGAGCTTTAATT	1110	TTAATAAATTAAAGCT	2879
		TATTAA		CCAT

2761	2783	CCTAACAAACCCACAGG	1111	TTAGGACCTGTGGGTT	2880
		TCCTAA		TGTT

2770	2792	CCCACAGGTCCTAAACT	1112	TTTGGTAGTTTAGGAC	2881
		ACCAAA		CTGT

2771	2793	CCACAGGTCCTAAACTA	1113	GTTTGGTAGTTTAGGA	2882
		CCAAAC		CCTG

7779	2801	CCTAAACTACCAAACCT	1114	TAATGCAGGTTTGGTA	2883
		GCATTA		GTTT

2788	2810	CCAAACCTGCATTAAAA	1115	CGAAATTTTTAATGCA	2884
		ATTTCG		GGTT

2793	2815	CCTGCATTAAAAATTTC	1116	CCAACCGAAATTTTTA	2885
		GGTTGG		ATGC

2821	2843	CCTCGGAGCAGAACCCA	1117	GGAGGTTGGGTTCTGC	2886
		ACCTCC		TCCG

2834	2856	CCCAACCTCCGAGCAGT	1118	GCATGTACTGCTCGGA	2887
		ACATGC		GGTT

2835	2857	CCAACCTCCGAGCAGTA	1119	AGCATGTACTGCTCGG	2888
		CATGCT		AGGT

2839	2861	CCTCCGAGCAGTACATG	1120	TCTTAGCATGTACTGC	2889
		CTAAGA		TCGG

2842	2864	CCGAGCAGTACATGCTA	1121	AAGTCTTAGCATGTAC	2890
		AGACTT		TGCT

2867	2889	CCAGTCAAAGCGAACTA	1122	GTATACTTAGTTCGCTT	2891
		CTATAC		TGAC

2899	2921	CCAATAACTTGACCAAC	1123	TGTTCCGTTGGTCAACG	2892
		GGAACA		TTAT

2911	2933	CCAACGGAACAAGTTAC	1124	CCTAGGGTAACTTGTT	2893
		CCTAGG		CCGT

2927	2949	CCCTAGGGATAACAGCG	1125	GGATTGCGCTGTTATC	2894
		CAATCC		CCTA

2928	2950	CCTAGGGATAACAGCGC	1126	AGGATTGCGCTGTTAT	2895
		AATCCT		CCCT

2948	2970	CCTATTCTAGAGTCCAT	1127	GTTGATATGGACTCTA	2896
		ATCAAC		GAAT

2961	2983	CCATATCAACAATAGGG	1128	CGTAAACCCTATTGTT	2897
		TTTACG		GATA

2985	3007	CCTCGATGTTGGATCAG	1129	GATGTCCTGATCCAAC	2898
		GACATC		ATCG

3007	3029	CCCGATGGTGCAGCCGC	1130	TTAATAGCGGCTGCAC	2899
		TATTAA		CATC

3008	3030	CCGATGGTGCAGCCGCT	1131	TTTAATAGCGGCTGCA	2900
		ATTAAA		CCAT

3020	3042	CCGCTATTAAAGGTTCG	1132	AACAAACGAACCTTTA	2901
		TTTGTT		ATAG

3056	3078	CCTACGTGATCTGAGTT	1133	GGTCTGAACTCAGATC	2902
		CAGACC		ACGT

3077	3099	CCGGAGTAATCCAGGTC	1134	GAAACCGACCTGGATT	2903
		GGTTTC		ACTC

3087	3109	CCAGGTCGGTTTCTATC	1135	AANGTAGATAGAAAC	2904
		TACNTT		CGACC

3116	3138	CCTCCCTGTACGAAAGG	1136	TCTTGTCCTTTCGTACA	2905
		ACAAGA		GGG

3119	3141	CCCTGTACGAAAGGACA	1137	TTCTCTTGTCCTTTCGT	2906
		AGAGAA		ACA

3120	3142	CCTGTACGAAAGGACA	1138	TTTCTCTTGTCCTTTCG	2907
		AGAGAAA		TAC

3148	3170	CCTACTTCACAAAGCGC	1139	GGGAAGGCGCTTTGTG	2908
		CTTCCC		AAGT

3164	3186	CCTTCCCCCGTAAATGA	1140	ATGATATCATTTACGG	2909
		TATCAT		GGGA

3168	3190	CCCCCGTAAATGATATC	1141	TGAGATGATATCATTT	2910
		ATCTCA		ACGG

3169	3191	CCCCGTAAATGATATCA	1142	TTGAGATGATATCATT	2911
		TCTCAA		TACG

3170	3192	CCCGTAAATGATATCAT	1143	GTTGAGATGATATCAT	2912
		CTCAAC		TTAC

3171	3193	CCGTAAATGATATCATC	1144	AGTTGAGATGATATCA	2913
		TCAACT		TTTA

3204	3226	CCCACACCCACCCAAGA	1145	CCCTGTTCTTGGGTGG	2914
		ACAGGG		GTGT

3205	3227	CCACACCCACCCAAGAA	1146	ACCCTGTTCTTGGGTG	2915
		CAGGGT		GGTG

3210	3232	CCCACCCAAGAACAGG	1147	AACAAACCCTGTTCTT	2916
		GTTTGTT		GGGT

3211	3233	CCACCCAAGAACAGGG	1148	TAACAAACCCTGTTCT	2917
		TTTGTTA		TGGG

3214	3236	CCCAAGAACAGGGTTTG	1149	TCTTAACAAACCCTGT	2918
		TTAAGA		TCTT

3215	3237	CCAAGAACAGGGTTTGT	1150	ATCTTAACAAACCCTG	2919
		TAAGAT		TTCT

3245	3267	CCCGGTAATCGCATAAA	1151	TTAAGTTTTATGCGAT	2920
		ACTTAA		TACC

3246	3268	CCGGTAATCGCATTAAAA	1152	TTTAAGTTTTATGCGA	2921
		CTTAAA		TTAC

3292	3314	CCTCTTCTTAACAACAT	1153	ATGGGTATGTTGTTAA	2922
		ACCCAT		GAAG

3310	3332	CCCATGGCCAACCTCCT	1154	AGGAGTAGGAGGTTG	2923
		ACTCCT		GCCAT

3311	3333	CCATGGCCAACCTCCTA	1155	GAGGAGTAGGAGGTT	2924
		CTCCTC		GGCCA

3317	3339	CCAACCTCCTACTCCTC	1156	TACAATGAGGAGTAG	2925
		ATTGTA		GAGGT

3321	3343	CCTCCTACTCCTATTGT	1157	TGGGTACAATGAGGA	2926
		ACCCA		GTAGG

3324	3346	CCTACTCCTCATTGTAC	1158	GAATGGGTACAATGA	2927
		CCATTC		GGAGT

3330	3352	CCTCATTGTACCCATTC	1159	CGATTAGAATGGGTAC	2928
		TAATCG		AATG

3340	3362	CCCATTCTAATCGCAAT	1160	AATGCCATTGCGATTA	2929
		GGCATT		GAAT

3341	3363	CCATTCTAATCGCAATG	1161	GAATGCCATTGCGATT	2930
		GCATTC		AGAA

3363	3385	CCTAATGCTTACCGAAC	1162	TTTTTCGTTCGGTAAG	2931
		GAAAAA		CATT

3374	3396	CCGAACGAAAAATTCTA	1163	ATAGCCTAGAATTTTT	2932
		GGCTAT		CGTT

3414	3436	CCCCAACGTTGTAGGCC	1164	CGTAGGGGCCTACAAC	2933
		CCTACG		GTTG

3415	3437	CCCAACGTTGTAGGCCC	1165	CCGTAGGGGCCTACAA	2934
		CTACGG		CGTT

3416	3438	CCAACGTTGTAGGCCCC	1166	CCCGTAGGGGCCTACA	2935
		TACGGG		ACGT

3429	3451	CCCCTACGGGCTACTAC	1167	AGGTTGTAGTAGCCC	2936
		AACCCT		GTAG

3430	3452	CCCTACGGGCTACTACA	1168	AAGGGTTGTAGTAGCC	2937
		ACCCTT		CGTA

3431	3453	CCTACGGGCTACTACAA	1169	GAAGGGTTGTAGTAGC	2938
		CCCTTC		CCGT

3448	3470	CCCTTCGCTGACGCCAT	1170	AGTTTTATGGCGTCAG	2939
		AAAACT		CGAA

3449	3471	CCTTCGCTGACGCCATA	1171	GAGTTTTATGGCGTCA	2940
		AAACTC		GCGA

3461	3483	CCATAAAACTCTTCACC	1172	CTCTTTGGTGAAGAGT	2941
		AAAGAG		TTTA

3476	3498	CCAAAGAGCCCCTAAA	1173	GGCGGGTTTTAGGGGC	2942
		ACCCGCC		TCTT

3484	3506	CCCCTAAAACCCGCCAC	1174	GTAGATGTGGCGGGTT	2943
		ATCTAC		TTAG

3485	3507	CCCTAAAACCCGCCACA	1175	GGTAGATGTGGCGGGT	2944
		TCTACC		TTTA

3486	3508	CCTAAAACCCGCCACAT	1176	TGGTAGATGTGGCGGG	2945
		CTACCA		TTTT

3493	3515	CCCGCCACATCTACCAT	1177	AGGGTGATGGTAGATG	2946
		CACCCT		TGGC

3494	3516	CCGCCACATCTACCATC	1178	GAGGGTGATGGTAGAT	2947
		ACCCTC		GTGG

3497	3519	CCACATCTACCATCACC	1179	GTAGAGGGTGATGGTA	2948
		CTCTAC		GATG

3506	3528	CCATCACCCTCTACATC	1180	GGCGGTGATGTAGAG	2949
		ACCGCC		GGTGA

3512	3534	CCCTCTACATCACCGCC	1181	GGTCGGGGCGGTGATG	2950
		CCGACC		TAGA

3513	3535	CCTCTACATCACCGCCC	1182	AGGTCGGGGCGGTGAT	2951
		CGACCT		GTAG

3524	3546	CCGCCCCGACCTTAGCT	1183	GGTGAGAGCTAAGGTC	2952
		CTCACC		GGGG

3527	3549	CCCCGACCTTAGCTCTC	1184	GATGGTGAGAGCTAA	2953
		ACCATC		GGTCG

3528	3550	CCCGACCTTAGCTCTCA	1185	CGATGGTGAGAGCTAA	2954
		CCATCG		GGTC

3529	3551	CCGACCTTAGCTCTCAC	1186	GCGATGGTGAGAGCTA	2955
		CATCGC		AGGT

3533	3555	CCTTAGCTCTCACCATC	1187	AAGAGCGATGGTGAG	2956
		GCTCTT		AGCTA

3545	3567	CCATCGCTCTTCTACTA	1188	GGTTCATAGTAGAAGA	2957
		TGAACC		GCGA

3566	3588	CCCCCCTCCCCATACCC	1189	GGGGTTGGGTATGGGG	2958
		AACCCC		AGGG

3567	3589	CCCCCTCCCCATACCA	1190	GGGGGTTGGGTATGGG	2959
		ACCCCC		GAGG

3568	3590	CCCCTCCCCATACCCAA	1191	AGGGGGTTGGGTATGG	2960
		CCCCCT		GGAG

3569	3591	CCCTCCCCATACCCAAC	1192	CAGGGGGTTGGGTATG	2961
		CCCCTG		GGGA

3570	3592	CCTCCCCATACCCAACC	1193	CCAGGGGGTTGGGTAT	2962
		CCCTGG		GGGG

3573	3595	CCCCATACCCAACCCCC	1194	TGACCAGGGGGTTGGG	2963
		TGGTCA		TATG

3574	3596	CCCATACCCAACCCCCT	1195	TTGACCAGGGGGTTGG	2964
		GGTCAA		GTAT

3575	3597	CCATACCCAACCCCCTG	1196	GTTGACCAGGGGGTTG	2965
		GTCAAC		GGTA

3580	3602	CCCAACCCCCTGGTCAA	1197	TTGAGGTTGACCAGGG	2966
		CCTCAA		GGTT

3581	3603	CCAACCCCCTGGTCAAC	1198	GTTGAGGTTGACCAGG	2967
		CTCAAC		GGGT

3585	3607	CCCCCTGGTCAACCTCA	1199	CTAGGTTGAGGTTGAC	2968
		ACCTAG		CAGG

3586	3608	CCCCTGGTCAACCTCAA	1200	CCTAGGTTGAGGTTGA	2969
		CCTAGG		CCAG

3587	3609	CCCTGGTCAACCTCAAC	1201	GCCTAGGTTGAGGTTG	2970
		CTAGGC		ACCA

3588	3610	CCTGGTCAACCTCAACC	1202	GGCCTAGGTTGAGGTT	2971
		TAGGCC		GACC

3597	3619	CCTCAACCTAGGCCTCC	1203	TAAATAGGAGGCCTAG	2972
		TATTTA		GTTG

3603	3625	CCTAGGCCTCCTATTTA	1204	CTAGAATAAATAGGA	2973
		TTCTAG		GGCCT

3609	3631	CCTCCTATTTATTCTAGC	1205	AGGTGGCTAGAATAA	2974
		CACCT		ATAGG

3612	3634	CCTATTTATTTAGCCA	1206	TAGAGGTGGCTAGAAT	2975
		CCTCTA		AAAT

3626	3648	CCACCTCTAGCCTAGCC	1207	GTAAACGGCTAGGCTA	2976
		GTTTAC		GAGG

3629	3651	CCTCTAGCCTAGCCGTT	1208	TGAGTAAACGGCTAGG	2977
		TACTCA		CTAG

3636	3658	CCTAGCCGTTTACTCAA	1209	AGAGGATTGAGTAAA	2978
		TCCTCT		CGGCT

3641	3663	CCGTTTACTCAATCCTC	1210	TGATCAGAGGATTGAG	2979
		TGATCA		TAAA

3654	3676	CCTCTGATCAGGGTGAG	1211	TTGATGCTCACCCTGA	2980
		CATCAA		TCAG

3689	3711	CCCTGATCGGCGCCTG	1212	TGCTCGCAGTGCGCCG	2981
		CGAGCA		ATCA

3690	3712	CCTGATCGGCACTGC	1213	CTGCTCGCAGTGCGCC	2982
		GAGCAG		GATC

3716	3738	CCCAAACAATCTCATAT	1214	GACTTCATATGAGATT	2983
		GAAGTC		GTTT

3717	3739	CCAAACAATCTCATATG	1215	TGACTTCATATGAGAT	2984
		AAGTCA		TGTT

3740	3762	CCCTAGCCATCATTCTA	1216	TGATAGTAGAATGATG	2985
		CTATCA		GCTA

3741	3763	CCTAGCCATCATTCTAC	1217	TTGATAGTAGAATGAT	2986
		TATCAA		GGCT

3746	3768	CCATCATTCTACTATCA	1218	TAATGTTGATAGTAGA	2987
		ACATTA		ATGA

3782	3804	CCTTTAACCTCTCCACC	1219	GATAAGGGTGGAGAG	2988
		CTTATC		GTTAA

3789	3811	CCTCTCCACCCTTATCA	1220	GTGTTGTGATAAGGGT	2989
		CAACAC		GGAG

3794	3816	CCACCCTTATCACAACA	1221	TTCTTGTGTTGTGATA	2990
		CAAGAA		AGGG

3797	3819	CCCTTATCACAACACAA	1222	GTGTTCTTGTGTTGTG	2991
		GAACAC		ATAA

3798	3820	CCTTATCACAACACAAG	1223	GGTGTTCTTGTGTTGT	2992
		AACACC		GATA

3819	3841	CCTCTGATTACTCCTGC	1224	ATGATGGCAGGAGTA	2993
		CATCAT		ATCAG

3831	3853	CCTGCCATCATGACCCT	1225	TGGCCAAGGGTCATGA	2994
		TGGCCA		GGC

3835	3857	CCATCATGACCCTTGGC	1226	ATTATGGCCAAGGGTC	2995
		CATAAT		ATGA

3844	3866	CCCTTGGCCATAATATG	1227	ATAAATCATATTATGG	2996
		ATTTAT		CCAA

3845	3867	CCTTGGCCATAATATGA	1228	GATAAATCATATTATG	2997
		TTTATC		GCCA

3851	3873	CCATAATATGATTTATC	1229	TGTGGAGATAAATCAT	2998
		TCCACA		ATTA

3869	3891	CCACACTAGCAGAGACC	1230	TCGGTTGGTCTCTGCT	2999
		AACCGA		AGTG

3884	3906	CCAACCGAACCCCCTTC	1231	AAGGTCGAAGGGGGT	3000
		GACCTT		TCGGT

3888	3910	CCGAACCCCCTTCGACC	1232	CGGCAAGGTCGAAGG	3001
		TTGCCG		GGGTT

3893	3915	CCCCCTTCGACCTTGCC	1233	CCCTTCGGCAAGGTCG	3002
		GAAGGG		AAGG

3894	3916	CCCCTTCGACCTTGCCG	1234	CCCCTTCGGCAAGGTC	3003
		AAGGGG		GAAG

3895	3917	CCCTTCGACCTTGCCGA	1235	TCCCCTTCGGCAAGGT	3004
		AGGGGA		CGAA

3896	3918	CCTTCGACCTTGCCGAA	1236	CTCCCCTTCGGCAAGG	3005
		GGGGAG		TCGA

3903	3925	CCTTGCCGAAGGGGAGT	1237	GTTCGGACTCCCCTTC	3006
		CCGAAC		GGCA

3908	3930	CCGAAGGGGAGTCCGA	1238	GACTAGTTCGGACTCC	3007
		ACTAGTC		CCTT

3920	3942	CCGAACTAGTCTCAGGC	1239	GTTGAAGCCTGAGACT	3008
		TTCAAC		AGTT

3953	3975	CCGCAGGCCCCTTCGCC	1240	GAATAGGGCGAAGGG	3009
		CTATTC		GCCTG

3960	3982	CCCCTTCGCCCTATTCTT	1241	CTATGAAGAATAGGGC	3010
		CATAG		GAAG

3961	3983	CCCTTCGCCCTATTCTTC	1242	GCTATGAAGAATAGG	3011
		ATAGC		GCGAA

3962	3984	CCTTCGCCCTATTCTTCA	1243	GGCTATGAAGAATAG	3012
		TAGCC		GGCGA

3968	3990	CCCTATTCTTCATAGCCG	1244	GTATTCGGCTATGAAG	3013
		GAATAC		AATA

3969	3991	CCTATTCTTCATAGCCG	1245	TGTATTCGGCTATGAA	3014
		AATACA		GAAT

3983	4005	CCGAATACACAAACATT	1246	TATAATAATGTTTGTG	3015
		ATTATA		TATT

4013	4035	CCCTCACCACTACAATC	1247	TAGGAAGATTGTAGTG	3016
		TTCCTA		GTGA

4014	4036	CCTCACCACTACAATCT	1248	CTAGGAAGATTGTAGT	3017
		TCCTAG		GGTG

4019	4041	CCACTACAATCTTCCTA	1249	TGTTCCTAGGAAGATT	3018
		GGAACA		CTTAG

4032	4054	CCTAGGAACAACATATG	1250	GTGCGTCATATGTTGT	3019
		ACGCAC		TCCT

4058	4080	CCCCTGAACTCTACACA	1251	ATATGTTGTGTAGAGT	3020
		ACATAT		TCAG

4059	4081	CCCTGAACTCTACACAA	1252	AATATGTTGTGTAGAG	3021
		CATATT		TTCA

4060	4082	CCTGAACTCTACCAAC	1253	AAATATGTTGTGTAGA	3022
		ATATTT		GTTC

4088	4110	CCAAGACCCTACTTCTA	1254	GGAGGTTAGAAGTAG	3023
		ACCTCC		GGTCT

4094	4116	CCCTACTTCTAACCTCC	1255	GAACAGGGAGGTTAG	3024
		CTGTTC		AAGTA

4095	4117	CCTACTTCTAACTCCC	1256	AGAACAGGGAGGTTA	3025
		TGTTCT		GAAGT

4106	4128	CCTCCCTGTTCTTATGA	1257	TCGAATTCATAAGAAC	3026
		ATTCGA		AGGG

4109	4131	CCCTGTTCTTATGAATT	1258	TGTTCGAATTCATAAG	3027
		CGAACA		AACA

4110	4132	CCTGTTCTTATGAATTC	1259	CTGTTCGAATTCATAA	3028
		GAACAG		GAAC

4137	4159	CCCCCGATTCCGCTACG	1260	GTTGGTCGTAGCGGAA	3029
		ACCAAC		TCGG

4138	4160	CCCCGATTCCGCTACGA	1261	AGTTGGTCGTAGCGGA	3030
		CCAACT		ATCG

4139	4161	CCCGATTCCGCTACGAC	1262	GAGTTGGTCGTAGCGG	3031
		CAACTC		AATC

4140	4162	CCGATTCCGCTACGACC	1263	TGAGTTGGTCGTAGCG	3032
		AACTCA		GAAT

4146	4168	CCGCTACGACCAACTCA	1264	GGTGTATGAGTTGGTC	3033
		TACACC		GTAG

4155	4177	CCAACTCATACACCTCC	1265	TTCATAGGAGGTGTAT	3034
		TATGAA		GAGT

4167	4189	CCTCCTATGAAAAAACT	1266	GTAGGAAGTTTTTTCA	3035
		TCCTAC		TAGG

4170	4192	CCTATGAAAAAACTTCC	1267	GTGGTAGGAAGTTTTT	3036
		TACCAC		TCAT

4185	4207	CCTACCACTCACCCTAG	1268	GTAATGCTAGGGTGAG	3037
		CATTAC		TGGT

4189	4211	CCACTCACCCTAGCATT	1269	ATAAGTAATGCTAGGG	3038
		ACTTAT		TGAG

4196	4218	CCCTAGCATTACTTATA	1270	ATATCATATAAGTAAT	3039
		TGATAT		GCTA

4197	4219	CCTAGCATTACTTATAT	1271	CATATCATATAAGTAA	3040
		GATATG		TGCT

4223	4245	CCATACCCATTACAATC	1272	GCTGGAGATTGTAATG	3041
		TCCAGC		GGTA

4228	4250	CCCATTACAATCTCCAG	1273	GGAATGCTGGAGATTG	3042
		CATTCC		TAAT

4229	4251	CCATTACAATCTCCAGC	1274	GGGAATGCTGGAGATT	3043
		ATTCCC		GTAA

4241	4263	CCAGCATTCCCCCTCAA	1275	TTAGGTTTGAGGGGGA	3044
		ACCTAA		ATGC

4249	4271	CCCCCTCAAACCTAAGA	1276	CATATTTCTTAGGTTT	3045
		AATATG		GAGG

4250	4272	CCCCTCAAACCTAAGAA	1277	ACATATTTCTTAGGTT	3046
		ATATGT		TGAG

4251	4273	CCCTCAAACCTAAGAAA	1278	GACATATTTCTTAGGT	3047
		TATGTC		TTGA

4252	4274	CCTCAAACCTAAGAAAT	1279	AGACATATTTCTTAGG	3048
		ATGTCT		TTTG

4259	4281	CCTAAGAAATATGTCTG	1280	TTTTATCAGACATATT	3049
		ATAAAA		TCTT

4318	4340	CCCCCTTATTTCTAGGA	1281	TCATAGTCCTAGAAAT	3050
		CTATGA		AAGG

4319	4341	CCCCTTATTTCTAGGAC	1282	CTCATAGTCCTAGAAA	3051
		TATGAG		TAAG

4320	4342	CCCTTATTTCTAGGACT	1283	TCTCATAGTCCTAGAA	3052
		ATGAGA		ATAA

4321	4343	CCTTATTTCTAGGACTA	1284	TTCTCATAGTCCTAGA	3053
		TGAGAA		AATA

4349	4371	CCATCCCTGAGAATCC	1285	AATTTTGGATTCTCAG	3054
		AAAATT		GGAT

4350	4372	CCATCCCTGAGAATCCA	1286	GAATTTTGGATTCTCA	3055
		AAATTC		GGGA

4354	4376	CCCTGAGAATCCAAAAT	1287	CGGAGAATTTTGGATT	3056
		TCTCCG		CTCA

4355	4377	CCTGAGAATCCAAAATT	1288	ACGGAGAATTTTGGAT	3057
		CTCCGT		TCTC

4364	4386	CCAAAATTCTCCGTGCC	1289	ATAGGTGGCACGGAG	3058
		ACCTAT		AATTT

4374	4396	CCGTGCCACCTATCACA	1290	ATGGGGTGTGATAGGT	3059
		CCCCAT		GGCA

4379	4401	CCACCTATCACACCCCA	1291	TTAGGATGGGGTGTGA	3060
		TCCTAA		TAGG

4382	4404	CCTATCACACCCCATCC	1292	ACTTTAGGATGGGGTG	3061
		TAAAGT		TGAT

4391	4413	CCCCATCCTAAAGTAAG	1293	GCTGACCTTACTTTAG	3062
		GTCAGC		GATG

4392	4414	CCCATCCTAAAGTAAGG	1294	AGCTGACCTTACTTTA	3063
		TCAGCT		GGAT

4393	4415	CCATCCTAAAGTAAGGT	1295	TAGCTGACCTTACTTT	3064
		CAGCTA		AGGA

4397	4419	CCTAAAGTAAGGTCAGC	1296	TATTTAGCTGACCTTA	3065
		TAAATA		CTTT

4430	4452	CCCATACCCCGAAAATG	1297	AACCAACATTTTCGGG	3066
		TTGGTT		GTAT

4431	4453	CCATACCCCGAAAATGT	1298	AACCAACATTTTCGGG	3067
		TGGTTA		GGTA

4436	4458	CCCCGAAAATGTTGGTT	1299	GGGTATAACCAACATT	3068
		ATACCC		TTCG

4437	4459	CCCGAAAATGTTGGTTA	1300	AGGGTATAACCAACAT	3069
		TACCCT		TTTC

4438	4460	CCGAAAATGTTGGTTAT	1301	AAGGGTATAACCAAC	3070
		ACCCTT		ATTTT

4456	4478	CCCTTCCCGTACTAATT	1302	GGGATTAATTAGTACG	3071
		AATCCC		GGAA

4457	4479	CCTTCCCGTACTAATTA	1303	GGGGATTAATTAGTAC	3072
		ATCCCC		GGGA

4461	4483	CCCGTACTAATTAATCC	1304	GCCAGGGGATTAATTA	3073
		CCTGGC		GTAC

4462	4484	CCGTACTAATTAATCCC	1305	GGCCAGGGGATTAATT	3074
		CTGGCC		AGTA

4476	4498	CCCCTGGCCCAACCCGT	1306	TAGATGACGGGTTGGG	3075
		CATCTA		CCAG

4477	4499	CCCTGGCCCAACCCGTC	1307	GTAGATGACGGGTTGG	3076
		ATCTAC		GCCA

4478	4500	CCTGGCCCAACCCGTCA	1308	AGTAGATGACGGGTTG	3077
		TCTACT		GGCC

4483	4505	CCCAACCCGTCATCTAC	1309	GGTAGAGTAGATGAC	3078
		TCTACC		GGGTT

4484	4506	CCAACCCGTCATCTACT	1310	TGGTAGAGTAGATGAC	3079
		CTACCA		GGGT

4488	4510	CCCGTCATCTACTCTAC	1311	AAGATGGTAGAGTAG	3080
		CATCTT		ATGAC

4489	4511	CCGTCATCTACTCTACC	1312	AAAGATGGTAGAGTA	3081
		ATCTTT		GATGA

4504	4526	CCATCTTTGCAGGCACA	1313	GATGAGTGTGCCTGCA	3082
		CTCATC		AAGA

4555	4577	CCTGAGTAGGCCTA	1314	GTTTATTTCTAGGCCT	3083
		ATAAAC		ACTC

4565	4587	CCTAGAAATAAACATGC	1315	AAGCTAGCATGTTTAT	3084
		TAGCTT		TTCT

4593	4615	CCAGTTCTAACCAAAAA	1316	TTTATTTTTTTGGTTAG	3085
		AATAAA		AAC

4603	4625	CCAAAAAAATAAACCCT	1317	GGAACGAGGGTTTATT	3086
		CGTTCC		TTTT

4616	4638	CCCTCGTTCCACAGAAG	1318	TGGCAGCTTCTGTGGA	3087
		CTGCCA		ACGA

4617	4639	CCTCGTTCCACAGAAGC	1319	ATGGCAGCTTCTGTGG	3088
		TGCCAT		AACG

4624	4646	CCACAGAAGCTGCCATC	1320	ATACTTGATGGCAGCT	3089
		AAGTAT		TCTG

4636	4658	CCATCAAGTATTTCCTC	1321	TTGCGTGAGGAAATAC	3090
		ACGCAA		TTGA

4649	4671	CCTCACGCAAGCAACCG	1322	TGGATGCGGTTGCTTG	3091
		CATCCA		CGTG

4663	4685	CCGCATCCATAATCCTT	1323	TATTAGAAGGATTATG	3097
		CTAATA		GATG

4669	4691	CCATAATCCTTCTAATA	1324	GATAGCTATTAGAAGG	3093
		GCTATC		ATTA

4676	4698	CCTTCTAATAGCTATCC	1325	TGAAGAGGATAGCTAT	3094
		TCTTCA		TAGA

4691	4713	CCTCTTCAACAATATAC	1326	CGGAGAGTATATTGTT	3095
		TCTCCG		GAAG

4711	4733	CCGGACAATGAACCATA	1327	ATTGGTTATGGTTCAT	3096
		ACCAAT		TGTC

4723	4745	CCATAACCAATACTACC	1328	TTGATTGGTAGTATTG	3097
		AATCAA		GTTA

4729	4751	CCAATACTACCAATCAA	1329	TGAGTATTGATTGGTA	3098
		TACTCA		GTAT

4738	4760	CCAATCAATACTCATCA	1330	TATTAATGATGAGTAT	3099
		TTAATA		TGAT

4795	4817	CCCCCTTTCACTTCTGA	1331	TGGGACTCAGAAGTGA	3100
		GTCCCA		AAGG

4796	4818	CCCCTTTCACTTCTGAG	1332	CTGGGACTCAGAAGTG	3101
		TCCCAG		AAAG

4797	4819	CCCTTTCACTTCTGAGT	1333	TCTGGGACTCAGAAGT	3102
		CCCAGA		GAAA

4798	4820	CCTTTCACTTCTGAGTC	1334	CTCTGGGACTCAGAAG	3103
		CCAGAG		TGAA

4814	4836	CCCAGAGGTTACCCAAG	1335	GGGTGCCTTGGGTAAC	3104
		GCACCC		CTCT

4815	4837	CCAGAGGTTACCCAAGG	1336	GGGGTGCCTTGGGTAA	3105
		CACCCC		CCTC

4825	4847	CCCAAGGCACCCCTCTG	1337	GGATGTCAGAGGGGT	3106
		ACATCC		GCCTT

4826	4848	CCAAGGCACCCCTCTGA	1338	CGGATGTCAGAGGGGT	3107
		CATCCG		GCCT

4834	4856	CCCCTCTGACATCCGGC	1339	AAGCAGGCCGGATGTC	3108
		CTGCTT		AGAG

4835	4857	CCCTCTGACATCCGGCC	1340	GAAGCAGGCCGGATG	3109
		TGCTTC		TCAGA

4836	4858	CCTCTGACATCCGGCCT	1341	AGAAGCAGGCCGGAT	3110
		GCTTCT		GTCAG

4846	4868	CCGGCCTGCTTCTTCTC	1342	TCATGTGAGAAGAAGC	3111
		ACATGA		AGGC

4850	4872	CCTGCTTCTTCTCACAT	1343	TTTGTCATGTGAGAAG	3112
		GACAAA		AAGC

4879	4901	CCCCCATCTCAATCATA	1344	TTGGTATATGATTGAG	3113
		TACCAA		ATGG

4880	4902	CCCCATCTCAATCATAT	1345	TTTGGTATATGATTGA	3114
		ACCAAA		GATG

4881	4903	CCCATCTCAATCATATA	1346	ATTTGGTATATGATTG	3115
		CCAAAT		AGAT

4882	4904	CCATCTCAATCATATAC	1347	GATTTGGTATATGATT	3116
		CAAATC		GAGA

4898	4920	CCAAATCTCTCCCTCAC	1348	CGTTTAGTGAGGGAGA	3117
		TAAACG		GATT

4908	4930	CCCTCACTAAACGTAAG	1349	AGAAGGCTTACGTTTA	3118
		CCTTCT		GTGA

4909	4931	CCTCACTAAACGTAAGC	1350	GAGAAGGCTTACGTTT	3119
		CTTCTC		AGTG

4925	4947	CCTTCTCCTCACTCTCTC	1351	AGATTGAGAGAGTGA	3120
		AATCT		GGAGA

4931	4953	CCTCACTCTCTCAATCTT	1352	TGGATAAGATTGAGAG	3121
		ATCCA		AGTG

4951	4973	CCATCATAGCAGGCAGT	1353	ACCTCAACTGCCTGCT	3122
		TGAGGT		ATGA

4982	5004	CCAAACCCAGCTACGCA	1354	AGATTTTGCGTAGCTG	3123
		AAATCT		GGTT

4987	5009	CCCAGCTACGCAAAATC	1355	TGCTAAGATTTTGCGT	3124
		TTAGCA		AGCT

4988	5010	CCAGCTACGCAAAATCT	1356	ATGCTAAGATTTTGCG	3125
		TAGCAT		TAGC

5014	5036	CCTCAATTACCCACATA	1357	TCATCCTATGTGGGTA	3126
		GGATGA		ATTG

5023	5045	CCCACATAGGATGAATA	1358	TGCTATTATTCATCCT	3127
		ATAGCA		ATGT

5024	5046	CCACATAGGATGAATAA	1359	CTGCTATTATTCATCCT	3128
		TAGCAG		ATG

5052	5074	CCGTACAACCCTAACAT	1360	ATGGTTATGTTAGGGT	3129
		AACCAT		TGTA

5060	5082	CCCTAACATAACCATTC	1361	AATTAAGAATGGTTAT	3130
		TTAATT		GTTA

5061	5083	CCTAACATAACCATTCT	1362	AAATTAAGAATGGTTA	3131
		TAATTT		TGTT

5071	5093	CCATTCTTAATTTAACT	1363	ATAAATAGTTAAATTA	3132
		ATTTAT		AGAA

5099	5121	CCTAACTACTACCGCAT	1364	GTAGGAATGCGGTAGT	3133
		TCCTAC		AGTT

5110	5132	CCGCATTCCTACTACTC	1365	TAAGTTGAGTAGTAGG	3134
		AACTTA		AATG

5117	5139	CCTACTACTCAACTTAA	1366	TGGAGTTTAAGTTGAG	3135
		ACTCCA		TAGT

5137	5159	CCAGCACCACGACCCTA	1367	TAGTAGTAGGGTCGTG	3136
		CTACTA		GTGC

5143	5165	CCACGACCCTACTACTA	1368	GCGAGATAGTAGTAG	3137
		TCTCGC		GGTCG

5149	5171	CCCTACTACTATCTCGC	1369	TCAGGTGCGAGATAGT	3138
		ACCTGA		AGTA

5150	5172	CCTACTACTATCTCGCA	1370	TTCAGGTGCGAGATAG	3139
		CCTGAA		TAGT

5167	5189	CCTGAAACAAGCTAACA	1371	TAGTCATGTTAGCTTG	3140
		TGACTA		TTTC

5193	5215	CCCTTAATTCCATCCAC	1372	AGGAGGGTGGATGGA	3141
		CCTCCT		ATTAA

5194	5216	CCTTAATTCCATCCACC	1373	GAGGAGGGTGGATGG	3142
		CTCCTC		AATTA
5202	5224	CCATCCACCCTCCTC	1374	CCTAGGGAGAGGAGG	3143
		CCTAGG		GTGGA

5206	5228	CCACCCTCCTCTCCCTA	1375	GCCTCCTAGGGAGAGG	3144
		GGAGGC		AGGG

5209	5231	CCCTCCTCTCCCTAGGA	1376	CAGGCCTCCTAGGGAG	3145
		GGCCTG		AGGA

5210	5232	GCTCCTCTCCCTAGGAG	1377	CCAGGCCTCCTAGGGA	3146
		GCCTGC		GAGG

5213	5235	CCTCTCCCTAGGAGGCC	1378	GGGGCAGGCCTCCTAG	3147
		TGCCCC		GGAG

5218	5240	CCCTAGGAGGCCTGCCC	1379	TAGCGGGGGCAGGCCT	3148
		CCGCTA		CCTA

5219	5241	CCTAGGAGGCCTGCCCC	1380	TTAGCGGGGGCAGGCC	3149
		CGCTAA		TCCT

5228	5250	CCTGCCCCCGCTAACCG	1381	AAAAGCCGGTTAGCG	3150
		GCTTTT		GGGGC

5232	5254	CCCCCGCTAACCGGCTT	1382	GGCAAAAAGCCGGTT	3151
		TTTGCC		AGCGG

5213	5255	CCCCGCTAACCGGCTTT	1383	GGGCAAAAAGCCGGT	3152
		TTGCCC		TAGCG

5234	5256	CCCGCTAACCGGCTTTT	1384	TGGGCAAAAAGCCGG	3153
		TGCCCA		TTAGC

5235	5257	CCGCTAACCGGCTTTTT	1385	TTGGGCAAAAAGCCG	3154
		GCCCAA		GTTAG

5242	5264	CCGGCTTTTTGCCCAAA	1386	GGCCCATTTGGGCAAA	3155
		TGGGCC		AAGC

5253	5275	CCCAAATGGGCCATTAT	1387	TCTTCGATAATGGCCC	3156
		CGAAGA		ATTT

5254	5276	CCAAATGGGCCATTATC	1388	TTCTTCGATAATGGCC	3157
		GAAGAA		CATT

5263	5285	CCATTATCGAAGAATTC	1389	TTTTGTGAATTCTTCG	3158
		ACAAAA		ATAA

5294	5316	CCTCATCATCCCCACCA	1390	CTATGATGGTGGGGAT	3159
		TCATAG		GATG

5303	5325	CCCCACCATCATAGCCA	1391	TGATGGTGGCTATGAT	3160
		CCATCA		GGTG

5304	5326	CCCACCATCATAGCCAC	1392	GTGATGGTGGCTATGA	3161
		CATCAC		TGGT

5305	5327	CCACCATCATAGCCACC	1393	GGTGATGGTGGCTATG	3162
		ATCACC		ATGG

5308	5330	CCATCATAGCCACCATC	1394	GAGGGTGATGGTGGCT	3163
		ACCCTC		ATGA

5317	5339	CCACCATCACCCTCCTT	1395	GAGGTTAAGGAGGGT	3164
		AACCTC		GATGG

5320	5342	CCATCACCCTCCTTAAC	1396	GTAGAGGTTAAGGAG	3165
		CTCTAC		GGTGA

5326	5348	CCCTCCTTAACCTCTAC	1397	GTAGAAGTAGAGGTTA	3166
		TTCTAC		AGGA

5327	5349	CCTCCTTAACCTCTACTT	1398	GGTAGAAGTAGAGGTT	3167
		CTACC		AAGG

5330	5352	CCTTAACCTCTACTTCT	1399	GTAGGTAGAAGTAGA	3168
		ACCTAC		GGTTA

5336	5358	CCTCTACTTCTACCTAC	1400	TTAGGCGTAGGTAGAA	3169
		GCCTAA		GTAG

5348	5370	CCTACGCCTAATCTACT	1401	AGGTGGAGTAGATTAG	3170
		CCACCT		GCGT

5354	5376	CCTAATCTACTCCACCT	1402	TGATTGAGGTGGAGTA	3171
		CAATCA		GATT

5365	5387	CCACCTCAATCACACTA	1403	GGGGAGTAGTGTGATT	3172
		CTCCCC		GAGG

5368	5390	CCTCAATCACACTACTC	1404	TATGGGGAGTAGTGTG	3173
		CCCATA		ATTG

5384	5406	CCCCATATCTAACAACG	1405	TTTTTACGTTGTTAGAT	3174
		TAAAAA		ATG

5385	5407	CCCATATCTAACAACGT	1406	ATTTTTACGTTGTTAG	3175
		AAAAAT		ATAT

5386	5408	CCATATCTAACAACGT	1407	TATTTTTACGTTGTTAG	3176
		AAAATA		ATA

5433	5455	CCCACCCCATTCCTCCC	1408	AGTGTGGGGAGGAAT	3177
		CACACT		GGGGT

5434	5456	CCACCCCATTCCTCCCC	1409	GAGTGTGGGGAGGAA	3178
		ACACTC		TGGGG

5417	5459	CCCCATTCCTCCCCACA	1410	GATGAGTGTGGGGAG	3179
		CTCATC		GAATG

5438	5460	CCCATTCCTCCCCACAC	1411	CGATGAGTGTGGGGA	3180
		TCATCG		GGAAT

5439	5461	CCATTCCTCCCCACACT	1412	GCGATGAGTGTGGGG	3181
		CATCGC		AGGAA

5444	5466	CCTCCCCACACTCATCG	1413	TAAGGGCGATGAGTGT	3182
		CCCTTA		GGGG

5447	5469	CCCCACACTCATCGCCC	1414	TGGTAAGGGCGATGA	3183
		TTACCA		GTGTG

5448	5470	CCCACACTCATCGCCCT	1415	GTGGTAAGGGCGATG	3184
		TACCAC		AGTGT

5449	5471	CCACACTCATCGCCCTT	1416	CGTGGTAAGGGCGATG	3185
		ACCACG		AGTG

5461	5483	CCCTTACCACGCTACTC	1417	AGGTAGGAGTAGCGT	3186
		CTACCT		GGTAA

5462	5484	CCTTACCACGCTACTCC	1418	TAGGTAGGAGTAGCGT	3187
		TACCTA		GGTA

5467	5489	CCACGCTACTCCTACCT	1419	GGAGATAGGTAGGAG	3188
		ATCTCC		TAGCG

5477	5499	CCTACCTATCTCCCCTTT	1420	GTATAAAAGGGGAGA	3189
		TATAC		TAGGT

5481	5503	CCTATCTCCCCTTTATA	1421	ATTAGTATAAAAGGGG	3190
		CTAAT		AGAT

5488	5510	CCCCTTTTATACTAATA	1422	TAAGATTATTAGTATA	3191
		ATCTTA		AAAG

5489	5511	CCCTTTTATACTAATAA	1423	ATAAGATTATTAGTAT	3192
		TCTTAT		AAAA

5490	5512	CCTTTTATACTAATAAT	1424	TATAAGATTATTAGTA	3193
		CTTATA		TAAA

5534	5556	CCAAGAGCCTTCAAAGC	1425	CTGAGGGCTTTGAAGG	3194
		CCTCAG		CTCT

5541	5563	CCTTCAAAGCCCTCAGT	1426	CAACTTACTGAGGGCT	3195
		AAGTTG		TTGA

5550	5572	CCCTCAGTAAGTTGCAA	1427	TAAGTATTGCAACTTA	3196
		TACTTA		CTGA

5551	5573	CCTCAGTAAGTTGCAAT	1428	TTAAGTATTGCAACTT	3197
		ACTTAA		ACTG

5601	5623	CCCCACTCTGCATCAAC	1429	CGTTCAGTTGATGCAG	3198
		TGAACG		AGTG

5602	5624	CCCACTCTGCATCAACT	1430	GCGTTCAGTTGATGCA	3199
		GAACGC		GAGT

5603	5625	CCACTCTGCATCAACTG	1431	TGCGTTCAGTTGATGC	3200
		AACGCA		AGAG

5632	5654	CCACTTTAATTAAGCTA	1432	AGGGCTTAGCTTAATT	3201
		AGCCCT		AAAG

5651	5673	CCCTTACTAGACCAATG	1433	AAGTCCCATTGGTCTA	3202
		GGACTT		GTAA

5652	5674	CCTTACTAGACCAATGG	1434	TAAGTCCCATTGGTCT	3203
		GACTTA		AGTA

5667	5684	CCAATGGGACTTAAACC	1435	TTTGTGGGTTTAAGTC	3204
		CACAAA		CCAT

5677	5699	CCCACAAACACTTAGTT	1436	GCTGTTAACTAAGTGT	3205
		AACAGC		TTGT

5678	5700	CCACAAACACTTAGTTA	1437	AGCTGTTAACTAAGTG	3206
		ACAGCT		TTTG

5706	5728	CCCTAATCAACTGGCTT	1438	AGATTGAAGCCAGTTG	3207
		CAATCT		ATTA

5707	5729	CCTAATCAACTGGCTTC	1439	TAGATTGAAGCCAGTT	3208
		AATCTA		GATT

5735	5757	CCCGCCGCCGGGAAAA	1440	CCGCCTTTTTTCCCGG	3209
		AAGGCGG		CGGC

5736	5758	CCGCCGCCGGGAAAAA	1441	CCCGCCTTTTTTCCCG	3210
		AGGCGGG		GCGG

5739	5761	CCGCCGGGAAAAAAGG	1442	TCTCCCGCCTTTTTTCC	3211
		CGGGAGA		CGG

5742	5764	CCGGGAAAAAAGGCGG	1443	GCTTCTCCCGCCTTTTT	3212
		GAGAAGC		TCC

5764	5786	CCCCGGCAGGTTTGAAG	1444	AACCAGCTTCAAACCT	3213
		CTGCTT		GCCG

5765	5787	CCCGGCAGGTTTGAAGC	1445	GAAGCAGCTTCAAACC	3214
		TGCTTC		TGCC

5766	5788	CCGGCAGGTTTGAAGCT	1446	AGAAGCAGCTTCAAAC	3215
		GCTTCT		CTGC

5817	5839	CCTCGGAGCTGGTAAAA	1447	GCCTCTTTTTACCAGC	3216
		AGAGGC		TCCG

5839	5861	CCTAACCCCTGTCTTTA	1448	TAAATCTAAAGACAGG	3217
		GATTTA		GGTT

5844	5866	CCCCTGTCTTTAGATTT	1449	GACTGTAAATCTAAAG	3218
		ACAGTC		ACAG

5845	5867	CCCTGTCTTTAGATTTA	1450	GGACTGTAAATCTAAA	3219
		CAGTCC		GACA

5846	5868	CCTGTCTTTAGATTTAC	1451	TGGACTGTAAATCTAA	3220
		AGTCCA		AGAC

5866	5888	CCAATGCTTCACTCAGC	1452	AAAATGGCTGAGTGA	3221
		CATTTT		AGCAT

5882	5904	CCATTTTACCTCACCCC	1453	TCAGTGGGGGTGAGGT	3222
		CACTGA		AAAA

5890	5912	CCTCACCCCCACTGATG	1454	GGCGAACATCAGTGG	3223
		TTCGCC		GGGTG

5895	5917	CCCCCACTGATGTTCGC	1455	CGGTCGGCGAACATCA	3224
		CGACCG		GTGG

5896	5918	CCCCACTGATGTTCGCC	1456	ACGGTCGGCGAACATC	3225
		GACCGT		AGTG

5897	5919	CCCACTGATGTTCGCCG	1457	AACGGTCGGCGAACAT	3226
		ACCGTT		CAGT

5898	5920	CCACTGATGTTCGCCGA	1458	CAACGGTCGGCGAAC	3227
		CCGTTG		ATCAG

5911	5933	CCGACCGTTGACTATTC	1459	TGTAGAGAATAGTCAA	3228
		TCTACA		CGGT

5915	5937	CCGTTGACTATTCTCTA	1460	GGTTTGTAGAGAATAG	3229
		CAAACC		TCAA

5936	5958	CCACAAAGACATTGGA	1461	ATAGTGTTCCAATGTC	3230
		ACACTAT		TTTG

5960	5982	CCTATTATTCGGCGCAT	1462	CAGCTCATGCGCCGAA	3231
		GAGCTG		TAAT

5987	6009	CCTAGGCACAGCTCTAA	1463	GGAGGCTTAGAGCTGT	3232
		GCCTCC		GCCT

6005	6027	CCTCCTTATTCGAGCCG	1464	CCAGCTCGGCTCGAAT	3233
		AGCTGG		AAGG

6008	6030	CCTTATTCGAGCCGAGC	1465	GGCCCAGCTCGGCTCG	3234
		TGGGCC		AATA

6019	6041	CCGAGCTGGGCCAGCCA	1466	GTTGCCTGGCTGGCCC	3235
		GGCAAC		AGCT

6029	6051	CCAGCCAGGCAACCTTC	1467	TACCTAGAAGGTTGCC	3236
		TAGGTA		TGGC

6033	6055	CCAGGCAACCTTCTAGG	1468	TCGTTACCTAGAAGGT	3237
		TAACGA		TGCC

6041	6063	CCTTCTAGGTAACGACC	1469	AGATGTGGTCGTTACC	3238
		ACATCT		TAGA

6056	6078	CCACATCTACAACGTTA	1470	TGACGATAACGTTGTA	3239
		TCGTCA		GATG

6082	6104	CCCATGCATTTGTAATA	1471	GAAGATTATTACAAAT	3240
		ATCTTC		GCAT

6083	6105	CCATGCATTTGTAATAA	1472	AGAAGATTATTACAAA	3241
		TCTTCT		TGCA

6117	6139	CCCATCATAATCGGAGG	1473	CCAAAGCCTCCGATTA	3242
		CTTTGG		TGAT

6118	6140	CCATCATAATCGGAGGC	1474	GCCAAAGCCTCCGATT	3243
		TTTGGC		ATGA

6153	6175	CCCCTAATAATCGGTGC	1475	TCGGGGGCACCGATTA	3244
		CCCCGA		TTAG

6154	6176	CCCTAATAATCGGTGCC	1476	ATCGGGGGCACCGATT	3245
		CCCGAT		ATTA

6155	6177	CCTAATAATCGGTGCCC	1477	TATCGGGGGCACCGAT	3246
		CCGATA		TATT

6169	6191	CCCCCGATATGGCGTTT	1478	GCGGGGAAACGCCAT	3247
		CCCCGC		ATCGG

6170	6192	CCCCGATATGGCGTTTC	1479	TGCGGGGAAACGCCAT	3248
		CCCGCA		ATCG

6171	6193	CCCGATATGGCGTTTCC	1480	ATGCGGGGAAACGCC	3249
		CCGCAT		ATATC

6172	6194	CCGATATGGCGTTTCCC	1481	TATGCGGGGAAACGCC	3250
		CGCATA		ATAT

6186	6208	CCCCGCATAAACAACAT	1482	AAGCTTATGTTGTTTA	3251
		AAGCTT		TGCG

6187	6209	CCCGCATAAACAACATA	1483	GAAGCTTATGTTGTTT	3252
		AGCTTC		ATGC

6188	6210	CCGCATAAACAACATAA	1484	AGAAGCTTATGTTGTT	3253
		GCTTCT		TATG

6219	6241	CCTCCCTCTCTCCTACTC	1485	AGCAGGAGTAGGAGA	3254
		CTGCT		GAGGG

6222	6244	CCCTCTCTCCTACTCCTG	1486	GCGAGCAGGAGTAGG	3255
		CTCGC		AGAGA

6223	6245	CCTCTCTCCTACTCCTGC	1487	TGCGAGCAGGAGTAG	3256
		TCGCA		GAGAG

6210	6252	CCTACTCCTGCTCGCAT	1488	TAGCAGATGCGAGCA	3257
		CTGCTA		GGAGT

6236	6258	CCTGCTCGCATCTGCTA	1489	CCACTATAGCAGATGC	3258
		TAGTGG		GAGC

6262	6284	CCGGAGCAGGAACAGG	1490	TGTTCAACCTGTTCCT	3259
		TTGAACA		GCTC

6290	6312	CCCTCCCTTAGCAGGGA	1491	AGTAGTTCCCTGCTAA	3260
		ACTACT		GGGA

6291	6313	CCTCCCTTAGCAGGGAA	1492	GAGTAGTTCCCTGCTA	3261
		CTACTC		AGGG

6294	6316	CCCTTAGCAGGGAACTAC	1493	TGGGAGTAGTTCCCTG	3262
		CTCCCA		CTAA

6295	6317	CCTTAGCAGGGAACTAC	1494	GTGGGAGTAGTTCCCT	3263
		TCCCAC		GCTA

6313	6335	CCCACCCTGGAGCCTCC	1495	GTCTACGGTGGCTCCA	3264
		GTAGAC		GGGT

6314	6336	CCACCCTGGAGCCTCCG	1496	GGTCTACGGAGGCTCC	3265
		TAGACC		AGGG

6317	6339	CCCTGGAGCCTCCGTAG	1497	TTAGGTCTACGGAGGC	3266
		ACCTAA		TCCA

6318	6340	CCTGGAGCCTCCGTAGA	1498	GTTAGGTCTACGGAGG	3267
		CCTAAC		CTCC

6325	6347	CCTCCGTAGACCTAACC	1499	GAAGATGGTTAGGTCT	3268
		ATCTTC		ACGG

6328	6350	CCGTAGACCTAACCATC	1500	GGAGAAGATGGTTAG	3269
		TTCTCC		GTCTA

6335	6357	CCTAACCATCTTCTCCTT	1501	GGTGTAAGGAGAAGA	3270
		ACACC		TGGTT

6340	6362	CCATCTTCTCCTTACAC	1502	TGCTAGGTGTAAGGAG	3271
		CTAGCA		AAGA

6349	6371	CTTACACCTAGCAGGT	1503	GGAGACACCTGCTAGG	3272
		GTCTCC		TGTA

6356	6378	CCTAGCAGGTGTCTCCT	1504	AGATAGAGGAGACAC	3273
		CTATCT		CTGCT

6370	6392	CCTCTATCTTAGGGGCC	1505	ATTGATGGCCCCTAAG	3274
		ATCAAT		ATAG

6385	6407	CCATCAATTTCATCACA	1506	AATTGTTGTGATGAAA	3275
		ACAATT		TTGA

6420	6442	CCCCCTGCCATAACCCA	1507	TGGTATTGGGTTATGG	3276
		ATACCA		CAGG

6421	6443	CCCCTGCCATAACCCAA	1508	TTGGTATTGGGTTATGG	3277
		TACCAA		GCAG

6422	6444	CCCTGCCATAACCCAAT	1509	TTTGGTATTGGGTTAT	3278
		ACCAAA		GGCA

6423	6445	CCTGCCATAACCCAATA	1510	GTTTGGTATTGGGTTA	3279
		CCAAAC		TGGC

6427	6449	CCATAACCCAATACCAA	1511	GGGCGTTTGGTATTGG	3280
		ACGCCC		GTTA

6433	6455	CCCAATACCAAACGCCC	1512	GAAGAGGGGCGTTTG	3281
		CTCTTC		GTATT

6434	6456	CCAATACCAAACGCCCC	1513	CGAAGAGGGGCGTTTG	3282
		TCTTCG		GTAT

6440	6462	CCAAACGCCCCTCTTCG	1514	ATCAGACGAAGAGGG	3283
		TCTGAT		GCGTT

6447	6469	CCCCTCTTCGTCTGATC	1515	AGGACGGATCAGACG	3284
		CGTCCT		AAGAG

6448	6470	CCCTCTTCGTCTGATCC	1516	TAGGACGGATCAGAC	3285
		GTCCTA		GAAGA

6449	6471	CCTCTTCGTCTGATCCG	1517	TTAGGACGGATCAGAC	3286
		TCCTAA		GAAG

6463	6485	CCGTCCTAATCACAGCA	1518	TAGGACTGCTGTGATT	3287
		GTCCTA		AGGA

6467	6489	CCTAATCACAGCAGTCC	1519	GAAGTAGGACTGCTGT	3288
		TACTTC		GATT

6482	6504	CCTACTTCTCCTATCTCT	1520	CTGGGAGAGATAGGA	3289
		CCCAG		GAAGT

6491	6513	CCTATCTCTCCCAGTCC	1521	CAGCTAGGACTGGGA	3290
		TAGCTG		GAGAT

6500	6522	CCCAGTCCTAGCTGCTG	1522	TGATGCCAGCAGCTAG	3291
		GCATCA		GACT

6501	6523	CCAGTCCTAGCTGCTGG	1523	GTGATGCCAGCAGCTA	3292
		CATCAC		GGAC

6506	6528	CCTAGCTGCTGGCATCA	1524	GTATAGTGATGCCAGC	3293
		CTATAC		AGCT

6539	6561	CCGCAACCTCAACACCA	1525	AGAAGGTGGTGTTGAG	3294
		CCTTCT		GTTG

6545	6567	CCTCAACACCCTTCT	1526	GGTCGAAGAAGGTGG	3295
		TCGACC		TGTTG

6553	6575	CCACCTTCTTCGACCCC	1527	TCCGGCGGGGTCGAAG	3296
		GCCGGA		AAGG

6556	6578	CCTTCTTCGACCCCGCC	1528	TCCTCCGGCGGGGTCG	3297
		GGAGGA		AAGA

6566	6588	CCCCGCCGGAGGAGGA	1529	TGGGGTCTCCTCCTCC	3298
		GACCCCA		GGCG

6567	6589	CCCGCCGGAGGAGGAG	1530	ATGGGGTCTCCTCCTC	3299
		ACCCCAT		CGGC

6568	6590	CCGCCGGAGGAGGAGA	1531	AATGGGGTCTCCTCCT	3300
		CCCCATT		CCGG

6571	6593	CCGGAGGAGGAGACCC	1532	TAGAATGGGGTCTCCT	3301
		CATTCTA		CCTC

6584	6606	CCCCATTCTATACCAAC	1533	ATAGGTGTTGGTATAG	3302
		ACCTAT		AATG

6585	6607	CCCATTCTATACCAACA	1534	AATAGGTGTTGGTATA	3303
		CCTATT		GAAT

6586	6608	CCATTCTATACCAACAC	1535	GAATAGGTGTTGGTAT	3304
		CTATTC		AGAA

6596	6618	CCAACACCTATTCTGAT	1536	CGAAAAATCAGAATA	3305
		TTTTCG		GGTGT

6602	6624	CCTATTCTGATTTTTCGG	1537	GGTGACCGAAAAATC	3306
		TCACC		AGAAT

6623	6645	CCCTGAAGTTTATATTC	1538	GGATAAGAATATAAA	3307
		TTATCC		CTTCA

6624	6646	CCTGAAGTTTATATTCT	1539	AGGATAAGAATATAA	3308
		TATCCT		ACTTC

6644	6666	CCTACCAGGCTTCGGAA	1540	AGATTATTCCGAAGCC	3309
		TAATCT		TGGT

6648	6670	CCAGGCTTCGGAATAAT	1541	TGGGAGATTATTCCGA	3310
		CTCCCA		AGCC

6667	6689	CCCATATTGTAACTAC	1542	GGAGTAGTAAGTTACA	3311
		TACTCC		ATAT

6668	6690	CCATATTGTAACTTACT	1543	CGGAGTAGTAAGTTAC	3312
		ACTCCG		AATA

6688	6710	CCGGAAAAAAAGAACC	1544	TCCAAATGGTTCTTTTT	3313
		ATTTGGA		TTC

6702	6724	CCATTTGGATACATAGG	1545	ACCATACCTATGTATC	3314
		TATGGT		CAAA

6749	6771	CCTAGGGTTTATCGTGT	1546	GTGCTCACACGATAAA	3315
		GAGCAC		CCCT

6773	6795	CCATATATTTACAGTAG	1547	CTATTCCTACTGTAAA	3316
		GAATAG		TATA

6820	6842	CCTCCGCTACCATAATC	1548	AGCGATGATTATGGTA	3317
		ATCGCTGCGG		GCGG

6823	6845	CCGCTACCATAATCATC	1549	GATAGCGATGATTATG	3318
		GCTATC		GTAG

6829	6851	CCATAATCATCGCTATC	1550	GGTGGGGATAGCGAT	3319
		CCCACC		GATTA

6845	6867	CCCCACCGGCGTCAAAG	1551	TAAATACTTTGACGCC	3320
		TATTTA		GGTG

6846	6868	CCCACCGGCGTCAAAGT	1552	CTAAATACTTTGACGC	3321
		ATTTAG		CGGT

6847	6869	CCACCGGCGTCAAAGTA	1553	GCTAAATACTTTGACG	3322
		TTTAGC		CCGG

6850	6872	CCGGCGTCAAAGTATTT	1554	TCAGCTAAATACTTTG	3323
		AGCTGA		ACGC

6877	6899	CCACACTCCACGGAAGC	1555	CATATTGCTTCCGTGG	3324
		AATATG		AGTG

6884	6906	CCACGGAAGCAATATG	1556	ATCATTTCATATTGCTT	3325
		AAATGAT		CCG

6925	6947	CCCTAGATTCATCTTT	1557	GAAAAGAAAGATGAA	3326
		CTTTTC		TCCTA

6926	6948	CCTAGGATTCATCTTTC	1558	TGAAAAGAAAGATGA	3327
		TTTTCA		ATCCT

6949	6971	CCGTAGGTGGCCTGACT	1559	AATGCCAGTCAGGCCA	3328
		GGCATT		CCTA

6959	6981	CCTGACTGGCATTGTAT	1560	TTGCTAATACAATGCC	3329
		TAGCAA		AGTC

7027	7049	CCCACTTCCACTATGTC	1561	TGATAGGACATAGTGG	3330
		CTATCA		AAGT

7028	7050	CCACTTCCACTATGTCC	1562	TTGATAGGACATAGTG	3331
		TATCAA		GAAG

7034	7056	CCACTATGTCCTATCAA	1563	CTCCTATTGATAGGAC	3332
		TAGGAG		ATAG

7043	7065	CCTATCAATAGGAGCTG	1564	CAAATACAGCTCCTAT	3333
		TATTTG		TGAT

7066	7088	CCATCATAGGAGGCTTC	1565	GTGAATGAAGCCTCCT	3334
		ATTCAC		ATGA

7095	7117	CCCCTATTCTCAGGCTA	1566	AGGGTGTAGCCTGAGA	3335
		CACCCT		ATAG

7096	7118	CCCTATTCTCAGGCTAC	1567	TAGGGTGTAGCCTGAG	3336
		ACCCTA		AATA

7097	7119	CCTATTCFCAGGCTACA	1568	CTAGGGTGTAGCCTGA	3337
		CCCTAG		GAAT

7114	7136	CCCTAGACCAAACCTAC	1569	TTTGGCGTAGGTTTGG	3338
		GCCAAA		TCTA

7115	7137	CCTAGACCAAACCTACG	1570	TTTTGGCGTAGGTTTG	3339
		CCAAAA		GTCT

7121	7143	CCAAACCTACGCCAAAA	1571	AATGGATTTTGGCGTA	3340
		TCCATT		GGTT

7126	7148	CCTACGCCAAAATCCAT	1572	AGTGAAATGGATTTTG	3341
		TTCACT		GCGT

7132	7154	CCAAAATCCATTTCACT	1573	TATGATAGTGAAATGG	3342
		ATCATA		ATTT

7139	7161	CCATTTCACTATCATAT	1574	CGATGAATATGATAGT	3343
		TCATCG		GAAA

7181	7203	CCCACAACACTTTCTCG	1575	ATAGGCCGAGAAAGT	3344
		GCCTAT		GTTGT

7182	7204	CCACAACACTTTCTCGG	1576	GATAGGCCGAGAAAG	3345
		CCTATC		TGTTG

7199	7221	CCTATCCGGAATGCCCC	1577	AACGTCGGGGCATTCC	3346
		GACGTT		GGAT

7204	7226	CCGGAATGCCCCGACGT	1578	CGAGTAACGTCGGGGC	3347
		TACTCG		ATTC

7212	7234	CCCCGACGTTACTCGGA	1579	GGGTAGTCCGAGTAAC	3348
		CTACCC		GTCG

7213	7235	CCCGACGTTACTCGGAC	1580	GGGGTAGTCCGAGTAA	3349
		TACCCC		CGTC

7214	7236	CCGACGTTACTCGGACT	1581	CGGGGTAGTCCGAGTA	3350
		ACCCCG		ACGT

7232	7254	CCCCGATGCATACACCA	1582	TTCATGTGGTGTATGC	3351
		CATGAA		ATCG

7233	7255	CCCGATGCATACACCAC	1583	TTTCATGTGGTGTATG	3352
		ATGAAA		CATC

7234	7256	CCGATGCATACACCACA	1584	GTTTCATGTGGTGTAT	3353
		TGAAAC		GCAT

7246	7268	CCACATGAAACATCCTA	1585	AGATGATAGGATGTTT	3354
		TCATCT		CATG

7259	7281	CCTATCATCTGTAGGCT	1586	TGAATGAGCCTACAGA	3355
		CATTCA		TGAT

7327	7349	CCTTCGCTTCGAAGCGA	1587	GACTTTTCGCTTCGAA	3356
		AAAGTC		GCGA

7349	7371	CCTAATAGTAGAAGAAC	1588	TGGAGGGTTCTTCTAC	3357
		CCTCCA		TATT

7365	7387	CCCTCCATAAACCTGGA	1589	AGTCACTCCAGGTTTA	3358
		GTGACT		TGGA

7366	7388	CCTCCATAAACCTGGAG	1590	TAGTCACTCCAGGTTT	3359
		TGACTA		ATGG

7369	7391	CCATAAACCTGGAGTGA	1591	ATATAGTCACTCCAGG	3360
		CTATAT		TTTA

7376	7398	CCTGGAGTGACTATATG	1592	GGCATCCATATAGTCA	3361
		GATGCC		CTCC

7397	7419	CCCCCCACCCTACCACA	1593	CGAATGTGTGGTAGGG	3362
		CATTCG		TGGG

7398	7420	CCCCCACCCTACCACAC	1594	TCGAATGTGTGGTAGG	3363
		ATTCGA		GTGG

7399	7421	CCCCACCCTACCACACA	1595	TTCGAATGTGTGGTAG	3364
		TTCGAA		GGTG

7400	7422	CCCACCCTACCACACAT	1596	CTTCGAATGTGTGGTA	3365
		TCGAAG		GGGT

7401	7423	CCACCCTACCACACATT	1597	TCTTCGAATGTGTGGT	3366
		CGAAGA		AGGG

7404	7426	CCCTACCACACATTCGA	1598	GGTTCTTCGAATGTGT	3367
		AGAACC		GGTA

7405	7427	CCTACCACACATTCGAA	1599	GGGTTCTTCGAATGTG	3368
		GAACCC		TGGT

7409	7431	CCACACATTCGAAGAAC	1600	ATACGGGTTCTTCGAA	3369
		CCGTAT		TGTG

7425	7447	CCCGTATACATAAAATC	1601	TGTCTAGATTTTATGT	3370
		TAGACA		ATAC

7426	7448	CCGTATACATAAAATCT	1602	TTGTCTAGATTTTATGT	3371
		AGACAA		ATA

7466	7488	CCCCCCAAAGCTGGTTT	1603	GGCTTGAAACCAGCTT	3372
		CAAGCC		TGGG

7467	7489	CCCCCAAAGCTGGTTTC	1604	TGGCTTGAAACCAGCT	3373
		AAGCCA		TTGG

7468	7490	CCCCAAAGTGGTTTCA	1605	TTGGCTTGAAACCAGC	3374
		AGCCAA		TTTG

7469	7491	CCCAAAGCTGGTTTCAA	1606	GTTGGCTTGAAACCAG	3375
		GCCAAC		CTTT

7470	7492	CCAAAGCTGGTTTCAAG	1607	GGTTGGCTTGAAACCA	3376
		CCAACC		GCTT

7487	7509	CCAACCCCATGGCCTCC	1608	AGTCATGGAGGCCATG	3377
		ATGACT		GGGT

7491	7513	CCCCATGGCCTCCATGA	1609	AAAAAGTCATGGAGG	3378
		CTTTTT		CCATG

7492	7514	CCCATGGCCTCCATGAC	1610	GAAAAAGTCATGGAG	3379
		TTTTTC		GCCAT

7493	7515	CCATGGCCTCCATGACT	1611	TGAAAAAGTCATGGA	3380
		TTTTCA		GGCCA

7499	7521	CCTCCATGACTTTTTCA	1612	CCTTTTTGAAAAAGTC	3381
		AAAAGG		ATGG

7502	7524	CCATGACTTTTTCAAAA	1613	ATACCTTTTTGAAAAA	3382
		AGGTAT		GTCA

7533	7555	CCATTTCATAACTTTGT	1614	ACTTTGACAAAGTTAT	3383
		CAAAGT		GAAA

7573	7595	CCTATATATCTTAATGG	1615	CATGTGCCATTAAGAT	3384
		CACATG		ATAT

7626	7648	CCCCTATCATAGAAGAG	1616	GATAAGCTCTTCTATG	3385
		CTTATC		ATAG

7627	7649	CCCTATCATAGAAGAGC	1617	TGATAAGCTCTTCTAT	3386
		TTATCA		GATA

7628	7650	CCTATCATAGAAGAGCT	1618	GTGATAAGCTCTTCTA	3387
		TATCAC		TGAT

7650	7672	CCTTTCATGATCACGCC	1619	TATGAGGGCGTGATCA	3388
		CTCATA		TGAA

7665	7687	CCCTCATAATCATTTTC	1620	GATAAGGAAAATGATT	3389
		CTTATC		ATGA

7666	7688	CCTCATAATCATTTTCCT	1621	AGATAAGGAAAATGA	3390
		TATCT		TTATG

7681	7703	CCTTATCTGCTTCCTAGT	1622	ACAGGACTAGGAAGC	3391
		CCTGT		AGATA

7693	7715	CCTAGTCCTGTATGCCC	1623	GGAAAAGGGCATACA	3392
		TTTTCC		GGACT

7699	7721	CCTGTATGCCCTTTTCCT	1624	GTGTTAGGAAAAGGG	3393
		AACAC		CATAC

7707	7729	CCCTTTTCCTAACACTC	1625	TGTTGTGAGTGTTAGG	3394
		ACAACA		AAAA

7708	7730	CCTTTTCTAACACTCA	1626	TTGTTGTGAGTGTTAG	3395
		CAACAA		GAAA

7714	7736	CCTAACACTCACAACAA	1627	TTAGTTTTGTTGTGAG	3396
		AACTAA		TGTT

7773	7795	CCGTCTGAACTATCCTG	1628	GGCGGGCAGGATAGTT	3397
		CCCGCC		CAGA

7786	7808	CCTGCCCGCCATCATCC	1629	GGACTAGGATGATGGC	3398
		TAGTCC		GGGC

7790	7812	CCCGCCATCATCCTAGT	1630	ATGAGGACTAGGATG	3399
		CCTCAT		ATGGC

7791	7813	CCGCCATCATCCTAGTC	1631	GATGAGGACTAGGAT	3400
		CTCATC		GATGG

7794	7816	CCATCATCCTAGTCCTC	1632	GGCGATGAGGACTAG	3401
		ATCGCC		GATGA

7801	7823	CCTAGTCCTCATCGCCC	1633	ATGGGAGGGCGATGA	3402
		TCCCAT		GGACT

7807	7829	CCTCATCGCCCTCCCAT	1634	GTAGGGATGGGAGGG	3403
		CCCTAC		CGATG

7815	7837	CCCTCCCATCCCTACGC	1635	AAGGATGCGTAGGGA	3404
		ATCCTT		TGG

7816	7838	CCTCCCATCCCTACGCA	1636	AAAGGATGCGTAGGG	3405
		TCCTTT		ATGGG

7819	7841	CCCATCCCTACGCATCC	1637	TGTAAAGGATGCGTAG	3406
		TTTACA		GGAT

7820	7842	CCATCCCTACGCATCCT	1638	ATGTAAAGGATGCGTA	3407
		TTACAT		GGGA

7824	7846	CCCTACGCATCCTTTAC	1639	TGTTATGTAAAGGATG	3408
		ATAACA		CGTA

7825	7847	CCTACGCATCCTTTACA	1640	CTGTTATGTAAAGGAT	3409
		TAACAG		GCGT

7834	7856	CCTTTACATAACAGACG	1641	TGACCTCGTCTGTTAT	3410
		AGGTCA		GTAA

7862	7884	CCCTCCCTTACCATCAA	1642	ATTGATTTGATGGTAA	3411
		ATCAAT		GGGA

7863	7885	CCTCCCTTACCATCAAA	1643	AATTGATTTGATGGTA	3412
		TCAATT		AGGG

7866	7888	CCCTTACCATCAAATCA	1644	GCCAATTGATTTGATG	3413
		ATTGGC		GTAA

7867	7889	CCTTACCATCAAATCAA	1645	GGCCAATTGATTTGAT	3414
		TTGGCC		GGTA

7872	7894	CCATCAAATCAATTGGC	1646	TTGGTGGCCAATTGAT	3415
		CACCAA		TTGA

7888	7910	CCACCAATGGTACTGAA	1647	CGTAGGTTCAGTACCA	3416
		CCTACG		TTGG

7891	7913	CCAATGGTACTGAACCT	1648	ACTCGTAGGTTCAGTA	3417
		ACGAGT		CCAT

7905	7927	CCTACGAGTACACCGAC	1649	GCCGTAGTCGGTGTAC	3418
		TACGGC		TCGT

7917	7939	CCGACTACGGCGGACTA	1650	GAAGATTAGTCCGCCG	3419
		ATCTTC		TAGT

7944	7966	CCTACATACTTCCCCCA	1651	GAATAATGGGGGAAG	3420
		TTATTC		TATGT

7955	7977	CCCCCATTATTCCTAGA	1652	CCTGGTTCTAGGAATA	3421
		ACCAGG		ATGG

7956	7978	CCCCATTTTCCTAGAA	1653	GCCTGGTTCTAGGAAT	3422
		CCAGGC		AATG

7957	7979	CCCATTATTCCTAGAAC	1654	CGCCTGGTTCTAGGAA	3423
		CAGGCG		TAAT

7958	7980	CCATTATTCCTAGAACC	1655	TCGCCTGGTTCTAGGA	3424
		AGGCGA		ATAA

7966	7988	CCTAGAACCAGGCGACC	1656	GTCGCAGGTCGCCTGG	3425
		TGCGAC		TTCT

7973	7995	CCAGGCGACCTGCGACT	1657	TCAAGGACTCGCAGGT	3426
		CCTTGA		CGCC

7981	8003	CCTGCGACTCCTTGACG	1658	TGTCAACGTCAAGGAG	3427
		TTGACA		TCGC

7990	8012	CCTTGACGTTGACAATC	1659	CTACTCGATTGTCAAC	3428
		GAGTAG		GTCA

8017	8039	CCCGATTGAAGCCCCCA	1660	TACGAATGGGGGCTTC	3429
		TTCCTTA		AATC

8018	8040	CCGATTGAAGCCCCCAT	1661	ATACGAATGGGGGCTT	3430
		TCGTAT		CAAT

8028	8050	CCCCCATTCGTATAATA	1662	TGTAATTATTATACGA	3431
		ATTACA		ATGG

8029	8051	CCCCATTCGTATAATAA	1663	ATGTAATTATTATACG	3432
		TTACAT		AATG

8030	8052	CCCATTCGTATAATAAT	1664	GATGTAATTATTATAC	3433
		TACATC		GAAT

8031	8053	CCATTCGTATAATAATT	1665	TGATGTAATTATTATA	3434
		ACATCA		CGAA

8080	8102	CCCCACATTAGGCTTAA	1666	CTGTTTTTAAGCCTAA	3435
		AAACAG		TGTG

8081	8103	CCCACATTAGGCTTAAA	1667	TCTGTTTTTAAGCCTA	3436
		AACAGA		ATGT

8082	8104	CCACATTAGGCTTAAAA	1668	ATCTGTTTTTAAGCCT	3437
		ACAGAT		AATG

8111	8133	CCCGGACGTCTAAACCA	1669	GTGGTTTGGTTTAGAC	3438
		AACCAC		GTCC

8112	8134	CCGGACGTCTAAACCAA	1670	AGTGGTTTGGTTTAGA	3439
		ACCACT		CGTC

8125	8147	CCAAACCACTTTCACCG	1671	GTGTAGCGGTGAAAGT	3440
		CTACAC		GGTT

8130	8152	CCACTTTCACCGCTACA	1672	CGGTCGTGTAGCGGTG	3441
		CGACCG		AAAG

8139	8161	CCGCTACACGACCGGGG	1673	GTATACCCCCGGTCGT	3442
		GTATAC		GTAG

8150	8172	CCGGGGGTATACTACGG	1674	CATTGACCGTAGTATA	3443
		TCAATG		CCCC

8194	8216	CCACAGTTTCATGCCCA	1675	GGACGATGGGCATGA	3444
		TCGTCC		AACTG

8207	8229	CCCATCGTCCTAGAATT	1676	GGAATTAATTCTAGGA	3445
		AATTCC		CGAT

8208	8230	CCATCGTCCTAGAATTA	1677	GGGAATTAATTCTAG	3446
		ATTCCC		ACGA

8215	8237	CCTAGAATTAATTCCCC	1678	TTTTTAGGGGAATTAA	3447
		TAAAAA		TTCT

8228	8250	CCCCTAAAAATCTTTGA	1679	CCTATTTCAAAGATTT	3448
		AATAGG		TTAG

8229	8251	CCCTAAAAATCTTTGAA	1680	CCCTATTTCAAAGATT	3449
		ATAGGG		TTTA

8230	8252	CCTAAAAATCTTTGAAA	1681	GCCCTATTTCAAAGAT	3450
		TAGGGC		TTTT

8252	8274	CCCGTATTTACCCTATA	1682	GGGTGCTATAGGGTAA	3451
		GCACCC		ATAC

8253	8275	CCGTATTTACCCTATAG	1683	GGGGTGCTATAGGGTA	3452
		CACCCC		AATA

8262	8284	CCCTATAGCACCCCCTC	1684	GGGGTAGAGGGGGTG	3453
		TACCCC		CTATA

8263	8285	CCTATAGCACCCCCTCT	1685	GGGGGTAGAGGGGGT	3454
		ACCCCC		GCTAT

8272	8294	CCCCCTCTACCCCCTCT	1686	GGCTCTAGAGGGGGTA	3455
		AGAGCC		GAGG

8273	8295	CCCCTCTACCCCCTCTA	1687	GGGCTCTAGAGGGGGT	3456
		GAGCCC		AGAG

8274	8296	CCCTCTACCCCCTCTAG	1688	TGGGCTCTAGAGGGGG	3457
		AGCCCA		TAGA

8275	8297	CCTCTACCCCCTCTAGA	1689	GTGGGCTCTAGAGGCG	3458
		GCCCAC		GTAG

8281	8303	CCCCCTCTAGAGCCCAC	1690	TTTACAGTGGGCTCTA	3459
		TGTAAA		GAGG

8282	8304	CCCCTCTAGAGCCCACT	1691	CTTTACAGTGGGCTCT	3460
		GTAAAG		AGAG

8283	8305	CCCTCTAGAGCCCACTG	1692	GCTTTACAGTGGGCTC	3461
		TAAAGC		TAGA

8284	8306	CCTCTAGAGCCCACTGT	1693	AGCTTTACAGTGGGCT	3462
		AAAGCT		CTAG

8293	8315	CCCACTGTAAAGCTAAC	1694	TGCTAAGTTAGCTTTA	3463
		TTAGCA		CAGT

8294	8316	CCACTGTAAAGCTAACT	1695	ATGCTAAGTTAGCTTT	3464
		TAGCAT		ACAG

8320	8342	CCTTTTAAGTTAAAGAT	1696	CTCTTAATCTTTAACTT	3465
		TAAGAG		AAA

8345	8367	CCAACACCTCTTTACAG	1697	ATTTCACTGTAAAGAG	3466
		TGAAAT		GTGT

8351	8373	CCTCTTTACAGTGAAAT	1698	TGGGGCATTTCACTGT	3467
		GCCCCA		AAAG

8369	8391	CCCCAACTAAATACTAC	1699	CATACGGTAGTATTTA	3468
		CGTATG		GTTG

8370	8392	CCCAACTAAATACTACC	1700	CCATACGGTAGTATTT	3469
		GTATGG		AGTT

8371	8393	CCAACTAAATACTACCG	1701	GCCATACGGTAGTATT	3470
		TATGGC		TAGT

8385	8407	CCGTATGGCCCACCATA	1702	GGTAATTATGGTGGGC	3471
		ATTACC		CATA

8393	8415	CCCACCATAATTACCCC	1703	AGTATGGGGGTAATTA	3472
		CATACT		TGGT

8394	8416	CCACCATAATTACCCCC	1704	GAGTATGGGGGTAATT	3473
		ATACTC		ATGG

8397	8419	CCATAATTACCCCCATA	1705	AAGGAGTATGGGGGT	3474
		CTCCTT		AATTA

8406	8428	CCCCCATACTCCTTACA	1706	GAATAGTGTAAGGAGT	3475
		CTATTC		ATGG

8407	8429	CCCCATACTCCTTACAC	1707	GGAATAGTGTAAGGA	3476
		TATTCC		GTATG

8408	8430	CCCATACTCCTTACACT	1708	AGGAATAGTGTAAGG	3477
		ATTCCT		AGTAT

8409	8431	CCATACTCCTTACACTTA	1709	GAGGAATAGTGTAAG	3478
		TTCCTC		GAGTA

8416	8438	CCTTACACTATTCCTCA	1710	GGGTGATGAGGAATA	3479
		TCACCC		GTGTA

8428	8450	CCTCATCACCCAACTAA	1711	ATATTTTTAGTTGGGT	3480
		AAATAT		GATG

8436	8458	CCCAACTAAAAATATTA	1712	TGTGTTTAATATTTTTA	3481
		AACACA		GTT

8437	8459	CCAACTAAAAATATTAA	1713	TTGTGTTTAATATTTTT	3482
		ACACAA		AGT

8464	8486	CCACCTACCTCCCTCAC	1714	GCTTTGGTGAGGGAGG	3483
		CAAAGC		GAGG

8467	8489	CCTACCTCCCTCACCAA	1715	TGGGCTTTGGTGAGGG	3484
		AGCCCA		AGGT

8471	8493	CCTCCCTCACCAAAGCC	1716	TTTATGGGCTTTGGTG	3485
		CATAAA		AGGG

8474	8496	CCCTCACCAAAGCCCAT	1717	ATTTTTATGGGCTTTG	3486
		AAAAAT		GTGA

8475	8497	CCTCACCAAAGCCCATA	1718	TATTTTTATGGGCTTTG	3487
		AAAATA		GTG

8480	8502	CCAAAGCCCATAAAAAT	1719	TTTTTTATTTTTATGG	3488
		AAAAAA		CTT

8486	8508	CCCATAAAAATAAAAA	1720	TTATAATTTTTTATTTT	3489
		ATTATAA		TAT

8487	8509	CCATAAAAATAAAAAA	1721	GTTATAATTTTTTATTT	3490
		TTATAAC		TTA

8513	8535	CCCTGAGAACCAAAATG	1722	TTCGTTCATTTTGGTTC	3491
		AACGAA		TCA

8514	8536	CCTGAGAACCAAAATG	17231	TTTCGTTCATTTTGGTT	3492
		AACGAAA		CTC

8522	8544	CCAAAATGAACGAAAA	1724	GAACAGATTTTCGTTC	3493
		TCTGTTC		ATTT

8558	8580	CCCCCACAATCCTAGGC	1725	GGGTAGGCCTAGGATT	3494
		CTACCC		GTGG

8559	8581	CCCCACAATCCTAGGCC	1726	CGGGTAGGCCTAGGAT	3495
		TACCCG		TGTG

8560	8582	CCCACAATCCTAGGCCT	1727	GCGGGTAGGCCTTAGG	3496
		ACCCGC		ATTGT

8561	8583	CCACAATCCTAGGCCTA	1728	GGCGGGTAGGCCTAG	3497
		CCCGCC		GATTG

8568	8590	CCTAGGCCTACCCGCCG	1729	GTACTGCGGCGGGTAG	3498
		CAGTAC		GCCT

8574	8596	CCTACCCGCCGCAGTAC	1730	TGATCAGTACTGCGGC	3499
		TGATCA		GGGT

8578	8600	CCCGCCGCAGTACTGAT	1731	AGAATGATCAGTACTG	3500
		CATTCT		CGGC

8579	8601	CCGCCGCAGTACTGATC	1732	TAGAATGATCAGTACT	3501
		ATTCTA		GCGG

8582	8604	CCGCAGTACTGATCATT	1733	AAATAGAATGATCAGT	3502
		CTATTT		ACTG

8605	8627	CCCCCTCTATTGATCCC	1734	GAGGTGGGGATCAAT	3503
		CACCTC		AGAGG

8606	8628	CCCCTCTATTGATCCCC	1735	GGAGGTGGGGATCAA	3504
		ACCTCC		TAGAG

8607	8629	CCCTCTATTGATCCCCA	1736	TGGAGGTGGGGATCA	3505
		CCTCCA		ATAGA

8608	8630	CCTCTATTGATCCCCAC	1737	TTGGAGGTGGGGATCA	3506
		CTCCAA		ATAG

8619	8641	CCCCACCTCCAAATATC	1738	TGATGAGATATTTGGA	3507
		TCATCA		GGTG

8620	8642	CCCACCTCCAAATATCT	1739	TTGATGAGATATTTGG	3508
		CATCAA		AGGT

8621	8643	CCACCTCCAAATATCTC	1740	GTTGATGAGATATTTG	3509
		ATCAAC		GAGG

8624	8646	CCTCCAAATATCTCATC	1741	GTTGTTGATGAGATAT	3510
		AACAAC		TTGG

8627	8649	CCAAATATCTCATCAAC	1742	TCGGTTGTTGATGAGA	3511
		AACCGA		TATT

8646	8668	CCGACTAATCACCACCC	1743	ATTGTTGGGTGGTGAT	3512
		AACAAT		TAGT

8657	8679	CCACCCAACAATGACTA	1744	TTTGATTAGTCATTGTT	3513
		ATCAAA		GGG

8660	8682	CCCAACAATGACTAATC	1745	TAGTTTGATTAGTCAT	3514
		AAACTA		TGTT

8661	8683	CCAACAATGACTAATCA	1746	TTAGTTTGATTAGTCA	3515
		AACTAA		TTGT

8684	8706	CCTCAAAACAAATGATA	1747	TATGGTTATCATTTGTT	3516
		ACCTA		TTG

8702	8724	CCATACACAACACTAAA	1748	TCGTCCTTTAGTGTTGT	3517
		GGACGA		GTA

8726	8748	CCTGATCTCTTATACTA	1749	GGATACTAGTATAAGA	3518
		GTATCC		GATC

8747	8769	CCTTAATCATTTTTATTG	1750	TGTGGCAATAAAAATG	3519
		CCACA		ATTA

8765	8787	CCACAACTAACCTCCTC	1751	GAGTCCGAGGAGGTTA	3570
		GGACTC		GTTG

8775	8797	CCTCCTCGGACTCCTGC	1752	AGTGAGGCAGGAGTC	3521
		CTCACT		CGAGG

8778	8800	CCTCGGACTCCTGCCTC	1753	ATGAGTGAGGCAGGA	3522
		ACTCAT		GTCCG

8787	8809	CCTGCCTCACTCATTTA	1754	TTGGTGTAAATGAGTG	3523
		CACCAA		AGGC

8791	8813	CCTCACTCATTTACACC	1755	GTGGTTGGTGTAAATG	3524
		AACCAC		AGTG

8806	8828	CCAACCACCCAACTATC	1756	TTTATAGATAGTTGGG	3525
		TATAAA		TGGT

8810	8832	CCACCCAACTATCTATA	1757	TAGGTTTATAGATAGT	3526
		AACCTA		TGGG

8813	8835	CCCAACTATCTATAAAC	1758	GGCTAGGTTTATAGAT	3527
		CTAGCC		AGTT

8814	8836	GCCAACTATCTATAAACC	1759	TGGCTAGGTTTATAGA	3528
		TAGCCA		TAGT

8829	8851	CCTAGCCATGGCCATCC	1760	ATAAGGGGATGGCCAT	3529
		CCTTAT		GGCT

8834	8856	CCATGGCCATCCCCTTA	1761	CGCTCATAAGGGGATG	3530
		TGAGCG		GCCA

8840	8862	CCATCCCCTTATGAGCG	1762	TGTGCCCGCTCATAAG	3531
		GGCACA		GGGA

8844	8866	CCCCTTATGAGCGGGCA	1763	TCACTGTGCCCGCTCA	3532
		CAGTGA		TAAG

8845	8867	CCCTTATGAGCGGGCAC	1764	ATCACTGTGCCCGCTC	3533
		AGTGAT		ATAA

8846	8868	CCTTATGAGCGGGCACA	1765	AATCACTGTGCCCGCT	3534
		GTGATT		CATA

8897	8919	CCCTAGCCCACTTCTTA	1766	TTGTGGTAAGAAGTGG	3535
		CCACAA		GCTA

8898	8920	CCTAGCCCACTTCTTAC	1767	CTTGTGGTAAGAAGTG	3536
		CACAAG		GGCT

8903	8925	CCCACTTCTTACCACAA	1768	TGTGCCTTGTGGTAAG	3537
		GGCACA		AAGT

8904	8926	CCACTTCTTACCACAAG	1769	GTGTGCCTTGTGGTAA	3538
		GCACAC		GAAG

8914	8936	CCACAAGGCACACCTAC	1770	AGGGGTGTAGGTGTGC	3539
		ACCCCT		CTTG

8926	8948	CCTACACCCCTTATCCC	1771	AGTATGGGGATAAGG	3540
		CATACT		GGTGT

8932	8954	CCCCTTATCCCCATACT	1772	ATAACTAGTATGGGGA	3541
		AGTTAT		TAAG

8933	8955	CCCTTATCCCCATACTA	1773	AATAACTAGTATGGGG	3542
		GTTATT		ATAA

8934	8956	CCTTATCCCCATACTAG	1774	TAATAACTAGTATGGG	3543
		TTATTA		GATA

8940	8962	CCCCATACTAGTTATTA	1775	TTTCGATAATAACTAC	3544
		TCGAAA		TATG

8941	8963	CCCATACTAGTTATTAT	1776	GTTTCGATAATAACTA	3545
		CGAAAC		GTAT

8942	8964	CCATACTAGTTATTATC	1777	GGTTTCGATAATAACT	3546
		GAAACC		AGTA

8963	8985	CCATCAGCCTACTCATT	1778	TGGTTGAATGAGTAGG	3547
		CAACCA		CTGA

8970	8992	CCTACTCATTCAACCAA	1779	GGGCTATTGGTTGAAT	3548
		TAGCCC		GAGT

8983	9005	CCAATAGCCCTGGCCGT	1780	AGGCGTACGGCCAGG	3549
		ACGCCT		GCTAT

8990	9012	CCCTGGCCGTACGCCTA	1781	AGCGGTTAGGCGTACG	3550
		ACCGCT		GCCA

8991	9013	CCTGGCCGTACGCCTAA	1782	TAGCGGTTAGGCGTAC	3551
		CCGCTA		GGCC

8996	9018	CCGTACGCCTAACCGCT	1783	AATGTTAGCGGTTAGG	3552
		AACATT		CGTA

9003	9025	CCTAACCGCTAACATTA	1784	CTGCAGTAATGTTAGC	3553
		CTGCAG		GGTT

9008	9030	CCGCTAACATTACTGCA	1785	GTGGCCTGCAGTAATG	3554
		GGCCAC		TTAG

9027	9049	CCACCTACTCATGCACC	1786	CAATTAGGTGCATGAG	3555
		TAATTG		TAGG

9030	9052	CCTACTCATGCACCTAA	1787	TTCCAATTAGGTGCAT	3556
		TTGGAA		GAGT

9042	9064	CCTAATTGGAAGCGCCA	1788	CTAGGGTGGCGCTTCC	3557
		CCCTAG		AATT

9056	9078	CCACCCTAGCAATATCA	1789	AATGGTTGATATTGCT	3558
		ACCATT		AGGG

9059	9081	CCCTAGCAATATCAACC	1790	GTTAATGGTTGATATT	3559
		ATTAAC		GCTA

9060	9082	CCTAGCAATATCAACCA	1791	GGTTAATGGTTGATAT	3560
		TTAACC		TGCT

9074	9096	CCATTAACCTTCCCTCT	1792	AAGTGTAGAGGGAAG	3561
		ACACTT		GTTAA

9081	9103	CCTTCCCTCTACACTTAT	1793	AGATGATAAGTGTAGA	3562
		CATCT		GGGA

9085	9107	CCCTCTACACTTATCAT	1794	GTGAAGATGATAAGTG	3563
		CTTCAC		TAGA

9086	9108	CCTCTACACTTATCATC	1795	TGTGAAGATGATAAGT	3564
		TTCACA		GTAG

9129	9151	CCTAGAAATCGCTGTCG	1796	TAAGGCGACAGCGAT	3565
		CCTTAA		TTCT

9146	9168	CCTTAATCCAAGCCTAC	1797	GAAAACGTAGGCTTGG	3566
		GTTTTC		ATTA

9153	9175	CCAAGCCTACGTTTTCA	1798	GAAGTGTGAAAACGT	3567
		CACTTTC		AGGCT

9158	9180	CCTACGTTTTCACACTT	1799	TACTAGAAGTGTGAAA	3568
		CTAGTA		ACGT

9183	9205	CCTCTACCTGCACGACA	1800	ATGTGTTGTCGTGCAG	3569
		ACACAT		GTAG

9189	9211	CCTGCACGACAACACAT	1801	GTCATTATGTGTTGTC	3570
		AATGAC		GTGC

9211	9233	CCCACCAATCACATGCC	1802	ATGATAGGCATGTGAT	3571
		TATCAT		TGGT

9212	9234	CCACCAATCACATGCCT	1803	TATGATAGGCATGTGA	3572
		ATCATA		TTGG

9215	9237	CCAATCACATGCCTATC	1804	CTATATGATAGGCATG	3573
		ATATAG		TGAT

9226	9248	CCTATCATATAGTAAAA	1805	GCTGGGTTTTACTATA	3574
		CCCAGC		TGAT

9243	9265	CCCAGCCCATGACCCCT	1806	CCTGTTAGGGGTCATG	3575
		AACAGG		GGCT

9244	9266	CCAGCCCATGACCCCTA	1807	CCCTGTTAGGGGTCAT	3576
		ACAGGG		GGGC

9248	9270	CCCATGACCCCTAACAG	1808	GGGCCCCTGTTAGGGG	3577
		GGGCCC		TCAT

9249	9271	CCATGACCCCTAACAGG	1809	AGGGCCCCTGTTAGGG	3578
		GGCCCT		GTCA

9255	9277	CCCCTAACAGGGGCCCT	1810	GCTGAGAGGGCCCCTG	3579
		CTCAGC		TTAG

9256	9278	CCCTAACAGGGGCCCTC	1811	GGCTGAGAGGGCCCCT	3580
		TCAGCC		GTTA

9257	9279	CCTAACAGGGGCCCTCT	1812	GGGCTGAGAGGGCCC	3581
		CAGCCC		CTGTT

9268	9290	CCCTCTCAGCCCTCCTA	1813	GGTCATTAGGAGGGCT	3582
		ATGACC		GAGA

9269	9291	CCTCTCAGCCCTCCTAA	1814	AGGTCATTAGGAGGGC	3583
		TGACCT		TGAG

9277	9299	CCCTCCTAATGACCTCC	1815	TAGGCCGGAGGTCATT	3584
		GGCCTA		AGGA

9278	9300	CCTCCTAATGACCTCCG	1816	CTAGGCCGGAGGTCAT	3585
		GCCTAG		TAGG

9281	9303	CCTAATGACCTCCGGCC	1817	TGGCTAGGCCGGAGGT	3586
		TAGCCA		CATT

9289	9311	CCTCCGGCCTAGCCATG	1818	AAATCACATGGCTAGG	3587
		TGATTT		CCGG

9292	9314	CCGGCCTAGCCATGTGA	1819	GTGAAATCACATGGCT	3588
		TTTCAC		AGGC

9296	9318	CCTAGCCATGTGATTTC	1820	GGAAGTGAAATCACAT	3589
		ACTTCC		GGCT

9301	9323	CCATGTGATTTCACTTC	1821	GGAGTGGAAGTGAAA	3590
		CACTCC		TCACA

9317	9339	CCACTCCATAACGCTCC	1822	GTATGAGGAGCGTTAT	3591
		TCATAC		GGAG

9322	9344	CCATAACGCTCCTCATA	1823	GCCTAGTATGAGGAGC	3592
		CTAGGC		GTTA

9332	9354	CCTCATACTAGGCCTAC	1824	TGGTTAGTAGGCCTAG	3593
		TAACCA		TATG

9344	9366	CCTACTAACCAACACAC	1825	TGGTTAGTGTGTTGGT	3594
		TAACCA		TAGT

9352	9374	CCAACACACTAACCATA	1826	TTGGTATATGGTFAGT	3595
		TACCAA		GTGT

9364	9386	CCATATACCAATGATGG	1827	ATCGCGCCATCATTGG	3596
		CGCGAT		TATA

9371	9393	CCAATGATGGCGCGATG	1828	GTGTTACATCGCGCCA	3597
		TAACAC		TCAT

9407	9429	CCAAGGCCACCACACAC	1829	CAGGTGGTGTGTGGTG	3598
		CACCTG		GCCT

9413	9435	CCACCACACACCACCTG	1830	TTTGGACAGGTGGTGT	3599
		TCCAAA		GTGG

9416	9438	CCACACACCACCTGTCC	1831	CTTTTTGGACAGGTGG	3600
		AAAAAG		TGTG

9423	9445	CCACCTGTCCAAAAAGG	1832	CGAAGGCCTTTTTGGA	3601
		CCTTCG		CAGG

9426	9448	CCTGTCCAAAAAGGCCT	1833	TATCGAAGGCCTTTTT	3602
		TCGATA		GGAC

9431	9453	CCAAAAAGGCCTTCGAT	1834	TCCCGTATCGAAGGCC	3603
		ACGGGA		TTTT

9440	9462	CCTTCGATACGGGATAA	1835	ATAGGATTATCCCGTA	3604
		TCCTAT		TCGA

9458	9480	CCTATTTATTACCTCAG	1836	AAACTTCTGAGGTAAT	3605
		AAGTTT		AAAT

9469	9491	CCTCAGAAGTTTTTTTCT	1837	TGCGAAGAAAAAAAC	3606
		TCGCA		TTCTG

9505	9527	CCTTTTACCACTCCAGC	1838	GGCTAGGCTGGAGTGG	3607
		CTAGCC		TAAA

9512	9534	CCACTCCAGCCTAGCCC	1839	GGGTAGGGGCTAGGCT	3608
		CTACCC		GGAG

9517	9539	CCAGCCTAGCCCCTACC	1840	TTGGGGGGTAGGGGCT	3609
		CCCCAA		AGGC

9521	9543	CCTAGCCCCTACCCCCC	1841	CTAATTGGGGGGTAGG	3610
		AATTAG		GGCT

9526	9548	CCCCTACCCCCCAATTA	1842	CCCTCCTAATTGGGGG	3611
		GGAGGG		GTAG

9527	9549	CCCTACCCCCCAATTAG	1843	GCCCTCCTAATTGGGG	3612
		GAGGGC		GGTA

9528	9550	CCTACCCCCCAATTAGG	1844	TGCCCTCCTAATTGGG	3613
		AGGGCA		GGGT

9532	9554	CCCCCCAATTAGGAGGG	1845	CCAGTGCCCTCCTAAT	3614
		CACTGG		TGGG

9533	9555	CCCCCAATTAGGAGGGC	1846	GCCAGTGCCCTCCTAA	3615
		ACTGGC		TTGG

9534	9556	CCCCAATTAGGAGGGCA	1847	GGCCAGTGCCCTCCTA	3616
		CTGGCC		ATTG

9535	9557	CCCAATTAGGAGGGCAC	1848	GGGCCAGTGCCCTCCT	3617
		TGGCCC		AATT

9536	9558	CCAATTAGGAGGGCACT	1849	GGGGCCAGTGCCCTCC	3618
		GGCCCC		TAAT

9555	9577	CCCCCAACAGGCATCAC	1850	AGCGGGGTGATGCCTG	3619
		CCCGCT		TTGG

9556	9578	CCCCAACAGGCATCACC	1851	TAGCGGGGTGATGCCT	3620
		CCGCTA		GTTG

9557	9579	CCCAACAGGCATCACCC	1852	TTAGCGGGGTGATGCC	3621
		CGCTAA		TGTT

9558	9580	CCAACAGGCATCACCCC	1853	TTTAGCGGGGTGATGC	3622
		GCTAAA		CTGT

9571	9593	CCCCGCTAAATCCCCTA	1854	GACTTCTAGGGGATTT	3623
		GAAGTC		AGCG

9572	9594	CCCGCTAAATCCCCTAG	1855	GGACTTCTAGGGGATT	3624
		AAGTCC		TAGC

9573	9595	CCGCTAAATCCCCTAGA	1856	GGGACTTCTAGGGGAT	3625
		AGTCCC		TTAG

9582	9604	CCCCTAGAAGTCCCACT	1857	TTTAGGAGTGGGACTT	3626
		CCTAAA		CTAG

9583	9605	CCCTAGAAGTCCCACTC	1858	GTTTAGGAGTGGGACT	3627
		CTAAAC		TCTA

9584	9606	CCTAGAAGTCCCACTCC	1859	TGTTTAGGAGTGGGAC	3628
		TAAACA		TTCT

9593	9615	CCCACTCCTAAACACAT	1860	ATACGGATGTGTTTAG	3629
		CCGTAT		GAGT

9594	9616	CCACTCCTAAACACATC	1861	AATACGGATGTGTTTA	3630
		CGTATT		GGAG

9599	9621	CCTAAACACATCCGTAT	1862	CGAGTAATACGGATGT	3631
		TACTCG		GTTT

9610	9632	CCGTATTACTCGCATCA	1863	TACTCCTGATGCGAGT	3632
		GGAGTA		AATA

9640	9662	CCTGAGCTCACCATAGT	1864	TATTAGACTATGGTGA	3633
		CTAATA		GCTC

9650	9672	CCATAGTCTAATAGAAA	1865	GGTTGTTTTCTATTAG	3634
		ACAACC		ACTA

9671	9693	CCGAAACCAAATAATTC	1866	GTGCTTGAATTATTTG	3635
		AAGCAC		GTTT

9677	9699	CCAAATAATTCAAGCAC	1867	TAAGCAGTGCTTGAAT	3636
		TGCTTA		TATT

9727	9749	CCCTCCTACAAGCCTCA	1868	GTACTCTGAGGCTTGT	3637
		GAGTAC		AGGA

9728	9750	CCTCCTACAAGCCTCAG	1869	AGTACTCTGAGGCTTG	3638
		AGTACT		TAGG

9731	9753	CCTACAAGCCTCAGAGT	1870	CGAAGTACTCTGAGGC	3639
		ACTTCG		TTGT

9739	9761	CCTCAGAGTACTTCGAG	1871	CGAAGTACTCTGAGGC	3640
		TCTCCC		CTCTG

9759	9781	CCCTTCACCATTTCCGA	1872	ATGCCGTCGGAAATGG	3641
		CGGCAT		TGAA

9760	9782	CCTTCACCATTTCCGAC	1873	GATGCCGTCGGAAATG	3642
		GGCATC		GTGA

9766	9788	CCATTTCCGACGGCATC	1874	GCCGTAGATGCCGTCG	3643
		TACGGC		GAAA

9772	9794	CCGACGGCATCTACGGC	1875	TGTTGAGCCGTAGATG	3644
		TCAACA		CCGT

9805	9827	CCACAGGCTTCCACGGA	1876	GTGAAGTCCGTGGAAG	3645
		CTTCAC		CCTG

9815	9837	CCACGGACTTCACGTCA	1877	CAATAATGACGTGAAG	3646
		TTATTG		TCCG

9848	9870	CCTCACTATCTGCTTCA	1878	GGCGGATGAAGCAGA	3647
		TCCGCC		TAGTG

9866	9888	CCGCCAACTAATATTTC	1879	TAAAGTGAAATATTAG	3648
		ACTTTA		TTGG

9869	9891	CCAACTAATATTTCACT	1880	ATGTAAAGTGAAATAT	3649
		TTACAT		TAGT

9892	9914	CCAAACATCACTTTGGC	1881	TTCGAAGCCAAAGTGA	3650
		TTCGAA		TGTT

9916	9938	CCGCCGCCTGATACTGG	1882	AAAATGCCAGTATCAG	3651
		CATTTT		GCGG

9919	9941	CCGCCTGATACTGGCAT	1883	TACAAAATGCCAGTAT	3652
		TTTGTA		CAGG

9922	9944	CCTGATACTGGCATTTT	1884	ATCTACAAAATGCCAG	3653
		GTAGAT		TATC

9970	9992	CCATCTATTGATGAGGG	1885	GTAAGACCCTCATCAA	3654
		TCTTAC		TAGA

10012	10034	CCGTTAACTTCCAATTA	1886	ACTAGTTAATTGGAG	3655
		ACTAGT		TTAA

10022	10044	CCAATTAACTAGTTTTG	1887	TGTTGTCAAAACTAGT	3656
		ACAACA		TAAT

10069	10091	CCTTAATTTTAATAATC	1888	GGTGTTGATTATTAAA	3657
		AACACC		ATTA

10090	10112	CCCTCCTAGCCTTACTA	1889	TATTAGTAGTAAGGCT	3658
		CTAATA		AGGA

10091	10113	CCTCCTAGCCTTACTAC	1890	TTATTAGTAGTAAGGC	3659
		TAATAA		TAGG

10094	10116	CCTAGCCTTACTACTAA	1891	TAATTATTAGTAGTAA	3660
		TAATTA		GGCT

10099	10121	CCTTACTACTAATAATT	1892	TGTAATAATTATTAGT	3661
		ATTACA		AGTA

10131	10153	CCACAACTCAACGGCT	1893	TCTATGTAGCCGTTGA	3662
		CATAGA		GTTG

10159	10181	CCACCCCTTACGAGTGC	1894	GAAGCCGCACTCGTAA	3663
		GGCTTC		GGGG

10162	10184	CCCCTTACGAGTGCGGC	1895	GTCGAAGCCGCACTCG	3664
		TTCGAC		TAAG

10163	10185	CCCTTACGAGTGCGGCT	1896	GGTCGAAGCCGCACTC	3665
		TCGACC		GTAA

10164	10186	CCTTACGAGTGCGGCTT	1897	GGGTCGAAGCCGCACT	3666
		CGACCC		CGTA

10184	10206	CCCTATATCCCCCGCCC	1898	GGACGCGGGCGGGGG	3667
		GCGTCC		ATATA

10185	10207	CCTATATCCCCCGCCCG	1899	GGGACGCGGGCGGGG	3668
		CGTCCC		GATAT

10192	10214	CCCCCGCCCGCGTCCCT	1900	GGAGAAAGGGACGCG	3669
		TTCTCC		GGCGG

10193	10215	CCCCGCCCGCGTCCCTT	1901	TGGAGAAAGGGACGC	3670
		TCTCCA		GGGCG

10194	10216	CCCGCCCGCGTCCCTTT	1902	ATGGAGAAAGGGACG	3671
		CTCCAT		CGGGC

10195	10217	CCGCCCGCGTCCCTTTC	1903	TATGGAGAAAGGGAC	3672
		TCCATA		GCGGG

10198	10220	CCCGCGTCCCTTTCTCC	1904	TTTTATGGAGAAAGGG	3673
		ATAAAA		ACGC

10199	10221	CCGCGTCCCTTTCTCCA	1905	ATTTTATGGAGAAAGG	3674
		TAAAAT		GACG

10205	10227	CCCTTTCTCCATAAAAT	1906	AGAAGAATTTTATGGA	3675
		TCTTCT		GAAA

10206	10228	CCTTTCTCCATAAAATT	1907	AAGAAGAATTTTATGG	3676
		CTTCTT		AGAA

10213	10235	CCATAAAATTCTTCTTA	1908	AGCTACTAAGAAGAAT	3677
		GTAGCT		TTTA

10240	10262	CCTTCTTATTATTTGATC	1909	TTCTAGATCAAATAAT	3678
		TAGAA		AAGA

10267	10289	CCCTCCTTTTACCCCTAC	1910	TCATGGTAGGGGTAAA	3679
		CATGA		AGGA

10268	10290	CCTCCTTTTACCCCTACC	1911	CTCATGGTAGGGGTAA	3680
		ATGAG		AAGG

10271	10293	CCTTTTACCCCTACCAT	1912	GGGCTCATGGTAGGGG	3681
		GAGCCC		TAAA

10278	10300	CCCCTACCATGAGCCCT	1913	GTTTGTAGGGCTCATG	3682
		ACAAAC		GTAG

10279	10301	CCCTACCATGAGCCCTA	1914	TGTTTGTAGGGCTCAT	3683
		CAAACA		GGTA

10280	10302	CCTACCATGAGCCCTAC	1915	TTGTTTGTAGGGCTCA	3684
		AAACAA		TGGT

10284	10306	CCATGAGCCCTACAAAC	1916	TTAGTTGTTTGTAGGG	3685
		AACTAA		CTCA

10291	10313	CCCTACAAACAACTAAC	1917	TGGCAGGTTAGTTGTT	3686
		CTGCCA		TGTA

10292	10314	CCTACAAACAACTAACC	1918	GTGGCAGGTTAGTTGT	3687
		TGCCAC		TTGT

10307	10329	CCTGCCACTAATAGTTA	1919	ATGACATAACTATTAG	3688
		TGTCAT		TGGC

10311	10333	CCACTAATAGTTATGTC	1920	AGGGATGACATAACTA	3689
		ATCCCT		TTAG

10330	10352	CCCTCTTATTAATCATC	1921	TAGGATGATGATTAAT	3690
		ATCCTA		AAGA

10331	10353	CCTCTTATTAATCATCA	1922	CTAGGATGATGATTAA	3691
		TCCTAG		TAAG

10349	10371	CCTAGCCCTAAGTCTGG	1923	CATAGCCAGACTTAG	3692
		CCTATG		GGCT

10354	10376	CCCTAAGTCTGGCCTAT	1924	TCACTCATAGGCCAGA	3693
		GAGTGA		CTTA

10355	10377	CCTAAGTCTGGCCTATG	1925	GTCACTCATAGGCCAG	3694
		AGTGAC		ACTT

10366	10388	CCTATGAGTGACTACAA	1926	TCCTTTTTGTAGTCACT	3695
		AAAGGA		CAT

10399	10421	CCGAATTGGTATATAGT	1927	GTTTAAACTATATACC	3696
		TTAAAC		AATT

10466	10488	CCAAATGCCCCTCATTT	1928	TTATGTAAATGAGGGG	3697
		ACATAA		CATT

10473	10495	CCCCTCATTTACATAAA	1929	ATAATATTTATGTAAA	3698
		TATTAT		TGAG

10474	10496	CCCTCATTTACATAAAT	1930	TATAATATTTATGTAA	3699
		ATTATA		ATGA

10475	10497	CCTCATTTACATAAATA	1931	GTATAATATTTATGTA	3700
		TTATAC		AATG

10507	10529	CCATCTCACTTCTAGGA	1932	TAGTATTCCTAGAAGT	3701
		ATACTA		GAGA

10544	10566	CCTCATATCCTCCCTAC	1933	GGCATAGTAGGGAGG	3702
		TATGCC		ATATG

10552	10574	CCTCCCTACTATGCCTA	1934	TCCTTCTAGGCATAGT	3703
		GAAGGA		AGGG

10555	10577	CCCTACTATGCCTAGAA	1935	TATTCCTTCTAGGCAT	3704
		GGAATA		AGTA

10556	10578	CCTACTATGCCTAGAAG	1936	TTATTCCTTCTAGCTCA	3705
		GAATAA		TAGT

10565	10587	CCTAGAAGGAATAATAC	1937	GCGATAGTATTATTCC	3706
		TATCGC		TTCT

10612	10634	CCCTCAACACCCACTCC	1938	TAAGAGGGAGTGGGT	3707
		CTCTTA		GTTGA

10613	10635	CCTCAACACCCACTCCC	1939	CTAAGAGGGAGTGGG	3708
		TCTTAG		TGTTG

10621	10643	CCCACTCCCTCTTAGCC	1940	AATATTGGCTAAGAGG	3709
		AATATT		GAGT

10622	10644	CCACTCCCTCTTAGCCA	1941	CAATATTGGCTAAGAG	3710
		ATATTG		GGAG

10627	10649	CCCTCTTAGCCAATATT	1942	AGGCACAATATTGGCT	3711
		GTGCCT		AAGA

10628	10650	CCTCTTAGCCAATATTG	1943	TAGGCACAATATTGGC	3712
		TGCCTA		TAAG

10636	10658	CCAATATTGTGCCTATT	1944	TATGGCAATAGGCACA	3713
		GCCATA		ATAT

10647	10669	CCTATTGCCATACTAGT	1945	GCAAAGACTAGTATGG	3714
		CTTTGC		CAAT

10654	10676	CCATACTAGTCTTTGCC	1946	GCAGGCGGCAAAGAC	3715
		GCCTGC		TAGTA

10669	10691	CCGCCTGCGAAGCAGCG	1947	GCCCACCGCTGCTTCG	3716
		GTGGGC		CAGG

10672	10694	CCTGCGAAGCAGCGGTG	1948	TAGGCCCACCGCTGCT	3717
		GGCCTA		TCGC

10691	10713	CCTAGCCCTACTAGTCT	1949	AGATTGAGACTAGTAG	3718
		CAATCT		GGCT

10696	10718	CCCTACTAGTCTCAATC	1950	GTTGGAGATTGAGACT	3719
		TCCAAC		AGTA

10697	10719	CCTACTAGTCTCAATCT	1951	TGTTGGAGATTGAGAC	3720
		CCAACA		TAGT

10714	10736	CCAACACATATGGCCTA	1952	GTAGTCTAGGCCATAT	3721
		GACTAC		GTGT

10727	10749	CCTAGACTACGTACATA	1953	TTAGGTTATGTACGTA	3722
		ACCTAA		GTCT

10745	10767	CCTAAACCTACTCCAAT	1954	TTTAGCATTGGAGTAG	3723
		GCTAAA		GTTT

10751	10773	CCTACTCCAATGCTAAA	1955	ATTAGTTTTAGCATTG	3724
		ACTAAT		GAGT

10757	10779	CCAATGCTAAAACTAAT	1956	GGGACGATTAGTTTTA	3725
		CGTCCC		GCAT

10777	10799	CCCAACAATTATATTAC	1957	GTGGTAGTAATATAAT	3726
		TACCAC		TGTT

10778	10800	CCAACAATTATATTACT	1958	AGTGGTAGTAATATAA	3727
		ACCACT		TTGT

10796	10818	CCACTGACATGACTTTC	1959	TTTTTGGAAAGTCATG	3728
		CAAAAA		TCAG

10812	10834	CCAAAAAACACATAATT	1960	GATTCAAATTATGTGT	3729
		TGAATC		TTTT

10842	10864	CCACCCACAGCCTAATT	1961	GCTAATAATTAGGCTG	3730
		ATTAGC		TGGG

10845	10867	CCCACAGCCTAATTATT	1962	GATGCTAATAATTAGG	3731
		AGCATC		CTGT

10846	10868	CCACAGCCTAATTATTA	1963	TGATGCTAATAATTAG	3732
		GCATCA		GCTG

10852	10874	CCTAATTATTAGCATCA	1964	GAGGGATGATGCTAAT	3733
		TCCCTC		AATT

10870	10892	CCCTCTACTATTTTTTAA	1965	TTTGGTTAAAAAATAG	3734
		CCAAA		TAGA

10871	10893	CCTCTACTATTTTTTAAC	1966	ATTTGGTTAAAAAATA	3735
		CAAAT		GTAG

10888	10910	CCAAATCAACAACAACC	1967	TAAATAGGTTGTTGTT	3736
		TATTTA		GATT

10903	10925	CCTATTTAGCTGTTCCC	1968	AGGTTGGGGAACAGCT	3737
		CAACCT		AAAT

10917	10939	CCCCAACCTTTTCCTCC	1969	GGGGTCGGAGGAAAA	3738
		GACCCC		GGTTG

10918	10940	CCCAACCTTTTCCTCCG	1970	GGGGGTCGGAGGAAA	3739
		ACCCCC		AGGTT

10919	10941	CCAACCTTTTCCTCCGA	1971	AGGGGGTCGGAGGAA	3740
		CCCCCT		AAGGT

10923	10945	CCTTTTCCTCCGACCCC	1972	TGTTAGGGGGTCGGAG	3741
		CTAACA		GAAA

10929	10951	CCTCCGACCCCCTAACA	1973	GGGGGTTGTTAGGGGG	3742
		ACCCCC		TCGG

10932	10954	CCGACCCCCTAACAACC	1974	GAGGGGGGTTGTTAGG	3743
		CCCCTC		GGGT

10936	10958	CCCCCTAACAACCCCCC	1975	TTAGGAGGGGGGTTGT	3744
		TCCTAA		TAGG

10937	10959	CCCCTAACAACCCCCCT	1976	ATTAGGAGGGGGGTTG	3745
		CCTAAT		TTAG

10938	10960	CCCTAACAACCCCCCTC	1977	TATTAGGAGGGGGGTT	3746
		CTAATA		GTTA

10939	10961	CCTAACAACCCCCCTCC	1978	GTATTAGGAGGGGGGT	3747
		TAATAC		TGTT

10947	10969	CCCCCCTCCTAATACTA	1979	GGTAGTTAGTATTAGG	3748
		ACTACC		AGGG

10948	10970	CCCCCTCCTAATACTAA	1980	AGGTAGTTAGTATTAG	3749
		CTACCT		GAGG

10949	10971	CCCCTCCTAATACTAAC	1981	CAGGTAGTTAGTATTA	3750
		TACCTG		GGAG

10950	10972	CCCTCCTAATACTAAC	1982	TCAGGTAGTTAGTATT	3751
		ACCTGA		AGGA

10951	10973	CCTCCTAATACTAACTA	1983	GTCAGGTAGTTAGTAT	3752
		CCTGAC		TAGG

10954	10976	CCTAATACTAACTACCT	1984	GGAGTCAGGTAGTTAG	3753
		GACTCC		TATT

10968	10990	CCTGACTCCTACCCCTC	1985	GATTGTGAGGGGTAGG	3754
		ACAATC		AGTC

10975	10997	CCTACCCCTCACAATCA	1986	TTGCCATGATTGTGAG	3755
		TGGCAA		GGGT

10979	11001	CCCCTCACAATCATGGC	1987	TGGCTTGCCATGATTG	3756
		AAGCCA		TGAG

10980	11002	CCCTCACAATCATGGCA	1988	TTGGCTTGCCATGATT	3757
		AGCCAA		GTGA

10981	11003	CCTCACAATCATGGCAA	1989	GTTGGCTTGCCATGAT	3758
		GCCAAC		GTG

10999	11021	CCAACGCCACTTATCCA	1990	GTTCACTGGATAAGTG	3759
		GTGAAC		GCGT

11005	11027	CCACTTATCCAGTGAAC	1991	ATAGTGGTTCACTGGA	3760
		CACTAT		TAAG

11013	11035	CCAGTGAACCACTATCA	1992	TTTTCGTGATAGTGGT	3761
		CGAAAA		TCAC

11021	11043	CCACTATCACGAAAAAA	1993	TAGAGTTTTTTTCGTG	3762
		ACTCTA		ATAG

11044	11066	CCTCTCTATACTAATCT	1994	GTAGGGAGATTAGTAT	3763
		CCCTAC		AGAG

11061	11083	CCCTACAAATCTCCTTA	1995	TATAATTAAGGAGATT	3764
		ATTATA		TGTA

11062	11084	CCTACAAATCTCCTTAA	1996	TTATAATTAAGGAGAT	3765
		TTATAA		TTGT

11073	11095	CCTTAATTATAACATTC	1997	GGCTGTGAATGTTATA	3766
		ACAGCC		ATTA

11094	11116	CCACAGAACTAATCATA	1998	ATAAAATATGATTAGT	3767
		TTTTAT		TCTG

11130	11152	CCACACTTATCCCCACC	1999	AGCCAAGGTGGGGAT	3768
		TTGGCT		AAGTG

11140	11162	CCCCACCTTGGCTATCA	2000	GGGTGATGATAGCCAA	3769
		TCACCC		GGTG

11141	11163	CCCACCTTGGCTATCAT	2001	CGGGTGATGATAGCCA	3770
		CACCCG		AGGT

11142	11164	CCACCTTGGCTATCATC	2002	TCGGGTGATGATAGCC	3771
		ACCCGA		AAGG

11145	11167	CCTTGGCTATCATCACC	2003	TCATCGGGTGATGATA	3772
		CGATGA		GCCA

11160	11182	CCCGATGAGGCAACCA	2004	TTCTGGCTGGTTGCCT	3773
		GCCAGAA		CATC

11161	11183	CCGATGAGGCAACCAG	2005	GTTCTGGCTGGTTGCC	3774
		CCAGAAC		TCAT

11173	11195	CCAGCCAGAACGCCTGA	2006	CTGCGTTCAGGCGTTC	3775
		ACGCAG		TGGC

11177	11199	CCAGAACGCCTGAACGC	2007	GTGCCTGCGTTCAGGC	3776
		AGGCAC		GTTC

11185	11207	CCTGAACGCAGGCACAT	2008	GGAAGTATGTGCCTGC	3777
		ACTTCC		GTTC

11206	11228	CCTATTCTACACCCTAG	2009	AGCCTACTAGGGTGTA	3778
		TAGGCT		GAAT

11217	11239	CCCTAGTAGGCTCCCTT	2010	TAGGGGAAGGGAGCC	3779
		CCCCTA		TACTA

11218	11240	CCTAGTAGGCTCCCTTC	2011	GTAGGGGAAGGGAGC	3780
		CCCTAC		CTACT

11229	11251	CCCTTCCCCTACTCATC	2012	TAGTGCGATGAGTAGG	3781
		GCACTA		GGAA

11230	11252	CCTTCCCCTACTCATCG	2013	TTAGTGCGATGAGTAG	3782
		CACTAA		GGGA

11234	11256	CCCCTACTCATCGCACT	2014	TAAATTAGTGCGATGA	3783
		AATTTA		GTAG

11235	11257	CCCTACTCATCGCACTA	2015	GTAAATTAGTGCGATG	3784
		ATTTAC		AGTA

11236	11258	CCTACTCATCGCACTAA	2016	TGTAAATTAGTGCGAT	3785
		TTTACA		GAGT

11268	11290	CCCTAGGCTCACTAAAC	2017	TAGAATGTTTAGTGAG	3786
		ATTCTA		CCTA

11269	11291	CCTAGGCTCACTAAACA	2018	GTAGAATGTTTAGTGA	3787
		TTCTAC		GCCT

11307	11329	CCCAAGAACTATCAAAC	2019	TCAGGAGTTTGATAGT	3788
		TCCTGA		TCTT

11308	11330	CCAAGAACTATCAAACT	2020	CTCAGGAGTTTGATAG	3789
		CCTGAG		TTCT

11325	11347	CCTGAGCCAACAACTTA	2021	TCATATTAAGTTGTTG	3790
		ATATGA		GCTC

11331	11353	CCAACAACTTAATATGA	2022	AGCTAGTCATATTAAG	3791
		CTAGCT		TTGT

11381	11403	CCTCTTTACGGACTCCA	2023	CATAAGTGGAGTCCGT	3792
		CTTTATG		AAAG

11395	11417	CCACTTATGACTCCCTA	2024	GGGCTTTAGGGAGTCA	3793
		AAGCCC		TAAG

11407	11429	CCCTAAAGCCCATGTCG	2025	GGGCTTCGACATGGGC	3794
		AAGCCC		TTTA

11408	11430	CCTAAAGCCCATGTCGA	2026	GGGGCTTCGACATGGG	3795
		AGCCCC		CTTT

11415	11437	CCCATGTCGAAGCCCCC	2027	AGCGATGGGGGCTTCG	3796
		ATCGCT		ACAT

11416	11438	CCATGTCGAAGCCCCCA	2028	CAGCGATGGGGGCTTC	3797
		TCGCTG		GACA

11427	11449	CCCCCATCGCTGGGTCA	2029	TACTATTGACCCAGCG	3798
		ATAGTA		ATGG

11428	11450	CCCCATCGCTGGGTCAA	2030	GTACTATTGACCCAGC	3799
		TAGTAC		GATG

11429	11451	CCCATCGCTGGGTCAAT	2031	AGTACTATTGACCCAG	3800
		AGTACT		CGAT

11430	11452	CCATCGCTGGGTCAATA	2032	AAGTACTATTGACCCA	3801
		GTACTT		GCGA

11454	11476	CCGCAGTACTCTTAAAA	2033	GCCTAGTTTTAAGAGT	3802
		CTAGGC		ACTG

11494	11516	CCTCACACTCATTCTCA	2034	GGGGGTTGAGAATGA	3803
		ACCCCC		GTGTG

11512	11534	CCCCCTGACAAAACACA	2035	AGGCTATGTGTTTTGT	3804
		TAGCCT		CAGG

11513	11535	CCCCTGACAAAACACAT	2036	TAGGCTATGTGTTTTG	3805
		AGCCTA		TCAG

11514	11536	CCCTGACAAAACACATA	2037	GTAGGCTATGTGTTTT	3806
		GCCTAC		GTCA

11515	11537	CCTGACAAAACACATAG	2038	GGTAGGCTATGTGTTT	3807
		CCTACC		TGTC

11532	11554	CCTACCCCTTTCCTGTA	2039	GGATAGTACAAGGAA	3808
		CTATCC		GGGGT

11536	11558	CCCCTTCCTTGTACTATC	2040	ATAGGGATAGTACAA	3809
		CCTAT		GGAAG

11537	11559	CCCTTCCTTGTACTATCC	2041	CATAGGGATAGTACAA	3810
		CTATG		GGAA

11538	11560	CCTTCCTTGTACTATCCC	2042	TCATAGGGATAGTACA	3811
		TATGA		AGGA

11542	11564	CCTTGTACTATCCCTAT	2043	TGCCTCATAGGGATAG	3812
		GAGGCA		TACA

11553	11575	CCCTATGAGGCATAATT	2044	TGTTATAATTATGCCT	3813
		ATAACA		CATA

11554	11576	CCTATGAGGCATAATTA	2045	TTGTTATAATTATGCC	3814
		TAACAA		TCAT

11580	11602	CCATCTGCCTACGACAA	2046	GTCTGTTTGTCGTAGG	3815
		ACAGAC		CAGA

11587	11609	CCTACGACAAACAGACC	2047	ATTTTAGGTCTGTTTGT	3816
		TAAAAT		CGT

11602	11624	CCTAAAATCGCTCATTG	2048	AGTATGCAATGAGCGA	3817
		CATACT		TTTT

11635	11657	CCACATAGCCCTCGTAG	2049	CTGTTACTACGAGGGC	3818
		TAACAG		TATG

11643	11665	CCCTCGTAGTAACAGCC	2050	GAGAATGGCTGTTACT	3819
		ATTCTC		ACGA

11644	11666	CCTCGTAGTAACAGCCA	2051	TGAGAATGGCTGTTAC	3820
		TTCTCA		TACG

11658	11680	CCATTCTCATCCAAACC	2052	TCAGGGGGTTTGGATG	3821
		CCCTGA		AGAA

11668	11690	CCAAACCCCCTGAAGCT	2053	CGGTGAAGCTTCAGGG	3822
		TCACCG		GGTT

116173	11695	CCCCCTGAAGCTTCACC	2054	TGCGCCGGTGAAGCTT	3823
		GGCGCA		CAGG

11674	11696	CCCCTGAAGCTTCACCG	2055	CTGCGCCGGTGAAGCT	3824
		GCGCAG		TCAG

11675	11697	CCCTGAAGCTTCACCGG	2056	ACTGCGCCGGTGAAGC	3825
		CGCAGT		TTCA

11676	11698	CCTGAAGCTTCACCGGC	2057	GACTGCGCCGGTGAAG	3826
		GCAGTC		CTTC

11688	11710	CCGGCGCAGTCATTCTC	2058	GATTATGAGAATGACT	3827
		ATAATC		GCGC

11712	11734	CCCACGGGCTTACATCC	2059	TAATGAGGATGTAAGC	3828
		TCATTA		CCGT

11713	11735	CCACGGGCTTACATCCT	2060	GTAATGAGGATGTAAG	3829
		CATTAC		CCCG

11727	11749	CCTCATTACTATTCTGC	2061	TGCTAGGCAGAATAGT	3830
		CTAGCA		AATG

11743	11765	CCTAGCAAACTCAAACT	2062	GTTCGTAGTTTGAGTT	3831
		ACGAAC		TGCT

11788	11810	CCTCTCTCAAGGACTTC	2063	GAGTTTGAAGTCCTTG	3832
		AAACTC		AGAG

11815	11837	CCCACTAATAGCTTTTT	2064	GTCATCAAAAAGCTAT	3833
		GATGAC		TAGT

11816	11838	CCACTAATAGCTTTTTG	2065	AGTCATCAAAAAGCTA	3834
		ATGACT		TTAG

11870	11848	CCTCGCTAACCTCGCCT	2066	GGGGTAAGGCGAGGT	3835
		TACCCC		TAGCG

11857	11879	CCTCGCCTTACCCCCCA	2067	TAATAGTGGGGGGTAA	3836
		CTATTA		GGCG

11862	11884	CCTTACCCCCCACTATT	2068	TAGGTTAATAGTGGGG	3837
		AACCTA		GGTA

11867	11889	CCCCCCACTATTAACCT	2069	CCCAGTAGGTTAATAG	3838
		ACTGGG		TGGG

11868	11890	CCCCCACTATTAACCTA	2070	TCCCAGTAGGTTAATA	3839
		CTGGGA		GTGG

11869	11891	CCCCACTATTAACCTAC	2071	CTCCCAGTAGGTTAAT	3840
		TGGGAG		AGTG

11870	11892	CCCACTATTAACCTACT	2072	TCTCCCAGTAGGTTAA	3841
		GGGAGA		TAGT

11871	11893	CCACTATTAACCTACTG	2073	TTCTCCCAGTAGGTTA	3842
		GGAGAA		ATAG

11881	11903	CCTACTGGGAGAACTCT	2074	GCACAGAGAGTTCTCC	3843
		CTGTGC		CAGT

11910	11932	CCACGTTCTCCTGATCA	2075	GATATTTGATCAGGAG	3844
		AATATC		AACG

11919	11941	CCTGATCAAATATCACT	2076	TAGGAGAGTGATATTT	3845
		CTCCTA		GATC

11938	11960	CCTACTTACAGGACTCA	2077	GTATGTTGAGTCCTGT	3846
		ACATAC		AAGT

11970	11992	CCCTATACTCCCTCTAC	2078	AAATATGTAGAGGGA	3847
		ATATTT		GTATA

11971	11993	CCTATACTCCCTCTACA	2079	TAAATATGTAGAGGGA	3848
		TATTTA		GTAT

11979	12001	CCCTCTACATATTTACC	2080	TGTTGTGGTAAATATG	3849
		ACAACA		TAGA

11980	12002	CCTCTACATATTTACCA	2081	GTGTTGTGGTAAATAT	3850
		CAACAC		GTAG

11994	12016	CCACAACACAATGGGG	2082	GAGTGAGCCCCATTGT	3851
		CTCACTC		GTTG

12018	12040	CCCACCACATTAACAAC	2083	TTTTATGTTGTTAATGT	3852
		ATAAAA		GGT

12019	12041	CCACCACATTAACAACA	2084	GTTTTATGTTGTTAAT	3853
		TAAAAC		GTGG

12022	12044	CCACATTAACAACATAA	2085	AGGGTTTTATGTTGTT	3854
		AACCCT		AATG

12041	12063	CCCTCATTCACACGAGA	2086	GTGTTTTCTCGTGTGA	3855
		AAACAC		ATGA

12042	12064	CCTCATTCACACGAGAA	2087	GGTGTTTTTTCGTGTG	3856
		AACACC		AATG

12063	12085	CCCTCATGTTCATACAC	2088	GGATAGGTGTATGAAC	3857
		CTATCC		ATGA

12064	12086	CCTCATGTTCATACACC	2089	GGGATAGGTGTATGAA	3858
		TATCCC		CATG

12079	12101	CCTATCCCCCATTCTCCT	2090	ATAGGAGGAGAATGG	3859
		CCTAT		GGGAT

12084	12106	CCCCCATTCTCCTCCTAT	2091	GAGGGATAGGAGGAG	3860
		CCCTC		AATGG

12085	12107	CCCCATTCTCCTCCTATC	2092	TGAGGGATAGGAGGA	3861
		CCTCA		GAATG

12086	12108	CCCATTCTCCTCCTATCC	2093	TTGAGGGATAGGAGG	3862
		CTCAA		AGAAT

12087	12109	CCATTCTCCTCCTATCCC	2094	GTTGAGGGATAGGAG	3863
		TCAAC		GAGAA

12094	12116	CCTCCTATCCCTCAACC	2095	TGTCGGGGTTGAGGGA	3864
		CCGACA		TAGG

12097	12119	CCTATCCCTCAACCCCG	2096	TGATGTCGGGGTTGAG	3865
		ACATCA		GGAT

12102	12124	CCCTCAACCCCGACATC	2097	GGTAATGATGTCGGGG	3866
		ATTACC		TTGA

12103	12125	CCTCAACCCCGACATCA	2098	CGGTAATGATGTCGGG	3867
		TTACCG		GTTG

12109	12131	CCCCGACATCATTACCG	2099	AAAACCCGGTAATGAT	3868
		GGTTTT		GTCG

12110	12132	CCCGACATCATTACCGG	2100	GAAAACCCGGTAATG	3869
		GTTTTC		ATGTC

12111	12133	CCGACATCATTACCGGG	2101	GGAAAACCCGGTAAT	3870
		TTTTCC		GATGT

12123	12145	CCGGGTTTTCCTCTTGT	2102	ATATTTACAAGAGGAA	3871
		AAATAT		AACC

12132	12154	CCTCTTGTAAATATAGT	2103	GGTTAAACTATATTTA	3872
		TTAACC		CAAG

12153	12175	CCAAAACATCAGATTGT	2104	AGATTCACAATCTGAT	3873
		GAATCT		GTTT

12194	12216	CCCCTTATTTACCGAGA	2105	GAGCTTTCTCGGTAAA	3874
		AAGCTC		TAAG

12195	12217	CCCTTATTTACCGAGAA	2106	TGAGCTTTCTCGGTAA	3875
		AGCTCA		ATAA

12196	12218	CCTTATTTACCGAGAAA	2107	GTGAGCTTTCTCGGTA	3876
		GCTCAC		AATA

12205	12227	CCGAGAAAGCTCACAA	2108	GCAGTTCTTGTGAGCT	3877
		GAACTGC		TTCT

12237	12259	CCCCCATGTCTAACAAC	2109	AGCCATGTTGTTAGAC	3878
		ATGGCT		ATGG

12238	12260	CCCCATGTCTAACAACA	2110	AAGCCATGTTGTTAGA	3879
		TGGCTT		CATG

12239	12261	CCCATGTCTAACAACAT	2111	AAAGCCATGTTGTTAG	3880
		GGCTTT		ACAT

12240	12262	CCATGTCTAACAACATG	2112	GAAAGCCATGTTGTTA	3881
		GCTTTC		GACA

12288	12310	CCATTGGTCTTAGGCCC	2113	TTTTTGGGGCCTAAGA	3882
		CAAAAA		CCAA

12302	12324	CCCCAAAAATTTTGGTG	2114	GAGTTGCACCAAAATT	3883
		CAACTC		TTTG

12303	12325	CCCAAAAATTTTGGTGC	2115	GGAGTTGCACCAAAAT	3884
		AACTCC		TTTT

12304	12326	CCAAAAATTTTGGTGCA	2116	TGGAGTTGCACCAAAA	3885
		ACTCCA		TTTT

12324	12346	CCAAATAAAAGTAATA	2117	GCATGGTTATTACTTT	3886
		ACCATGC		TATT

12341	12363	CCATGCACACTACTATA	2118	GGTGGTTATAGTAGTG	3887
		ACCACC		TGCA

12359	12381	CCACCCTAACCCTGACT	2119	TAGGGAAGTCAGGGTT	3888
		TCCCTA		AGGG

12362	12384	CCCTAACCCTGACTTCC	2120	AATTAGGGAAGTCAG	3889
		CTAATT		GGTTA

12363	12385	CCTAACCCTGACTTCCC	2121	GAATTAGGGAAGTCA	3890
		TAATTC		GGGTT

12368	12390	CCCTGACTTCCCTAATT	2122	GGGGGGAATTAGGGA	3891
		CCCCCC		AGTCA

12369	12391	CCTGACTTCCCTAATTC	2123	TGGGGGGAATTAGGG	3892
		CCCCCA		AAGTC

12377	12399	CCCTAATTCCCCCCATC	2124	CTGTAAGGATGGGGGG	3893
		CTTACC		AATTA

12378	12400	CCTAATTCCCCCCATCC	2125	TGGTAAGGATGGGGG	3894
		TTACCA		GAATT

12385	12407	CCCCCCATCCTTACCAC	2126	ACGAGGGTGGTAAGG	3895
		CCTCGT		ATGGG

12386	12408	CCCCCATCCTTACCACC	2127	AACGAGGGTGGTAAG	3896
		CTCGTT		GATGG

12387	12409	CCCCATCCTTACCACCC	2128	TAACGAGGGTGGTAA	3897
		TCGTTA		GGATG

12388	12410	CCCATCCTTACCACCCT	2129	TTAACGAGGGTGGTAA	3898
		CGTTAA		GGAT

12389	12411	CCATCCTTACCACCCTC	2130	GTTAACGAGGGTGGTA	3899
		GTTAAC		AGGA

12393	12415	CCTTACCACCCTCGTTA	2131	TAGGGTTAACGAGGGT	3900
		ACCCTA		GGTA

12398	12420	CCACCCTCGTTAACCCT	2132	TTTGTTAGGGTTAACG	3901
		AACAAA		AGGG

12401	12423	CCCTCGTTAACCCTAAC	2133	TTTTTTGTTAGGGTTA	3902
		AAAAAA		ACGA

12402	12424	CCTCGTTAACCCTAACA	2134	TTTTTTTGTTAGGGTTA	3903
		AAAAAA		ACG

12411	12433	CCCTAACAAAAAAAACT	2135	GGTATGAGTTTTTTTT	3904
		CATACC		GTTA

12412	12434	CCTAACAAAAAAAACTC	2136	GGGTATGAGTTTTTTT	3905
		ATACCC		TGTT

12432	12454	CCCCCATTATGTAAAAT	2137	CAATGGATTTTACATA	3906
		CCATTG		ATGG

12433	12455	CCCCATTATGTAAAATC	2138	ACAATGGATTTTACAT	3907
		CATTGT		AATG

12434	12456	CCCATTATGTAAAATCC	2139	GACATGGATTTTACA	3908
		ATTGTC		TAAT

12435	12457	CCATTATGTAAAATCCA	2140	CGACAATGGATTTTAC	3909
		TTGTCG		ATAA

12449	12471	CCATTGTCGCATCCACC	2141	AATAAAGGTGGATGC	3910
		TTTATT		GACAA

12461	12483	CCACCTTTATTATCAGT	2142	GAAGAGACTGATAAT	3911
		CTCTTC		AAAGG

12464	12486	CCTTTATTATCAGTCTCT	2143	GGGGAAGAGACTGAT	3912
		TCCCC		AATAA

12483	12505	CCCCACAACAATATTCA	2144	GGCACATGAATATTGT	3913
		TGTGCC		TGTG

12484	12506	CCCACAACAATATTCAT	2145	AGGCACATGAATATTG	3914
		GTGCCT		TTGT

12485	12507	CCACAACAATATTCATG	2146	TAGGCACATGAATATT	3915
		TGCCTA		GTTG

12504	12526	CCTAGACCAAGAAGTTA	2147	AGATAATAACTTCTTG	3916
		TTATCT		GTCT

12510	12532	CCAAGAAGTTATTATCT	2148	AGTTCGAGATAATAAC	3917
		CGAACT		TTCT

12542	12564	CCACAACCCAAACAACC	2149	GAGCTGGGTTGTTTGG	3918
		CAGCTC		GTTG

12548	12570	CCCAAACAACCCAGCTC	2150	TAGGGAGAGCTGGGTT	3919
		TCCCTA		GTTT

12549	12571	CCAAACAACCCAGCTCT	2151	TTAGGGAGAGCTGGGT	3920
		CCCTAA		TGTT

12557	12579	CCCAGCTCTCCCTAAGC	2152	TTTGAAGCTTAGGGAG	3921
		TTCAAA		AGCT

12558	12580	CCAGCTCTCCCTAAGCT	2153	GTTTGAAGCTTAGGGA	3922
		TCAAAC		GAGC

12566	12588	CCCTAACTTCAAACTA	2154	GTAGTCTAGTTTGAAG	3923
		GACTAC		CTTA

12567	12589	CCTAAGCTTCAAACTAG	2155	AGTAGTCTAGTTTGAA	3924
		ACTACT		GCTT

12593	12615	CCATAATATTCATCCCT	2156	TGCTACAGGGATGAAT	3925
		GTAGCA		ATTA

12606	12628	CCCTGTAGCATTGTTCG	2157	ATGTAACGAACAATGC	3926
		TTACAT		ACA

12607	12629	CCTGTAGCATTGTTCGT	2158	CATGTAACGAACAATG	3927
		TACATG		CTAC

12632	12654	CCATCATAGAATTCTCA	2159	TCACAGTGAGAATTCT	3928
		CTGTGA		ATGA

12669	12691	CCCAAACATTAATCAGT	2160	TGAAGAACTGATTAAT	3929
		TCTTCA		GTTT

12670	12692	CCAAACATTAATCAGTT	2161	TTGAAGAACTGATTAA	3930
		CTTCAA		TGTT

12708	12730	CCTAATTACCATACTAA	2162	CTAAGATTAGTATGGT	3931
		TCTTAG		AATT

12716	12738	CCATACTAATCTTAGTT	2163	AGCGGTAACTAAGATT	3932
		ACCGCT		AGTA

12734	12756	CCGCTAACAACCTATTC	2164	CAGTTGGAATAGGTTG	3933
		CAACTG		TTAG

12744	12766	CCTATTCCAACTGTTCA	2165	AGCCGATGAACAGTTG	3934
		TCGGCT		GAAT

12750	12772	CCAACTGTTCATCGGCT	2166	CCTTTCAGCCGATGAA	3935
		GAGAGG		CAGT

12788	12810	CCTTCTTGCTCATCAGTT	2167	TCATCAACTGATGAGC	3936
		GATGA		AAGA

12815	12837	CCCGAGCAGATGCCAAC	2168	TGCTGTGTTGGCATCT	3937
		ACAGCA		GCTC

12816	12838	CCGAGCAGATGCCAAC	2169	CTGCTGTGTTGGCATC	3938
		ACAGCAG		TGCT

12827	12849	CCAACACAGCAGCCATT	2170	TGCTTGAATGGCTGCT	3939
		CAAGCA		GTGT

12839	12861	CCATTCAAGCAATCCTA	2171	GTTGTATAGGATTGCT	3940
		TACAAC		TGAA

12852	12874	CCTATACAACCGTATCG	2172	TATCGCCGATACGGTT	3941
		GCGATA		GTAT

12861	12883	CCGTATCGGCGATATCG	2173	TGAAAACCGATATCGCC	3942
		GTTTCA		GATA

12885	12907	CCTCGCCTTAGCATGAT	2174	GGATAAATCATGCTAA	3943
		TTATCC		GGCG

12890	12912	CCTTAGCATGATTTATC	2175	GTGTAGGATAAATCAT	3944
		CTACAC		GCTA

12906	12928	CCTACACTCCAACTCAT	2176	GGTCTCATGAGTTGGA	3945
		GAGACC		GTGT

12914	12936	CCAACTCATGAGACCCA	2177	TTGTTGTGGGTCTCAT	3946
		CAACAA		GAGT

12927	12949	CCCACAACAAATAGCCC	2178	TTAGAAGGGCTATTTG	3947
		TTCTAA		TTGT

12928	12950	CCACAACAAATAGCCCT	2179	TTTAGAAGGGCTATTT	3948
		TCTAAA		GTTG

12941	12963	CCCTTCTAAACGCTAAT	2180	GCTTGGATTAGCGTTT	3949
		CCAAGC		AGAA

12942	12964	CCTTCTAAACGCTAATC	2181	GGCTTGGATTAGCGTT	3950
		CAAGCC		TAGA

12958	12980	CCAAGCCTCACCCCACT	2182	CCTAGTAGTGGGGTGA	3951
		ACTAGG		GGCT

12963	12985	CCTCACCCCACTACTAG	2183	GGAGGCCTAGTAGTGG	3952
		GCCTCC		GGTG

12968	12990	CCCCACTACTAGGCCTC	2184	TAGGAGGAGGCCTAGT	3953
		CTCCTA		AGTG

12969	12991	CCCACTACTAGGCCTCC	2185	CTAGGAGGAGGCCTA	3954
		TCCTAG		GTAGT

12970	12992	CCACTACTAGGCCTCCT	2186	GCTAGGAGGAGGCCT	3955
		CCTAGC		AGTAG

12981	13003	CCTCCTCCTAGCAGCAG	2187	TGCCTGCTGCTGCTAG	3956
		CAGGCA		GAGG

12984	13006	CCTCCTAGCAGCAGCAG	2188	ATTTGCCTGCTGCTGC	3957
		GCAAAT		TAGG

12987	13009	CCTAGCAGCAGCAGGC	2189	CTGATTTGCCTGCTGC	3958
		AAATCAG		TGCT

13010	13032	CCCAATTAGGTCTCCAC	2190	TCAGGGGTGGAGACCT	3959
		CCCTGA		AATT

13011	13033	CCAATTAGGTCTCCACC	2191	GTCAGGGGTGGAGAC	3960
		CCTGAC		CTAAT

13023	13045	CCACCCCTGACTCCCCT	2192	TGGCTGAGGGGAGTCA	3961
		CAGCCA		GGGG

13026	13048	CCCCTGACTCCCCTCAG	2193	CTATGGCTGAGGGGAG	3962
		CCATAG		TCAG

13027	13049	CCCTGACTCCCCTCAGC	2194	TCTATGGCTGAGGGGA	3963
		CATAGA		GTCA

13028	13050	CCTGACTCCCCTCAGCC	2195	TTCTATGGCTGAGGGG	3964
		ATAGAA		AGTC

13035	13057	CCCCTCAGCCATAGAAG	2196	TGGGGCCTTCTATGGC	3965
		GCCCCA		TGAG

13036	13058	CCCTCAGCCATAGAAGG	2197	GTGGGGCCTTCTATGG	3966
		CCCCAC		CTGA

13037	13059	CCTCAGCCATAGAAGGC	2198	GGTGGGGCCTTCTATG	3967
		CCCACC		GCTG

13043	13065	CCATAGAAGGCCCCACC	2199	GACTGGGGTGGGGCCT	3968
		CCAGTC		TCTA

13053	13075	CCCCACCCCAGTCTCAG	2200	GTAGGGCTGAGACTGG	3969
		CCCTAC		GGTG

13054	13076	CCCACCCCAGTCTCAGC	2201	AGTAGGGCTGAGACTG	3970
		CCTACT		GGGT

13055	13077	CCACCCCAGTCTCAGCC	2202	GAGTAGGGCTGAGACT	3971
		CTACTC		GGGG

13058	13080	CCCCAGTCTCAGCCCTA	2203	GTGGAGTAGGGCTGA	3972
		CTCCAC		GACTG

13059	13081	CCCAGTCTCAGCCCTAC	2204	AGTGGAGTAGGGCTG	3973
		TCCACT		AGACT

13060	13082	CCAGTCTCAGCCCTACT	2205	GAGTGGAGTAGGGCT	3974
		CCACTC		GAGAC

13070	13092	CCCTACTCCACTCAAGC	2206	TATAGTGCTTGAGTGG	3975
		ACTATA		AGTA

13071	13093	CCTACTCCACTCAAGCA	2207	CTATAGTGCTTGAGTG	3976
		CTATAG		GAGT

13077	13099	CCACTCAAGCACTATAG	2208	CTACAACTATAGTGCT	3977
		TTGTAG		TGAG

13119	13141	CCGCTTCCACCCCCTAG	2209	TTTCTGCTAGGGGGTG	3978
		CAGAAA		GAAG

13125	13147	CCACCCCCTAGCAGAAA	2210	GGCTATTTTCTGCTAG	3979
		ATAGCC		GGGG

13128	13150	CCCCCTAGCAGAAAATA	2211	GTGGGCTATTTTCTGC	3980
		GCCCAC		TAGG

13129	13151	CCCCTAGCAGAAAATAG	2212	AGTGGGCTATTTTCTG	3981
		CCCACT		CTAG

13130	13152	CCCTAGCAGAAAATAGC	2213	TAGTGGGCTATTTTCT	3982
		CCACTA		GCTA

13131	13153	CCTAGCAGAAAATAGCC	2214	TAGTGGCCTATTTTC	3983
		CACTAA		TGCT

13146	13168	CCCACTAATCCAAACTC	2215	GTGTTAGAGTTTGGAT	3984
		TAACAC		TAGT

13147	13169	CCACTAATCCAAACTCT	2216	AGTGTTAGAGTTTGGA	3985
		AACACT		TTAG

13155	13177	CCAAACTCTAACACTAT	2217	CTAAGCATAGTGTTAG	3986
		GCTTAG		AGTT

13187	13209	CCACTCTGTTCGCAGCA	2218	GCAGACTGCTGCGAAC	3987
		GTCTGC		AGAG

13211	13233	CCCTTACACAAAATGAC	2219	TTTGATGTCATTTTGTG	3988
		ATCAAA		TAA

13212	13234	CCTTACACAAAATGACA	2220	TTTTGATGTCATTTTGT	3989
		TCAAAA		GTA

13244	13266	CCTTCTCCACTTCAAGT	2221	TAGTTGACTTGAAGTG	3990
		CAACTA		GAGA

13250	13272	CCACTTCAAGTCAACTA	2222	GAGTCCTAGTTGACTT	3991
		GGACTC		GAAG

13296	13318	CCAACCACACCTAGCAT	2223	GCAGGAATGCTAGGTG	3992
		TCCTGC		TGGT

13300	13322	CCACACCTAGCATTCCT	2224	ATGTGCAGGAATGCTA	3993
		GCACAT		GGTG

13305	13327	CCTAGCATTCCTGCACA	2225	TACAGATGTGCAGGAA	3994
		TCTGTA		TGCT

13314	13336	CCTGCACATCTGTACCC	2226	AGGCGTGGGTACAGAT	3995
		ACGCCT		GTGC

13328	13350	CCCACGCCTTCTTCAAA	2227	TATGGCTTTGAAGAAG	3996
		GCCATA		GCGT

13329	13351	CCACGCCTTCTTCAAAG	2228	GTATGGCTTTGAAGAA	3997
		CCATAC		GGCG

13334	13356	CCTTCTTCAAAGCCATA	2229	AAATAGTATGGCTTTG	3998
		CTATTT		AAGA

13346	13368	CCATACTATTTATGTGC	2230	CCCGGAGCACATAAAT	3999
		TCCGGG		AGTA

13364	13386	CCGGGTCCATCATCCAC	2231	AAGGTTGTGGATGATG	4000
		AACCTT		GACC

13370	13392	CCATCATCCACAACCTT	2232	ATTGTTAAGGTTGTGG	4001
		AACAAT		ATGA

13377	13399	CCACAACCTTAACAATG	2233	CTTGTTCATTGTTAAG	4002
		AACAAG		GTTG

13383	13405	CCTTAACAATGAACAAG	2234	GAATATCTTGTTCATT	4003
		ATATTC		GTTA

13430	13452	CCATACCTCTCACTTCA	2235	GGAGGTTGAAGTGAG	4004
		ACCTCC		AGGTA

13435	13457	CCTCTCACTTCAACCTC	2236	GTGAGGGAGGTTGAA	4005
		CCTCAC		GTGAG

13448	13470	CCTCCCTCACCATTGGC	2237	TAGGCTGCCAATGGTG	4006
		AGCCTA		AGGG

13451	13473	CCCTCACCATTGGCAGC	2238	TGCTAGGCTGCCAATG	4007
		CTAGCA		GTGA

13452	13474	CCTCACCATTGGCAGCC	2239	ATGCTAGGCTGCCAAT	4008
		TAGCAT		GGTG

13457	13479	CCATTGGCAGCCTAGCA	2240	TGCTAATGCTAGGCTG	4009
		TTAGCA		CCAA

13467	13489	CCTAGCATTAGCAGGAA	2241	AAGGTATTCCTGCTAA	4010
		TACCTT		TGCT

13486	13508	CCTTTCCTCACAGGTTT	2242	GAGTAGAAACCTGTGA	4011
		CTACTC		GGAA

13491	13513	CCTCACAGGTTTCTACT	2243	CTTTGGAGTAGAAACC	4012
		CCAAAG		TGTG

13508	13530	CCAAAGACCACATCATC	2244	GGTTTCGATGATGTGG	4013
		GAAACC		TCTT

13515	13537	CCACATCATCGAAACCG	2245	TGTTTGCGGTTTCGAT	4014
		CAAACA		GATG

13529	13551	CCGCAAACATATCATAC	2246	GTTTGTGTATGATATG	4015
		ACAAAC		TTTG

13553	13575	CCTGAGCCCTATCTATT	2247	GAGAGTAATAGATAG	4016
		ACTCTC		GGCTC

13559	13581	CCCTATCTATTACTCTC	2248	AGCGATGAGAGTAAT	4017
		ATCGCT		AGATA

13560	13582	CCTATCTATTACTCTCAT	2249	TAGCGATGAGAGTAAT	4018
		CGCTA		AGAT

13583	13605	CCTCCCTGACAAGCGCC	2250	GCTATAGGCGCTTGTC	4019
		TATAGC		AGGG

13586	13608	CCCTGACAAGCGCCTAT	2251	AGTGCTATAGGCGCTT	4020
		AGCACT		GTCA

13587	13609	CCTGACAAGCGCCTATA	2252	GAGTGCTATAGGCGCT	4021
		GCACTC		TGTC

13598	13620	CCTATAGCACTCGAATA	2253	AAGAATTATTCGAGTG	4022
		ATTCTT		CTAT

13625	13647	CCCTAACAGGTCAACCT	2254	GAAGCGAGGTTGACCT	4023
		CGCTTC		GTTA

13626	13648	CCTAACAGGTCAACCTC	2255	GGAAGCGAGGTTGAC	4024
		GCTTCC		CTGTT

13639	13661	CCTCGCTTCCCCACC	2256	TAGTAAGGGTGGGGA	4025
		TACTAA		AGCG

13647	13669	CCCCACCCTTACTAACA	2257	CGTTAATGTTAGTAAG	4026
		TTAACG		GGTG

13648	13670	CCCACCCTTACTAACAT	2258	TCGTTAATGTTAGTAA	4027
		TAACGA		GGGT

13649	13671	CCACCCTTACTAACATT	2259	TTCGTTAATGTTAGTA	4028
		AACGAA		AGGG

13652	13674	CCCTTACTAACATTAAC	2260	ATTTTCGTTAATGTTA	4029
		GAAAAT		GTAA

13653	13675	CCTTACTAACATTAACG	2261	TATTTTCGTTAATGTTA	4030
		AAAATA		GTA

13677	13699	CCCCACCCTACTATACC	2262	TAATGGGGTTTAGTAG	4031
		CCATTA		GGTG

13678	13700	CCCACCCTACTAAACCC	2263	TTAATGGGGTTTAGTA	4032
		CATTAA		GGGT

13679	13701	CCACCCTACTAAACCCC	2264	TTTAATGGGGTTTAGT	4033
		ATTAAA		AGGG

13682	13704	CCCTACTAAACCCCATT	2265	GCGTTTAATGGGGTTT	4034
		AAACGC		AGTA

13683	13705	CCTACTAAACCCCATTA	2266	GGCGTTTAATGGGGTT	4035
		AACGCC		TAGT

13692	13714	CCCCATTAAACGCCTGG	2267	CGGCTGCCAGGCGTTT	4036
		CAGCCG		AATG

13693	13715	CCCATTAAACGCCTGGC	2268	CCGGCTGCCAGGCGTT	4037
		AGCCGG		TAAT

13694	13716	CCATTAAACGCCTGGCA	2269	TCCGGCTGCCAGGCGT	4038
		GCCGGA		TTAA

13704	13726	CCTGGCAGCCGGAAGCC	2270	CGAATAGGCTTCCGGC	4039
		TATTCG		TGCC

13712	13734	CCGGAAGCCTATTCGCA	2271	AAATCCTGCGAATAGG	4040
		GGATTT		CTTC

13719	13741	CCTATTCGCAGGATTTC	2272	TAATGAGAAATCCTGC	4041
		TCATTA		GAAT

13754	13776	CCCCCGCATCCCCCTTC	2773	TGTTTGGAAGGGGGAT	4042
		CAAACA		GCGG

13755	13777	CCCCGCATCCCCCTTCC	2274	TTGTTTGGAAGGGGGA	4043
		AAACAA		TGCG

13756	13778	CCCGCATCCCCCTTCCA	7275	GTTGTTTGGAAGGGGG	4044
		AACAAC		ATGC

13757	13779	CCGCATCCCCCTTCCAA	2276	TGTTGTTTGGAAGGGG	4045
		ACAACA		GATG

13763	13785	CCCCCTTCCAAACAACA	2277	GGGGATTGTTGTTTGG	4046
		ATCCCC		AAGG

13764	13786	CCCCTTCCAAACAACAA	2278	GGGGGATTGTTGTTTG	4047
		TCCCCC		GAAG

13765	13787	CCCTTCCAAACAACAAT	2279	AGGGGGATTGTTGTTT	4048
		CCCCCT		GGAA

13766	13788	CCTTCCAAACAACAATC	2280	GAGGGGGATTGTTGTT	4049
		CCCCTC		TGGA

13770	13792	CCAAACAACAATCCCCC	2281	GGTAGAGGGGGATTGT	4050
		TCTACC		TGTT

13782	13804	CCCCCTCTACCTAAAAC	2282	CTGTGAGTTTTAGGTA	4051
		TCACAG		GAGG

13783	13805	CCCCTCTACCTAAAACT	2283	GCTGTGAGTTTTAGGT	4052
		CACAGC		AGAG

13784	13806	CCCTCTACCTAAAACTC	2284	GGCTGTGAGTTTTAGG	4053
		ACAGCC		TAGA

13785	13807	CCTCTACCTAAAACTCA	2285	GGGCTGTGAGTTTTAG	4054
		CAGCCC		GTAG

13791	13813	CCTAAAACTCACAGCCC	2286	CAGCGAGGGCTGTGA	4055
		TCGCTG		GTTTT

13805	13827	CCCTCGCTGTCACTTTC	2287	TCCTAGGAAAGTGACA	4056
		CTAGGA		GCGA

13806	13828	CCTCGCTGTCACTTTCCT	2288	GTCCTAGGAAAGTGAC	4057
		AGGAC		AGCG

13821	13843	CCTAGGACTTCTAACAG	2289	CTAGGGCTGTTAGAAG	4058
		CCCTAG		TCCT

13838	13860	CCCTAGACCTCAACTAC	2290	GGTTAGGTAGTTGAGG	4059
		CTAACC		TCTA

13839	13861	CCTAGACCTCAACTACC	2291	TGGTTAGGTAGTTGAG	4060
		TAACCA		GTCT

13845	13867	CCTCAACTACCTAACCA	2292	GTTTGTTGGTTAGGTA	4061
		ACAAAC		GTTG

13854	13876	CCTAACCAACAAACTTA	2293	TTATTTTAAGTTTGTTG	4062
		AAATAA		GTT

13859	13881	CCAACAAACTTAAAATA	2294	GGATTTTATTTTAAGT	4063
		AAATCC		TTGT

13880	13902	CCCCACTATGCACATTT	2295	GAAATAAAATGTGCAT	4064
		TATTTC		AGTG

13881	13903	CCCACTATGCACATTTT	2296	AGAAATAAAATGTGC	4065
		ATTTCT		ATAGT

13882	13904	CCACTATGCACATTTTA	2297	GAGAAATAAAATGTG	4066
		TTTCTC		CATAG

13904	13926	CCAACATACTCGGATTC	2298	AGGGTAGAATCCGAGT	4067
		TACCCT		ATGT

13923	13945	CCCTAGCATCACACACC	2299	TTGTGCGGTGTGTGAT	4068
		GCACAA		GCTA

13924	13946	CCTAGCATCACACACCG	2300	ATTGTGCGGTGTGTGA	4069
		CACAAT		TGCT

13938	13960	CCGCACAATCCCCTATC	2301	GGCCTAGATAGGGGAT	4070
		TAGGCC		TGTG

13947	13969	CCCCTATCTAGGCCTTC	2302	TCGTAAGAAGGCCTAG	4071
		TTACGA		ATAG

13948	13970	CCCTATCTAGGCCTTCT	2303	CTCGTAAGAAGGCCTA	4072
		TACGAG		GATA

13949	13971	CCTATCTAGGCCTTCTT	2304	GCTCGTAAGAAGGCCT	4073
		ACGAGC		AGAT

13959	13981	CCTTCTTACGAGCCAAA	2305	GCAGGTTTTGGCTCGT	4074
		ACCTGC		AAGA

13971	13993	CCAAAACCTGCCCCTAC	2306	GGAGGAGTAGGGGCA	4075
		TCCTCC		GGTTT

13977	13999	CCTGCCCCTACTCCTCC	2307	GGTCTAGGAGGAGTA	4076
		TAGACC		GGGGC

13981	14003	CCCCTACTCCTCCTAGA	2308	GTTAGGTCTAGGAGGA	4077
		CCTAAC		GTAG

13982	14004	CCCTACTCCTCCTAGAC	2309	GGTTAGGTCTAGGAGG	4078
		CTAACC		AGTA

13983	14005	CCTACTCCTCCTAGACC	2310	AGGTTAGGTCTAGGAG	4079
		TAACCT		GAGT

13989	14011	CCTCCTAGACCTAACCT	2311	CTAGTCAGGTTAGGTC	4080
		GACTAG		TAGG

13992	14014	CCTAGACCTAACCTGAC	2312	TTTCTAGTCAGGTTAG	4081
		TAGAAA		GTCT

13998	14020	CCTAACCTGACTAGAAA	2313	ATAGCTTTTCTAGTCA	4082
		AGCTAT		GGTT

14003	14025	CCTGACTAGAAAAGCTA	2314	AGGTAATAGCTTTTCT	4083
		TTACCT		AGTC

14023	14045	CCTAAAACAATTTCACA	2315	TGGTGCTGTGAAATTG	4084
		GCACCA		TTTT

14043	14065	CCAAATCTCCACCTCCA	2316	TGATGATGGAGGTGGA	4085
		TCATCA		GATT

14051	14073	CCACCTCCATCATCACC	2317	GGTTGAGGTGATGATG	4086
		TCAACC		GAGG

14054	14076	CCTCCATCATCACCTCA	2318	TTGGGTTGAGGTGATG	4087
		ACCCAA		ATGG

14057	14079	CCATCATCACCTCAACC	2319	TTTTTGGGTTGAGGTG	4088
		CAAAAA		ATGA

14066	14088	CCTCAACCCAAAAAGGC	2320	AATTATGCCTTTTTGG	4089
		ATAATT		GTTG

14072	14094	CCCAAAAAGGCATAATT	2321	AAGTTTAATTATGCCT	4090
		AAACTT		TTTT

14073	14095	CCAAAAAGGCATAATTA	2322	AAAGTTTAATTATGCC	4091
		AACTTT		TTTT

14100	14122	CCTCTCTTTCTTCTTCCC	2323	TGAGTGGGAAGAAGA	4092
		ACTCA		AAGAG

14115	14137	CCCACTCATCCTAACCC	2324	GGAGTAGGGTTAGGAT	4093
		TACTCC		GAGT

14116	14138	CCACTCATCCTAACCCT	2325	AGGAGTAGGGTTAGG	4094
		ACTCCT		ATGAG

14124	14146	CCTAACCCTACTCCTAA	2326	ATGTGATTAGGAGTAG	4095
		TCACAT		GGTT

14129	14151	CCCTACTCCTAATCACA	2327	AGGTTATGTGATTAGG	4096
		TAACCT		AGTA

14130	14152	CCTACTCCTAATCACAT	2328	TAGGTTATGTGATTAG	4097
		AACCTA		GAGT

14136	14158	CCTAATCACATAACCTA	2329	GGGGAATAGGTTATGT	4098
		TTCCCC		GATT

14149	14171	CCTATTCCCCCGAGCAA	2330	TTGAGATTGCTCGGGG	4099
		TCTCAA		GAAT

14155	14177	CCCCCGAGCAATCTCAA	2331	TTGTAATTGAGATTGC	4100
		TTACAA		TCGG

14156	14178	CCCCGAGCAATCTCAAT	2332	ATTGTAATTGAGATTG	4101
		TACAAT		CTCG

14157	14179	CCCGAGCAATCTCAATT	2333	TATTGTAATTGAGATT	4102
		ACAATA		GCTC

14158	14180	CCGAGCAATCTCAATTA	2334	ATATTGTAATTGAGAT	4103
		CAATAT		TGCT

14186	14208	CCAACAAACAATGTTCA	2335	ACTGGTTGAACATTGT	4104
		ACCAGT		TTGT

14204	14226	CCAGTAACTACTACTAA	2336	CGTTGATTAGTAGTAG	4105
		TCAACG		TTAC

14227	14249	CCCATAATCATACAAAG	2337	CGGGGGCTTTGTATGA	4106
		CCCCCG		TTAT

14228	14250	CCATAATCATACAAAGC	2338	GCGGGGGCTTTGTATG	4107
		CCCCGC		ATTA

14244	14266	CCCCCGCACCAATAGGA	2339	GGAGGATCCTATTGGT	4108
		TCCTCC		GCGG

14245	14267	CCCCGCACCAATAGGAT	2340	GGGAGGATCCTATTGG	4109
		CCTCCC		TGCG

14246	14268	CCCGCACCAATAGGATC	2341	CGGGAGGATCCTATTG	4110
		CTCCCG		GTGC

14247	14269	CCGCACCAATAGGATCC	2342	TCGGGAGGATCCTATT	4111
		TCCCGA		GGTG

14252	14274	CCAATAGGATCCTCCCG	2343	TTGATTCGGGAGGATC	4112
		AATCAA		CTAT

14262	14284	CCTCCCGAATCAACCCT	2344	GGGGTCAGGGTTGATT	4113
		GACCCC		CGGG

14265	14287	CCCGAATCAACCCTGAC	2345	AGAGGGGTCAGGGTT	4114
		CCCTCT		GATTC

14266	14288	CCGAATCAACCCTGACC	2346	GAGAGGGGTCAGGGT	4115
		CCTCTC		TGATT

14275	14297	CCCTGACCCCTCTCCTT	2347	TTTATGAAGGAGAGGG	4116
		CATAAA		GTCA

14276	14298	CCTGACCCCTCTCCTTC	2348	ATTTATGAAGGAGAGG	4117
		ATAAAT		GGTC

14281	14303	CCCCTCTCCTTCATAAA	2349	GAATAATTTATGAAGG	4118
		TTATTC		AGAG

14282	14304	CCCTCTCCTTCATAAAT	2350	TGAATAATTTATGAAG	4119
		TATTCA		GAGA

14283	14305	CCTCTCCTTCATAAATT	2351	CTGAATAATTTATGAA	4120
		ATTCAG		GGAG

14288	14310	GCTTCATAAATTATTCA	2352	GGAAGCTGAATAATTT	4121
		GCTTCC		ATGA

14309	14331	CCTACACTATTAAAGTT	2353	GTGGTAAACTTTAATA	4122
		TACCAC		GTGT

14328	14350	CCACAACCACCACCCCA	2354	GTATGATGGGGTGGTG	4123
		TCATAC		GTTG

14334	14356	CCACCACCCCATCATAC	2355	GAAAGAGTATGATGG	4124
		TCTTTC		GGTGG

14337	14359	CCACCCCATCATACTCT	2356	GGTGAAAGAGTATGAT	4125
		TTCACC		GGGG

14340	14362	CCCCATCATACTCTTTT	2357	CTGGGTGAAAGAGTAT	4126
		ACCCAC		GATG

14341	14363	CCCATCATACTCTTTCA	2358	TGTGGGTGAAAGAGTA	4127
		CCCACA		TGAT

14342	14364	CCATCATACTCTTTCAC	2359	CTGTGGGTGAAAGAGT	4128
		CCACAG		ATGA

14358	14380	CCCACAGCACCAATCCT	2360	GGAGGTAGGATTGGTG	4129
		ACCTCC		CTGT

14359	14381	CCACAGCACCAATCCTA	2361	TGGAGGTAGGATTGGT	4130
		CCTCCA		GCTG

14367	14389	CCAATCCTACCTCCATC	2362	GTTAGCGATGGAGGTA	4131
		GCTAAC		GGAT

14372	14394	CCTACCTCCATCGCTAA	2363	GTGGGGTTAGCGATGG	4132
		CCCCAC		AGGT

14376	14398	CCTCCATCGCTAACCCC	2364	TTTAGTGGGGTTAGCG	4133
		ACTAAA		ATGG

14379	14401	CCATCGCTAACCCCACT	2365	TGTTTTAGTGGGGTTA	4134
		AAAACA		GCGA

14389	14411	CCCCACTAAAACACTCA	2366	TCTTGGTGAGTGTTTT	4135
		CCAAGA		AGTG

14390	14412	CCCACTAAAACACTCAC	2367	GTCTTGGTGAGTGTTT	4136
		CAAGAC		TAGT

14391	14413	CCACTAAAACACTCACC	2368	GGTCTTGGTGAGTGTT	4137
		AAGACC		TTAG

14406	14428	CCAAGACCTCAACCCCT	2369	GGGGTCAGGGGTTGA	4138
		GACCCC		GGTCT

14412	14434	CCTCAACCCCTGACCCC	2370	GGCATGGGGGTCAGG	4139
		CATGCC		GGTTG

14418	14440	CCCCTGACCCCCATGCC	2371	TCCTGAGGCATGGGGG	4140
		TCAGGA		TCAG

14419	14441	CCCTGACCCCCATGCCT	2372	ATCCTGAGGCATGGGG	4141
		CAGGAT		GTCA

14420	14442	CCTGACCCCCATGCCTC	2373	TATCCTGAGGCATGGG	4142
		AGGATA		GGTC

14425	14447	CCCCCATGCCTCAGGAT	2374	AGGAGTATCCTGAGGC	4143
		ACTCCT		ATGG

14426	14448	CCCCATGCCTCAGGATA	2375	GAGGAGTATCCTGAGG	4144
		CTCCTC		CATG

14427	14449	CCCATGCCTCAGGATAC	2376	TGAGGAGTATCCTGAG	4145
		TCCTCA		GCAT

14428	14450	CCATGCCTCAGGATACT	2377	TTGAGGAGTATCCTGA	4146
		CCTCAA		GGCA

14433	14455	CCTCAGGATACTCCTCA	2378	GGCTATTGAGGAGTAT	4147
		ATAGCC		CCTG

14445	14467	CCTCAATAGCCATCGCT	2379	TACTACAGCGATGGCT	4148
		GTAGTA		ATTG

14454	14476	CCATCGCTGTAGTATAT	2380	CTTTGGATATACTACA	4149
		CCAAAG		GCGA

14471	14493	CCAAAGACAACCATCAT	2381	GGGGGAATGATGGTTG	4150
		TCCCCC		TCTT

14481	14503	CCATCATTCCCCCTAAA	2382	AATTTATTTAGGGGGA	4151
		TAAATT		ATGA

14489	14511	CCCCCTAAATAAATTAA	2383	GTTTTTTTAATTTATTT	4152
		AAAAAC		AGG

14490	14512	CCCCTAAATAAATTAA	2384	AGTTTTTTTAATTTATT	4153
		AAAACT		TAG

14491	14513	CCCTAAATAAATTAAAA	2385	TAGTTTTTTTAATTTAT	4154
		AAACTA		TTA

14492	14514	CCTAAATAAATTAAAAA	2386	ATAGTTTTTTTAATTTA	4155
		AACTAT		TTT

14519	14541	CCCATATAACCTCCCCC	2387	AATTTTGGGGGAGGTT	4156
		AAAATT		ATAT

14520	14542	CCATATAACCTCCCCCA	2388	GAATTTTGGGGGAGGT	4157
		AAATTC		TATA

14528	14550	CCTCCCCCAAAATTCAG	2389	ATTATTCTGAATTTTG	4158
		AATAAT		GGGG

14531	14553	CCCCCAAAATTCAGAAT	2390	GTTATTATTCTGAATTT	4159
		AATAAC		TGG

14532	14554	CCCCAAAATTCAGAATA	2391	TGTTATTATTCTGAATT	4160
		ATAACA		TTG

14533	14555	CCCAAAATTCAGAATAA	2392	GTGTTATTATTCTGAA	4161
		TAACAC		TTTT

14534	14556	CCAAAATTCAGAATAAT	2393	TGTGTTATTATTCTGA	4162
		AACACA		ATTT

14557	14579	CCCGACCACACCGCTAA	2394	TGATTGTTAGCGGTGT	4163
		CAATCA		GGTC

14558	14580	CCGACCACACCGCTAAC	2395	TTGATTGTTAGCGGTG	4164
		AATCAA		TGGT

14562	1484	CCACACCGCTAACAATC	2396	AGTATTGATTGTTAGC	4165
		AATACT		GGTG

14567	14589	CCGCTAACAATCAATAC	2397	GGTTTAGTATTGATTG	4166
		TAAACC		TTAG

14588	14610	CCCCCATAAATAGGAGA	2398	AAGCCTTCTCCTATTT	4167
		AGGCTT		ATGG

14589	14611	CCCCATAAATAGGAGA	2399	TAAGCCTTCTCCTATTT	4168
		AGGCTTA		ATG

14590	14612	CCCATAAATAGGAGAA	2400	CTAAGCCTTCTCCTAT	4169
		GGCTTAG		TTAT

14591	14613	CCATAAATAGGAGAAG	2401	TCTAAGCCTTCTCCTA	4170
		GCTTAGA		TTTA

14620	14642	CCCCACAAACCCCATTA	2402	GTTTAGTAATGGGGTT	4171
		CTAAAC		TGTG

14621	14643	CCCACAAACCCCATTAC	2403	GGTTTAGTAATGGGGT	4172
		TAAACC		TTGT

14622	14644	CCACAAACCCCATTACT	2404	GGGTTTAGTAATGGGG	4173
		AAACCC		TTTG

14629	14651	CCCCATTACTAAACCCA	2405	TGAGTGTGGGTTTAGT	4174
		CACTCA		AATG

14630	14652	CCCATTACTAAACCCAC	2406	TTGAGTGTGGGTTTAG	4175
		ACTCAA		TAAT

14631	14653	CCATTACTAAACCCACA	2407	GTTGAGTGTGGGTTTA	4176
		CTCAAC		GTAA

14642	14664	CCCACACTCAACAGAAA	2408	GCTTTGTTTCTGTTGA	4177
		CAAAGC		GTGT

14643	14665	CCACACTCAACAGAAAC	2409	TGCTTTGTTTCTGTTGA	4178
		AAAGCA		GTG

14694	14716	CCACGACCAATGATATG	2410	GTTTTTCATATCATTG	4179
		AAAAAC		GTCG

14700	14722	CCAATGATATGAAAAAC	2411	ACGATGGTTTTTCATA	4180
		CATCGT		TCAT

14716	14738	CCATCTTGTATTTCAA	2412	TTGTAGTTGAAATACA	4181
		CTACAA		ACGA

14744	14766	CCAATGACCCCAATACG	2413	GTTTTGCGTATTGGGG	4182
		CAAAAC		TCAT

14751	14773	CCCCAATACGCAAAACT	2414	GGGGTTAGTTTTGCGT	4183
		AACCCC		ATTG

14752	14774	CCCAATACGCAAAACTA	2415	GGGGGTTAGTTTTGCG	4184
		ACCCCC		TATT

14753	14775	CCAATACGCAAAACTAA	2416	AGGGGGTTAGTTTTGC	4185
		CCCCCT		GTAT

14770	14792	CCCCCTAATAAAATTAA	2417	GGTTAATTAATTTTAT	4186
		TTAACC		TAGG

14771	14793	CCCCTAATAAAATTAAT	2418	TGGTTAATTAATTTTA	4187
		TAACCA		TTAG

14772	14794	CCCTAATAAAATTAATT	2419	GTGGTTAATTAATTTT	4188
		AACCAC		ATTA

14773	14795	CCTAATAAAATFAATTA	2420	AGTGGTTAATTAATTT	4189
		ACCACT		TATT

14791	14813	CCACTCATTCATCGACC	2421	TGGGGAGGTCGATGA	4190
		TCCCCA		ATGAG

14806	14828	CCTCCCCACCCCATCCA	2422	AGATGTTGGATGGGGT	4191
		ACATCT		GGGG

14809	14831	CCCCACCCCATCCAACA	2423	CGGAGATGTTGGATGG	4192
		TCTCCG		GGTG

14810	14832	CCCACCCCATCCAACAT	2424	GCGGAGATGTTGGATG	4193
		CTCCGC		GGGT

14811	14833	CCACCCCATCCAACATC	2425	TGCGGAGATGTTGGAT	4194
		TCCGCA		GGGG

14814	14836	CCCCATCCAACATCTCC	2426	TCATGCGGAGATGTTG	4195
		GCATGA		GATG

14815	14837	CCCATCCAACATCTCCG	2427	ATCATGCGGAGATGTT	4196
		CATGAT		GGAT

14816	14838	CCATCCAACATCTCCGC	2428	CATCATGCGGAGATGT	4197
		ATGATG		TGGA

14820	14842	CCAACATCTCCGCATGA	2429	GTTTCATCATGCGGAG	4198
		TGAAAC		ATGT

14829	14851	CCGCATGATGAAACTTC	2430	TGAGCCGAAGTTTCAT	4199
		GGCTCA		CATG

14854	14876	CCTTGGCGCCTGCCTGA	2431	GGAGGATCAGGCAGG	4200
		TCCTCC		CGCCA

14862	14884	CCTGCCTGATCCTCCAA	2432	GGTGATTTGGAGGATC	4201
		ATCACC		AGGC

14866	14888	CCTGATCCTCCAAATCA	2433	CTGTGGTGATTTGGAG	4202
		CCACAG		GATC

14872	14894	CCTCCAAATCACCACAG	2434	ATAGTCCTGTGGTGAT	4203
		GACTAT		TTGG

14875	14897	CCAAATCACCACAGGAC	2435	GGAATAGTCCTGTGGT	4204
		TATTCC		GATT

14883	14905	CCACAGGACTATTCCTA	2436	CATGGCTAGGAATAGT	4205
		GCCATG		CCTG

14896	14918	CCTAGCCATGCACTACT	2437	CTGGTGAGTAGTGCAT	4206
		CACCAG		GGCT

14901	14923	CCATGCACTACTCACCA	2438	GGCGTCTGGTGAGTAG	4207
		GACGCC		TGCA

14915	14937	CCAGACGCCTCAACCGC	2439	GAAAAGGCGGTTGAG	4208
		CTTTTC		GCGTC

14922	14944	CCTCAACCGCCTTTTCA	2440	GATTGATGAAAAGGC	4209
		TCAATC		GGTTG

14928	14950	CCGCCTTTTCATCAATC	2441	GTGGGCGATTGATGAA	4210
		GCCCAC		AAGG

14931	14953	CCTTTTCATCAATCGCC	2442	GATGTGGGCGATTGAT	4211
		CACATC		GAAA

14946	14968	CCCACATCACTCGAGAC	2443	ATTTACGTCTCGAGTG	4212
		GTAAAT		ATGT

14947	14969	CCACATCACTCGAGACG	2444	AATTTACGTCTCGAGT	4213
		TAAATT		GATG

14983	15005	CCGCTACCTTCACGCCA	2445	CGCCATTGGCGTGAAG	4214
		ATGGCG		GTAG

14989	15011	CCTTCACGCCAATGGCG	2446	TTGAGGCGCCATTGGC	4215
		CCTCAA		GTGA

14997	15019	CCAATGGCGCCTCAATA	2447	AAAGAATATTGAGGC	4216
		TTCTTT		GCCAT

15006	15028	CCTCAATATTCTTTATCT	2448	GAGGCAGATAAAGAA	4217
		GCCTC		TATTG

15025	15047	CCTCTTCCTACACATCG	2449	CTCGCCCGATGTGTAG	4218
		GGCGAG		GAAG

15031	15053	CCTACACATCGGGCGAG	2450	ATAGGCCTCGCCCGAT	4219
		GCCTAT		GTGT

15049	15071	CCTATATTACGGATCAT	2451	AGAGAAATGATCCGTA	4220
		TTCTCT		ATAT

15081	15103	CCTGAAACTTCGGCATT	2452	GAGGATAATGCCGATG	4221
		ATCCTC		TTTC

15100	15122	CCTCCTGCTTGCAACTA	2453	TTGCTATAGTTGCAAG	4222
		TAGCAA		CAGG

15103	15125	CCTGCTTGCAACTATAG	2454	CTGTTGCTATAGTTGC	4223
		CAACAG		AAGC

15126	15148	CCTTCATAGGCTATGTC	2455	CGGGAGGACATAGCCT	4224
		CTCCCG		ATGA

15142	15164	CCTCCCGTGAGGCCAAA	2456	ATGATATTTGGCCTCA	4225
		TATCAT		CGGG

15145	15167	CCCGTGAGGCCAAATAT	2457	AGAATGATATTTGGCC	4226
		CATTCT		TCAC

15146	15168	CCGTGAGGCCAAATATC	2458	CAGAATGATATTTGGC	4227
		ATTCTG		CTCA

15154	15176	CCAAATATCATTCTGAG	2459	TGGCCCCTCAGAATGA	4228
		GGGCCA		TATT

15174	15196	CCACAGTAATTACAAAC	2460	TAGTAAGTTTGTAATT	4229
		TTACTA		ACTG

15198	15220	CCGCCATCCCATACATT	2461	TGTCCCAATGTATGGG	4230
		GGGACA		ATGG

15201	15223	CCATCCCATACATTGGG	2462	GTCTGTCCCAATGTAT	4231
		ACAGAC		GGGA

15205	15727	CCCATACATTGGGACAG	2463	CTAGGTCTGTCCCAAT	4232
		ACCTAG		GTAT

15206	15228	CCATACATTGGGACAGA	2464	ACTAGGTCTGTCCCAA	4233
		CCTAGT		TGTA

15223	15245	CCTAGTTCAATGAATCT	2465	CTCCTCAGATTCATTG	4234
		GAGGAG		AACT

15263	15285	CCCACCCTCACACGATT	2466	GTAAAGAATCGTGTGA	4235
		CTTTAC		GGGT

15264	15286	CCACCCTCACACGATTC	2467	GGTAAAGAATCGTGTG	4236
		TTTACC		AGGG

15267	15289	CCCTCACACGATTCTTT	2468	AAAGGTAAAGAATCG	4237
		ACCTTT		TGTGA

15268	15290	CCTCACACGATTCTTTA	2469	GAAAGGTAAAGAATC	4238
		CCTTTC		GTGTG

15285	15307	CCTTTCACTTCATCTTGC	2470	GAAGGGCAAGATGAA	4239
		CCTTC		GTGAA

15302	15324	CCCTTCATTATTGCAGC	2471	GCTAGGGCTGCAATAA	4240
		CCTAGC		TGAA

15303	15325	CCTTCATTATTGCAGCC	2472	TGCTAGGGCTGCAATA	4241
		CTAGCA		ATGA

15318	15340	CCCTAGCAACACTCCAC	2473	TAGGAGGTGGAGTGTT	4242
		CTCCTA		GCTA

15319	15341	CCTAGCAACACTCCACC	2474	ATAGGAGGTGGAGTGT	4243
		TCCTAT		TGCT

15331	15353	CCACCTCCTATTCTTGC	2475	TTTCGTGCAAGAATAG	4244
		ACGAAA		GAGG

15334	15356	CCTCCTATTCTTGCACG	2476	CCGTTTCGTGCAAGAA	4245
		AAACGG		TAGG

15337	15359	CCTATTCTTGCACGAAA	2477	ATCCCGTTTCGTGCAA	4246
		CGGGAT		GAAT

15367	15389	CCCCCTAGGAATCACCT	2478	AATGGGAGGTGATTCC	4247
		CCCATT		TAGG

15368	15390	CCCCTAGGAATCACCTC	2479	GAATGGGAGGTGATTC	4248
		CCATTC		CTAG

15369	15391	CCCTAGGAATCACCTCC	2480	GGAATGGGAGGTGATT	4249
		CATTCC		CCTA

15370	15392	CCTAGGAATCACCTCCC	2481	CGGAATGGGAGGTGA	4250
		ATTCCG		TTCCT

15381	15403	CCTCCCATTCCGATAAA	2482	GGTGATTTTATCGGAA	4251
		ATCACC		TGGG

15384	15406	CCCATTCCGATAAAATC	2483	GAAGGTGATTTTATCG	4252
		ACCTTC		GAAT

15385	15407	CCATTCCGATAAAATCA	2484	GGAAGGTGATTTTATC	4253
		CCTTCC		GGAA

15390	15412	CCGATAAAATCACCTTC	2485	AGGGTGGAAGGTGATT	4254
		CACCCT		TTAT

15402	15424	CCTTCCACCCTTACTAC	2486	GATTGTGTAGTAAGGG	4255
		ACAATC		TGGA

15406	15428	CCACCCTTACTACACAA	2487	CTTTGATTGTGTAGTA	4256
		TCAAAG		AGGG

15409	15431	CCCTTACTACACAATCA	2488	CGTCTTTGATTGTGTA	4257
		AAGACG		GTAA

15410	15432	CCTTACTACACAATCAA	2489	GCGTCTTTGATTGTGT	4258
		AGACGC		AGTA

15432	15454	CCCTCGGCTTACTTCTCT	2490	AAGGAAGAGAAGTAA	4259
		TCCTT		GCCGA

15433	15455	CCTCGGCTTACTTCTCTT	2491	GAAGGAAGAGAAGTA	4260
		CCTTC		AGCCG

15451	15473	CCTTCTCTCCTTAATGA	2492	TTAATGTCATTAAGGA	4261
		CATTAA		GAGA

15459	15481	CCTTAATGACATTAACA	2493	GAATAGTGTTAATGTC	4262
		CTATTC		ATTA

15485	15507	CCAGACCTCCTAGGCGA	2494	TCTGGGTCGCCTAGGA	4263
		CCCAGA		GGTC

15490	15512	CCTCCTAGGCGACCCAG	2495	AATTGTCTGGGTCGCC	4264
		ACAATT		TAGG

15493	15515	CCTAGGCGACCCAGACA	2496	TATAATTGTCTGGGTC	4265
		ATTATA		GCCT

15502	15524	CCCAGACAATTATACCC	2497	TGGCTAGGGTATAATT	4266
		TAGCCA		GTCT

15503	15525	CCAGACAATTATACCCT	2498	TTGGCTAGGGTATAAT	4267
		AGCCAA		TGTC

15516	15538	CCCTAGCCAACCCCTTA	2499	GGTGTTTAAGGGGTTG	4268
		AACACC		GCTA

15517	15539	CCTAGCCAACCCCTTAA	2500	GGGTGTTTAAGGGGTT	4269
		ACACCC		GGCT

15522	15544	CCAACCCCTTAAACACC	2501	GGGAGGGGTGTTTAAG	4270
		CCTCCC		GGGT

15526	15548	CCCCTTAAACACCCCTC	2502	TGTGGGGAGGGGTGTT	4271
		CCCACA		TAAG

15527	15549	CCCTTAAACACCCCTCC	2503	ATGTGGGGAGGGGTGT	4272
		CCACAT		TTAA

15528	15550	CCTTAAACACCCCTCCC	2504	GATGTGGGGAGGGGT	4273
		CACATC		GTTTA

15537	15559	CCCCTCCCCACATCAAG	2505	TTCGGGCTTGATGTGG	4274
		CCCGAA		GGAG

15538	15560	CCCTCCCCACATCAAGC	2506	ATTCGGGCTTGATGTG	4275
		CCGAAT		GGGA

15539	15561	CCTCCCCACATCAAGCC	2507	CATTCGGGCTTGATGT	4276
		CGAATG		GGGG

15542	15564	CCCCACATCAAGCCCGA	2508	TATCATTCGGGCTTGA	4277
		ATGATA		TGTG

15543	15565	CCCACATCAAGCCCGAA	2509	ATATCATTCGGGCTTG	4278
		TGATAT		ATGT

15544	15566	CCACATCAAGCCCGAAT	2510	AATATCATCGGGCTT	4279
		GATATT		GATG

15554	15576	CCCGAATGATATTTCCT	2511	GCGAATAGGAAATATC	4280
		ATTCGC		ATTC

15555	15577	CCGAATGATATTTCCTA	2512	GGCGAATAGGAAATA	4281
		TTCGCC		TCATT

15568	15590	CCTATTCGCCTACACAA	2513	GGAGAATTGTGTAGGC	4282
		TTCTCC		GAAT

15576	15598	CCTACACAATTCTCCGA	2514	GACGGATCGGAGAATT	4283
		GTGTGT		GTGT

15589	15611	CCGATCCGTCCCTAACA	2515	CTAGTTTGTTAGGGAC	4284
		AACTAG		GGAT

15594	15616	CCGTCCCTAACAAACTA	2516	GCCTCCTAGTTTGTTA	4285
		GGAGGC		GGGA

15598	15620	CCCTAACAAACTAGGAG	2517	GGACGCCTCCTAGTTT	4286
		GCGTCC		GTTA

15599	15621	CCTAACAAACTAGGAG	2518	AGGACGCCTCCTAGTT	4287
		GCGTCCT		TGTT

15619	15641	CCTTGCCCTATTACTAT	2519	GGATGGATAGTAATAG	4288
		CCATCC		GGCA

15624	15646	CCCTATTACTATCCATC	2520	GATGAGGATGGATAGT	4289
		CTCATC		AATA

15625	15647	CCTATTACTATCCATCC	2521	GGATGAGGATGGATA	4290
		TCATCC		GTAAT

15636	15658	CCATCCTCATCCTAGCA	2522	GATTATTGCTAGGATG	4291
		ATAATC		AGGA

15640	15662	CCTCATCCTAGCAATAA	2523	TGGGGATTATTGCTAG	4292
		TCCCCA		GATG

15646	15668	CCTAGCAATAATCCCCA	2524	GGAGGATGGGGATTAT	4293
		TCCTCC		TGCT

15658	15680	CCCCATCCTCCATATAT	2525	GTTTGGATATATGGAG	4294
		CCAAAC		GATG

15659	15681	CCCATCCTCCATATATC	2526	TGTTTGGATATATGGA	4295
		CAAACA		GGAT

15660	15682	CCATCCTCCATATATCC	2527	TTGTTTGGATATATGG	4296
		AAACAA		AGGA

15664	15686	CCTCCATATATCCAAAC	2528	TTTGTTGTTTGGATAT	4297
		AACAAA		ATGG

15667	15689	CCATATATCCAAACAAC	2529	TGCTTTGTTGTTTGGAT	4298
		AAAGCA		ATA

15675	15697	CCAAACAACAAAGCAT	2530	AAATATTATGCTTTGT	4299
		AATATTT		TGTT

15700	15722	CCCACTAAGCCAATCAC	2531	AATAAAGTGATTGGCT	4300
		TTTATT		TAGT

15701	15723	CCACTAACCAATCACT	2532	CAATAAAGTGATTGGC	4301
		TTATTG		TTAG

15709	15731	CCAATCACTTTATTGAC	2533	CTAGGAGTCAATAAAG	4302
		TCCTAG		TGAT

15727	15749	CCTAGCCGCAGACCTCC	2534	GAATGAGGAGGTCTGC	4303
		TCATTC		GGCT

15732	15754	CCGCAGACCTCCTCATT	2535	GGTTAGAATGAGGAG	4304
		CTAACC		GTCTG

15739	15761	CCTCCTCATTCTAACCT	2536	CGATTCAGGTTAGAAT	4305
		GAATCG		GAGG

15742	15764	CCTCATTCTAACCTGAA	2537	CTCCGATTCAGGTTAG	4306
		TCGGAG		AATG

15753	15775	CCTGAATCGGAGGACA	2538	TACTGGTTGTCCTCCG	4307
		ACCAGTA		ATTC

15770	15792	CCAGTAAGCTACCCTTT	2539	ATGGTAAAAGGGTAG	4308
		TACCAT		CTTAC

15781	15803	CCCTTTTACCATCATTG	2540	CTTGTCCAATGATGGT	4309
		GACAAG		AAAA

15782	15804	CCTTTTACCATCATTGG	2541	ACTTGTCCAATGATGG	4310
		ACAAGT		TAAA

15789	15811	CCATCATTGGACAAGTA	2542	GGATGCTACTTGTCCA	4311
		GCATCC		ATGA

15810	15832	CCGTACTATACTTCACA	2543	GATTGTTGTGAAGTAT	4312
		ACAATC		AGTA

15832	15854	CCTAATCCTAATACCAA	2544	AGATAGTTGGTATTAG	4313
		CTATCT		GATT

15838	15860	CCTAATACCAACTATCT	2545	TTAGGGAGATAGTTGG	4314
		CCCTAA		TATT

15845	15867	CCAACTATCTCCCTAAT	2546	TTTTCAATTAGGGAGA	4315
		TGAAAA		TAGT

15855	15877	CCCTAATTGAAAACAAA	2547	GAGTATTTTGTTTTCA	4316
		ATACTC		ATTA

15856	15878	CCTAATTGAAAACAAAA	2548	TGAGTATTTTGTTTTCA	4317
		TACTCA		ATT

15885	15907	CCTGTCCTTGTAGTATA	2549	TTAGTTTATACTACAA	4318
		AACTAA		GGAC

15890	15912	CCTTGTAGTATAAACTA	2550	GTGTATTAGTTTATAC	4319
		ATACAC		TACA

15912	15934	CCAGTCTTGTAAACCGG	2551	TCATCTCCGGTTTACA	4320
		AGATGA		AGAC

15925	15947	CCGGAGATGAAAACCTT	2552	TGGAAAAAGGTTTTCA	4321
		TTTCCA		TCTC

15938	15960	CCTTTTTCCAAGGACAA	2553	TCTGATTTGTCCTTGG	4322
		ATCAGA		AAAA

15945	15967	CCAAGGACAAATCAGA	2554	CTTTTTCTCTGATTTGT	4323
		GAAAAAG		CCT

15977	15999	CCACCATTAGCACCCAA	2555	TTAGCTTTGGGTGCTA	4324
		AGCTAA		ATGG

15980	16002	CCATTAGCACCCAAAGC	2556	ATCTTAGCTTTGGGTG	4325
		TAAGAT		CTAA

15989	16011	CCCAAAGCTAAGATTCT	2557	TAAATTAGAATCTTAG	4326
		AATTTA		CTTT

15990	16012	CCAAAGCTAAGATTCTA	2558	TTAAATTAGAATCTTA	4327
		ATTTAA		GCTT

16052	16074	CCACCCAAGTATTGACT	2559	TGGGTGAGTCAATACT	4328
		CACCCA		TGGG

16055	16077	CCCAAGTATTGACTCAC	2560	TGATGGGTGAGTCAAT	4329
		CCATCA		ACTT

16056	16078	CCAAGTATTGACTCACC	2561	TTGATGGGTGAGTCAA	4330
		CATCAA		TACT

16071	16093	CCCATCAACAACCGCTA	2562	AATACATAGCGGTTGT	4331
		TGTATT		TGAT

16072	16094	CCATCAACAACCGCTAT	2563	AAATACATAGCGGTTG	4332
		GTATTT		TTGA

16082	16104	CCGCTATGTATTTCGTA	2564	GTAATGTACGAAATAC	4333
		CATTAC		ATAG

16107	16129	CCAGCCACCATGAATAT	2565	CGTACAATATTCATGG	4334
		TGTACG		TGGC

16111	16133	CCACCATGAATATTGTA	2566	GTACCGTACAATATTC	4335
		CGGTAC		ATGG

16114	16136	CCATGAATATTGTACGG	2567	ATGGTACCGTACAATA	4336
		TACCAT		TTCA

16133	16155	CCATAAATACTTGACCA	2568	TACAGGTGGTCAAGTA	4337
		CCTGTA		TTTA

16147	16169	CCACCTGTAGTACATAA	2569	GGGTTTTTATGTACTA	4338
		AAACCC		CAGG

16150	16172	CCTGTAGTACATAAAAA	2570	ATTGGGTTTTTATGTA	4339
		CCCAAT		CTAC

16167	16189	CCCAATCCACATCAAAA	2571	AGGGGGTTTTGATGTG	4340
		CCCCCT		GATT

16168	16190	CCAATCCACATCAAAAC	2572	GAGGGGGTTTTGATGT	4341
		CCCCTC		GGAT

16173	16195	CCACATCAAAACCCCCT	2573	ATGGGGAGGGGGTTTT	4342
		CCCCAT		GATG

16184	16206	CCCCCTCCCCATGCTTA	2574	TGCTTGTAAGCATGGG	4343
		CAAGCA		GG

16185	16207	CCCCTCCCCATGCTTAC	2575	TTGCTTGTAAGCATGG	4344
		AAGCAA		GGAG

16186	16208	CCCTCCCCATGCTTACA	2576	CTTGCTTGTAAGCATG	4345
		AGCAAG		GGGA

16187	16209	CCTCCCCATGCTTACAA	2577	ACTTGCTTGTAAGCAT	4346
		GCAAGT		GGGG

16190	16212	CCCCATGCTTACAAGCA	2578	TGTACTTGCTTGTAAG	4347
		AGTACA		CATG

16191	16213	CCCATGCTTACAAGCAA	2579	CTGTACTTGCTTGTAA	4348
		GTACAG		GCAT

16192	16214	CCATGCTTACAAGCAAG	2580	GCTGTACTTGCTTGTA	4349
		TACAGC		AGCA

16221	16243	CCCTCAACTATCACACA	2581	AGTTGATGTGTGATAG	4350
		TCAACT		TTGA

16222	16244	CCTCAACTATCACACAT	2582	CAGTTGATGTGTGATA	4351
		CAACTG		GTTG

16250	16272	CCAAAGCCACCCCTCAC	2583	TAGTGGGTGAGGGGTG	4352
		CCACTA		GCTT

16256	16278	CCACCCCTCACCCACTA	2584	GTATCCTAGTGGGTGA	4353
		GGATAC		GGGG

16259	16281	CCCCTCACCCACTAGGA	2585	TTGGTATCCTAGTGGG	4354
		TACCAA		TGAG

16260	16282	CCCTCACCCACTAGGAT	2586	GTTGGTATCCTAGTGG	4355
		ACCAAC		GTGA

16261	16283	CCTCACCCACTAGGATA	2587	TGTTGGTATCCTAGTG	4356
		CCAACA		GGTG

16266	16288	CCCACTAGGATACCAAC	2588	AGGTTTGTTGGTATCC	4357
		AAACCT		TAGT

16267	16289	CCACTAGGATACCAACA	2589	TAGGTTTGTTGGTATC	4358
		AACCTA		CTAG

16278	16300	CCAACAAACCTACCCAC	2590	TTAAGGGTGGGTAGGT	4359
		CCTTAA		TTGT

16286	16308	CCTACCCACCCTTAACA	2591	ATGTACTGTTAAGGGT	4360
		GTACAT		GGGT

16290	16312	CCCACCCTTAACAGTAC	2592	TACTATGTACTGTTAA	4361
		ATAGTA		GGGT

16291	16313	CCACCCTTAACAGTACA	2593	GTACTATGTACTGTTA	4362
		TAGTAC		AGGG

16294	16316	CCCTTAACAGTACATAG	2594	TATGTACTATGTACTG	4363
		TACATA		TTAA

16295	16317	CCTTAACAGTACATAGT	2595	TTATGTACTATGTACT	4364
		ACATAA		GTTA

16320	16342	CCATTTACCGTACATAG	2596	AATGTGCTATGTACGG	4365
		CACATT		TAAA

16327	16349	CCGTACATAGCACATTA	2597	TGACTGTAATGTGCTA	4366
		CAGTCA		TGTA

16353	16375	CCCTTCTCGTCCCCATG	2598	GTCATCCATGGGGACG	4367
		GATGAC		AGAA

16354	16376	CCTTCTCGTCCCCATGG	2599	GGTCATCCATGGGGAC	4368
		ATGACC		GAGA

16363	16385	CCCCATGGATGACCCCC	2600	TCTGAGGGGGGTCAT	4369
		CTCAGA		CATG

16364	16386	CCCATGGATGACCCCCC	2601	ATCTGAGGGGGGTCAT	4370
		TCAGAT		CCAT

16365	16387	CCATGGATGACCCCCCT	2602	TATCTGAGGGGGGTCA	4371
		CAGATA		TCCA

16375	16397	CCCCCCTCAGATAGGGG	2603	AAGGGACCCCTATCTG	4372
		TCCCTT		AGGG

16376	16398	CCCCCTCAGATAGGGGT	2604	CAAGGGACCCCTATCT	4373
		CCCTTG		GAGG

16377	16399	CCCCTCAGATAGGGGTC	2605	TCAAGGGACCCCTATC	4374
		CCTTGA		TGAG

16378	16400	CCCTCAGATAGGGGTCC	2606	GTCAAGGGACCCCTAT	4375
		CTTGAC		CTGA

16379	16401	CCTCAGATAGGGGTCCC	2607	GGTCAAGGGACCCCTA	4376
		TTGACC		TCTG

16393	16415	CCCTTGACCACCATCCT	2608	TCACGGAGGATGGTGG	4377
		CCGTGA		TCAA

16394	16416	CCTTGACCACCATCCTC	2609	TTCACGGAGGATGGTG	4378
		CGTGAA		GTCA

16400	16422	CCACCATCCTCCGTGAA	2610	ATTGATTTCACGGAGG	4379
		ATCAAT		ATGG

16403	16425	CCATCCTCCGTGAAATC	2611	GATATTGATTTCACGG	4380
		AATATC		AGGA

16407	16429	CCTCCGTGAAATCAATA	2612	GCGGGATATTGATTTC	4381
		TCCCGC		ACGG

16410	16432	CCGTGAAATCAATATCC	2613	TGTGCGGGATATTGAT	4382
		CGCACA		TTCA

16425	16447	CCCGCACAAGAGTGCTA	2614	GGAGAGTAGCACTCTT	4383
		CTCTCC		GTGC

16426	16448	CCGCACAAGAGTGCTAC	2615	AGGAGAGTAGCACTCT	4384
		TCTCCT		TGTG

16446	16468	CCTCGCTCCGGGCCCAT	2616	AGTGTTATGGGCCCGG	4385
		AACACT		AGCG

16453	16475	CCGGGCCCATAACACTT	2617	ACCCCCAAGTGTTATG	4386
		GGGGGT		GGCC

16458	16480	CCCATAACACTTGGGGG	2618	TAGCTACCCCCAAGTG	4387
		TAGCTA		TTAT

16459	16481	CCATAACACTTGGGGGT	2619	TTAGCTACCCCCAAGT	4388
		AGCTAA		GTTA

16494	16516	CCGACATCTGGTTCCTA	2620	CTGAAGTAGGAACCA	4389
		CTTCAG		GATGT

16507	16529	CCTACTTCAGGGTCATA	2621	AGGCTTTATGACCCTG	4390
		AAGCCT		AAGT

16527	16549	CCTAAATAGCCCACACG	2622	GGGGAACGTGTGGGCT	4391
		TTCCCC		ATTT

16536	16558	CCCACACGTTCCCCTTA	2623	CTTATTTAAGGGGAAC	4392
		AATAAG		GTGT

16537	16559	CCACACGTTCCCCTTAA	2624	TCTTATTTAAGGGGAA	4393
		ATAAGA		CGTG

16546	16568	CCCCTTAAATAAGACAT	2625	ATCGTGATGTCTTATT	4394
		CACGAT		TAAG

16547	16569	CCCTTAAATAAGACATC	2626	CATCGTGATGTCTTAT	4395
		ACGATG		TT

16548	16570	CCTTAAATAAGACATCA	2627	CCATCGTGATGTCTTA	4396
		CGATGG		TTTA

Applications

The gNAs (e.g., gRNAs) and collections of gNAs (e.g., gRNAs) provided herein are useful for a variety of applications, including depletion, partitioning, capture, or enrichment of target sequences of interest, genome-wide labeling; genome-wide editing, genome-wide function screens; and genome-wide regulation.
In one embodiment, the gNAs are selective for host nucleic acids in abiological sample from a host, but are not selective for non-host nucleic acids in the sample from a host. In one embodiment, the gNAs are selective for non-host nucleic acids from a biological sample from a host but are not selective for the host nucleic acids in the sample. In one embodiment, the gNAs are selective for both host nucleic acids and a subset of the non-host nucleic acids in abiological sample from a host. For example, where a complex biological sample comprises host nucleic acids and nucleic acids from more than one non-host organisms, the gRNAs may be selective for more than one of the non-host species. In such embodiments, the gNAs are used to serially deplete or partition the sequences that are not of interest. For example, saliva from a human contains human DNA, as well as the DNA of more than one bacterial species, but may also contain the genomic material of an unknown pathogenic organism. In such an embodiment, gNAs directed at the human DNA and the known bacteria can be used to serially deplete the human DNA, and the DNA of the known bacterial, thus resulting in a sample comprising the genomic material of the unknown pathogenic organism.
In an exemplary embodiment, the gNAs are selective for human host DNA obtained from a biological sample from the host, but do not hybridize with DNA from an unknown pathogen(s) also obtained from the sample.
In some embodiments, the gNAs are useful for depleting and partitioning of targeted sequences in a sample, enriching a sample for non-host nucleic acids, or serially depleting targeted nucleic acids in a sample comprising: providing nucleic acids extracted from a sample; and contacting the sample with a plurality of complexes comprising (i) any one of the collection of gNAs described herein and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins.
In some embodiments, the gNAs are useful for method of depletion and partitioning of targeted sequences in a sample comprising: providing nucleic acids extracted from a sample, wherein the extracted nucleic acids comprise sequences of interest and targeted sequences for one of depletion and partitioning; contacting the sample with a plurality of complexes comprising (i) a collection of gNAs provided herein; and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins, under conditions in which the nucleic acid-guided nuclease system proteins cleave the nucleic acids in the sample.
In some embodiments, the gNAs are useful for enriching a sample for non-host nucleic acids comprising: providing a sample comprising host nucleic acids and non-host nucleic acids; contacting the sample with a plurality of complexes comprising (i) a collection of gNAs provided herein comprising targeting sequences directed at the host nucleic acids; and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins, under conditions in which the nucleic acid-guided nuclease system proteins cleave the host nucleic acids in the sample, thereby depleting the sample of host nucleic acids, and allowing for the enrichment of non-host nucleic acids.
In some embodiments, the gNAs are useful for one method for serially depleting targeted nucleic acids in a sample comprising: providing a biological sample from a host comprising host nucleic acids and non-host nucleic acids, wherein the non-host nucleic acids comprise nucleic acids from at least one known non-host organism and nucleic acids from an unknown non-host organism; providing a plurality of complexes comprising (i) a collection of gNAs provided herein, directed at the host nucleic acids; and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins; mixing the nucleic acids from the biological sample with the gNA-nucleic acid-guided nuclease system protein complexes (e.g., gRNA-CRISPR/Cas system protein complexes) configured to hybridize to targeted sequences in the host nucleic acids, wherein at least a portion of the complexes hybridizes to the targeted sequences in the host nucleic acids, and wherein at least a portion of the host nucleic acids are cleaved; mixing the remaining nucleic acids from the biological sample with the gNA-nucleic acid-guided nuclease system protein complexes configured to hybridize to targeted sequences in the at least one known non-host nucleic acids, wherein at least a portion of the complexes hybridizes to the targeted sequences in the at least one non-host nucleic acids, and wherein at least a portion of the non-host nucleic acids are cleaved; and isolating the remaining nucleic acids from the unknown non-host organism and preparing for further analysis.
In some embodiments, the gNAs generated herein are used to perform genome-wide or targeted functional screens in a population of cells. In such an embodiment, libraries of in vitro-transcribed gNAs (e.g., gRNAs) or vectors encoding the gNAs can be introduced into a population of cells via transfection or other laboratory techniques known in the art, along with a nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein, in a way that gNA-directed nucleic acid-guided nuclease system protein editing can be achieved to sequences across the entire genome or to a specific region of the genome. In one embodiment, the nucleic acid-guided nuclease system protein can be introduced as a DNA. In one embodiment, the nucleic acid-guided nuclease system protein can be introduced as mRNA. In one embodiment, the nucleic acid-guided nuclease system protein can be introduced as protein. In one exemplary embodiment, the nucleic acid-guided nuclease system protein is Cas9.
In some embodiments, the gNAs generated herein are used for the selective capture and/or enrichment of nucleic acid sequences of interest. For example, in some embodiments, the gNAs generated herein are used for capturing target nucleic acid sequences comprising: providing a sample comprising a plurality of nucleic acids; and contacting the sample with a plurality of complexes comprising (i) a collection of gNAs provided herein; and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins. Once the sequences of interest are captured, they can be further ligated to create, for example, a sequencing library.
In some embodiments, the gNAs generated herein are used for introducing labeled nucleotides at targeted sites of interest comprising: (a) providing a sample comprising a plurality of nucleic acid fragments; (b) contacting the sample with a plurality of complexes comprising (i) a collection of gNAs provided herein; and (ii) nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein-nickases (e.g. Cas9-nickases), wherein the gNAs are complementary to targeted sites of interest in the nucleic acid fragments, thereby generating a plurality of nicked nucleic acid fragments at the targeted sites of interest; and (c) contacting the plurality of nicked nucleic acid fragments with an enzyme capable of initiating nucleic acid synthesis at a nicked site, and labeled nucleotides, thereby generating a plurality of nucleic acid fragments comprising labeled nucleotides in the targeted sites of interest.
In some embodiments, the gNAs generated herein are used for capturing target nucleic acid sequences of interest comprising: (a) providing a sample comprising a plurality of adapter-ligated nucleic acids, wherein the nucleic acids are ligated to a first adapter at one end and are ligated to a second adapter at the other end; and (b) contacting the sample with a collection of gNAs which comprise a plurality of dead nucleic acid-guided nuclease-gNA complexes (e.g., dCas9-gRNA complexes), wherein the dead nucleic acid-guided nuclease (e.g., dCas9) is fused to a transposase, wherein the gNAs are complementary to targeted sites of interest contained in a subset of the nucleic acids, and wherein the dead nucleic acid-guided nuclease-gNA transposase complexes (e.g., dCas9-gRNA transposase complexes) are loaded with a plurality of third adapters, to generate a plurality of nucleic acids fragments comprising either a first or second adapter at one end and a third adapter at the other end. In one embodiment the method further comprises amplifying the product of step (b) using first or second adapter and third adapter-specific PCR.
In some embodiments, the gNAs generated herein are used to perform genome-wide or targeted activation or repression in a population of cells. In such an embodiment, libraries of in vitro-transcribed gNAs (e.g., gRNAs) or vectors encoding the gNAs can be introduced into a population of cells via transfection or other laboratory techniques known in the art, along with a catalytically dead nucleic acid-guided nuclease (e.g., CRISPR/Cas) system protein fused to an activator or repressor domain (catalytically dead nucleic acid-guided nuclease system protein-fusion protein), in a way that gNA-directed catalytically dead nucleic acid-guided nuclease system protein-mediated activation or repression can be achieved at sequences across the entire genome or to a specific region of the genome. In one embodiment, the catalytically dead nucleic acid-guided nuclease system protein-fusion protein can be introduced as DNA. In one embodiment, the catalytically dead nucleic acid-guided nuclease system protein-fusion protein can be introduced as mRNA. In one embodiment, the catalytically dead nucleic acid-guided nuclease system protein-fusion protein can be introduced as protein. In some embodiments, the collection of gNAs or nucleic acids encoding for gNAs exhibit specificity for more than one nucleic acid-guided nuclease system protein. In one exemplary embodiment, the catalytically dead nucleic acid-guided nuclease system protein is dCas9.
In some embodiments, the collection comprises gRNAs or nucleic acids encoding for gRNAs with specificity for Cas9 and one or more CRISPR/Cas system proteins selected from selected from the group consisting of Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5. In some embodiments, the collection comprises gRNAs or nucleic acids encoding for gRNAs with specificity for various catalytically dead CRISPR/Cas system proteins fused to different fluorophores, for example for use in the labeling and/or visualization of different genomes or portions of genomes, for use in the labeling and/or visualization of different chromosomal regions, or for use in the labeling and/or visualization of the integration of viral genes/genomes into a genome.
In some embodiments, the collection of gNAs (or nucleic acids encoding for gNAs) have specificity for different nucleic acid-guided nuclease (e.g., CRISPR/Cas) system proteins, and target different sequences of interest, for example from different species. For example, a first subset of gNAs from a collection of gNAs (or transcribed from a population of nucleic acids encoding such gNAs) targeting a genome from a first species can be first mixed with a first nucleic acid-guided nuclease system protein member (or an engineered version); and a second subset of gNAs from a collection of gNAs (or transcribed from a population of nucleic acids encoding such gNAs) targeting a genome from a second species can be mixed with a second different nucleic acid-guided nuclease system protein member (or an engineered version). In one embodiment, the nucleic acid-guided nuclease system proteins can be a catalytically dead version (for example dCas9) fused with different fluorophores, so that different targeted sequence of interest, e.g. different species genome, or different chromosomes of one species, can be labeled by different fluorescent labels. For example, different chromosomal regions can be labeled by different gRNA-targeted dCas9-fluorophores, for visualization of genetic translocations. For example, different viral genomes can be labeled by different gRNA-targeted dCas9-fluorophores, for visualization of integration of different viral genomes into the host genome. In another embodiment, the nucleic acid-guided nuclease system protein can be dCas9 fused with either activation or repression domain, so that different targeted sequence of interest, e.g. different chromosomes of a genome, can be differentially regulated. In another embodiment, the nucleic acid-guided nuclease system protein can be dCas9 fused different protein domain which can be recognized by different antibodies, so that different targeted sequence of interest, e.g. different DNA sequences within a sample mixture, can be differentially isolated.

Exemplary Compositions of the Invention

In one embodiment, provided herein is a composition comprising a nucleic acid fragment, a nickase nucleic acid-guided nuclease-gNA complex, and labeled nucleotides. In one exemplary embodiment, provided herein is a composition comprising a nucleic acid fragment, a nickase Cas9-gRNA complex, and labeled nucleotides. In such embodiments, the nucleic acid may comprise DNA. The nucleotides can be labeled, for example with biotin. The nucleotides can be part of an antibody-conjugate pair.
In one embodiment, provided herein is a composition comprising a nucleic acid fragment and a catalytically dead nucleic acid-guided nuclease-gNA complex, wherein the catalytically dead nucleic acid-guided nuclease is fused to a transposase. In one exemplary embodiment, provided herein is a composition comprising a DNA fragment and a dCas9-gRNA complex, wherein the dCas9 is fused to a transposase.
In one embodiment, provided herein is a composition comprising a nucleic acid fragment comprising methylated nucleotides, a nickase nucleic acid-guided nuclease-gNA complex, and unmethylated nucleotides. In an exemplary embodiment, provided herein is a composition comprising a DNA fragment comprising methylated nucleotides, a nickase Cas9-gRNA complex, and unmethylated nucleotides.
In one embodiment, provided herein is a gDNA complexed with a nucleic acid-guided-DNA endonuclease. In an exemplary embodiment, the nucleic acid-guided-DNA endonuclease is NgAgo.
In one embodiment, provided herein is a gDNA complexed with a nucleic acid-guided-RNA endonuclease.
In one embodiment, provided herin is a gRNA complexed with a nucleic acid-guided-DNA endonuclease.
In one embodiment, provided herein is a gRNA complexed with a nucleic acid-guided-RNA endonuclease. In one embodiment, the nucleic acid-guided-RNA endonuclease comprises C2c2.

Kits and Articles of Manufacture

The present application provides kits comprising any one or more of the compositions described herein, not limited to adapters, gNAs (e.g., gRNAs), gNA collections (e.g., gRNA collections), nucleic acid molecules encoding the gNA collections, and the like.
In one exemplary embodiment, the kit comprises a collection of DNA molecules capable of transcribing into a library of gRNAs wherein the gRNAs are targeted to human genomic or other sources of DNA sequences.
In one embodiment, the kit comprises a collection of gNAs wherein the gNAs are targeted to human genomic or other sources of DNA sequences.
In some embodiments, provided herein are kits comprising any of the collection of nucleic acids encoding gNAs, as described herein. In some embodiments, provided herein are kits comprising any of the collection of gNAs, as described herein.
The present application also provides all essential reagents and instructions for carrying out the methods of making the gNAs and the collection of nucleic acids encoding gNAs, as described herein. In some embodiments, provided herein are kits that comprise all essential reagents and instructions for carrying out the methods of making individual gNAs and collections of gNAs as described herein.
Also provided herein is computer software monitoring the information before and after contacting a sample with a gNA collection produced herein. In one exemplary embodiment, the software can compute and report the abundance of non-target sequence in the sample before and after providing gNA collection to ensure no off-target targeting occurs, and wherein the software can check the efficacy of targeted-depletion/encrichment/capture/partitioning/labeling/regulation/editing by comparing the abundance of the target sequence before and after providing gNA collection to the sample.
The following examples are included for illustrative purposes and are not intend to limit the scope of the invention.

Examples

Example 1: Construction of a gRNA Library from a T7 Promoter Human DNA Library

T7 Promoter Library Construction

Human genomic DNA (400 ng) was fragmented using an S2 Covaris sonicator (Covaris) for 8 cycles, to yield fragments of 200-300 bp in length. Fragmented DNA was repaired using the NEBNext End Repair Module (NEB) and incubated at 25° C. for 30 min, then heat inactivated at 75° C. for 20 min. To make T7 promoter adapters, oligos T7-1 (5′GCCTCGAGC*T*A*ATACGACTCACTATAGAG3′, * denotes a phosphorothioate backbone linkage)(SEQ ID NO: 4397) and T7-2 (sequence 5′Phos-CTCTATAGTGAGTCGTATTA3′) (SEQ ID NO: 4398) were admixed at 15 μM, heated to 98° C. for 3 min then cooled slowly (0.1° C./min) to 30° C. T7 promoter blunt adapters (15 pmol total) were then added to the blunt-ended human genomic DNA fragments, and incubated with Blunt/TA Ligase Master Mix (NEB) at 25° C. for 30 min ((2) in FIG. 1). Ligations were amplified with 2 μM oligo T7-1, using Hi-Fidelity 2× Master Mix (NEB) for 10 cycles of PCR (98° C. for 20 s, 63° C. for 20 s, 72° C. for 35 s). Amplification was verified by running a small aliquot on agarose gel electrophoresis. PCR amplified products were recovered using 0.6×AxyPrep beads (Axygen) according to the manufacturer's instructions, and resuspended in 15 μL of 10 mM Tris-HCl pH 8.

Digestion of DNA

PCR amplified T7 promoter DNA (2 μg total per digestion) was digested with 0.1 μL of Nt.CviPII (NEB) in 10 μL of NEB buffer 2 (50 mM NaCl, 10 mM Tris-HCl pH 7.9, 10 mM MgCl₂, 100 μg/mL BSA) for 10 min at 37° C. ((3) in FIG. 1), then heat inactivated at 75° C. for 20 min. An additional 10 μL of NEB buffer 2 with 1 μL of T7 Endonuclease I (NEB) was added to the reaction, and incubated at 37° C. for 20 min ((4) in FIG. 1). Enzymatic digestion of DNA was verified by agarose gel electrophoresis. Digested DNA was recovered by adding 0.6×AxyPrep beads (Axygen), according to the manufacturer's instructions, and resuspended in 15 μL of 10 mM Tris-HCl pH 8.

Ligation of Adapters and Removal of HGG

DNA was then blunted using T4 DNA Polymerase (NEB) for 20 min at 25° C., followed by heat inactivation at 75° C. for 20 min ((5) in FIG. 1).
To make MlyI adapters, oligos MlyI-1 (sequence 5′>3′, 5′Phos-GGGACTCGGATCCCTATAGTGATACAAAGACGATGACGACAAGCG) (SEQ ID NO: 4399) and MlyI-2 (sequence 5′>3′, TCACTATAGGGATCCGAGTCCC) (SEQ ID NO: 4400) were admixed at 15 μM, heated to 98° C. for 3 min then cooled slowly (0.1° C./min) to 30° C. MlyI adapters (15 pmol total) were then added to T4 DNA Polymerase-blunted DNA, and incubated with Blunt/TA Ligase Master Mix (NEB) at 25° C. for 30 min ((6) in FIG. 1). Ligations were heat inactivated at 75° C. for 20 min, then digested with MlyI and XhoI (NEB) for 1 hr at 37° C., so that HGG motifs are eliminated ((7) in FIG. 1). Digests were then cleaned using 0.8×AxyPrep beads (Axygen), and DNA was resuspended in 10 μL of 10 mM Tris-Cl pH 8.
To make StlgR adapters, oligos stlgR (sequence 5′>3′, 5′Phos-GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCG AGTCGGTGCTTTTTTTGGATCCGATGC) (SEQ ID NO: 4401) and stlgRev (sequence 5′>3′, GGATCCAAAAAAAGCACCGACTCGGTGCCACUITTITCAAGTTGATAACGGACTAGCCTTATTTTAAC TTGCTATTTCTAGCTCTAAAAC) (SEQ ID NO: 4402) were admixed at 15 μM, heated to 98° C. for 3 min then cooled slowly (0.1° C./min) to 60° C. StlgR adapters (5 pmol total) were added to HGG-removed DNA fragments, and incubated with Blunt/TA Ligase Master Mix (NEB) at 25° C. for 30 min ((8) in FIG. 1). Ligations were then incubated with Hi-Fidelity 2× Master Mix (NEB), using 2 μM of both oligos T7-1 and gRU (sequence 5′>3′, AAAAAAAGCACCGACTCGGTG) (SEQ ID NO: 4403), and amplified using 20 cycles of PCR (98° C. for 20 s, 60° C. for 20 s, 72° C. for 35 s). Amplification was verified by running a small aliquot on agarose gel electrophoresis. PCR amplified products were recovered using 0.6×AxyPrep beads (Axygen) according to the manufacturer's instructions, and resuspended in 15 μL of 10 mM Tris-HCl pH 8.

In Vitro Transcription

The T7/gRU amplified library of PCR products was then used as template for in vitro transcription, using the HiScribe T7 In Vitro Transcription Kit (NEB). 500-1000 ng of template was incubated overnight at 37° C. according to the manufacturer's instructions. To transcribe the guide libraries into gRNAs, the following in vitro transcription reaction mixture was assembled: 10 μL of purified library (˜500 ng), 6.5 μL of H₂O, 2.25 μL of ATP, 2.25 μL of CTP, 2.25 μL of GTP, 2.25 μL of UTP, 2.25 μL of 10× reaction buffer (NEB) and 2.25 μL of T7 RNA Polymerase mix. The reaction was incubated at 37° C. for 24 hr, then purified using the RNA cleanup kit (Life Technologies), eluted with 100 μL of RNase-free water, quantified and stored at −20° C. until use.

Example 2: Construction of gRNA Library from Intact Human Genomic DNA

Digestion of DNA

Human genomic DNA ((1) in FIG. 2; 20 μg total per digestion) was digested with 0.1 μL of Nt.CviPII (NEB) in 40 μL of NEB buffer 2 (50 mM NaCl, 10 mM Tris-HC pH 7.9, 10 mM MgCl₂, 100 μg/mL BSA) for 10 min at 37° C., then heat inactivated at 75° C. for 20 min. An additional 40 μL of NEB buffer 2 and 1 μL of T7 Endonuclease I (NEB) was added to the reaction, with 20 min incubation at 37° C. (e.g., (2) in FIG. 2). Fragmentation of genomic DNA was verified with a small aliquot by agarose gel electrophoresis. DNA fragments between 200 and 600 bp were recovered by adding 0.3×AxyPrep beads (Axygen), incubating at 25° C. for 5 min, capturing beads on a magnetic stand and transferring the supernatant to a new tube. DNA fragments below 600 bp do not bind to beads at this bead/DNA ratio and remain in the supernatant. 0.7×AxyPrep beads (Axygen) were then added to the supernatant (this will bind all DNA molecules longer than 200 bp), allowed to bind for 5 min. Beads were captured on a magnetic stand and washed twice with 80% ethanol, air dried. DNA was then resuspended in 15 μL of 10 mM Tris-HCl pH 8. DNA concentration was determined using a Qbit assay (Life Technologies).

Ligation of Adapters

To make T7/MlyI adapters, oligos MlyI-1 (sequence 5′>3′, 5′Phos-GGGGGACTCGGATCCCTATAGTGATACAAAGACGATGACGACAAGCG) (SEQ ID NO: 4404) and T7-7 (sequence 5′>3′, GCCTCGAGC*T*A*ATACGACTCACTATAGGGATCCAAGTCCC, * denotes a phosphorothioate backbone linkage) (SEQ ID NO: 4405) were admixed at 15 μM, heated to 98° C. for 3 min then cooled slowly (0.1° C./min) to 30° C. The purified, Nt.CviPII/T7 Endonuclease I digested DNA (100 ng) was then ligated to 15 pmol of T7/MlyI adapters using Blunt/TA Ligase Master Mix (NEB) at 25° C. for 30 min ((3) in FIG. 2). Ligations were then amplified by 10 cycles of PCR (98° C. for 20 s, 60° C. for 20 s, 72° C. for 35 s) using Hi-Fidelity 2× Master Mix (NEB), and 2 μM of both oligos T7-17 (GCCTCGAGC*T*A*ATACGACTCACTATAGGG * denotes a phosphorothioate backbone linkage) (SEQ ID NO: 4406) and Flag (sequence 5′>3′, CGCTTGTCGTCATCGTCTTTGTA) (SEQ ID NO: 4407). PCR amplification increases the yield of DNA and, given the nature of the Y-shaped adapters we used, always resulted in T7 promoter being added distal to the HGG site and MlyI site being added next to the HGG motif ((4) in FIG. 2).
PCR products were then digested with MlyI and XhoI (NEB) for 1 hr at 37° C., and heat inactivated at 75° C. for 20 min ((5) in FIG. 2). Following that, 5 pmol of adapter StlgR (in Example 1) was ligated using Blunt/TA Ligase Master Mix (NEB) at 25° C. for 30 min ((6) in FIG. 2). Ligations were then amplified by PCR using Hi-Fidelity 2× Master Mix (NEB), 2 μM of both oligos T7-7 and gRU (in Example 1) and 20 cycles of PCR (98° C. for 20 s, 60° C. for 20 s, 72° C. for 35 s). Amplification was verified by running a small aliquot on agarose gel electrophoresis. PCR amplified products were recovered using 0.6×AxyPrep beads (Axygen) according to the manufacturer's instructions, and resuspended in 15 μL of 10 mM Tris-HCl pH 8.
Samples were then used as templates for in vitro transcription reaction as described in Example 1.

Example 3: Direct Cutting with CviPII

30 μg of human genomic DNA was digested with 2 units of NtCviPII (New England Biolabs) for 1 hour at 37° C., followed by heat inactivation at 75° C. for 20 minutes. The size of the fragments was verified to be 200-1,000 base pairs using a fragment analyzer instrument (Advanced Analytical). The 5′ or 3′ protruding ends (as shown, for example, in FIG. 3) were converted to blunt ends by adding 100 units of T4 DNA polymerase (New England Biolabs), 100 μM dNTPs and incubating at 12° C. for 30 minutes. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 20 μL elution buffer. The DNA was then ligated to MlyI adapter (see, for example, Example 4) or BaeI/EcoP15I adapters (see, for example, Example 4) or BaeI/EcoP15I adapters (see, for example, Example 5)

Example 4: Use of MlyI Adapter

Adapter MlyI was made by combining 2 μmoles of MlyI Ad1 and MlyAd2 in 40 μL water. Adapter BsaXI/MmeI was made by combining 2 μmoles oligo BsMm-Ad1 and 2 μmoles oligo BsMm-Ad2 in 40 μL water. T7 adapter was made by combining 1.5 μmoles of T7-Ad1 and T7-Ad2 oligos in 100 μL water. Stem-loop adapter was made by combining 1.5 μmoles of gR-top and gR-bot oligos in 100 μL water. In all cases, after mixing adapters were heated to 98° C. for 3 min then cooled to room temperature at a cooling rate of 1° C./min in a thermal cycler.

TABLE 5

Oligonucleotides used with MlyI Adapter.

SEQ
ID	Oligo
NO	name	Sequence (5′>3′)	Modification

4408	MlyI-	gagatcagcttctgcattgatgccagcagcccgagtcag	none
	Ad1

4409	MlyI-	ctgactcgggctgctgtacaaagacgatgacgacaagcgtta	5′phosphate
	Ad2

4410	BsMm-	gagatcagcttctgcattgatgcGGAGCCGCAGTACACTATCCAAC	none
	Ad1

4411	BsMm-	GTTGGATAGTGTACTGCGGCTCCtacaaagacgatgacgacaagcg	5′phosphate
	Ad2

4412	T7-Ad1	gcctcgagctaatacgactcactatagagNN	none

4398	T7-Ad2	Ctctatagtgagtcgtatta		5′phosphate

4413	gR-top	ttagagctagaaatagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggt		5′phosphate
		gctttttt

4414	gR-bot	aaaaaagcaccgactcggtgccactttttcaagttgataacggactagccttattttaacttgctatttct	none
		agctctaaaac

The DNA containing the CCD blunt ends (from earlier section) was then ligated to 50 pmoles of adapter MlyI, using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. The DNA was then recovered by incubating with 0.6× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4 (50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 100 μg/mL BSA, pH 7.9). These steps eliminate small (<100 nucleotides) DNA and MlyI adapter dimers.
Purified DNA was then digested by adding 20 units of MlyI (New England Biolabs) and incubating at 37° C. for 1 hour to eliminate both the adapter derived sequences and the CCD (and complementary HGG) motifs. DNA was recovered from the digest by incubating with 0.6× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 30 μL buffer 4.
The purified DNA was then ligated to 50 pmoles of adapter BsaXI/MmeI, using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. The DNA was then recovered by incubating with 0.6× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4 (50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 100 μg/mL BSA, pH 7.9). DNA was then digested by addition of 20 units MmeI (New England Biolabs) and 40 pmol/μL SAM (S-adenosyl methionine) at 37° C. for 1 hour, followed by heat inactivation at 75° C. for 20 minutes. DNA was then ligated to 30 pmoles T7 adapter using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 20 μL buffer 4, then digested with 20 units of BsaXI for 1 hour at 37° C. The guide RNA stem-loop sequences were added by adding 15 pmoles stem-loop adapter and using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 min. DNA was then recovered using a PCR cleanup kit (Zymo), eluted in 20 μL elution buffer and PCR amplified using HiFidelity 2× master mix (New England Biolabs). Primers T7-Ad1 and gRU (sequence 5′>3′ AAAAAAGCACCGACTCGGTG) (SEQ ID NO: 4419) were used to amplify with the following settings (98° C. 3 min; 98° C. for 20 sec, 60° C. for 30 secs, 72° C. for 20 sec, 30 cycles). The PCR amplicon was cleaned up using the PCR cleanup kit and verified by DNA sequencing, then used as template for an in vitro transcription reaction to generate guide RNAs.

Example 5: Use of BaeI/EcoP15I Adapter

Adapter Bae/EcoP15I was made by combining 2 μmoles of BE Ad1 and BE Ad2 in 40 μL water. T7-E adapter was made by combining 1.5 μmoles of T7-Ad3 and T7-Ad4 oligos in 100 μL water. In all cases, after mixing adapters were heated to 98° C. for 3 min then cooled to room temperature at a cooling rate of 1° C./min in a thermal cycler.

TABLE 6

Oligonucleotides used with BaeI/EcoP15I Adapter.

SEQ
ID	Oligo
NO:	name	Sequence (5′>3′)	Modification

4415	BE	ActgctgacACAAgtatcTTTTTTTTTTgtttaaacTTTTTTTTTTgatacACAAgtcagcagA		5′phosphate
	Ad1

4416	Be	TagctgacTTGTgtatcAAAAAAAAAAgtttaaacAAAAAAAAAAgatacTTGTgtcagcagT		5′phosphate
	Ad2

12	T7-	gcctcgagctaatacgactcactatagag	none
	Ad3

4417	T7-	NNctctatagtgagtcgtatta	5′phosphate
	Ad4

4418	stlgR	ttagagctagaaatagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccg	5′adenylation
		agtcggtgctttttt

The DNA containing the CCD blunt ends (from earlier section) was then ligated to 50 pmoles of adapter BaeI/EcoP15I, using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. The DNA was then recovered by incubating with 0.6× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4 (50 mM potassium acetate 20 mM Tris-acetate, 10 mM magnesium acetate, 100 μg/mL BSA, pH 7.9). Recovered DNA was then digested with 20 units PmeI for 30 min at 37° C.; DNA was then recovered by incubating with 1.2× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4. These steps eliminate small (<100 nucleotides) DNA and BaeI/EcoP15I adapter multimers.
DNA was then digested by addition of 20 units EcoP15I (New England Biolabs) and 1 mM ATP at 37° C. for 1 hour, followed by heat inactivation at 75° C. for 20 minutes. DNA was then ligated to 30 pmoles T7-E adapter using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 20 μL buffer 4.
Purified DNA was then digested by adding 20 units of BaeI (New England Biolabs), 40 pmol/μL SAM (S-adenosyl methionine) and incubating at 37° C. for 1 hour to eliminate both the adapter derived sequences and the CCD (and complementary HGG) motifs. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 20 μL elution buffer.
Recovered DNA was then ligated to the stlgR oligo using Thermostable 5′ AppDNA/RNA Ligase
(New England Biolabs) by adding 20 units ligase, 20 pmol stlgR oligo, in 20 μL ss ligation buffer (10 mM Bis-Tris-Propane-HCl, 10 mM MgCl₂, 1 mM DTT, 2.5 mM MnCl₂, pH 7 @ 25° C.) and incubating at 65° C. for 1 hour followed by heat inactivation at 90° C. for 5 min. DNA product was then PCR amplified using HiFidelity 2× master mix (New England Biolabs). Primers T7-Ad3 and gRU (sequence 5′>3′ AAAAAAGCACCGACTCGGTG) (SEQ ID NO: 4419) were used to amplify with the following settings (98° C. 3 min; 98° C. for 20 sec, 60° C. for 30 secs, 72° C. for 20 see, 30 cycles). The PCR amplicon was cleaned up using the PCR cleanup kit and verified by DNA sequencing, then used as template for an in vitro transcription reaction to generate the guide RNAs.

Example 6: NEMDA Method

NEMDA (Nicking Endonuclease Mediated DNA Amplification) was performed using 50 ng of human genomic DNA. The DNA was incubated in 100 μL thermo polymerase buffer (20 mM Tris-HCl, 10 mM (NH₄)₂SO₄, 10 mM KCl, 6 mM MgSO₄, 0.1% Triton® X-100, pH 8.8) supplemented with 0.3 mM dNTPs, 40 units of Bst large fragment DNA polymerase, and 0.1 units of NtCviPII (New England Biolabs) at 55° C. for 45 min, followed by 65° C. for 30 min and finally 80° C. for 20 min in a thermal cycler.
The DNA was then diluted with 300 μL of buffer 4 supplemented with 200 pmoles of T7-RND8 oligo (sequence 5′>3′ gcctcgagctaatacgactcactatagagnnnnnnnn) (SEQ ID NO: 4420) and boiled at 98° C. for 10 min followed by rapid cooling to 10° C. for 5 min. The reaction was then supplemented with 40 units of E. coli DNA polymerase I and 0.1 mM dNTPs (New England Biolabs) and incubated at room temperature for 20 min followed by heat inactivation at 75° C. for 20 min. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 30 μL elution buffer.
DNA was then ligated to 50 pmoles of adapter BaeI/EcoP15I, using the blunt/TA ligation master mix (New England Biolabs) at room temperature for 30 minutes. The DNA was then recovered by incubating with 0.6× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80/o ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4 (50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 100 μg/mL BSA, pH 7.9). Recovered DNA was then digested with 20 units PmeI for 30 min at 37° C.; DNA was then recovered by incubating with 1.2× Kapa SPRI beads (Kapa Biosystems) for 5 minutes, capturing the beads with a magnetic rack, washing twice with 80% ethanol, air drying the beads for 5 minutes and finally resuspending the DNA in 50 μL buffer 4. These steps eliminate small (<100 nucleotides) DNA and BaeI/EcoP15I adapter multimers.
Purified DNA was then digested by adding 20 units of BaeI (New England Biolabs), 40 pmol/μL SAM (S-adenosyl methionine) and incubating at 37° C. for 1 hour to eliminate both the adapter derived sequences and the CCD (and complementary HGG) motifs. DNA was then recovered using a PCR cleanup kit (Zymo) and eluted in 20 μL elution buffer.
Recovered DNA was then ligated to the stlgR oligo using Thermostable 5′ AppDNA/RNA Ligase (New England Biolabs) by adding 20 units ligase, 20 pmol stlgR oligo, in 20 μL ss ligation buffer (10 mM Bis-Tris-Propane-HCl, 10 mM MgCl₂, 1 mM DTT, 2.5 mM MnCl₂. pH 7 @ 25° C.) and incubating at 65° C. for 1 hour followed by heat inactivation at 90° C. for 5 min. DNA product was then PCR amplified using HiFidelity 2× master mix (New England Biolabs). Primers T7-Ad3 (sequence 5′>3′ gctcgagctaatacgactcactatagag) (SEQ ID NO: 12) and gRU (sequence 5′>3′ AAAAAAGCACCGACTCGGTG) (SEQ ID NO: 4419) were used to amplify with the following settings (98° C. for 3 min; 98° C. for 20 sec, 60° C. for 30 secs, 72° C. for 20 sec, 30 cycles). The PCR amplicon was cleaned up using the PCR cleanup kit and verified by DNA sequencing, then used as template for an in vitro transcription reaction to generate the guide RNAs.

Claims

1. A collection of nucleic acids the nucleic acids in the collection comprising:

a second segment encoding a targeting sequence; and

a third segment encoding a nucleic acid-guided nuclease system protein-binding sequence, wherein the collection of nucleic acids comprises at least 10⁵unique nucleic acid molecules.

2. The collection of claim 1, wherein the nucleic acid-guided nuclease system protein is a CRISPR/Cas system protein.

3. The collection of claim 1, wherein the size of the second segment varies from 15-250 bp across the collection of nucleic acids.

4. The collection of claim 1, wherein at least 10% of the second segments in the collection are greater than 21 bp.

5. The collection of claim 1, wherein the size of the second segment is not 20 bp and is not 21 bp.

6. (canceled)

7. The collection of claim 1, wherein the collection of nucleic acids is a collection of DNA.

8. The collection of claim 7, wherein the second segment is single stranded DNA.

9. The collection of claim 7, wherein the third segment is single stranded DNA.

10. The collection of claim 7, wherein the third segment is double stranded DNA.

11. The collection of claim 1, further comprising a first segment comprising a regulatory region, wherein the regulatory region is a region capable of binding a transcription factor.

12. The collection of claim 1, further comprising a first segment comprising a regulatory region, wherein the regulatory region comprises a promoter.

13. The collection of claim 13, wherein the promoter is selected from the group consisting of T7, SP6, and T3.

14. The collection of claim 1, wherein the targeting sequence is directed at a mammalian genome, eukaryotic genome, prokaryotic genome, or a viral genome.

15. The collection of claim 1, wherein the targeting sequence is directed at repetitive or abundant DNA.

16. The collection of claim 1, wherein the targeting sequence is directed at mitochondrial DNA, ribosomal DNA, Alu DNA, centromeric DNA, SINE DNA, LINE DNA, or STR DNA.

17. The collection of claim 1, wherein the sequence of the second segments is selected from Table 3 and/or Table 4.

18. (canceled)

19. The collection of claim 1, wherein the targeting sequence is at least 80% complementary to the strand opposite to a sequence of nucleotides 5′ to a PAM sequence.

20. The collection of claim 1, wherein the collection comprises targeting sequences directed to sequences of interest spaced about every 10,000 bp or less across the genome of an organism.

21. The collection of claim 20, wherein the PAM sequence is AGG, CGG, or TGG.

22. The collection of claim 20, wherein the PAM sequence is specific for a CRISPR/Cas system protein selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, and Cm5.

23. The collection of claim 1, wherein the third segment comprises DNA encoding a gRNA stem-loop sequence.

24. The collection of claim 1, wherein the sequence of the third segment encodes for a RNA comprising the sequence GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAA AGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 1) or encodes for a RNA comprising the sequence GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUC AACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUUC (SEQ ID NO: 2).

25. The collection of claim 1, wherein the sequence of the third segment encodes for a crRNA and a tracrRNA.

26. The collection of claim 1, wherein the nucleic acid-guided nuclease system protein is from a bacterial species.

27. The collection of claim 1, wherein the nucleic acid-guided nuclease system protein is from an archaea species.

28. The collection of claim 2, wherein the CRISPR/Cas system protein is a Type I, Type II, or Type III protein.

29. The collection of claim 2, wherein the CRISPR/Cas system protein is selected from the group consisting of Cas9, Cpf1, Cas3, Cas8a-c, Cas10, Cse1, Csy1, Csn2, Cas4, Csm2, Cm5, dCas9 and cas9 nickase.

30. The collection of claim 1, wherein the third segment comprises DNA encoding a Cas9-binding sequence.

31. The collection of claim 1, wherein a plurality of third segments of the collection encode for a first nucleic acid-guided nuclease system protein binding sequence, and a plurality of the third segments of the collection encode for a second nucleic acid-guided nuclease system protein binding sequence.

32. The collection of claim 1, wherein the third segments of the collection encode for a plurality of different binding sequences of a plurality of different nucleic acid-guided nuclease system proteins.

33.-192. (canceled)

193. A kit comprising the collection of nucleic acids of claim 1.

194.-235. (canceled)

236. The collection of claim 1, wherein at least 10% of the nucleic acids in the collection vary in size.

237. The collection of claim 1, further comprising a first segment comprising a regulatory region.

238. A collection of guide RNAs generated by transcribing the collection of claim 1.