Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003992.1 Hibiscus syriacus cultivar Beakdansim tig00008693_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 69950
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1084 original size:20 final size:20
Alignment explanation
Indices: 1059--1104 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1049 AACTATAATC
1059 TAAAATCAATTTTTAAACAT
1 TAAAATCAATTTTTAAACAT
*
1079 TAAAATCGATTTTTAAACAT
1 TAAAATCAATTTTTAAACAT
*
1099 CAAAAT
1 TAAAAT
1105 AATCCAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATCAATTTTTAAACAT
Found at i:5985 original size:42 final size:42
Alignment explanation
Indices: 5702--5974 Score: 287
Period size: 42 Copynumber: 6.5 Consensus size: 42
5692 TACTGTGACT
* * *
5702 ATCATCTGGAGAGTAGGAACGATCTCGCCTTCTGTAGTACCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* *
5744 ATCTTCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTACCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* **
5786 ATCTTCTGGTGAGTAGGAACGATCCCGCCTTCTACAGTATCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* * * *
5828 ATCATCTCGTGAATAGGAACGATCCCGCCTTCTATAGCATCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* * * *
5870 ATCATCAGGTGAGTAGGAACGATCTCGCCTACGGTAGTAAT-G
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGT-ATCG
* * * * * * * * *
5912 TTCATCTGGAGTGTAAGACCTATCCCGTCTTCTGTAGCATCT
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* *
5954 ATCATCAGGAGAGTAGGAACG
1 ATCATCTGGTGAGTAGGAACG
5975 GTCACGTCTT
Statistics
Matches: 191, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
41 2 0.01
42 187 0.98
43 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
Found at i:14892 original size:32 final size:32
Alignment explanation
Indices: 14856--14920 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
14846 TAGCTCCCCA
*
14856 ACACTTCTAGGATATTTAACAGTGGATTCTGT
1 ACACTTCTAGGATATTTAACAGTGGATTATGT
* *
14888 ACACTTCTAGGATATTTTACTGTGGATTATGT
1 ACACTTCTAGGATATTTAACAGTGGATTATGT
14920 A
1 A
14921 GTCCATGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (32 bp):
ACACTTCTAGGATATTTAACAGTGGATTATGT
Found at i:15630 original size:40 final size:40
Alignment explanation
Indices: 15551--15630 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 40
15541 TGTAGGACTT
**
15551 AGTTCAATGACTTATAGGAAAACAATTTCGCAATGAGCCA
1 AGTTCAATGACTTATAGGAAAACAATTTCGCAACAAGCCA
* * * *
15591 AGTTCAATGACTT-TCAGGAATATATTTTGGCAACAAGCCA
1 AGTTCAATGACTTAT-AGGAAAACAATTTCGCAACAAGCCA
15631 TTGATAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
AGTTCAATGACTTATAGGAAAACAATTTCGCAACAAGCCA
Found at i:24646 original size:21 final size:22
Alignment explanation
Indices: 24613--24655 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
24603 AGATTAAGCC
24613 TTAATGAGAACTT-TTAAAAAA
1 TTAATGAGAACTTATTAAAAAA
* *
24634 TTAATGGGGACTTAATTAAAAA
1 TTAATGAGAACTT-ATTAAAAA
24656 CCATTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (22 bp):
TTAATGAGAACTTATTAAAAAA
Found at i:31755 original size:23 final size:23
Alignment explanation
Indices: 31728--31800 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
31718 ATACTTTACA
*
31728 ATATAAGCGCTACCTATTTCATT
1 ATATAAGCGCTACCTATTACATT
31751 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* * *
31774 ATATAAACGCTACATATTACATC
1 ATATAAGCGCTACCTATTACATT
31797 ATAT
1 ATAT
31801 TTTTACCTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:32243 original size:21 final size:22
Alignment explanation
Indices: 32218--32290 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 22
32208 ATACTTTACA
32218 ATATAAGCACTACCTATTACATT
1 ATATAAG-ACTACCTATTACATT
* *
32241 ATATAAAAACTATCTATTACATT
1 ATAT-AAGACTACCTATTACATT
*
32264 ATATAAGAGCTACCTATTACATC
1 ATATAAGA-CTACCTATTACATT
32287 ATAT
1 ATAT
32291 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 3 0.07
23 38 0.88
24 2 0.05
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATAAGACTACCTATTACATT
Found at i:32252 original size:23 final size:23
Alignment explanation
Indices: 32226--32290 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
32216 CAATATAAGC
32226 ACTACCTATTACATTATATAAAA
1 ACTACCTATTACATTATATAAAA
* *
32249 ACTATCTATTACATTATATAAGA
1 ACTACCTATTACATTATATAAAA
* *
32272 GCTACCTATTACATCATAT
1 ACTACCTATTACATTATAT
32291 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (23 bp):
ACTACCTATTACATTATATAAAA
Found at i:32540 original size:489 final size:488
Alignment explanation
Indices: 31343--33688 Score: 4029
Period size: 489 Copynumber: 4.8 Consensus size: 488
31333 GTCTATATTT
*
31343 TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAG
1 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
*
31407 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTAATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
31472 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
131 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
* * *
31537 AAATATGTAATATATATGTTTATTATTTTTAATTTAATGATAATATATACCGTAACATAAAAAAT
196 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
* *
31602 AAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAA
261 AAATCATTAGACAC-TATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
* * * *
31667 TTAATGTTTTCCACAGCGAAATAAGTATGAACACTTCTATAAAAAGGATAGATACTTTACAATAT
325 TTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATAT
* * * *
31732 AAGCGCTACCTATTTCATTATATAAGCGCTACCTATTACATTATATAA-ACGCTACATATTACAT
390 AAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGA-GCTACCTATTACAT
* * *
31796 CATATTTTTACCTGA-TATATTGTAAAGTATTGATCC
454 CATATTTTTACCT-ATTATATTG-AAAGTGTTCATAC
*
31832 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAAATAG
1 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
*
31897 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
*
31962 GTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
131 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
32027 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
196 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
32092 AAATCATTAGACATCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
261 AAATCATTAGACA-CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
* * *
32157 TTAATGATTTCTACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATACTTTACAATAT
325 TTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATAT
** *
32222 AAGCACTACCTATTACATTATATAAAAACTATCTATTACATTATATAAGAGCTACCTATTACATC
390 AAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGAGCTACCTATTACATC
*
32287 ATATTTTTACCTATTATATTGAAAGTGTCCATAC
455 ATATTTTTACCTATTATATTGAAAGTGTTCATAC
*
32321 TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
1 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
* *
32386 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGTACAAAAAATTATTTAATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
32451 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
131 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
*
32516 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAACAT
196 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
*
32581 AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
261 AAATCATTAGAC-ACTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
* * * *
32646 TTAATGTTTTCCACAGTGAAATAAGTATGAACACTTCTATAAAAAGGATTGATACTTTACAATAT
325 TTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATAT
*
32711 AAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATC
390 AAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGAGCTACCTATTACATC
32776 ATATTTTTACCTATTATATTGAAAGTGTTCATAC
455 ATATTTTTACCTATTATATTGAAAGTGTTCATAC
*
32810 TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAG
1 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
32874 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC-AAAAATTATTTGATT
66 TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
*
32938 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAAT
131 GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
* *
33003 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAAAAAT
196 AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
* *
33068 AAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAA
261 AAATCATTAGACAC-TATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
*
33133 TTAATGTTTTCCACAGTGAAAAAAGTATGGATACTTTTATAAAAAGGATAGATACTTTACAATAT
325 TTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATAT
* * * *
33198 AAACACTACATATTACATTATATAAACGCTACATATTACATTATATAAGCGCTACCTATTACATC
390 AAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGAGCTACCTATTACATC
33263 ATATTTTTACCTATTATATTGAAAGTGTTCATAC
455 ATATTTTTACCTATTATATTGAAAGTGTTCATAC
* *
33297 TTTTTATAAAAAGGATCGATA-TTTTTTTTAAGTTATGTAATTTATGTTTCAATTTTTTTTAACA
1 TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATA
* * *
33361 GTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAACTATTTGAT
65 GTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGAT
* *
33426 TGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGATAATAA
130 TGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAA
33491 TAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAA
195 TAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAA
* *
33556 TAAATCATTAGACACCTATAATTACTAATTTAATATCTTAAAACTCACTCAAAATATAACCTTAA
260 TAAATCATTAGACA-CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAA
* *
33621 ATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAAGATAGATACTTTACAATA
324 ATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATA
33686 TAA
389 TAA
33689 CAGGTAAAAA
Statistics
Matches: 1764, Mismatches: 83, Indels: 20
0.94 0.04 0.01
Matches are distributed among these distances:
486 31 0.02
487 376 0.21
488 116 0.07
489 845 0.48
490 394 0.22
491 2 0.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (488 bp):
TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAG
TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATT
GTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT
AAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT
AAATCATTAGACACTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAAT
TAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATA
AGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGAGCTACCTATTACATCA
TATTTTTACCTATTATATTGAAAGTGTTCATAC
Found at i:32742 original size:23 final size:23
Alignment explanation
Indices: 32707--32779 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
32697 ATACTTTACA
*
32707 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
32730 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
32753 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
32776 ATAT
1 ATAT
32780 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:33224 original size:23 final size:23
Alignment explanation
Indices: 33194--33266 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
33184 ATACTTTACA
*
33194 ATATAAACACTACATATTACATT
1 ATATAAACGCTACATATTACATT
33217 ATATAAACGCTACATATTACATT
1 ATATAAACGCTACATATTACATT
* * *
33240 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACATATTACATT
33263 ATAT
1 ATAT
33267 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACATATTACATT
Found at i:33377 original size:976 final size:979
Alignment explanation
Indices: 31325--33688 Score: 4116
Period size: 976 Copynumber: 2.4 Consensus size: 979
31315 TTATAATATG
* *
31325 TTGAAAGTGTCTATATTTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCCATA--CTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATG
31390 TTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
64 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
31454 ACAAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
* *
31519 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATGATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* * * *
31584 TACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCAC
259 TACCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCAC
*
31649 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGCGAAATAAGTATGAACACTTCTATAAAAAGG
324 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGAACACTTCTATAAAAAGG
* * *
31714 ATAGATACTTTACAATATAAGCGCTACCTATTTCATTATATAAGCGCTACCTATTACATTATATA
389 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
* *
31779 AACGCTACATATTACATCATATTTTTACCTGATATATTGTAAAGTATTGATCCTTTTTATAAAAA
454 AACGCTACATATTACATCATATTTTTACCTGATATATTGTAAAGTATTCATACTTTTTATAAAAA
31844 GGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAAATAGTGTTTCATGTTT
519 GGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAAATAGTGTTTCATGTTT
31909 TCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTT
584 TCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTT
*
31974 TATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATA
649 TATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATA
*
32039 TATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGAC
714 TATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGAC
*
32104 ATCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGATTTCT
779 ATCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGATTTCC
* *
32169 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATACTTTACAATATAAGCACTACCTA
844 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATACTTTACAATATAAACACTACATA
32234 TTACATTATATAAAAACTATCTATTACATTATATAAGAGCTACCTATTACATCATATTTTTACCT
909 TTACATTATATAAAAACTATCTATTACATTATATAAGAGCTACCTATTACATCATATTTTTACCT
32299 ATTATA
974 ATTATA
*
32305 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
32370 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGTAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
32435 AAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
32500 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
32565 CCGTAACGTAAAACATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTC
32630 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGAACACTTCTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGAACACTTCTATAAAAAGGAT
* *
32695 TGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAA
* * *
32760 CGCTACCTATTACATCATATTTTTACCT-ATTATATTG-AAAGTGTTCATACTTTTTATAAAAAT
456 CGCTACATATTACATCATATTTTTACCTGA-TATATTGTAAAGTATTCATACTTTTTATAAAAAG
32823 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT-AATAGTGTTTCATGTTTT
520 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAAATAGTGTTTCATGTTTT
*
32887 CCACCTACAATATTAATTTAATAATTTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTT
585 CCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTT
*
32951 ATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATAT
650 ATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATAT
* *
33016 ATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAAAAATAAATCATTAGATA
715 ATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACA
* *
33081 -CATATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
780 TC-TATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGATTTCC
* *
33145 ACAGTGAAAAAAGTATGGATACTTTTATAAAAAGGATAGATACTTTACAATATAAACACTACATA
844 ACAGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATACTTTACAATATAAACACTACATA
** *
33210 TTACATTATATAAACGCTA-CATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
909 TTACATTATATAAAAACTATC-TATTACATTATATAAGAGCTACCTATTACATCATATTTTTACC
33274 TATTATA
973 TATTATA
* * *
33281 TTGAAAGTGTTCATACTTTTTATAAAAAGGATCGATA-TTTTTTTTAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * *
33345 TCAATTTTTTTTAACAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* * * *
33410 CAAAAAACTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATAT
130 CAAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
33475 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
33540 ACCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAATTTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACT
* * * *
33605 CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT-AGACACTTTTATAAAAAAG
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGA-ACACTTCTATAAAAAGG
33669 ATAGATACTTTACAATATAA
389 ATAGATACTTTACAATATAA
33689 CAGGTAAAAA
Statistics
Matches: 1320, Mismatches: 58, Indels: 16
0.95 0.04 0.01
Matches are distributed among these distances:
975 33 0.03
976 695 0.53
977 53 0.04
978 121 0.09
979 404 0.31
980 14 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (979 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTAATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGAACACTTCTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAA
CGCTACATATTACATCATATTTTTACCTGATATATTGTAAAGTATTCATACTTTTTATAAAAAGG
ATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTAAATAGTGTTTCATGTTTTC
CACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
TAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATA
TATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAGACAT
CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGATTTCCAC
AGTGAAAAAAGTATGGACACTTTTATAAAAAAGATAGATACTTTACAATATAAACACTACATATT
ACATTATATAAAAACTATCTATTACATTATATAAGAGCTACCTATTACATCATATTTTTACCTAT
TATA
Found at i:34907 original size:70 final size:70
Alignment explanation
Indices: 34789--34923 Score: 168
Period size: 70 Copynumber: 1.9 Consensus size: 70
34779 ACTATTGAAT
* * *
34789 AGCTCTTTTCAAGTTTGATATTTATCCTCATTTGAATGGTTACAATTTGCT-TGTAGATGTATTA
1 AGCTCTTTTCAAGGTTGATATTTATCCTCATTTGAA-GGTCACAATTTG-TACGTAGATGTATTA
34853 AAGGTTC
64 AAGGTTC
**
34860 AGCTC-TTTCAAGGTTGATATTTATCCTCACTTTAGAA-GTCATTATTTGTACGTAGATGTATTA
1 AGCTCTTTTCAAGGTTGATATTTATCCTCA-TTT-GAAGGTCACAATTTGTACGTAGATGTATTA
34923 A
64 A
34924 CGGTGAACCA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
69 1 0.02
70 44 0.79
71 8 0.14
72 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (70 bp):
AGCTCTTTTCAAGGTTGATATTTATCCTCATTTGAAGGTCACAATTTGTACGTAGATGTATTAAA
GGTTC
Found at i:39986 original size:2 final size:2
Alignment explanation
Indices: 39979--40014 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39969 ACTAAAGTAA
39979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40015 TAGGGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40298 original size:19 final size:19
Alignment explanation
Indices: 40276--40317 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40266 ATTCATATGA
*
40276 AATAAAATAATAATTAAA-T
1 AATAAAATAA-AATAAAATT
40295 AATAAAATAAAATAAAATT
1 AATAAAATAAAATAAAATT
40314 AATA
1 AATA
40318 TTGATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAATAAAATAAAATT
Found at i:41570 original size:3 final size:3
Alignment explanation
Indices: 41564--41634 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
41554 TATTTATTAT
* * *
41564 TAA TAA TAA TAA GAA -AA TAA TAA TAA TAA TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
41611 TAA TTA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
41635 AAAAGAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:42289 original size:177 final size:176
Alignment explanation
Indices: 41969--42372 Score: 607
Period size: 177 Copynumber: 2.3 Consensus size: 176
41959 AACGAAAATG
* * * *
41969 TTGAAAACATTCTGC-CCGAAGGTCTTATGAATGGCCCGA-AAGACTTACAAATCAAGAAACCCC
1 TTGAAAACATCCTGCACTGAAGGTCTTATG-ATGACCC-ATAGGACTTACAAATCAAGAAACCCC
* *
42032 CGAAGGCTTAGTTTCTTAATTGTCAATGAACCCCTTTGTTAGGCTTAGTTTCCTTTAACAACTCT
64 CGAAGGCTTAGTTTCTTAATTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
*
42097 TTTGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAGAAT-TTCAT
129 TTTGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAAAATCTT-AT
*
42145 TTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCATAGGACTTATAAATCAAGAAACCCCC
1 TTGAAAACATCCTGCACTGAAGGTCTTAT-GATGACCCATAGGACTTACAAATCAAGAAACCCCC
* * *
42210 GAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTT
65 GAAGGCTTAGTTTCTTAATTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTT
*
42275 TTGAGATGATTAGGAAACCCCTGAAGGCTTAGTTTCTAAAATCTTAT
130 TTGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAAAATCTTAT
* * *
42322 TTGAAAACATCCTGCAATGAAGGTCTTATGGATGTCCCGTAGGACTTACAA
1 TTGAAAACATCCTGCACTGAAGGTCTTAT-GATGACCCATAGGACTTACAA
42373 TTCTGGGAAA
Statistics
Matches: 207, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
176 15 0.07
177 189 0.91
178 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (176 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGATGACCCATAGGACTTACAAATCAAGAAACCCCCG
AAGGCTTAGTTTCTTAATTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTT
TGAGATAATTAGGAAACCCCTGAAGGCTTAGTTTCTAAAATCTTAT
Found at i:43046 original size:22 final size:22
Alignment explanation
Indices: 42988--43047 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
42978 AATAAAGCTT
*
42988 TCATCTTTGAA-AAGAGAATCTA
1 TCATCTTTGAAGAA-TGAATCTA
43010 TCATCTTTGAAGAATGAATCTA
1 TCATCTTTGAAGAATGAATCTA
43032 TCATCTTTGAAGAATG
1 TCATCTTTGAAGAATG
43048 TAGATGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAATGAATCTA
Found at i:43493 original size:54 final size:54
Alignment explanation
Indices: 43411--43518 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
43401 ATAATAACTG
* * *
43411 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTACTGTAGCTTCTGCACAGAT
* *
43465 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTAGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTACTGTAGCTTCTGCACAGAT
43519 TTCTCGATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTACTGTAGCTTCTGCACAGAT
Found at i:45090 original size:18 final size:18
Alignment explanation
Indices: 45067--45141 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
45057 ATGGATTATC
*
45067 AGTGGTCCTTCCGGACAT
1 AGTGGTCCTTCGGGACAT
*
45085 AGTGGTTCTTCGGGGAACAAT
1 AGTGGTCCTTC-GGG-AC-AT
*
45106 AAGTGGTCCTTCGGGATAT
1 -AGTGGTCCTTCGGGACAT
* *
45125 AGTTGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
45142 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
18 24 0.52
19 4 0.09
20 3 0.07
21 5 0.11
22 10 0.22
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:51962 original size:18 final size:18
Alignment explanation
Indices: 51939--52011 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
51929 AGGGATTATC
51939 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
51957 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
51976 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
51995 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
52012 AATATTCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 31 0.63
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:51987 original size:38 final size:38
Alignment explanation
Indices: 51936--52012 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
51926 TCGAGGGATT
*
51936 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
*
51974 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
52012 A
1 A
52013 ATATTCATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACA
Found at i:52173 original size:13 final size:14
Alignment explanation
Indices: 52150--52196 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
52140 TGGTATGAGA
*
52150 ATGTATGTGTTATC
1 ATGTATATGTTATC
52164 -TGTATATGTTATC
1 ATGTATATGTTATC
*
52177 ATCATATATGTTATC
1 AT-GTATATGTTATC
*
52192 GTGTA
1 ATGTA
52197 ATTGATACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 12 0.44
14 3 0.11
15 12 0.44
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (14 bp):
ATGTATATGTTATC
Found at i:53995 original size:72 final size:71
Alignment explanation
Indices: 53878--54011 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 71
53868 TATATCAAGT
*
53878 TAGCTGAATATTATCTATAAAGTCAGGGCTATCAACCAATTGCTTTAAGGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAGTCAGGGCTATCAACCAATTGCTTT-AGGGGACAACTCAAGCAT
53943 AACAGAC
65 AACAGAC
* * **
53950 TAGCTGAATATTATCCATAAAG-CCGGGCCTATTAACCAATTGCTTTAGGGGGTAACTCAAGC
1 TAGCTGAATATTATCCATAAAGTCAGGG-CTATCAACCAATTGCTTTAGGGGACAACTCAAGC
54012 TTTATTGCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 18 0.32
72 38 0.68
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (71 bp):
TAGCTGAATATTATCCATAAAGTCAGGGCTATCAACCAATTGCTTTAGGGGACAACTCAAGCATA
ACAGAC
Found at i:56201 original size:42 final size:42
Alignment explanation
Indices: 56127--56210 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
56117 TTAATTTTGT
* * * ** *
56127 CATTTGCTCCTTTGAATCATCTTGGATTTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCATCCTAGAACTTTTTTACTTGATC
*
56169 CATTTGTTCATTTGAATCATCCTAGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCATCCTAGAACTTTTTTACTTGATC
56211 AATCATCTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCATCCTAGAACTTTTTTACTTGATC
Found at i:57579 original size:16 final size:16
Alignment explanation
Indices: 57558--57599 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
57548 AAAATGCATG
57558 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
* *
57574 AAAAAAGAAGAAAAAT
1 AAAAAATAAAAAAAAT
57590 -AAAAATAAAA
1 AAAAAATAAAA
57600 TGGTTAGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:60738 original size:4 final size:4
Alignment explanation
Indices: 60729--60881 Score: 212
Period size: 4 Copynumber: 39.8 Consensus size: 4
60719 AGCCTATTGT
60729 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
60777 CA-A CATAA CATA -TTA CATA C-TA -ATA CATA CATA CATA CATA CATA
1 CATA CAT-A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
60822 C-TA CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
60867 TACA TATA CATA CAT
1 CATA CATA CATA CAT
60882 TTACATAGGT
Statistics
Matches: 135, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
2 2 0.01
3 12 0.09
4 117 0.87
5 4 0.03
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:60985 original size:25 final size:25
Alignment explanation
Indices: 60957--61006 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
60947 TTTAACACCA
60957 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
60982 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
61007 ACCCCTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:63134 original size:35 final size:35
Alignment explanation
Indices: 63099--63174 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
63089 GCCTGTAATA
* *
63099 AATAAAATTAT-TTATATTA-TTATTATAATAAAAT
1 AATAAAATTATAATA-ATTATTTATAATAATAAAAT
**
63133 AATATTATTATAATAATTATTTATAATAATAAAAT
1 AATAAAATTATAATAATTATTTATAATAATAAAAT
63168 AATAAAA
1 AATAAAA
63175 AAGAAAAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
AATAAAATTATAATAATTATTTATAATAATAAAAT
Found at i:63140 original size:16 final size:17
Alignment explanation
Indices: 63119--63168 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
63109 TTTATATTAT
63119 TATTATAATAA-AATAA
1 TATTATAATAATAATAA
* *
63135 TATTATTATAATAATTA
1 TATTATAATAATAATAA
63152 T-TTATAATAATAA-AA
1 TATTATAATAATAATAA
63167 TA
1 TA
63169 ATAAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 21 0.75
17 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTATAATAATAATAA
Found at i:63140 original size:19 final size:19
Alignment explanation
Indices: 63116--63171 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
63106 TTATTTATAT
63116 TATTATTATAATAAAATAA
1 TATTATTATAATAAAATAA
*
63135 TATTATTATAAT--AATTA
1 TATTATTATAATAAAATAA
*
63152 T-TTATAATAATAAAATAA
1 TATTATTATAATAAAATAA
63170 TA
1 TA
63172 AAAAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTATTATAATAAAATAA
Found at i:63158 original size:13 final size:12
Alignment explanation
Indices: 63100--63162 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
63090 CCTGTAATAA
63100 ATAA-AATTATT
1 ATAATAATTATT
*
63111 -TATATTATTATT
1 ATA-ATAATTATT
63123 ATAATAA--A--
1 ATAATAATTATT
63131 ATAAT-ATTATT
1 ATAATAATTATT
63142 ATAATAATTATTT
1 ATAATAATTA-TT
63155 ATAATAAT
1 ATAATAAT
63163 AAAATAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
7 1 0.02
8 5 0.12
9 1 0.02
10 3 0.07
11 6 0.15
12 13 0.32
13 12 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:65581 original size:21 final size:21
Alignment explanation
Indices: 65557--65607 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
65547 AGACTCAGGT
65557 TGCTTCTCAGGCAGGAACAGC
1 TGCTTCTCAGGCAGGAACAGC
65578 TGCTTCTCA-GCAGGAACAGC
1 TGCTTCTCAGGCAGGAACAGC
65598 TGCTTCTCAG
1 TGCTTCTCAG
65608 TCCCAGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (21 bp):
TGCTTCTCAGGCAGGAACAGC
Done.