Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_028254
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 677434
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Found at i:2629 original size:17 final size:17
Alignment explanation
Indices: 2607--2642 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2597 GGGAAGATAG
2607 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
2624 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
2641 AG
1 AG
2643 CTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.31, T:0.03
Consensus pattern (17 bp):
AGAAAGAGAGACAAGAA
Left flanking sequence: Indices 2107 -- 2606
TTATCCAGAAACAACTCAATCAATCAATTACCTTATTTAAGATACGCCCAAATCCATTCAACCAG
CCACTCAAGGGTTTGGAGTTACCATTTCCGCTATTCCTGCCAAGGAATAAAGTAAAGGGACTACC
GATACCCCTTCGCGTTCGCTTTGGTTTAGAGTAATCGCTTGTTCCTTCAGTCTTCAGAGGTAAGC
TCTTTTGCCTTCTTCCTAATGGACTACGAGGACCCTAGGATTTAGGACTCTTATAAAGAAGGATT
ATTGGCCTACTGCTGCCTTACCACTAGCTTAACACTAGCAGCACAGGCTTACCTATTAATCACAG
ACCCCCTTCCTTACTTGCTTACTTCCTTGCTTGCCTGGAGAGAAAGAATATTAAAAAGAAAGAAA
GGATCCCCTACTTACTTAGTACAAGGAAGGGAAAGACTTACTAAAAGACCAAAGACTGGCTTACT
TACTGTCTTGGCTCCTAGGACTTCTTACAAGGAATGGGAAGATAG
Right flanking sequence: Indices 2643 -- 3142
CTAAGGATATAACGAAGGGCGAAAGGGAGCACAGAAAGGCGCAATACCAAAGCTTTTTTGAAAGA
GAAGAATGCGCCATAGGTTTCTTCCTGCTTTGCTTTGGGAAGGGGCATTGAAAGAACACAGACAT
AGTGGAAATGCTCCTAGACTAGAGAAGGTTCCCCCGTAAGTCTGATCCTCTCAACTCATACTACA
GCAGGGAAATCCACTTTTCTGGACAGGGTCTTCCTTCTCGGAGAATAGGTCTACTATGCTGAAGC
AGAAGGGAACAGGATGCTCATTTAAATGTCAATGAGACTAGTCAGGATGCTCCCTGTAGTACATT
CCCAGATCTGAGCTACCTGGATCAACCCACCAATTAGTACAGTTCGTCAGTGAGTACGTGGGAAT
AGCCCAGTAATGAATAGAAATTTAAGTCACCGGGTAAAGAAGCGAGGGGATCAGCTCAATTGAAA
GAGAGGGCGCGATCGGCATACAATTATTCGATTTCATTTCTTGCC
Found at i:58966 original size:19 final size:19
Alignment explanation
Indices: 58930--58966 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58920 ATGCTATAGA
*
58930 CATGCTATAGAGTAGTCAG
1 CATGCTATAGAGCAGTCAG
*
58949 CATGCTATAGAGCGGTCA
1 CATGCTATAGAGCAGTCA
58967 AAATCCCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (19 bp):
CATGCTATAGAGCAGTCAG
Left flanking sequence: Indices 58430 -- 58929
CATACCTAGCGCCGGGGGTCTCTTTTTACCTTCGCCGAGGGTTTGGTTTGCTTTATGTGTAGTAA
AATCTCTCCCTCATTGTTAGGAGCGGAATAGCTTATTATATATATGAGAAGGGAGGTGTAAAATG
CGGTCTCTGAAAGAAGAAATTCCAGTTTAGGACACCTTGTAGGGAATCGGAGAAGTTGCATGAAG
AGGTCCTTAGACTCTATTGGAACAAAGCTAAGTTTCGACTACTTCTCTCTCGGGTTCAATGAAAG
CAGCCTCGAAAGAACCAAGGCATAATAGTGTGGTACCTCGATTAGTCGCTGGTCAAAGCCCAAAC
TCAAAGGGTAGAAAATGCGGTGGAATAAAAGAGAAAATAGGAGATTGAACTCCTCATTGGGCATT
CAGGGATGAATGCTTTATATCATTACAATAGGCAGTGGAAATACATCCTTTGAGGAGTAAGAGCA
GGTACCTCGAACTCAAGTGAAGCTGTCGGTGAAGCATGCTATAGA
Right flanking sequence: Indices 58967 -- 59466
AAATCCCCAATGCTTGGCTGGAAGCAAGGTGCGTAGCCTCTTCAGCAGTAGGAGTCGGAGTAATA
GGTTCTGAAAGAAGGGAACAAAGGCTTGATGCAATTAAGCAGTAGCAGTAGCTAAAAGAGTAGTA
GCTGTAGGTTCTGAAAGAAGGGAACAAGAGTGAGACTTTCTTCCCACTCCCATACTCCTCTAAGA
GTCTCTCTCCTTTAATCAATTACATCGAACCAAAGGCTATATACTCAAATGGAGTGAGTTCTGGC
GTTCAGGTAATCCTCTCGTGGAGCACTTTACCAATTGATCAACCAGATTTGGGCTTTATGTGTAA
AAAAGAGAAGTTCTCACCAACAGCAGAAAGATACCAAGCAGCAGATACGGGTTTAGCGGGAACAG
CTAGCTTTATCGGAAGGAGCTGAATCCACATCTGCTATAGCTAAAATACCTGTTTCTGACCCATG
TGGTTTTACTCAACTTGAGGCCAAAACGCCTAATTTGAGCATCTT
Found at i:128281 original size:19 final size:19
Alignment explanation
Indices: 128254--128295 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
128244 TAGCAGCACC
128254 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
128273 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
128292 AAAA
1 AAAA
128296 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Left flanking sequence: Indices 127754 -- 128253
GAACATATTAAAGCACTCCTTGGAGTTCCTAAAAAATCCACTCTTTCTGCCATATTGTTGGTTGT
GCTTTTTGATTGTGCGCAGCTTTTCCAGACCATATTCTTTCTTCTTCGAGCATTTCGACGATTTG
TTGAATCTTATTAGGTGAGGGTACTTCGGATTTTCGTAAATCGATAATAAGGTCAGCTACCTGAT
TTTCCAATGGGGTGAGCTTTCGCATATGTGAGGCCTTGTTAGCTTAGCTCCACCCGTTGGTGCCG
GTTGCTCCTGCTGCTCCAACTCCCTCCAGATGTCCTCTTGGTTGACTTCAGCAGCTTGGATTTCA
AACGAAGGAGAAACAGGCTCCTGAGCTAGTGGTAGTGGCTCAGAAGCTTCCGGCACCGGGGGGAG
GGCTTGCTGCACCTCCATCGAATCGACCTTATCTTCCTCAAACTCGCAAGCTGCGACGATGATGA
TAGGAATTAAAAAATGTTAGTATGGAGTTGAACAGTAGCAGCACC
Right flanking sequence: Indices 128296 -- 128795
ATATCTGAAGAAATTTTAGGGTTCGTGATAATAGATCTGGGCCGGTTGAAAAGGCTCTTTTTCTT
CTTCTTCATTCTCGACAGGAATACATCAACAAAACAGCCCTTCCATATAGGTGCATGAACTTTGT
CAATAGATTCCTAGCTAACTCCTCTTCCTATTGATCTTGATTAGTTCCAGCTTGTTGAGAGTTCT
CTTTTTTTTTTTTGAATCGGACCCATTTTTAGACCGTCTCCTGAAATACCTGCTTATCCCGCATG
TGCTTTCGGAGCCCCCCACTCATTCAATCACTTGCTTGTGATTGCAGCCATTCCCCGAAAAGGGA
ATTGTCCGCTCCCGTTCATGGGACGAACCGAACATCGTTAGGTCCCGAATTCTGCGAACCACCGG
ATCTAGACCAAGATCTCCATTACGTCGTACGAGATATCGATCCGAAGAACTTACTTTCAGTTGTA
AGTTATCCATTCTGCTTCTATCTAAAGTGATGCTAGGCTGCTTCA
Found at i:141135 original size:15 final size:15
Alignment explanation
Indices: 141115--141144 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
141105 GGAGGCAGGC
141115 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
141130 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
141145 AATATACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAGTGAAATAAAAT
Left flanking sequence: Indices 140615 -- 141114
ACGGCTTTCAAAAGACGAGTAAGAGACGGGGAGGGGGAGGCTCTCGAAACCAAGCGAGACTAAAA
AGAACATGGGAATTCGCACCATTCCTATGAGTGCTTTTTTTCGAAAAGCCAACAAAGGGACAGCC
CTCTTTCTCTATCTCGGTCTCGGTTTAGCATCATCATATATCGATCCGGAGATAATTTGGATTGG
TTGTAGTGCGGATTAAGGAGCTGCTCCTCCATGCTGTGGCTGTGGAGGTGGGGGCTGCCGCCGCC
TGATAGAGGCAGAAGCCGGGGCCACCGGAGCTATCTGCGTCGAGTGTGTCGATTGAAAGAGGAGG
GGAGACAAAATGAATTCCAGCGAAAAAATAGAAAGAGTCGTGCCGTTCAAAGTGGAATTCTTCTA
AGATCCATCCATTGCTCGATCGATTTTGCATGCTCTGCTCCCAAAATGCAGAGAGACTTGCGAGG
GCAGATCTGGGTTGGTTGGTCCGGAAAGTCATGGGGGAGGCAGGC
Right flanking sequence: Indices 141145 -- 141644
AATATACTGGTGCTACTATAGAATCTTTTGAATCACGCACGGCACACTTTCTATATCTCCTCCGT
CTACAAGGTGAACAGCTTGGCTTACAGCACAGCGTGTTCGCCACCACACCGGCTGGCTGGTGCAT
TGGCCCTTTGAATGAATAAGAGAAGGGCTTTGTATAGACACCCTTGAGCCATATTCGTCGCCCTA
GGCTCACCATTATTTCATTCTATTTATGGGTTCTAGCTCCAAAGAACATATACATGGAGCTATGT
CGACTTACGTACGTCTCGTTGACCAAACGATTAGGTATACCACGCCACGTATCATCCCCTCTTTC
CATAAAAAAAAAAAAAAAAAGAAAAGATATAGTGATCGATCGTGCCGTAAGACCTTGTTCGTTTC
TACTTGACGTTATTTTCCTCGGTTTTTTTTACATTACATAAGGTAGCTTGCTTACTTAGCGCTTG
CGCTAAGGATCTAATCAGAGTCAAACTTCAATTTTAAATGAAAAA
Found at i:186964 original size:21 final size:21
Alignment explanation
Indices: 186938--186984 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
186928 TTAAGGGATG
186938 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
186959 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
186980 TAACA
1 TAACA
186985 ATCGATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (21 bp):
TAACAGAAGTTTCAAGAGAAC
Left flanking sequence: Indices 186438 -- 186937
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTTAAATTGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTAAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 186985 -- 187484
ATCGATGGACTGGAAGGGCGAGAGACAGAAGAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:250425 original size:2 final size:2
Alignment explanation
Indices: 250418--250454 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
250408 ATTATAAAAG
*
250418 TA TA TA TA CTA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250455 CTAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 249918 -- 250417
TTTCCGAAAGCGCAGTGCCCCACGGATAGAAGACGACTCCCCTGATTTGGTGTCGCCCATTTTTT
ATATTTATGGGGTTTACACCGTCGTGCACTAATGCTGTTTCTATCTTTTTTTCTAGCAGCATCCG
CTTTTCCAGAACACTAAAAAATGCTGACACCTCGTGGTGTCTCCCGACAAAATGCACTGCTAAGC
GGTCGAACAGTTCCATCCTTCTCGTGTGATCCGGCATCAGGGGTTGCTCGAGAATCGGGACGAGA
ACAGCCTGTGCTATTTCAGGATCAGTCAGGGGCCTCGGGAGCGCGCGGTTGGACCGCTTGATGGA
AATCCGCTGCGCCAGACGGGGAACCACTTCTTACGTCGCACATGGCTATCTCCAGGAGGGGCCCC
TGACTGATTATTCCAACGATAGATAGAATAAGACCCAGAAGTTGGATGGGACTGCCATGAAAGAT
CTCCTCCGGGATTGGATCCCGGTGAAAAGAGATCCATTATAAAAG
Right flanking sequence: Indices 250455 -- 250954
CTAAAAAGGTGGATTTCGCCCTGCAATCCTAAGGGCCAGGATTCAATCTCCACTGGAGCCATTGT
GAGGAATAACCATTCTAGAACAATCATTTGGTTTGTTTCATTCTTTTTTTGTTCTGCTCCCCCCA
AAAAAAAGGGAGACTTCCTCAGGAAATCGCTGGTTTTTCCAACCCAACCGAGGATTTCCGACAAG
TCCTTCTTCATTTTTAGAGCAAGAAGGGGAACTATAGAGATTCAATGAACAGTGTTTCTTACGAT
TACGCCCAGCCCAAAAAAGCCCTTCGGAGTTGAACCGAAAAAAAAGCCTATTACTTAGGGCCCTT
CAAGAAGTTTGTGTTAAGCATATAGCCGGGCCCTCTTTCTGAGCCAGGATCAAACTCTTCTTTTT
TTACTATGATTGGGCCCTGCAGACGTACTACTTTCAATCAAACCTTTTCTTTCCTTTCCTTAAGA
TATATATGTTACCCACCATATTAATAAGGCACCAAACGCGCACTG
Found at i:257772 original size:22 final size:22
Alignment explanation
Indices: 257740--257782 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
257730 GGTTGATCAA
257740 CTACGGAGGATCCATTAGCATT
1 CTACGGAGGATCCATTAGCATT
*
257762 CTACGGGGGATCCATTAGCAT
1 CTACGGAGGATCCATTAGCAT
257783 CCCCTCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (22 bp):
CTACGGAGGATCCATTAGCATT
Left flanking sequence: Indices 257240 -- 257739
ATATCAAATATGGTGTGCTAATGGTGATGTGGTTACTAACCCACCAACATATATCATTCCGGAAT
GGACGACTGGAGCACAAACTCCTATTTATATACTTTCTTCCTTGCCAGGCCAGCTGGAAGCGAAA
GAAGCTATCTTTACGGAATGAAAAAGTGCTTCACTGCGCATATGCATATGCTACAGCTGATATGC
GACAGTCAGTATAATTGAACAATATTTTATCCACTTGAAGCTGATACGCTGCTAGAGTTGACTTG
CAAGGTTTTCGCAGATGAGTTGTAGCTTCCTTTGTCCTTCTCTTCCCCTCCGAGCAGTAGCAGGA
GATAATTCAATTGGGATAGTAGGGGACGGTGCTTCGGGTTAGCACTCTCTCTCTTTCCGTCGGTG
AACAAGTCTCATTCGTTTGGCCGGCCCTAAATCAGCATTGAAATCCTTTTTTCCATGGTCATAGA
ATGATTGTGACTTACGAGTAACAGGCTCTGAAAGAGGTTGATCAA
Right flanking sequence: Indices 257783 -- 258282
CCCCTCCCCCGAAATTGGCACATGAGCACTCGAACCCGCCTCTCTTCTTGTCCCACCAGTGTTTA
AAAACAAACCTCCGCTATTATTATACTTTCTACCACGGAAACGTCGATGGGATGTACTTAGGTGC
AGAAGCCATGATCGGTATAGTGAGGCTAGCTTTCCCTCTTGACCTAGGCTTAGGCTGGTATAGAA
GAGTGGGAACAGTCTCCAGGGTATGTGTGATATTGGTATTTGAATACACAGTTATCAAGAAGTCA
AGACAGCAAGAGTCGGATGCGCCAGAATGAATATATGCGGCCAATTCCTTCTTACTGATATCCAA
AGATTCCCTTTAACAGGATGGTTTTAAATGATGGTTTATTACAGGTTCTGGTGGCATGAATAGGA
TGAGCATACGAATGAGCCGGAACATGGATAACGTAGTGGTTCGAGCCGGTCGAGAGTACGAGATT
ACTGACCGAAGACTCTTCAATTGAGATGGGCCGAAGCCCTGCTAG
Found at i:259750 original size:14 final size:14
Alignment explanation
Indices: 259731--259761 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
259721 TATCTAAACT
259731 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
259745 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
259759 ATT
1 ATT
259762 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Left flanking sequence: Indices 259231 -- 259730
AAGAAAAGCTTTTTCAGATGTTAAAAAAAGCATTGTAGGATAATCGGCATCTGTCCCTCGAGAAA
GAGTAAGATAGGCAAAAAGGCATAGAGACTACAGCGGTAATGCCGCATCTCTCGATGAGAAGGAA
TCCTGGAAAGAAGAGCAAAGAAAAGCCCTTCTTCTTCTGCCTTTTGACTCTATCTTGCCCTTTCT
TTAGGGAATTGCGGAGTGAATGAGTGCAACAAAACAAGGAAAGAAGGCTATAAGCTGCCTACATG
GAATTACTCTTCATGCACATTTCCCAGAAAGAGTATATTGCGATAATCGGATGCTAAGTCTCCCT
GGCTTCCTTCCTCCAGCGGATCTGTGGGCATTAAAAGAAGAAAGACTTTCAGGTTCTTCGCCACA
TTCCTTCTTAGGAAAGAAAGGCTCCCGTTCGTGCCCTGTAAGAAGGAAAATTAGAAAGGAAGGCA
TAGTCGAAAAGACTAGCAGCTTCTCTGTGCATGGATATCTAAACT
Right flanking sequence: Indices 259762 -- 260261
ATAATTCAAAAAGACTTTCGCGAAGCAGGAAAACAATCAGGTAATCAGGAAAGGCAGAAAGGGTA
GAGCCTTAGTTACCCGCAGCTCAAATAGCCAAGGTCGGTGGAAAAGGAATAGTACAGCTTGTTTG
GATAAAGGAAGCATTCATACTCGACCCGCGTCTGGACGCCCCTCTCGGGCTCACTTCCTGACAAC
CCAGCCCACAACAGGAAATGGACAGGCATTGACAAAAGCCGAAGCCTCTAACGATTTTTAAGCTG
GGTAACGGGTACCCTATCGGAAAGGGGTTTTCGTCTACCTCCCAAGCATATGGCGGGCTTATAGG
GCGCTGGTCTCCGTTAGGCTTTGAGTCTAGGAGTATAGCGATGGCTTCATCCACCGGTCCTACCA
TGGAACGAGTTTCTTCGCGCTTGGCCTTGAAATTTCGAGGCATCTTTCCCAAGACAAGAAGCGGC
GTCGGATCCCGGTAGTGCGGTAGTACGCCCAGCAGAATGTCGTAG
Found at i:268307 original size:26 final size:26
Alignment explanation
Indices: 268278--268330 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
268268 GACACGCTAT
268278 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
268304 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
268330 G
1 G
268331 CCTTTGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.15
Consensus pattern (26 bp):
GATCGCCGTCAAAGACAGGATTCGAG
Left flanking sequence: Indices 267778 -- 268277
GTGGTAGTGGCTCTATTGACTATAGCCGTCCCAATGTGAAATATAGTATTCAGTAGACGCAAATG
CAGATACTATCCCCTACGGAATAAAACTTTCTTTCATTCCGTAGGGGTAAGACTCTTCAAATAAA
ACTCAAAATTCACCTAGGACTTTTTTCTTTTATAGGGACTTCTGGCTCTGATCCTTCTATAGTAG
GAAGACAAGATCGCAAGGGAATCACTAGTTCGAGTTCCATGCCTTCCTTCTGGTCCCAAACACTG
GGTTATTAACCGATGAGTTAATTTTCCCCTTACCCATTTCTTGTCCATGTGTCCCTTGCTTCTTA
GTGCTCCGTTGGACGGGGACTCCTTCTTCATTTGAATGCTTTGATGCTGGCCAACTGGGAGTAGG
TTCTGGCTGCTCTTTCTGTGATGCTATTTCGACCTCGTAAAGATATTAGGACTTTCACACTGACA
TTGAGACAGAAAACATTCGATCAGTTTCCCAGCGTGACACGCTAT
Right flanking sequence: Indices 268331 -- 268830
CCTTTGTCCCCATTGCTTGTTAGTTAAGTAGGGAGAGAGAACGCCCCATCTCTTGATTACGAAGA
TCACTTTCACAGCAAGCACGAAGCTTAACTATTATGTAAATTGAAACGATCTCCCCAGGAAAGCA
TGATGCCTGACTTGCCCCTGCTTTCCAAAACGGTAGACCAAAAGCACTGAAATGAATATGAGAAA
TGTGGCCTATCTATGGAAGGAATCTTTCGTTACTAGAACCCCTTCCTAGTGACTGTAAGCGAAAT
GCATTTAGCGAACGCCTGGGGGTACTGAGTTCCATATTTTTTATTATAGAAATGTTATCTCTATC
TAAACGACTAAGTCTTCCAGTGATCTCTCCCCCACCCAAAACCATCCCTTCCAGCGTTAGCGCAC
AAGAAGGAGCTTTTGGCAGTGAGTCGAAAGTCTTAGTGAGAAGCCCTCTTAGGACTCTTTCCACT
CTTCTCTGAGTGCCTTCAACAGTGCTTAGGTAGCGCTCACTGCGA
Found at i:295397 original size:17 final size:17
Alignment explanation
Indices: 295354--295399 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
295344 GCAGTAAATG
*
295354 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
295371 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
295387 GAATGAACTAACC
1 GAATAAACTAACC
295400 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 294854 -- 295353
TAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTCCTATCTGCCTATAAGGATTCGATAAAGAAA
GAGAATGTGAGTGGGCAGGAGATCAATAAACACAGAAAGCGAAGAGCAAAAGGAGCAGAAGACAC
TCAGTTGTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTCCCAAAGCAAAGAGA
GCTCAAAGCAATAAGATGAAAGCTGGGATGAGATGCTAGCCTTAGCTAGGAAGATCCATCATTGA
GCCTTAGGCCACTACCGAGCAGAAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAA
AGGCGGAGACAATACCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCAATCACATTT
TCAGGCACACCAGTCAAAGAGCCATCGGACCCATTAAAGTCCCCTTTTTTACTAATATACAAGGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 295400 -- 295899
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGATAAATTCCT
AAAACAGAAAATAAAAGTAAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGATGGATTTTAAG
TCATTTTGGACGAAGCAGCGGGCATACCAGAAATGGCTTGTCAGGAATGGTAGATGGAGCAAGAA
TGCATAGCAGGCTTAAAACACGACACAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTC
ATTGGAGCTAGCATACGAAATTATCCGTTGAAGGGTTCAACTCTCAGGGCGGCCATTGCGAGCGA
TATTCACTTTCAAGAATCATCGAGCCTACGCCTATTTCATTACTCTCGAAGAGCTCATCAAAGAG
CTAAGGCTAAGGGATGAGAAAAAAAAAGGAGGAGGTGGAATTTCTTTCAACTATAACATTTATTA
CAACACTTAATATTACAGACAGAGAATTCGGTAAGGGGATAGAAG
Found at i:360937 original size:52 final size:50
Alignment explanation
Indices: 360834--360937 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 50
360824 GTAATCTCTT
*
360834 ATGTTGAAGCGAATGATAAAACTGGCATCCCCCTATGCGGCTCCCCTGCC
1 ATGTTGAAGCGAATGATAAAACTGGCACCCCCCTATGCGGCTCCCCTGCC
*
360884 ATGTTGAGGCGAATGATAAAACTGGGGCACCCCCCTATGCGGCTCCCCTGCC
1 ATGTTGAAGCGAATGATAAAACT--GGCACCCCCCTATGCGGCTCCCCTGCC
360936 AT
1 AT
360938 TCCAGCCAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 22 0.44
52 28 0.56
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (50 bp):
ATGTTGAAGCGAATGATAAAACTGGCACCCCCCTATGCGGCTCCCCTGCC
Left flanking sequence: Indices 360334 -- 360833
GCAAGGATCTATGTCGTGGAGGATGGTAGTGAAGAAGGAATCCCTCAAAGCGAGAGCACTGACCT
CGCACACGGAGTTTCGATGGCCTGTCCCCTGGGGTCTAGCGAAAGGAACTAAAAAGCCAGCAAAA
AGCCTTCTGTCGGCCGCTCAAACCAACTGACGATACGGAGGAGCGTACCGTATGGATTGACGAAA
ATAGTTTAAGCACAATAGGTAGAATGAGAATCGAACTCACTTGTGTACCATTTGGGGAGAAAGAC
CGATGCCGTTCCTACCTTTTAGCTAGTCGCATGATCAATTGATTTAATACAATATATCGCTTCTC
CAATCCGTGATAAGCTGTGCCATGTGCTTTCAGTTCTTCGTACGCTGAGAAAGGAGAATGCCTTC
TTTTGGTCGAATAAGAGATACTTTTGCTTCCAAACAAACATAGGTCATCCCGGAAGTTAACTATG
TAAAGCCCGTTTGTCTGCCTTAGACAGAAAAAGCTGTAATCTCTT
Right flanking sequence: Indices 360938 -- 361437
TCCAGCCAGATAAAGCAATGCAATGAGTCGGAGGAGAAACATTAAAAAATTCCAACGACTACTCA
TATCTGGCCTTGTGTAAGTAAAGCCCTCGGTAGGTAGTTCTTCTTCCTAAGCTACAAGCGTGAGA
CCGCCAGGGAACTCATATCGAAAGAACTACTTGCATAGAATAAGAAAGAAGTCTGGTATTTGGCG
ATCGGACGGCGTTTTGTCTTTGAGGCAATGGAAAAAAAAACCTCGATATATATATAGTGAAAAAA
GTGCCTATTTCTTTTCTTTTAAAGAAGGAGATTGGATCAAGAAGCCGAGGGCCCAGTGTGGCTTT
ATTAAAGCGGGTAACCTGTTCGACGTCAGAACCGCTCTCAAAACCCTCATATCACCCTCCCTTTG
AAGAGAAACGACTTTCTCCATATCTATATCTATGCAACTAGTTCTTTCAAAGGCTTCCAAATCTA
TCCATCTTACTTACTCAAAAGCTTTGAATATTCGACTCGAAACCT
Found at i:366451 original size:15 final size:14
Alignment explanation
Indices: 366431--366485 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
366421 TCATTAGAAG
366431 AACCAGCGGTAGCTA
1 AACCAGCGGTAGC-A
*
366446 AACCAGCGATAGCAA
1 AACCAGCGGTAGC-A
366461 AACCAGCGGTAGCA
1 AACCAGCGGTAGCA
366475 GAACCAGCGGT
1 -AACCAGCGGT
366486 TTTTGGCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.09
Consensus pattern (14 bp):
AACCAGCGGTAGCA
Left flanking sequence: Indices 365931 -- 366430
TAAAAAGCTTAAAAAATGTATCCCATTTCTTTGAAATCCCACTATAGTAATGCCAATAAAAAGAG
AAAATGAGAGACCCAAAGTAATGAGAAAATGACTTGTAACTGTGAAGCTATAAGGTATCATACCC
TGGGGATTACGAAATAACGAAAAAGTAAAAGTGACCGAGATGCAAGGGAAATACTTTTGTTTCAC
ATTACTGGAAAGACCGCCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCATAAATAAGCTCTA
CCAAGGATTGCCAAGCATTTGGTACTAACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGA
AGTAGGAACAAACTGAGAGTTAGCAGCATAAACAAAGATGGATTTGTGAATGAGAAATACAAGTT
TCCAATCTTCAAATCAATCAATGGCACAATCTCAAATTGCTCAAGGGGGCTGGGGACGATGGGTG
GTTGGGGTGGTTCCATTTGCCCCCCCACCCCCAGGTCATTAGAAG
Right flanking sequence: Indices 366486 -- 366985
TTTTGGCCAAGGCCAAGACAAACATTTTGAAAAAAAATCTTTTGAATTTTGAATAGCCGTGGTCA
TTTTTCTTTCATTCTTTTCATTCTCCGCTCCCCCCAAAAAAAGGAGAGACTTCATTTTCACTGTA
CGAGTAGTGAAAAACTATAGTTTACTTTTATTGGTTGTTGACCAACGGAAAGCATGGGAGTCTTT
GGGCATTTCTTCTTCTCTTACGATATTTCTAATTACCTAATAGAATAAATACTTTAGTTCGAACT
AGTTTTTAGCTTGAACGTGGCGAATGCTATCTCTTTCCCGCAACTCGACTGTTTAACAGGATGGT
ACGAATCCGCTCTTTGACTTAGTTAAGGAAGGAAGCAATTGTTCTCTTTGCGTTTAGCTGGGCAA
AGCAAAGTGAAGGGAAGGATGAATCGCTCCCGAAAAGGAATCTATTGATTCTCTCCCAATTGGTT
GGACCGTAGGTGCGATGATTTACTTCACGGGCGAGGTCTCTGGTT
Found at i:442431 original size:9 final size:9
Alignment explanation
Indices: 442417--442441 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
442407 TTCGATACAA
442417 TTTATTTAT
1 TTTATTTAT
442426 TTTATTTAT
1 TTTATTTAT
442435 TTTATTT
1 TTTATTT
442442 TAGTTCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Left flanking sequence: Indices 441917 -- 442416
TTCATATTCCCAAAATGGAATTAGATGCGAAATCTATAAAGCCCCTTTTCGTGGTTGTAGAAAAG
GTTTTTTTGTTCGAATCCTTTCATTTTAAGGAATTGGTTGGTCGTACAATAACAAGTATTATAGT
ATATAGTCTTCGATAAAAGAAACAAAACAAACAATAAAATAATTGGAACAATTAATATTCGTGAT
GCAAGCATTGCTGTATTAGATCCAAAGGTTTTTCTTGACCTAGCTACAAGGATGGGACTCTAAAA
TATTGAAAGAAAAAATGTAGAACCTAAAAGGAAAAGAACATAGGAATTACTAGTCTTAGAATCGA
GTTAGACCAAAATAAAGGTTTGATTTCTTCGAGCGATCGTGCGATACTTTTTTTCTTCTTATTCG
AGATATTATGTGCAATTAATAAACCTACTACTGAATCTAATAAGTTAAAGTAAAGTCAAAGTGTT
AGTTGGTTGTTGTTCGTTCCAAAATAGAAAATGGATTCGATACAA
Right flanking sequence: Indices 442442 -- 442941
TAGTTCCCATATCTCGGTAATGGGGTCTGTTGATTCGTAATCACGCTCTGTAGGATTTGAACCTA
CGACATCGGGTTTTGGAGACCCACGTTCTACCGAACTGAACTAAGAGCGCTTTCTTATCACAGTA
GATACAATTGTAAAGAAAAGGATGATTTTTGTACCTTCACTACATCTTGCATGCATCTAGTATCA
TTAAATTAAAAATTTGTCATGTCTTGAATCGATCTTAACCTTCGTTACTGCCCAGAGGAGAAGGT
AGGGATGACAAGATTGGAACCCGTGACATTTTGTATCCAATCCAAAACAAAGACGCTACCAAGCT
GCGCCACATCCCTTTCAATTGGTCTACGGTGTCATTGTAGAGAATCTCTGCCCTGTTTTCCACAT
CGTTATTTCCTCCATCGATATCCAATTTATCTTGCCATTTCTTCTTTTTGGTTTTCATTTTTTTA
TATACTAAATATCATCCCGCCGCTCCTACCAACGCTTACTTACTT
Found at i:456331 original size:24 final size:24
Alignment explanation
Indices: 456289--456337 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
456279 ATTCGGATTC
* *
456289 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
456313 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
456337 G
1 G
456338 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 455789 -- 456288
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTAGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 456338 -- 456837
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:473711 original size:26 final size:26
Alignment explanation
Indices: 473677--473734 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
473667 TTCCATACTT
* *
473677 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
473703 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
473729 A-AGAAA
1 AGAGAAA
473735 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Left flanking sequence: Indices 473177 -- 473676
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 473735 -- 474234
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:524493 original size:19 final size:19
Alignment explanation
Indices: 524466--524507 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
524456 TAGCAGCACC
524466 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
524485 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
524504 AAAA
1 AAAA
524508 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Left flanking sequence: Indices 523966 -- 524465
GAACATATTAAAGCACTCCTTGGAGTTCCTAAAAAATCCACTCTTTCTGCCATATTGTTGGTTGT
GCTTTTTGATTGTGCGCAGCTTTTCCAGACCATATTCTTTCTTCTTCGAGCATTTCGACGATTTG
TTGAATCTTATTAGGTGAGGGTACTTCGGATTTTCGTAAATCGATAATAAGGTCAGCTACCTGAT
TTTCCAATGGGGTGAGCTTTCGCATATGTGAGGCCTTGTTAGCTTAGCTCCACCCGTTGGTGCCG
GTTGCTCCTGCTGCTCCAACTCCCTCCAGATGTCCTCTTGGTTGACTTCAGCAGCTTGGATTTCA
AACGAAGGAGAAACAGGCTCCTGAGCTAGTGGTAGTGGCTCAGAAGCTTCCGGCACCGGGGGGAG
GGCTTGCTGCACCTCCATCGAATCGACCTTATCTTCCTCAAACTCGCAAGCTGCGACGATGATGA
TAGGAATTAAAAAATGTTAGTATGGAGTTGAACAGTAGCAGCACC
Right flanking sequence: Indices 524508 -- 525007
ATATCTGAAGAAATTTTAGGGTTCGTGATAATAGATCTGGGCCGGTTGAAAAGGCTCTTTTTCTT
CTTCTTCATTCTCGACAGGAATACATCAACAAAACAGCCCTTCCATATAGGTGCATGAACTTTGT
CAATAGATTCCTAGCTAACTCCTCTTCCTATTGATCTTGATTAGTTCCAGCTTGTTGAGAGTTCT
CTTTTTTTTTTTTGAATCGGACCCATTTTTAGACCGTCTCCTGAAATACCTGCTTATCCCGCATG
TGCTTTCGGAGCCCCCCACTCATTCAATCACTTGCTTGTGATTGCAGCCATTCCCCGAAAAGGGA
ATTGTCCGCTCCCGTTCATGGGACGAACCGAACATCGTTAGGTCCCGAATTCTGCGAACCACCGG
ATCTAGACCAAGATCTCCATTACGTCGTACGAGATATCGATCCGAAGAACTTACTTTCAGTTGTA
AGTTATCCATTCTGCTTCTATCTAAAGTGATGCTAGGCTGCTTCA
Found at i:537347 original size:15 final size:15
Alignment explanation
Indices: 537327--537356 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
537317 GGAGGCAGGC
537327 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
537342 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
537357 AATATACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAGTGAAATAAAAT
Left flanking sequence: Indices 536827 -- 537326
ACGGCTTTCAAAAGACGAGTAAGAGACGGGGAGGGGGAGGCTCTCGAAACCAAGCGAGACTAAAA
AGAACATGGGAATTCGCACCATTCCTATGAGTGCTTTTTTTCGAAAAGCCAACAAAGGGACAGCC
CTCTTTCTCTATCTCGGTCTCGGTTTAGCATCATCATATATCGATCCGGAGATAATTTGGATTGG
TTGTAGTGCGGATTAAGGAGCTGCTCCTCCATGCTGTGGCTGTGGAGGTGGGGGCTGCCGCCGCC
TGATAGAGGCAGAAGCCGGGGCCACCGGAGCTATCTGCGTCGAGTGTGTCGATTGAAAGAGGAGG
GGAGACAAAATGAATTCCAGCGAAAAAATAGAAAGAGTCGTGCCGTTCAAAGTGGAATTCTTCTA
AGATCCATCCATTGCTCGATCGATTTTGCATGCTCTGCTCCCAAAATGCAGAGAGACTTGCGAGG
GCAGATCTGGGTTGGTTGGTCCGGAAAGTCATGGGGGAGGCAGGC
Right flanking sequence: Indices 537357 -- 537856
AATATACTGGTGCTACTATAGAATCTTTTGAATCACGCACGGCACACTTTCTATATCTCCTCCGT
CTACAAGGTGAACAGCTTGGCTTACAGCACAGCGTGTTCGCCACCACACCGGCTGGCTGGTGCAT
TGGCCCTTTGAATGAATAAGAGAAGGGCTTTGTATAGACACCCTTGAGCCATATTCGTCGCCCTA
GGCTCACCATTATTTCATTCTATTTATGGGTTCTAGCTCCAAAGAACATATACATGGAGCTATGT
CGACTTACGTACGTCTCGTTGACCAAACGATTAGGTATACCACGCCACGTATCATCCCCTCTTTC
CATAAAAAAAAAAAAAAAAAGAAAAGATATAGTGATCGATCGTGCCGTAAGACCTTGTTCGTTTC
TACTTGACGTTATTTTCCTCGGTTTTTTTTACATTACATAAGGTAGCTTGCTTACTTAGCGCTTG
CGCTAAGGATCTAATCAGAGTCAAACTTCAATTTTAAATGAAAAA
Found at i:635883 original size:26 final size:26
Alignment explanation
Indices: 635847--635897 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
635837 CACGGCGGGG
635847 AAAGAGGGGCCGGC-CAAGCCCCATTT
1 AAAGAGGGGCC-GCTCAAGCCCCATTT
* *
635873 AAAGAGTGGCCGCTCAAGCCGCATT
1 AAAGAGGGGCCGCTCAAGCCCCATT
635898 ATTTACGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.14
Consensus pattern (26 bp):
AAAGAGGGGCCGCTCAAGCCCCATTT
Left flanking sequence: Indices 635347 -- 635846
AGATAAGTCGATCTTCACATTGATCGATTACATGGTCTTAAGCTCGACCTTTCTCATGCTCCAGT
CCTTGACTTGGCTTTGGCTCCTACTCTACCAGACGGTGACCGGCTCAATAGAGCACCTTTGGGCG
CTGGCTTTTCGAAAGCAAGTTAGGAAAGAGCTTGAGATCGTGTACCCACCGTTCCGGGTTCCGGC
TAGACAGGGTAGACTGAACACAAAGACAATCTATATATAGAAAGTCATAGGTTCGGTAGACTGAA
CACAAAGAAAATCTATAAAGAAAAAGTCAAGTATGACGCGCTTTTTTCTTTGTTTACTCAAGGCG
AATCAAAACCTTTACTTTTCTTCTTCTCTTATGAAATTTCTCTAGTTAGCGTATCACTCCTAAAT
GCAGCCTTTCCTTTATATTTTATACGATAAACTAAAGAAAGCATTTCTATATCTATATTATTCGA
TACCACCAAATGAAAATGACTTCCTGAGTCTTGCGCACGGCGGGG
Right flanking sequence: Indices 635898 -- 636397
ATTTACGCAATTCCTTGATCTGATCGGTACCTTACCCTCCAAAGAAAGCACCCTCGGTCCTTCCC
TTCCTCTTCAGGTATGAATTTCCCAGCCCAACCTCTTTTGAGGAGAGGCCTAAAAAGGGGAATAA
GTTTCCCATTGGCCACTCCACGGATGAATGCCCATTTTGGAATAAGGAGTTGTTGGGGTAGCTGG
ATCAGAACGTTCGCCTAGCGCTAGTGTAACCCTCAAACGAGAAGGGAGATTAGCAAGTGTTGAGC
ATGTCGAACTGGTAGCTTGATTGGGGAACCAGAACTCGTTCTATTCGATATTGATTTCCGTAGAG
CAGTACCTAGGCAAAAGAGAAAGACCTTAGGGGCGCAAGGAAGAGCCGAAACCTATAATCCCCAA
TCAGCCTCTTTTCGCAAGAACAACGAATCTCCAAATCGAGAATTTCGTATTTTAATTAAGATTAA
GATGACCAACTTTTTCTTTACTTTAGGTTTCCAACCGGGGTACAA
Found at i:641423 original size:24 final size:24
Alignment explanation
Indices: 641396--641468 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
641386 CTTTCCTTTT
641396 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
* **
641420 TGTCTTGGCT-T-T-CCTT---TT
1 TGTCTTGACTCTATGCCTTCCAGC
641438 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
641462 TGTCTTG
1 TGTCTTG
641469 GTGAAGACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 9 0.24
19 1 0.03
20 1 0.03
21 8 0.22
22 1 0.03
23 1 0.03
24 16 0.43
ACGTcount: A:0.08, C:0.29, G:0.18, T:0.45
Consensus pattern (24 bp):
TGTCTTGACTCTATGCCTTCCAGC
Left flanking sequence: Indices 640896 -- 641395
AAAACGTTCTTTCTTTTCTACGCTACGATCTTTCTTCTCTTATGATATTTCTAACCAAATGAAAC
TGATTCAATGGCAGCCCCTCTTCCTTGTTCACAGAAACCATTTTATAAAGAGCAAAGAGAACAAG
AGCAATCGCAGCTGAGTCAACTCTATCCATTCTTGTTCCAAGCTAAAAGCTTGAGGAAGAAGAGC
TTATTCAACTCGAGGGTCAAAGAAGACCAAGAAAATATCGATTCAGCATAAGCAAGGGATGAGAG
AGGCCTTTGTCGGGTAAGAGATGAATGAGGCCTTACGAGTGAACTGCCTTACCTTAAGGAGACGT
CGGACTTACCTTTGGAAACTTCCCATGAAGTAGTGCTTTCTTCTTTGCTAAAGAGAATGTCAAAC
CTGCAAACAAGCCATTCAAGCAAAGAGTCTATTCTGAGCCCTTTTCATGTACAGGGTATTCTCTT
GATTAACGCCTTTTCCGCTCTCATTCCTGGCTTGGCTTTCCTTTT
Right flanking sequence: Indices 641469 -- 641968
GTGAAGACTGTGGTAGTGGTATCGGTTCTTTGCTGGGTTGATTGAATATCTCTTTCGCTTGCTTC
TTTGCGGCAGAAAGACCGAGGGCAAGATCTCTTTATATAAGGATATAAGGAAAACCTCACATCCG
ATTCGTAAACAGACAGGAGACAGGCAAGAAAGTCACTAGAAGCACCGGAATGACTACCATCGACT
GGCTTGCCCGGAATACCAGGACTTAGACCGACAGACTGCTTTCAACCGCTTTGCTACTGGTTCGC
TTTGAATGAACCCTTACTGCACTGCTAGCGTTGGAGAGCTTGAAAGCGGCTTGGCTGGCACTCAT
ACTCACACGGATTGGACTTCAACCGTGCTACTAGGCCTAAATTTCCCTCTTCCTTCGGGTGTACT
AAGACTATCTCTTTCATAGACTATTCCTTCTCCCCTCGAGTCAGGAGCTAGCTTTCAATCTCCCA
CTCCTACTGCTACTACTCCTGATACAATCTTGCTTGGAAAAAACC
Found at i:641440 original size:42 final size:42
Alignment explanation
Indices: 641381--641469 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
641371 TCATTCCTGG
641381 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
641423 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
641465 CTTGG
1 CTTGG
641470 TGAAGACTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.07, C:0.28, G:0.18, T:0.47
Consensus pattern (42 bp):
CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
Left flanking sequence: Indices 640881 -- 641380
TCGTAAAGGCGAATCAAAACGTTCTTTCTTTTCTACGCTACGATCTTTCTTCTCTTATGATATTT
CTAACCAAATGAAACTGATTCAATGGCAGCCCCTCTTCCTTGTTCACAGAAACCATTTTATAAAG
AGCAAAGAGAACAAGAGCAATCGCAGCTGAGTCAACTCTATCCATTCTTGTTCCAAGCTAAAAGC
TTGAGGAAGAAGAGCTTATTCAACTCGAGGGTCAAAGAAGACCAAGAAAATATCGATTCAGCATA
AGCAAGGGATGAGAGAGGCCTTTGTCGGGTAAGAGATGAATGAGGCCTTACGAGTGAACTGCCTT
ACCTTAAGGAGACGTCGGACTTACCTTTGGAAACTTCCCATGAAGTAGTGCTTTCTTCTTTGCTA
AAGAGAATGTCAAACCTGCAAACAAGCCATTCAAGCAAAGAGTCTATTCTGAGCCCTTTTCATGT
ACAGGGTATTCTCTTGATTAACGCCTTTTCCGCTCTCATTCCTGG
Right flanking sequence: Indices 641470 -- 641969
TGAAGACTGTGGTAGTGGTATCGGTTCTTTGCTGGGTTGATTGAATATCTCTTTCGCTTGCTTCT
TTGCGGCAGAAAGACCGAGGGCAAGATCTCTTTATATAAGGATATAAGGAAAACCTCACATCCGA
TTCGTAAACAGACAGGAGACAGGCAAGAAAGTCACTAGAAGCACCGGAATGACTACCATCGACTG
GCTTGCCCGGAATACCAGGACTTAGACCGACAGACTGCTTTCAACCGCTTTGCTACTGGTTCGCT
TTGAATGAACCCTTACTGCACTGCTAGCGTTGGAGAGCTTGAAAGCGGCTTGGCTGGCACTCATA
CTCACACGGATTGGACTTCAACCGTGCTACTAGGCCTAAATTTCCCTCTTCCTTCGGGTGTACTA
AGACTATCTCTTTCATAGACTATTCCTTCTCCCCTCGAGTCAGGAGCTAGCTTTCAATCTCCCAC
TCCTACTGCTACTACTCCTGATACAATCTTGCTTGGAAAAAACCG
Done.