Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 2 of 75
Found at i:352560 original size:5 final size:5
Alignment explanation
Indices: 352552--352588 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
352542 AAAAGGAAAC
* *
352552 AAAAT AAAAT AAAAT AAAAT AAAAT GAAAC AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
352589 TCACCTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:352560 original size:15 final size:15
Alignment explanation
Indices: 352542--352588 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
352532 GAAATGAAAG
*
352542 AAAAGGAAACAAAAT
1 AAAATGAAACAAAAT
* *
352557 AAAATAAAATAAAAT
1 AAAATGAAACAAAAT
352572 AAAATGAAACAAAAT
1 AAAATGAAACAAAAT
352587 AA
1 AA
352589 TCACCTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAATGAAACAAAAT
Found at i:353838 original size:17 final size:16
Alignment explanation
Indices: 353812--353851 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
353802 AAAATCAATT
353812 AAAATTACATAATATA
1 AAAATTACATAATATA
*
353828 AAAAGTTACATTATATA
1 AAAA-TTACATAATATA
353845 AAAATTA
1 AAAATTA
353852 AATGAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATTACATAATATA
Found at i:354039 original size:60 final size:60
Alignment explanation
Indices: 353966--354087 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
353956 ATACTAAACT
* * * * *
353966 AAACACAATAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
354026 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
354086 AA
1 AA
354088 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:354104 original size:19 final size:19
Alignment explanation
Indices: 354080--354123 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
354070 ATTATAAAAT
354080 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
354099 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
354118 AATTAC
1 AATTAC
354124 CCATTGGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:355319 original size:6 final size:7
Alignment explanation
Indices: 355299--355324 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
355289 GCAATTTGTA
355299 TTATTTT
1 TTATTTT
355306 TTATTTT
1 TTATTTT
355313 TTATTTT
1 TTATTTT
355320 TTATT
1 TTATT
355325 ATAAAACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTATTTT
Found at i:360590 original size:22 final size:21
Alignment explanation
Indices: 360539--360599 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 21
360529 ATTTAGATGG
*
360539 TATTTAAATAGTTATATATTAAA
1 TATTTAAA-AATTA-ATATTAAA
360562 TATTTTAAAGAATTAATA-TAAA
1 TA-TTTAAA-AATTAATATTAAA
360584 TTATTTATAAAATTAA
1 -TATTTA-AAAATTAA
360600 CGATACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 14 0.42
23 9 0.27
24 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TATTTAAAAATTAATATTAAA
Found at i:365270 original size:29 final size:29
Alignment explanation
Indices: 365215--365269 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
365205 CGCGGAAAAT
365215 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
*
365244 GGCCCATTTCGGTAAAT-ATTAAAAAA
1 GGCCCATTCCGGTAAATAATTAAAAAA
365270 AAGGGGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:368267 original size:23 final size:22
Alignment explanation
Indices: 368241--368283 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
368231 GGTTTTGCCA
*
368241 ATTTGTGATTTGGATTGTTTTTT
1 ATTTGGGATTTGG-TTGTTTTTT
*
368264 ATTTGGGTTTTGGTTGTTTT
1 ATTTGGGATTTGGTTGTTTT
368284 ATGACCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.09, C:0.00, G:0.26, T:0.65
Consensus pattern (22 bp):
ATTTGGGATTTGGTTGTTTTTT
Found at i:370714 original size:16 final size:16
Alignment explanation
Indices: 370693--370727 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
370683 AATATCATAA
370693 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
370709 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
370725 AAA
1 AAA
370728 AAAATAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:389249 original size:19 final size:19
Alignment explanation
Indices: 389174--389255 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
389164 NNNNNNNNNT
*
389174 AAAAA-TAATAAAATAAATA
1 AAAAATTAATAAAA-ATATA
* *
389193 AATAA-TATTAAAAATAT-
1 AAAAATTAATAAAAATATA
* *
389210 AAAAATTGATATAAACT-TA
1 AAAAATTAATA-AAAATATA
389229 AAAAATTAATAAAAATATA
1 AAAAATTAATAAAAATATA
*
389248 AAATATTA
1 AAAAATTA
389256 TAAGTATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.08
18 11 0.22
19 34 0.69
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAAATTAATAAAAATATA
Found at i:389721 original size:19 final size:19
Alignment explanation
Indices: 389688--389741 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
389678 GAGTTCAAGT
389688 TTTTATATATTTTTAAAT-AA
1 TTTT-TATA-TTTTAAATGAA
*
389708 TTTTTATATGTTTATATGAA
1 TTTTTATAT-TTTAAATGAA
*
389728 TTTTAATATTTTAA
1 TTTTTATATTTTAA
389742 TAAATTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATATTTTAAATGAA
Found at i:389809 original size:14 final size:15
Alignment explanation
Indices: 389790--389819 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
389780 GTTTATAACA
389790 ATTTTA-ATATTTTT
1 ATTTTATATATTTTT
389804 ATTTTATATATTTTT
1 ATTTTATATATTTTT
389819 A
1 A
389820 ATGATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATATATTTTT
Found at i:394073 original size:50 final size:50
Alignment explanation
Indices: 394014--394114 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
394004 TAGCCAAAAA
394014 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
1 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
394064 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
1 CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
394114 C
1 C
394115 ATTCTCTCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (50 bp):
CCTCTACTATAGTTGGAAGATTCTTCTCACCTACAGTCATACATATGCAG
Found at i:406122 original size:18 final size:19
Alignment explanation
Indices: 406067--406117 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
406057 TTACAAAAAC
406067 AAAATT-AAAATAATTT-TCA
1 AAAATTCAAAAT-ATTTAT-A
406086 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
406105 AAAATTTCAAAAT
1 AAAA-TTCAAAAT
406118 TTATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:411627 original size:142 final size:143
Alignment explanation
Indices: 411359--411644 Score: 529
Period size: 142 Copynumber: 2.0 Consensus size: 143
411349 GAATGACTCT
411359 GAACTAGACCTATCTATGGGTCCGGTAGTCCTCCCAGTTCAGTAGGCACAACTCAAATTGGGCCA
1 GAACTAGACC-ATCTATGGGTCCGGTAGTCCTCCCAGTTCAGTAGGCACAACTCAAATTGGGCCA
*
411424 AGCATGAATAAATATTTTTGCACCTCGAGTCGGCTCGGGTTCAATTTAAATAATAAAAATATTTT
65 AGCATGAATAAATATTTTTGCACCTCGAGACGGCTCGGGTTCAATTTAAATAATAAAAATATTTT
411489 TAAATTTAAATTTA
130 TAAATTTAAATTTA
411503 GAACTAGACC-TCTATGGGTCCGGTAGTCCTCCCAGTTCAGTAGGCACAACTCAAATTGGGCCAA
1 GAACTAGACCATCTATGGGTCCGGTAGTCCTCCCAGTTCAGTAGGCACAACTCAAATTGGGCCAA
* *
411567 GCATGAATAAATATTTTTGCACCTCGCGAGGGCTCGGGTTCAATTTAAATAATAAAAATATTTTT
66 GCATGAATAAATATTTTTGCACCTCGAGACGGCTCGGGTTCAATTTAAATAATAAAAATATTTTT
411632 AAATTTAAATTTA
131 AAATTTAAATTTA
411645 ATCATATAAA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
142 129 0.93
144 10 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (143 bp):
GAACTAGACCATCTATGGGTCCGGTAGTCCTCCCAGTTCAGTAGGCACAACTCAAATTGGGCCAA
GCATGAATAAATATTTTTGCACCTCGAGACGGCTCGGGTTCAATTTAAATAATAAAAATATTTTT
AAATTTAAATTTA
Found at i:424537 original size:2 final size:2
Alignment explanation
Indices: 424532--424556 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
424522 TGTGATAGGC
424532 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
424557 AGGTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:430585 original size:15 final size:16
Alignment explanation
Indices: 430560--430590 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
430550 TATTATATGT
430560 AATATATAATTAATTA
1 AATATATAATTAATTA
430576 AATA-ATAATTAATTA
1 AATATATAATTAATTA
430591 TTAAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATATAATTAATTA
Found at i:436617 original size:31 final size:29
Alignment explanation
Indices: 436556--436641 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
436546 GGTTGAAAAA
* *
436556 ATAATTTATAT-AAGATTTATGGTTTAATG
1 ATAATTTATATAAAAATTT-TGATTTAATG
*
436585 TATAATTATATATAAAAATTTTGATTTTATG
1 -ATAATT-TATATAAAAATTTTGATTTAATG
*
436616 -TAATTTTATACATAAAATTTTGATTT
1 ATAA-TTTATATA-AAAATTTTGATTT
436642 GATTCAATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 8 0.17
30 21 0.44
31 13 0.27
32 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (29 bp):
ATAATTTATATAAAAATTTTGATTTAATG
Found at i:436675 original size:12 final size:12
Alignment explanation
Indices: 436658--436687 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
436648 ATTCTTGTGC
436658 ATTATTAACATA
1 ATTATTAACATA
436670 ATTATTAACATA
1 ATTATTAACATA
436682 A-TATTA
1 ATTATTA
436688 TTTTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATTAACATA
Found at i:436853 original size:30 final size:30
Alignment explanation
Indices: 436781--436866 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 30
436771 GATTAAATTA
*
436781 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * * * *
436811 ACAATTAGAGTTTCACGTGTATAATTGTACT
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
*
436842 AAATTAAAGTTT-ATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
436867 TATATTAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 10 0.23
30 11 0.25
31 23 0.52
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:439516 original size:18 final size:18
Alignment explanation
Indices: 439493--439527 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
439483 TTTGTAAAAA
439493 GTTTAAACTATAAAAATG
1 GTTTAAACTATAAAAATG
*
439511 GTTTAATCTATAAAAAT
1 GTTTAAACTATAAAAAT
439528 TTTCATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
GTTTAAACTATAAAAATG
Found at i:446968 original size:2 final size:2
Alignment explanation
Indices: 446956--446987 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
446946 TCAAATACAG
446956 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
446988 CTTTTGCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:447106 original size:80 final size:81
Alignment explanation
Indices: 446972--447134 Score: 319
Period size: 80 Copynumber: 2.0 Consensus size: 81
446962 ATATATATAT
446972 ATATATATATATATATCTTTTGCTCCCTCAAATTGGTCACTTGTATTATTTGACCTAATTAGTAT
1 ATATATATATATATATCTTTTGCTCCCTCAAATTGGTCACTTGTATTATTTGACCTAATTAGTAT
447037 TTAAACTTCAACTCCG
66 TTAAACTTCAACTCCG
447053 ATATATATATAT-TATCTTTTGCTCCCTCAAATTGGTCACTTGTATTATTTGACCTAATTAGTAT
1 ATATATATATATATATCTTTTGCTCCCTCAAATTGGTCACTTGTATTATTTGACCTAATTAGTAT
447117 TTAAACTTCAACTCCG
66 TTAAACTTCAACTCCG
447133 AT
1 AT
447135 TTACACTTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 70 0.85
81 12 0.15
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (81 bp):
ATATATATATATATATCTTTTGCTCCCTCAAATTGGTCACTTGTATTATTTGACCTAATTAGTAT
TTAAACTTCAACTCCG
Found at i:456115 original size:2 final size:2
Alignment explanation
Indices: 456108--456133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
456098 NNATATTAAA
456108 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
456134 GGGAGCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:456607 original size:30 final size:30
Alignment explanation
Indices: 456563--456624 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
456553 ACTTAACAAG
456563 CAAATGCCTATAAAAAAATAACAAAATTAA
1 CAAATGCCTATAAAAAAATAACAAAATTAA
* * *
456593 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAAAAATAACAAAATTAA
456623 CA
1 CA
456625 GTAAAATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTATAAAAAAATAACAAAATTAA
Found at i:457065 original size:2 final size:2
Alignment explanation
Indices: 457058--457093 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
457048 TAGTACATGC
457058 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
457094 TCAACATACT
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:460592 original size:28 final size:29
Alignment explanation
Indices: 460557--460614 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
460547 TGTCCTTAAA
* *
460557 ATTTTTAAAAAAA-TTGATTAAATCCCTT
1 ATTTTTAAAAAAATTTCATTAAACCCCTT
460585 ATTTTTAAAAAAATTTCATTAAACCCCTT
1 ATTTTTAAAAAAATTTCATTAAACCCCTT
460614 A
1 A
460615 AAATTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (29 bp):
ATTTTTAAAAAAATTTCATTAAACCCCTT
Found at i:461503 original size:31 final size:30
Alignment explanation
Indices: 461468--461584 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 30
461458 AGTTTAGAAG
461468 GGTCTAATGAAAATTTTAAAAAAATTTGGGA
1 GGTCTAATGAAAATTTT-AAAAAATTTGGGA
* * *
461499 GGTCTAATTAAATATTTTTTAAAACTTTGAGG-
1 GGTCTAATGAAA-A-TTTTAAAAAATTTG-GGA
* * *
461531 GGTC-AAT-AAAATTTT-TAAATTTTGAGA
1 GGTCTAATGAAAATTTTAAAAAATTTGGGA
*
461558 GGAT-TAATGAAAATTTCCAAAAAATTT
1 GG-TCTAATGAAAATTT-TAAAAAATTT
461585 AGAGAGCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 1 0.01
27 9 0.13
28 8 0.12
29 8 0.12
30 3 0.04
31 20 0.29
32 13 0.19
33 6 0.09
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (30 bp):
GGTCTAATGAAAATTTTAAAAAATTTGGGA
Found at i:468638 original size:116 final size:117
Alignment explanation
Indices: 468495--468727 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 117
468485 TAAAATCATG
468495 TGATATTAGAAAAAAAATAGCTTATTAAAAGCTTCTATTTTAATTTTATAATTACTTTTATTTAA
1 TGATATTAGAAAAAAAATAGCTTATTAAAAGCTTCTATTTTAATTTTATAATTACTTTTATTTAA
468560 TTTAATTATAATTTCTTAATTATTAAAAATAACATATATTTTAATATTATGA
66 TTTAATTATAATTTCTTAATTATTAAAAATAACATATATTTTAATATTATGA
468612 TGATATTAG-AAAAAAATAGCTTATTAAAAGCTTCTATTTTAATTTTATAATTACTTTTATTTAA
1 TGATATTAGAAAAAAAATAGCTTATTAAAAGCTTCTATTTTAATTTTATAATTACTTTTATTTAA
468676 TTTAATTATAATTTCTTAATTATTAAAAATAACATATATTTTAATATTATGA
66 TTTAATTATAATTTCTTAATTATTAAAAATAACATATATTTTAATATTATGA
468728 ATTTTTGTTA
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 107 0.92
117 9 0.08
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (117 bp):
TGATATTAGAAAAAAAATAGCTTATTAAAAGCTTCTATTTTAATTTTATAATTACTTTTATTTAA
TTTAATTATAATTTCTTAATTATTAAAAATAACATATATTTTAATATTATGA
Found at i:487950 original size:15 final size:14
Alignment explanation
Indices: 487930--487975 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
487920 TAAAAAGTAG
487930 AAAAATTAAATTCAT
1 AAAAATTAAATT-AT
* *
487945 AAAAATAAAAATAT
1 AAAAATTAAATTAT
*
487959 AAAAACTAAATTAT
1 AAAAATTAAATTAT
487973 AAA
1 AAA
487976 TTTGTGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:487962 original size:29 final size:29
Alignment explanation
Indices: 487920--487975 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
487910 TTTTAAAATT
*
487920 TAAAAAGTAGAAAAATTAAATTCATAAAAA
1 TAAAAAGTAGAAAAACTAAATT-ATAAAAA
*
487950 TAAAAA-TATAAAAACTAAATTATAAA
1 TAAAAAGTAGAAAAACTAAATTATAAA
487976 TTTGTGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (29 bp):
TAAAAAGTAGAAAAACTAAATTATAAAAA
Found at i:489558 original size:109 final size:109
Alignment explanation
Indices: 489419--489625 Score: 362
Period size: 109 Copynumber: 1.9 Consensus size: 109
489409 ATGAATTTCT
*
489419 CCCCCCCCCTTTGTAGATGATTGAGAATTAGAGTGAAATCAACCTTGTATGGTGGGTTATATTAT
1 CCCCCCCCCTTTGTAGATGATT-AGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
*
489484 GTTATGTTCCTCCTTTCTCAGTATGGTTACCATCTCTCCCTCCTC
65 GTTATGTTCCTCCTTGCTCAGTATGGTTACCATCTCTCCCTCCTC
489529 CCCCCCCCCTTTTGTAGATGATT-GAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
1 CCCCCCCCC-TTTGTAGATGATTAGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTAT
*
489593 GTTATTTTCCTCCTTGCTCAGTATGGTTACCAT
65 GTTATGTTCCTCCTTGCTCAGTATGGTTACCAT
489626 GATGATGGTA
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
109 71 0.76
110 9 0.10
111 13 0.14
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (109 bp):
CCCCCCCCCTTTGTAGATGATTAGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATG
TTATGTTCCTCCTTGCTCAGTATGGTTACCATCTCTCCCTCCTC
Found at i:496175 original size:24 final size:24
Alignment explanation
Indices: 496148--496197 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
496138 CTTACTAATC
496148 GAACAATTCCAAACTACAACCGAG
1 GAACAATTCCAAACTACAACCGAG
*
496172 GAACAATTCCAAACTACAATCGAG
1 GAACAATTCCAAACTACAACCGAG
496196 GA
1 GA
496198 TACGGGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (24 bp):
GAACAATTCCAAACTACAACCGAG
Found at i:497025 original size:26 final size:27
Alignment explanation
Indices: 496996--497052 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
496986 GGCGAAGGAA
496996 AATTTT-TTTTTTGGGGGTTAGAATTG
1 AATTTTATTTTTTGGGGGTTAGAATTG
*
497022 AATTTTAATTTTTTGGGTGTTAGAATTG
1 AATTTT-ATTTTTTGGGGGTTAGAATTG
497050 AAT
1 AAT
497053 GGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
28 22 0.79
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (27 bp):
AATTTTATTTTTTGGGGGTTAGAATTG
Found at i:497043 original size:28 final size:28
Alignment explanation
Indices: 497002--497063 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
496992 GGAAAATTTT
**
497002 TTTTTTGGGGGTTAGAATTGAATTTTAA
1 TTTTTTGGGGGTTAGAATTGAATGGTAA
*
497030 TTTTTTGGGTGTTAGAATTGAATGGTAA
1 TTTTTTGGGGGTTAGAATTGAATGGTAA
497058 TTTTTT
1 TTTTTT
497064 TAGGTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTTTTTGGGGGTTAGAATTGAATGGTAA
Found at i:497454 original size:17 final size:17
Alignment explanation
Indices: 497427--497470 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
497417 TAAAATGTGT
497427 TAATATTGAACTTAAACA
1 TAAT-TTGAACTTAAACA
*
497445 TAATTTGAACTTAATCA
1 TAATTTGAACTTAAACA
*
497462 TAATATGAA
1 TAATTTGAA
497471 TACATGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (17 bp):
TAATTTGAACTTAAACA
Found at i:502224 original size:2 final size:2
Alignment explanation
Indices: 502217--502248 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
502207 GGTTTCAATT
502217 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
502249 CCCCCCTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:505665 original size:16 final size:16
Alignment explanation
Indices: 505629--505668 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
505619 AAAGTCTAAA
505629 AAAAAATATATTTAAT
1 AAAAAATATATTTAAT
* *
505645 AAAAAGTATATTTGAT
1 AAAAAATATATTTAAT
*
505661 TAAAAATA
1 AAAAAATA
505669 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
AAAAAATATATTTAAT
Found at i:505761 original size:131 final size:130
Alignment explanation
Indices: 505617--505868 Score: 461
Period size: 131 Copynumber: 1.9 Consensus size: 130
505607 TAATTGGGAT
505617 TAAAAGTCT-AAAAAAAAATATATTTAATAAAAAGTATATTTGATTAAAAATAAAAATAAAAATA
1 TAAAAGTCTAAAAAAAAAAT-TATTTAATAAAAAGTATATTTGATTAAAAATAAAAATAAAAATA
*
505681 AAATATTTAATATATAATTCAGGCCGAGCCGGGCCGGGCCCGGGCCGGGGCAAAAAAAACATGTC
65 AAATATTTAATATATAATTCAGGCCGAGCCGGGCCGGG-CCGGGCCCGGGCAAAAAAAACATGTC
505746 CG
129 CG
505748 TAAAAGTCTAAAAAAAAAATTATTTAATAAAAAGTATATTTGATTAAAAATAAAAATAAAAATAA
1 TAAAAGTCTAAAAAAAAAATTATTTAATAAAAAGTATATTTGATTAAAAATAAAAATAAAAATAA
*
505813 AATATTTAATATATAATTCAGGCCGAGCCGGGCCGGGCCGGGCCCGGGCCAAAAAA
66 AATATTTAATATATAATTCAGGCCGAGCCGGGCCGGGCCGGGCCCGGGCAAAAAAA
505869 GTCTTACCCG
Statistics
Matches: 118, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
130 17 0.14
131 91 0.77
132 10 0.08
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (130 bp):
TAAAAGTCTAAAAAAAAAATTATTTAATAAAAAGTATATTTGATTAAAAATAAAAATAAAAATAA
AATATTTAATATATAATTCAGGCCGAGCCGGGCCGGGCCGGGCCCGGGCAAAAAAAACATGTCCG
Found at i:508208 original size:31 final size:31
Alignment explanation
Indices: 508167--508226 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
508157 TTATGAAATG
508167 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTGAAAGTTTTCATTTAA
* *
508198 GTCATTGAACTATTTGAAAGTTTTTATTT
1 GTCACTGAACTATTTGAAAGTTTTCATTT
508227 GAGCCACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (31 bp):
GTCACTGAACTATTTGAAAGTTTTCATTTAA
Found at i:509865 original size:31 final size:32
Alignment explanation
Indices: 509830--509910 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
509820 TTGGGTTCAA
* **
509830 AACTAAAATTTTA-AAATTTGAAAAATACAAG
1 AACTAAAATTTGACAAATTCAAAAAATACAAG
* *
509861 AACTAAAA-TTGACCAATTCAAAAAATACAGG
1 AACTAAAATTTGACAAATTCAAAAAATACAAG
509892 AACTAAAA-TTGATCAAATT
1 AACTAAAATTTGA-CAAATT
509911 ACAACTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.07
31 34 0.81
32 5 0.12
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (32 bp):
AACTAAAATTTGACAAATTCAAAAAATACAAG
Found at i:514173 original size:223 final size:223
Alignment explanation
Indices: 513773--514213 Score: 623
Period size: 223 Copynumber: 2.0 Consensus size: 223
513763 AACATGCTAG
* * * * *
513773 CATCACTAACTCATGAAACTCTTTCCTTAAAATATTAGTATCTTACTAAATCTTTATTTTCTCTC
1 CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
* ** * *
513838 TCCTCTAACATGAACATACAACTTTTCCACTTGAATATAACCTTTCTATGTTGTTCTAAACTTAA
66 TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
*
513903 TTCCACTAAGAATTTCAATGGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
131 TTCCACTAAGAATTTCAATAGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
*
513968 GAGACCAAACTGTATGGAAATGAGTTAA
196 GAGACCAAACTGTAAGGAAATGAGTTAA
* * *
513996 CATCACTAACTCATGAAAGTCTTACCTTAAACCCTTAGTATATCACTAAATCTTAATTTTCTCTC
1 CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
* * *
514061 TCCTTTAACATGAACATATAACCTCGCCACTTGAATATAACATTGCTATGTTGTTGTAAACTTAA
66 TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
* * * * * * *
514126 TTTCATTAAGAATTTCAATAG-AATTTTGTTGGTTTTTGGCTAAGGTTTGATGGCTATCGTGAAG
131 TTCCACTAAGAATTTCAATAGAAATTTTG-TGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAA
* *
514190 AGGGACCAAATTGTAAGGAAATGA
195 AGAGACCAAACTGTAAGGAAATGA
514214 AATTTTCCTT
Statistics
Matches: 190, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
222 7 0.04
223 183 0.96
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (223 bp):
CATCACTAACTCATGAAACTCTTACCTTAAAACATTAGTATATCACTAAATCTTAATTTTCTCTC
TCCTCTAACATGAACATACAACCTCGCCACTTGAATATAACATTGCTATGTTGTTCTAAACTTAA
TTCCACTAAGAATTTCAATAGAAATTTTGTGGTTTCTGACAAAGGTTTGATAGCTATCGTGAAAA
GAGACCAAACTGTAAGGAAATGAGTTAA
Found at i:526017 original size:147 final size:148
Alignment explanation
Indices: 525850--526144 Score: 583
Period size: 147 Copynumber: 2.0 Consensus size: 148
525840 ATAAGATTAT
525850 TATTTTAATAAATAAATTTCATGTTAGAAAAATAAGAAAAATGGGTATTCATTTATTTATAAATA
1 TATTTTAATAAATAAATTTCATGTTAGAAAAATAAGAAAAATGGGTATTCATTTATTTATAAATA
525915 TTTTTATAAAAATCTTATATATTTTTATCAAAAAATAAACTTTTAAACATTTTTTTTATTTTTAA
66 TTTTTATAAAAATCTTATATATTTTTATCAAAAAATAAACTTTTAAACATTTTTTTTATTTTTAA
525980 GAATCAAGATTAAATTGA
131 GAATCAAGATTAAATTGA
525998 TATTTTAAT-AATAAATTTCATGTTAGAAAAATAAGAAAAATGGGTATTCATTTATTTATAAATA
1 TATTTTAATAAATAAATTTCATGTTAGAAAAATAAGAAAAATGGGTATTCATTTATTTATAAATA
526062 TTTTTATAAAAATCTTATATATTTTTATCAAAAAATAAACTTTTAAACATTTTTTTTATTTTTAA
66 TTTTTATAAAAATCTTATATATTTTTATCAAAAAATAAACTTTTAAACATTTTTTTTATTTTTAA
526127 GAATCAAGATTAAATTGA
131 GAATCAAGATTAAATTGA
526145 AAAAACTATA
Statistics
Matches: 147, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 138 0.94
148 9 0.06
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (148 bp):
TATTTTAATAAATAAATTTCATGTTAGAAAAATAAGAAAAATGGGTATTCATTTATTTATAAATA
TTTTTATAAAAATCTTATATATTTTTATCAAAAAATAAACTTTTAAACATTTTTTTTATTTTTAA
GAATCAAGATTAAATTGA
Found at i:529863 original size:36 final size:35
Alignment explanation
Indices: 529823--529892 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
529813 CATCTCCGGA
529823 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
529859 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATA
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATA
529893 CGTGATCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:530266 original size:48 final size:48
Alignment explanation
Indices: 530194--530285 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
530184 AGGGATTCTG
** * *
530194 TTGAATCCTTTATTGTTGCGAGTTAAGTTGACTTAGGCATTTTTACTA
1 TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTACTA
* *
530242 TTGAATCCTTTATTACTGCAAGTTAGGCTGACTTAGGCGTTTTT
1 TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTT
530286 GAGCAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (48 bp):
TTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTACTA
Found at i:535044 original size:36 final size:35
Alignment explanation
Indices: 535004--535075 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
534994 CATCTCCGGA
535004 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
535040 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
535075 G
1 G
535076 TGATCCTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:541765 original size:128 final size:129
Alignment explanation
Indices: 541533--541827 Score: 393
Period size: 128 Copynumber: 2.3 Consensus size: 129
541523 ACAGAAGAAT
** * ** *
541533 ATCAGATCTTATCTCATTGAGATTACAGCGGAGCAGACTGAAGCTGGTAATCCTATCTCCCTGAG
1 ATCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACTCAAGCTACTAATCCCATCTCCCTGAG
* *
541598 ATTACAGTGGAGTGGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGT
66 ATTACAGTGGAGTGGATTAAAATAAAGAATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGC
*
541662 ATTAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCCAAGAC-ACT-ATCCCATCTCCCTG
1 ATCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACT-CAAG-CTACTAATCCCATCTCCCTG
*
541724 A-AGTTACAGTGGAGCT-GATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGAT
64 AGA-TTACAGTGGAG-TGGATTAAAATAAAGAATCTCATCTCTCTGAAGTTACAGTAGAGTAGAT
541787 CGC
127 CGC
* * * *
541790 ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAC
1 ATCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGAC
541828 CGAAGAATTT
Statistics
Matches: 146, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
127 1 0.01
128 105 0.72
129 39 0.27
130 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (129 bp):
ATCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGACTCAAGCTACTAATCCCATCTCCCTGAG
ATTACAGTGGAGTGGATTAAAATAAAGAATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGC
Found at i:541846 original size:46 final size:44
Alignment explanation
Indices: 541586--542086 Score: 222
Period size: 44 Copynumber: 11.5 Consensus size: 44
541576 CTGGTAATCC
* * ** *
541586 TATCTCCCTGAGATTACAGTGGAGTGGA-TTAA-AATAAAGAATCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAT-CAG-ATCT
* * * * * *
541630 TATCTCTCTGAAGTTACAGTAGAGTAGATC---GTATTAGATCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATCAGATCT
* * * * *
541671 TATCTCCCTGAGATTACAGCGGAGCAGATCC-AAG-A-CACTATCC
1 TATCTCCCTGAGGTTACAGTGGAGTAGA-CCGAAGAATCA-GATCT
* * ** *
541714 CATCTCCCTGAAGTTACAGTGGAGCT-GA-TTAA-AATAAAGGATCT
1 TATCTCCCTGAGGTTACAGTGGAG-TAGACCGAAGAAT-CA-GATCT
* * * * * * *
541758 CATCTCTCTGAAGTTACAGTAGAGTAGATC---GCATCAGGTCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATCAGATCT
541799 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAA--TCAGATCT
* ** * *
541845 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGATCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AATCAGATCT
* * * * *
541889 TATCTCCCTGAGATTACAGCGGAGCAGATCC-AAG-A-CACTATCC
1 TATCTCCCTGAGGTTACAGTGGAGTAGA-CCGAAGAATCA-GATCT
* * ** *
541932 CATCTCCCTGAAGTTACAGTGGAGCT-GA-TTAA-AATAAAGGATCT
1 TATCTCCCTGAGGTTACAGTGGAG-TAGACCGAAGAAT-CA-GATCT
* * * * * * *
541976 CATCTCTCTGAAGTTACAGTAGAGTAGATC---GCATCAGGTCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATCAGATCT
542017 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCT
1 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAA--TCAGATCT
*
542063 TATCTCCTTGAGGTTACAGTGGAG
1 TATCTCCCTGAGGTTACAGTGGAG
542087 CTGGTTAAAG
Statistics
Matches: 345, Mismatches: 77, Indels: 68
0.70 0.16 0.14
Matches are distributed among these distances:
41 84 0.24
42 14 0.04
43 59 0.17
44 119 0.34
46 68 0.20
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATCAGATCT
Found at i:541907 original size:218 final size:218
Alignment explanation
Indices: 541665--542087 Score: 837
Period size: 218 Copynumber: 1.9 Consensus size: 218
541655 AGATCGTATT
541665 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
541730 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
541795 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
541860 ACAGTGGAGCAGATTGAAGCCAG
196 ACAGTGGAGCAGATTGAAGCCAG
541883 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
541948 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
542013 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAGGTT
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
542078 ACAGTGGAGC
196 ACAGTGGAGC
542088 TGGTTAAAGA
Statistics
Matches: 204, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 204 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (218 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
ACAGTGGAGCAGATTGAAGCCAG
Found at i:542005 original size:87 final size:87
Alignment explanation
Indices: 541846--542005 Score: 189
Period size: 87 Copynumber: 1.8 Consensus size: 87
541836 TTCAGATCTT
* * ** * *
541846 ATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGG
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTCATCTCCCTGAGATTACAGCAG
541911 AGCAGATCCAAGACACTATCCC
66 AGCAGATCCAAGACACTATCCC
* * * *
541933 ATCTCCCTGAAGTTACAGTGGAGCTGATTAAAATAAAG-GATCTCATCTCTCTGA-AGTTACAGT
1 ATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGAAAGAGATCTCATCTCCCTGAGA-TTACAGC
*
541996 AGAGTAGATC
64 AGAGCAGATC
542006 GCATCAGGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
86 1 0.02
87 55 0.92
88 4 0.07
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (87 bp):
ATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTCATCTCCCTGAGATTACAGCAG
AGCAGATCCAAGACACTATCCC
Found at i:542186 original size:218 final size:217
Alignment explanation
Indices: 541665--542182 Score: 713
Period size: 218 Copynumber: 2.4 Consensus size: 217
541655 AGATCGTATT
* * * ** *
541665 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
1 AGATCTTACCTCCCTGAGATTACAGCGAAGCAGATCCAAGACACCAAACCATCTCCATG-AGTTA
541730 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
65 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
541795 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
130 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* * *
541860 ACAGTGGAGCAGATTGAAGCCAG
195 ACAGTGGAGCAGATTAAAGCAAC
* * * ** *
541883 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACACTATCCCATCTCCCTGAAGTTA
1 AGATCTTACCTCCCTGAGATTACAGCGAAGCAGATCCAAGACACCAAACCATCTCCATG-AGTTA
541948 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
65 CAGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
542013 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAGGTT
130 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* * *
542078 ACAGTGGAGCTGGTTAAAGATAAC
195 ACAGTGGAGCAGATTAAAG-CAAC
* * * *
542102 AGATCTTGCCTTCCTGCG-TTAACAGCGAAGCAGA-CCAA-A-ACCAAACCTTGCCTCCATCG-G
1 AGATCTTACCTCCCTGAGATT-ACAGCGAAGCAGATCCAAGACACCAAACCAT--CTCCAT-GAG
* *
542162 TTGCAGTGGAGCTGGTTAAAA
62 TTACAGTGGAGCTGATTAAAA
542183 ATAACAGATC
Statistics
Matches: 276, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
216 6 0.02
217 21 0.08
218 221 0.80
219 28 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (217 bp):
AGATCTTACCTCCCTGAGATTACAGCGAAGCAGATCCAAGACACCAAACCATCTCCATGAGTTAC
AGTGGAGCTGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
CAGTGGAGCAGATTAAAGCAAC
Found at i:542376 original size:87 final size:87
Alignment explanation
Indices: 542074--542357 Score: 500
Period size: 87 Copynumber: 3.3 Consensus size: 87
542064 ATCTCCTTGA
* *
542074 GGTTACAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGA-CC
1 GGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
542138 AAAACCAAA-CCTTGCCTCCATC
66 AAAA-CAAAGCCTTGCCTCCATC
* * *
542160 GGTTGCAGTGGAGCTGGTTAAAAATAACAGATCTTGTCTTCCTGCGTTAACAGGGAAGCAGATCG
1 GGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
542225 AAAACAAAGCCTTGCCTCCATC
66 AAAACAAAGCCTTGCCTCCATC
542247 GGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
1 GGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
542312 AAAACAAAGCCTTGCCTCCATC
66 AAAACAAAGCCTTGCCTCCATC
542334 GGTTGCAGTGGAGCTGGTTAAAGA
1 GGTTGCAGTGGAGCTGGTTAAAGA
542358 CATCAAGTCT
Statistics
Matches: 188, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
86 62 0.33
87 126 0.67
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (87 bp):
GGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
AAAACAAAGCCTTGCCTCCATC
Found at i:542540 original size:84 final size:85
Alignment explanation
Indices: 542448--542983 Score: 373
Period size: 84 Copynumber: 6.4 Consensus size: 85
542438 TAAGCCACGA
* * * *
542448 ATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAACAGTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGTA
*
542513 GTGGAGCAGATCGTATTAAG
66 GTGGAGCAGATCGTATCAAG
* * * * * * ** * * **
542533 A-CTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCT---TCAAGTGTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGT-
* * * *
542594 AG-GAAGCAGAT-TTAAGCCACG
65 AGTGGAGCAGATCGT-A-TCAAG
* * *
542615 AATCCTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGT
542680 AGTGGAGCAGATCGTATCAAG
65 AGTGGAGCAGATCGTATCAAG
* * * * * ** * * **
542701 A-CTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTAAATCTTATCT---TCAAGTGTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGT-
* * * *
542762 AG-GAAGCAGAT-TTAAGCCACG
65 AGTGGAGCAGATCGT-A-TCAAG
* * * * *
542783 AATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGCA-T-TAGATCTTATCTCCCTAAGCAG
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAG-ATTGTAGATCTTATCTCCCTAAACAG
* * ** *
542846 TAGTGGAGCAGATAGAAGAAACCA
64 TAGTGGAGCAGATCGTATCAA--G
* *
542870 ATCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGTA
* *
542935 GTGGAGCAGATCGCAT-TAG
66 GTGGAGCAGATCGTATCAAG
* *
542954 ATCTTATCTCTCTAAGCAGTAGTGGAGTAG
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAG
542984 ATCGCATCAA
Statistics
Matches: 332, Mismatches: 94, Indels: 51
0.70 0.20 0.11
Matches are distributed among these distances:
80 2 0.01
81 27 0.08
82 9 0.03
83 13 0.04
84 171 0.52
85 7 0.02
86 53 0.16
87 49 0.15
88 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (85 bp):
ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGTA
GTGGAGCAGATCGTATCAAG
Found at i:542560 original size:168 final size:168
Alignment explanation
Indices: 542359--542858 Score: 896
Period size: 168 Copynumber: 3.0 Consensus size: 168
542349 GGTTAAAGAC
*
542359 ATCAAGTCTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
1 ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
*
542424 TAAAGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTG
66 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTG
*
542489 TAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGT
*
542527 ATTAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
1 ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
* *
542592 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTG
66 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTG
542657 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGT
131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGT
*
542695 ATCAAGACTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
1 ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
* *
542760 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGCA-T
66 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAG-ATT
542824 -TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
130 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
542859 AGAAGAAACC
Statistics
Matches: 319, Mismatches: 12, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
167 35 0.11
168 283 0.89
169 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (168 bp):
ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTG
TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGT
Found at i:542951 original size:127 final size:128
Alignment explanation
Indices: 542615--542985 Score: 382
Period size: 127 Copynumber: 2.9 Consensus size: 128
542605 TTAAGCCACG
*
542615 AATCCTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AATCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* * * * **
542680 AGTGGAGCAGATCGTATCAAGA-CTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTA
66 AGTGGAGCAGATCGCAT-TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGACAACA
* * * * * * * * *
542743 AATCTTATCT-TC-AAGT-GTAAG-GAAGCAGATTTAAGCCA-CG-A-ATCCTATCTCCCTGAGC
1 AATCCTATCTCCCTAAGTAGT-AGTGGAGTAGGTTGAAG--ATTGTAGATCTTATCTCCCTAAGC
* * * **
542801 AGCAATGGAGTAGGTTAAAGCATTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGA-
63 AGTAGTGGAGCA-G--ATCGCATTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGAC
*
542865 AACC
125 AACA
* *
542869 AATCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGT
1 AATCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
* *
542934 AGTGGAGCAGATCGCATTAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGAT
66 AGTGGAGCAGATCGCATTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
542986 CGCATCAAAG
Statistics
Matches: 189, Mismatches: 40, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
124 24 0.13
125 13 0.07
126 20 0.11
127 80 0.42
128 15 0.08
129 14 0.07
130 23 0.12
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (128 bp):
AATCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGCATTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGACAACA
Found at i:542974 original size:40 final size:41
Alignment explanation
Indices: 542911--543046 Score: 168
Period size: 40 Copynumber: 3.3 Consensus size: 41
542901 TTGAAGATTG
* * *
542911 TAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGCAT-
1 TAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATC
542951 TAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATC
1 TAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATC
* ** *
542992 AAAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATC
1 -TAGATCTTATCTCTCT-AAGCAGTAGTGGAGTAGATCGCATC
*
543035 CAG-TCTTATCTC
1 TAGATCTTATCTC
543047 CCTGAAGTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
40 37 0.44
41 9 0.11
42 17 0.20
43 22 0.26
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (41 bp):
TAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATC
Found at i:543000 original size:336 final size:334
Alignment explanation
Indices: 542359--543005 Score: 795
Period size: 336 Copynumber: 1.9 Consensus size: 334
542349 GGTTAAAGAC
*
542359 ATCAAGTCTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
1 ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
* *
542424 TAAAGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAGATTG
66 TAAAGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGATTG
* * ** * * *
542489 TAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGTATTAAGACTTATCTTCCTAAGCAGTAG
131 TAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATAGAAGAAAAACCTATCTCCCTAAGCAGTAG
* **
542554 CGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAATC
196 CGGAGCAGATCGAAGACAGTAAATCTTATCTTAAACAGTAAGGAAGCAGA-TTAAGCCACGAATC
* * * * ***
542619 CTATCTCCCTAAGTAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
260 CTATCTCCCTAAGCAGCAGTGGAGTAGATCG-ACATCAAAGATCTTATCTCCCTAAGCAGTAGTG
542684 GAGCAGATCGT
324 GAGCAGATCGT
*
542695 ATCAAGACTTATCTTCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
1 ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
*
542760 TAAGGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGCA-T
66 TAAAGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAG-ATT
* * *
542824 -TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTGAGTA
130 GTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATAGAAGAAA--AA-CCTATCTCCCTAAGCA
* * * * ** * * *
542888 GTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGT-AGTGGAGCAGA-T-CG-C
192 GTAGCGGAGCAGATCGAAGACAGTAAATCTTATCT---TAAACAGTAAG-GAAGCAGATTAAGCC
** * * *
542949 ATTAGATCTTATCTCTCTAAGCAGTAGTGGAGTAGATCG-CATCAAAGATCTTATCTC
253 ACGA-ATCCTATCTCCCTAAGCAGCAGTGGAGTAGATCGACATCAAAGATCTTATCTC
543006 TCTGAAGTTG
Statistics
Matches: 263, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
335 38 0.14
336 136 0.52
337 5 0.02
338 69 0.26
339 1 0.00
340 2 0.01
341 12 0.05
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (334 bp):
ATCAAGACTTATCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACAGTAAATCTTATCTTCAAGTG
TAAAGAAGCAGATTTAAGCCACGAATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGATTG
TAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATAGAAGAAAAACCTATCTCCCTAAGCAGTAG
CGGAGCAGATCGAAGACAGTAAATCTTATCTTAAACAGTAAGGAAGCAGATTAAGCCACGAATCC
TATCTCCCTAAGCAGCAGTGGAGTAGATCGACATCAAAGATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGT
Found at i:543019 original size:127 final size:125
Alignment explanation
Indices: 542636--543026 Score: 336
Period size: 127 Copynumber: 3.1 Consensus size: 125
542626 CCTAAGTAGC
* *
542636 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGTATCAAG
1 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAT-TAG
542701 A-CTTATCT-TCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTAAATCTTATCT-TC--AAG-TG
65 ATCTTATCTCT-CTAAGCAGTAGTGGAGCAGATCG-A-ACA--AAATCTTATCTCTCTGAAGTTG
542760 T
125 T
* * * * * * * * * * **
542761 AAG-GAAGCAGATTTAAGCCA-CG-A-ATCCTATCTCCCTGAGCAGCAATGGAGTAGGTTAAAGC
1 -AGTGGAGTAGGTTGAAG--ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCA-G--ATCGC
* * * * *
542822 ATTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTG-AG
60 ATTAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAA-CAA--AATCTTATCTCTCTGAAG
*
542886 TAGT
122 TTGT
*
542890 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGCATTAGA
1 AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATTAGA
* *
542955 TCTTATCTCTCTAAGCAGTAGTGGAGTAGATCGCATCAAAGATCTTATCTCTCTGAAGTTGT
66 TCTTATCTCTCTAAGCAGTAGTGGAGCAGATCG-AACAAA-ATCTTATCTCTCTGAAGTTGT
*
543017 AGTAGAGTAG
1 AGTGGAGTAG
543027 ATCGCATCCA
Statistics
Matches: 202, Mismatches: 42, Indels: 41
0.71 0.15 0.14
Matches are distributed among these distances:
124 25 0.12
125 14 0.07
126 29 0.14
127 91 0.45
128 6 0.03
129 14 0.07
130 23 0.11
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (125 bp):
AGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATTAGA
TCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAACAAAATCTTATCTCTCTGAAGTTGT
Found at i:543030 original size:43 final size:42
Alignment explanation
Indices: 542932--543055 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 42
542922 TCCCTAAACA
* * * **
542932 GTAGTGGAGCAGATCGCAT-TAGATCTTATCTCTCT-AAGCA
1 GTAGTAGAGTAGATCGCATCAAGATCTTATCTCTCTGAAGTT
*
542972 GTAGTGGAGTAGATCGCATCAAAGATCTTATCTCTCTGAAGTT
1 GTAGTAGAGTAGATCGCATC-AAGATCTTATCTCTCTGAAGTT
* *
543015 GTAGTAGAGTAGATCGCATCCAG-TCTTATCTCCCTGAAGTT
1 GTAGTAGAGTAGATCGCATCAAGATCTTATCTCTCTGAAGTT
543056 ACAGTGGAGC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 18 0.24
41 17 0.23
42 17 0.23
43 22 0.30
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (42 bp):
GTAGTAGAGTAGATCGCATCAAGATCTTATCTCTCTGAAGTT
Found at i:550953 original size:22 final size:22
Alignment explanation
Indices: 550927--550982 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
550917 TTATTTTTAC
550927 TATTAATTA-ACTTATTATTATT
1 TATT-ATTACACTTATTATTATT
*
550949 TATTATTACTCTTATTATTATT
1 TATTATTACACTTATTATTATT
550971 GATATTATTACA
1 --TATTATTACA
550983 TTTGGTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.14
22 16 0.55
24 9 0.31
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTATTACACTTATTATTATT
Found at i:550980 original size:12 final size:10
Alignment explanation
Indices: 550938--550979 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
550928 ATTAATTAAC
550938 TTATTATTAT
1 TTATTATTAT
550948 TTATTATTACT
1 TTATTATTA-T
550959 CTTATTATTAT
1 -TTATTATTAT
*
550970 TGA-TATTAT
1 TTATTATTAT
550979 T
1 T
550980 ACATTTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 7 0.24
10 11 0.38
11 2 0.07
12 9 0.31
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (10 bp):
TTATTATTAT
Found at i:553693 original size:14 final size:14
Alignment explanation
Indices: 553676--553705 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
553666 AGGTGAACTA
553676 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
553690 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
553704 GC
1 GC
553706 TGCAATCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:553910 original size:14 final size:14
Alignment explanation
Indices: 553891--553920 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
553881 CATCGGGAAA
553891 TCCGGAAAATATTT
1 TCCGGAAAATATTT
553905 TCCGGAAAATATTT
1 TCCGGAAAATATTT
553919 TC
1 TC
553921 TCCCTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
TCCGGAAAATATTT
Found at i:554047 original size:3 final size:3
Alignment explanation
Indices: 554039--554091 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
554029 ATTCTCACTC
* *
554039 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TTA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
554086 TTA ATA
1 ATA ATA
554092 CTTACATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 1 0.02
3 42 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:554805 original size:14 final size:17
Alignment explanation
Indices: 554786--554823 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
554776 ATTTATTTCT
554786 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
554800 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
554817 TAATATA
1 TAATATA
554824 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:554831 original size:12 final size:11
Alignment explanation
Indices: 554803--554846 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
554793 ATATTTATAA
554803 TATAATTAATT
1 TATAATTAATT
*
554814 TAATAATATACTT
1 T-ATAAT-TAATT
554827 TATAATTAATT
1 TATAATTAATT
554838 TATATATTA
1 TATA-ATTA
554847 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:554850 original size:20 final size:23
Alignment explanation
Indices: 554798--554860 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
554788 ATATAATATT
554798 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
554820 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
554845 TATATAAATAAATAAT
1 TATATATATAATTAAT
554861 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:554862 original size:20 final size:20
Alignment explanation
Indices: 554815--554863 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
554805 TAATTAATTT
*
554815 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
554835 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
554855 AATAATATA
1 AATAATATA
554864 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:556344 original size:51 final size:52
Alignment explanation
Indices: 556286--556401 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 52
556276 ATTGGTATAA
* * * *
556286 TAACAAATTTAGTCCACAAA-AGTTTACACATTGTGTCAAATTGGTATTG-TT
1 TAACAAATTTAGCCCACAAACA-TTTACACATTCTATCAAATTGGCATTGATT
* * * *
556337 TAACAAATTTAACCCACAAACATTTACATATTCTATCAATTTGGCCTTGATT
1 TAACAAATTTAGCCCACAAACATTTACACATTCTATCAAATTGGCATTGATT
556389 TAACAAATTTAGC
1 TAACAAATTTAGC
556402 TCGTAATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
51 39 0.72
52 15 0.28
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (52 bp):
TAACAAATTTAGCCCACAAACATTTACACATTCTATCAAATTGGCATTGATT
Found at i:557516 original size:124 final size:126
Alignment explanation
Indices: 557395--557626 Score: 297
Period size: 127 Copynumber: 1.8 Consensus size: 126
557385 GTGTTTTCTG
* * * * * * * *
557395 GTTTGAATGTTTTTGTAGTTTAGAGTTTGAGTGTTAGTGTTG-GGTAAGTATAAAGGT-AGAATT
1 GTTTGAATATTTTTGTAGTTCAAAGTTTGAGTGTGAATGTTGTGGTAAGTATAAAGATAACAACT
** * *
557458 TGATTTGGGTTTAGATCATTTAATTTTGGGTTTTAATTGTTTCAAGTTCAAGTATTTTCGA
66 TGATTCAGGTTTAGATCATGTAATTTTCGGTTTTAATTGTTTCAAGTTCAAGTATTTTCGA
* *
557519 GTTTGAATATTTTTGTAGTTCAAAGTTTGAGTGTGAATGTTGTTTGTAGGTATAAAGATAACAAC
1 GTTTGAATATTTTTGTAGTTCAAAGTTTGAGTGTGAATGTTG-TGGTAAGTATAAAGATAACAAC
* *
557584 TTGATTCAGGTTTAGATCATGTAATTTTCTGTTTTAGTTGTTT
65 TTGATTCAGGTTTAGATCATGTAATTTTCGGTTTTAATTGTTT
557627 TAGGATTTTG
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
124 37 0.42
126 12 0.13
127 40 0.45
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.47
Consensus pattern (126 bp):
GTTTGAATATTTTTGTAGTTCAAAGTTTGAGTGTGAATGTTGTGGTAAGTATAAAGATAACAACT
TGATTCAGGTTTAGATCATGTAATTTTCGGTTTTAATTGTTTCAAGTTCAAGTATTTTCGA
Found at i:562022 original size:3 final size:3
Alignment explanation
Indices: 562014--562039 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
562004 AACAATAACC
562014 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
562040 CTTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:562136 original size:42 final size:42
Alignment explanation
Indices: 562077--562198 Score: 190
Period size: 42 Copynumber: 2.8 Consensus size: 42
562067 CATTGTTTTT
562077 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
1 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
*
562119 GCCTCAACAATGACTTCTGCTTTCTTTGGGGCCTCCTTTGGA
1 GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
* *
562161 GCCTCAACAATGGCTTCTTCCACTTTCTTTGGCGCCTC
1 GCCTCAACAATGACTTCTT---CTTTCTTTGGGGCCTC
562199 AACAATGGCG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
42 58 0.79
45 15 0.21
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (42 bp):
GCCTCAACAATGACTTCTTCTTTCTTTGGGGCCTCCTTTGGA
Found at i:563755 original size:16 final size:17
Alignment explanation
Indices: 563736--563777 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
563726 AATATACTAA
563736 TTATTTATT-AAACATT
1 TTATTTATTCAAACATT
* *
563752 TTATTAATTCAAATATT
1 TTATTTATTCAAACATT
563769 TTAGTTTAT
1 TTA-TTTAT
563778 AATAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 8 0.38
17 9 0.43
18 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTTATTCAAACATT
Found at i:564727 original size:26 final size:26
Alignment explanation
Indices: 564698--564748 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
564688 TACAAACAGC
*
564698 AGCCATTGATAAAAAAAAAAAAAAAT
1 AGCCATTGAAAAAAAAAAAAAAAAAT
*
564724 AGCCATTTAAAAAAAAAAAAAAAAA
1 AGCCATTGAAAAAAAAAAAAAAAAA
564749 AAAGAACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.14
Consensus pattern (26 bp):
AGCCATTGAAAAAAAAAAAAAAAAAT
Found at i:564737 original size:24 final size:25
Alignment explanation
Indices: 564698--564746 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
564688 TACAAACAGC
564698 AGCCATTGATAAAAAAAAAAAAAAAT
1 AGCCATT-ATAAAAAAAAAAAAAAAT
564724 AGCCATT-TAAAAAAAAAAAAAAA
1 AGCCATTATAAAAAAAAAAAAAAA
564747 AAAAAGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 16 0.70
26 7 0.30
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.14
Consensus pattern (25 bp):
AGCCATTATAAAAAAAAAAAAAAAT
Found at i:567745 original size:21 final size:22
Alignment explanation
Indices: 567720--567761 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
567710 ACCACCTTCT
567720 TCATCA-AA-ATTATTCCAATTA
1 TCATCACAAGATT-TTCCAATTA
567741 TCATCACAAGATTTTCCAATT
1 TCATCACAAGATTTTCCAATT
567762 TCTTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (22 bp):
TCATCACAAGATTTTCCAATTA
Found at i:577113 original size:17 final size:18
Alignment explanation
Indices: 577091--577128 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
577081 AAGTTTTAAT
577091 TTTATATT-TTATAAAAA
1 TTTATATTCTTATAAAAA
*
577108 TTTATATTCTTTTAAAAA
1 TTTATATTCTTATAAAAA
577126 TTT
1 TTT
577129 TCAGGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATATTCTTATAAAAA
Found at i:577595 original size:17 final size:17
Alignment explanation
Indices: 577570--577616 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
577560 TGGAATGAGC
*
577570 CTCAAGTAAGATTTTGG
1 CTCAGGTAAGATTTTGG
577587 CTCAGGTAAGATTTTGG
1 CTCAGGTAAGATTTTGG
*
577604 CTCAGGTCAGATT
1 CTCAGGTAAGATT
577617 GACCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (17 bp):
CTCAGGTAAGATTTTGG
Found at i:578193 original size:14 final size:14
Alignment explanation
Indices: 578178--578227 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
578168 ATATTCAAAT
*
578178 AATAACAATAAAAT
1 AATAACAATAAAAC
* *
578192 AATAATAATAATAC
1 AATAACAATAAAAC
*
578206 AATAAAAATAACAAC
1 AATAACAATAA-AAC
578221 AATAACA
1 AATAACA
578228 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 21 0.72
15 8 0.28
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAACAATAAAAC
Found at i:578195 original size:17 final size:17
Alignment explanation
Indices: 578175--578219 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
578165 AAAATATTCA
578175 AATAATAACAATAAAAT
1 AATAATAACAATAAAAT
* *
578192 AATAATAATAATACAAT
1 AATAATAACAATAAAAT
*
578209 AAAAATAACAA
1 AATAATAACAA
578220 CAATAACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAATAACAATAAAAT
Found at i:586869 original size:14 final size:14
Alignment explanation
Indices: 586827--586886 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
586817 TTTTAATATT
586827 ATATTTTATATAAAA
1 ATATTTTATAT-AAA
*
586842 ACAATTTTA-A-AAA
1 A-TATTTTATATAAA
586855 ATATTTTATATAAA
1 ATATTTTATATAAA
** *
586869 ATATAATATATCAA
1 ATATTTTATATAAA
586883 ATAT
1 ATAT
586887 ACTAAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.16
13 5 0.14
14 18 0.49
15 2 0.05
16 6 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATTTTATATAAA
Found at i:599082 original size:3 final size:3
Alignment explanation
Indices: 599074--599109 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
599064 TATATAACTT
*
599074 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
599110 GTATAATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:601271 original size:54 final size:54
Alignment explanation
Indices: 601210--601317 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
601200 AGCATATGGT
* *
601210 TAACCATATTATTTCATTTTCTGAATCATACAAACTATGGTTGACATTGATAAC
1 TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
*
601264 TAACCATATTATCTCATTTTCTGAAACATATAAACTATGGTTGACATTGATAAC
1 TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
601318 AATTCGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (54 bp):
TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
Found at i:604196 original size:22 final size:24
Alignment explanation
Indices: 604169--604225 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
604159 ATAAATTTTA
604169 ATTTTTATAATAATAAA-AATATA-
1 ATTTTTATAAT-ATAAATAATATAT
* *
604192 A-TTTTATCATTTAAATAATATAT
1 ATTTTTATAATATAAATAATATAT
604215 ATTTTTATAAT
1 ATTTTTATAAT
604226 TTTTAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 14 0.50
23 2 0.07
24 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTTATAATATAAATAATATAT
Found at i:604208 original size:28 final size:28
Alignment explanation
Indices: 604156--604211 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
604146 TTAGGGGTCG
*
604156 AAAATAAATTTTAATTTTTATAATAATA
1 AAAATAAATTTTAATATTTATAATAATA
604184 AAAATATAATTTT-ATCATTTA-AATAATA
1 AAAATA-AATTTTAAT-ATTTATAATAATA
604212 TATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATAAATTTTAATATTTATAATAATA
Found at i:612220 original size:15 final size:16
Alignment explanation
Indices: 612200--612233 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
612190 AGTCCCTAAA
*
612200 GTTTTTTGG-TTTAGG
1 GTTTTTAGGATTTAGG
612215 GTTTTTAGGATTTAGG
1 GTTTTTAGGATTTAGG
612231 GTT
1 GTT
612234 AAGGTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (16 bp):
GTTTTTAGGATTTAGG
Found at i:612313 original size:34 final size:33
Alignment explanation
Indices: 612275--612398 Score: 105
Period size: 34 Copynumber: 3.7 Consensus size: 33
612265 GTTTAAGGAA
*
612275 TAAATTAAGGTTTAAGGTTTTTTAAAAAAATAAT
1 TAAATTAAGGTTT-AGGTTTTTTAAAAAATTAAT
*
612309 TAAATT-AGGTTTTTGGGTTTAGGGTTT---AAATTAAT
1 TAAATTAAGG--TTTAGGTTT----TTTAAAAAATTAAT
*
612344 TAAATTAAGGTTTAGGGTTTTTAAGAAAATTAAT
1 TAAATTAAGGTTTAGGTTTTTTAA-AAAATTAAT
*
612378 TAAATTATGGTTTA-GTTTTTT
1 TAAATTAAGGTTTAGGTTTTTT
612399 CTTAAATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 23
0.72 0.06 0.23
Matches are distributed among these distances:
30 3 0.04
33 9 0.12
34 39 0.53
35 16 0.22
36 3 0.04
38 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (33 bp):
TAAATTAAGGTTTAGGTTTTTTAAAAAATTAAT
Found at i:612352 original size:69 final size:68
Alignment explanation
Indices: 612257--612390 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 68
612247 AATAATTTAT
*
612257 GGTTTAGGGTTTAAGGAATAAATTAAGGTTTAAGGTTTTTTAA-AAAAATAATTAAATTA-GGTT
1 GGTTTAGGGTTTAAGGAATAAATTAAGGTTT-AGGGTTTTTAAGAAAAATAATTAAATTATGGTT
612320 TTTG
65 TTTG
** *
612324 GGTTTAGGGTTTAAATTAATTAAATTAAGGTTTAGGGTTTTTAAGAAAATTAATTAAATTATGGT
1 GGTTTAGGGTTT-AAGGAA-TAAATTAAGGTTTAGGGTTTTTAAGAAAAATAATTAAATTATGGT
612389 TT
64 TT
612391 AGTTTTTTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 12 0.20
68 14 0.24
69 28 0.47
70 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (68 bp):
GGTTTAGGGTTTAAGGAATAAATTAAGGTTTAGGGTTTTTAAGAAAAATAATTAAATTATGGTTT
TTG
Found at i:612674 original size:125 final size:125
Alignment explanation
Indices: 612467--612857 Score: 460
Period size: 125 Copynumber: 3.2 Consensus size: 125
612457 TTTTGTTTTT
* * * * * *
612467 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTAAGAAGATGATTCTGAAAAGATAATGCCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGACAA-ATAGTGTCAAAA
* * * *
612532 CCACTTCAAGCAAGATGCACTGTCAGCAAAATTACTAAAAAAAACTCCCACGTGGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* *
612593 TTTTTCTACAGTAGTTCCT-AAAAAATAATTCTGAA-AAGACGGTTCCGAGCAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATT-TTAAGAAGACGGTTCTGA-CAAATAGTGTCAAA
* ** *
612656 AACTCTTCAAGCAGGATGCACTGTCAGCAAAAACACTGAAAAAAGC-CCCTACATGGACGCTC
64 AACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCC-ACGTGGACGCTC
* * *
612718 TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTAAGAAGACGGTTCTGAACAAAT-G-GT----G
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTG-ACAAATAGTGTCAAAA
* *
612777 ACGCTTCAAGCAGGATGCACTGTCAGTAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTC
*
612838 TTTTTCTACAATAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
612858 TTTGGCTTTA
Statistics
Matches: 228, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
120 67 0.29
121 4 0.02
124 5 0.02
125 101 0.44
126 50 0.22
127 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGACAAATAGTGTCAAAAA
CACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:615332 original size:25 final size:25
Alignment explanation
Indices: 615303--615350 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
615293 ACTTAAATTT
*
615303 TATTAAAA-ATATAAAAATAATTTAC
1 TATTAAAATAT-TAAAAACAATTTAC
615328 TATTAAAATATTAAAAACAATTT
1 TATTAAAATATTAAAAACAATTT
615351 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAATATTAAAAACAATTTAC
Found at i:615355 original size:24 final size:24
Alignment explanation
Indices: 615300--615355 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
615290 AGAACTTAAA
*
615300 TTTTATTAAAAATATAAAAATAAT
1 TTTTATTAAAAATATAAAAACAAT
*
615324 TTACTATT-AAAATATTAAAAACAAT
1 TT-TTATTAAAAATA-TAAAAACAAT
615349 TTTTATT
1 TTTTATT
615356 TTATTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTATTAAAAATATAAAAACAAT
Found at i:615524 original size:21 final size:21
Alignment explanation
Indices: 615491--615545 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
615481 GTTTTCGGTG
*
615491 GGGATTTTGGTTGCTCCGGCGA
1 GGGATTGTGGTTGCTCCGGC-A
*
615513 TGG-TTGTGGTTGCTCCGGCA
1 GGGATTGTGGTTGCTCCGGCA
615533 GGGATTGTGGTTG
1 GGGATTGTGGTTG
615546 TGGGTGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.44, T:0.35
Consensus pattern (21 bp):
GGGATTGTGGTTGCTCCGGCA
Found at i:616421 original size:7 final size:7
Alignment explanation
Indices: 616411--616435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
616401 TTATATACAT
616411 AATACTA
1 AATACTA
616418 AATACTA
1 AATACTA
616425 AATACTA
1 AATACTA
616432 AATA
1 AATA
616436 TGAAACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:621383 original size:2 final size:2
Alignment explanation
Indices: 621376--621404 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
621366 TTAGAAAATT
621376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
621405 CTTTTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:622581 original size:50 final size:51
Alignment explanation
Indices: 622527--622624 Score: 189
Period size: 50 Copynumber: 1.9 Consensus size: 51
622517 TTTGTTAATT
622527 TATTTAAAATTTTAATTAGCTCCTAAATTTTTTAAAAA-TTTAATTAGCTC
1 TATTTAAAATTTTAATTAGCTCCTAAATTTTTTAAAAATTTTAATTAGCTC
622577 TATTTAAAATTTTAATTAGCTCCTAAATTTTTTAAAAATTTTAATTAG
1 TATTTAAAATTTTAATTAGCTCCTAAATTTTTTAAAAATTTTAATTAG
622625 ACCTCCAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 38 0.81
51 9 0.19
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (51 bp):
TATTTAAAATTTTAATTAGCTCCTAAATTTTTTAAAAATTTTAATTAGCTC
Found at i:622582 original size:22 final size:22
Alignment explanation
Indices: 622557--622598 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
622547 TCCTAAATTT
622557 TTTAAAAATTTAATTAGCTCTA
1 TTTAAAAATTTAATTAGCTCTA
*
622579 TTTAAAATTTTAATTAGCTC
1 TTTAAAAATTTAATTAGCTC
622599 CTAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTAAAAATTTAATTAGCTCTA
Found at i:622734 original size:31 final size:30
Alignment explanation
Indices: 622582--622727 Score: 86
Period size: 31 Copynumber: 4.8 Consensus size: 30
622572 AGCTCTATTT
*
622582 AAAATTTTAATTAG--C-TCCTAAATTTTTTA
1 AAAATTTTAATTAGATCTTCC-AAA-ATTTTA
* ** *
622611 AAAATTTTAATTAGA-CCTCCAATTTTTTTG
1 AAAATTTTAATTAGATCTTCCAA-AATTTTA
* * * *
622641 AAAATTCTCACTA-AGCTTTCCAAAATTTTA
1 AAAATTTTAATTAGATC-TTCCAAAATTTTA
* * *
622671 GAAGATTTTAATTAGATCCTCCATAATTTTTA
1 -AAAATTTTAATTAGATCTTCCA-AAATTTTA
*
622703 AAAATTTTAATTAGGTCTTCCAAAA
1 AAAATTTTAATTAGATCTTCCAAAA
622728 CCTTTAATAG
Statistics
Matches: 89, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
29 15 0.17
30 25 0.28
31 40 0.45
32 9 0.10
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (30 bp):
AAAATTTTAATTAGATCTTCCAAAATTTTA
Found at i:623613 original size:16 final size:17
Alignment explanation
Indices: 623594--623630 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
623584 AATTTTTGAA
*
623594 TATTTT-AGGTTTGATC
1 TATTTTGAGGTTCGATC
623610 TATTTTGAGGTTCGATC
1 TATTTTGAGGTTCGATC
623627 -ATTT
1 TATTT
623631 GGGTTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (17 bp):
TATTTTGAGGTTCGATC
Found at i:627845 original size:15 final size:16
Alignment explanation
Indices: 627819--627849 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
627809 TACATTTTTT
627819 TGCCCCCTGGGGGGGG
1 TGCCCCCTGGGGGGGG
627835 TGCCCCC-GGGGGGGG
1 TGCCCCCTGGGGGGGG
627850 GGGGGGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.32, G:0.58, T:0.10
Consensus pattern (16 bp):
TGCCCCCTGGGGGGGG
Found at i:627850 original size:16 final size:16
Alignment explanation
Indices: 627819--627850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
627809 TACATTTTTT
*
627819 TGCCCCCTGGGGGGGG
1 TGCCCCCGGGGGGGGG
627835 TGCCCCCGGGGGGGGG
1 TGCCCCCGGGGGGGGG
627851 GGGGGAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.31, G:0.59, T:0.09
Consensus pattern (16 bp):
TGCCCCCGGGGGGGGG
Found at i:630863 original size:3 final size:3
Alignment explanation
Indices: 630850--630884 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
630840 AAGGGGAAAA
630850 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
630885 TAAGCGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:631203 original size:18 final size:18
Alignment explanation
Indices: 631165--631204 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
631155 CTATTGGTTT
* *
631165 ATTAGTTTGATCGGTTCG
1 ATTAGTTTAATCGATTCG
*
631183 ATTAGTTTAATCGATTTG
1 ATTAGTTTAATCGATTCG
631201 ATTA
1 ATTA
631205 AAAATTCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (18 bp):
ATTAGTTTAATCGATTCG
Found at i:637864 original size:16 final size:16
Alignment explanation
Indices: 637843--637894 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
637833 TTTGGTTCGC
637843 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
*
637859 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
* *
637875 TGTAATAGAATAGAGG
1 TGTATTAGATTAGAGG
637891 TGTA
1 TGTA
637895 ATGGAAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:638166 original size:18 final size:17
Alignment explanation
Indices: 638145--638179 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
638135 TTATTATTAA
*
638145 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
638163 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
638180 TCTTAANNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:643594 original size:12 final size:12
Alignment explanation
Indices: 643579--643608 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
643569 AATACAAACA
643579 ACAGAAGCTGCT
1 ACAGAAGCTGCT
643591 ACAGAAGCTGCT
1 ACAGAAGCTGCT
*
643603 AAAGAA
1 ACAGAA
643609 ATTAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
ACAGAAGCTGCT
Found at i:643892 original size:14 final size:14
Alignment explanation
Indices: 643873--643903 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
643863 AAAATATTAA
643873 CAACAAATAGTTCC
1 CAACAAATAGTTCC
643887 CAACAAATAGTTCC
1 CAACAAATAGTTCC
643901 CAA
1 CAA
643904 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:644309 original size:35 final size:36
Alignment explanation
Indices: 644263--644334 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
644253 TAAGCTAATT
644263 CAGCCAATGATTTGGCTAAAGAATG-GGAGAAACTG
1 CAGCCAATGATTTGGCTAAAGAATGAGGAGAAACTG
644298 CAGCCAATGATTTGGCTAAAGAATGTAGGAGAAACTG
1 CAGCCAATGATTTGGCTAAAGAATG-AGGAGAAACTG
644335 AATTTCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 25 0.71
37 10 0.29
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (36 bp):
CAGCCAATGATTTGGCTAAAGAATGAGGAGAAACTG
Found at i:647613 original size:17 final size:17
Alignment explanation
Indices: 647591--647625 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
647581 ACCAAATTTC
647591 AATATTTATCGGGCATT
1 AATATTTATCGGGCATT
647608 AATATTTATCGGGCATT
1 AATATTTATCGGGCATT
647625 A
1 A
647626 GAAGACCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (17 bp):
AATATTTATCGGGCATT
Found at i:652654 original size:6 final size:6
Alignment explanation
Indices: 652645--652673 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
652635 AAATAAAATT
652645 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
652674 TTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:654038 original size:21 final size:21
Alignment explanation
Indices: 653999--654040 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
653989 GTCTACATAA
* *
653999 AAAATTAAAATTTGAAAAATG
1 AAAATGAAAATTTCAAAAATG
654020 AAAATGAAAATTTCTAAAAAT
1 AAAATGAAAATTTC-AAAAAT
654041 TTTAAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAATGAAAATTTCAAAAATG
Found at i:654722 original size:14 final size:15
Alignment explanation
Indices: 654698--654735 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
654688 ATTTAAAATA
654698 TTTTTATAATTAGT-T
1 TTTTTA-AATTAGTAT
654713 TTTTTAAATTAGTAT
1 TTTTTAAATTAGTAT
*
654728 ATTTTAAA
1 TTTTTAAA
654736 ATGACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTTAAATTAGTAT
Found at i:654828 original size:29 final size:29
Alignment explanation
Indices: 654771--654828 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
654761 ATTATTGTAA
* *
654771 AAGGAAATATCATAATGATATCTACATAT
1 AAGGAAATATCAGAATGATATCCACATAT
* *
654800 AAGGAAATATTAGAATGATATCCATATAT
1 AAGGAAATATCAGAATGATATCCACATAT
654829 TAATTATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (29 bp):
AAGGAAATATCAGAATGATATCCACATAT
Found at i:661514 original size:17 final size:17
Alignment explanation
Indices: 661492--661526 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
661482 ATTTACAAAA
661492 AGGGAAAAAGAATTCCC
1 AGGGAAAAAGAATTCCC
661509 AGGGAAAAAGAATTCCC
1 AGGGAAAAAGAATTCCC
661526 A
1 A
661527 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (17 bp):
AGGGAAAAAGAATTCCC
Found at i:662576 original size:4 final size:4
Alignment explanation
Indices: 662567--662592 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
662557 TTTCTTGGAG
662567 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
662593 GTTTATGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:666618 original size:17 final size:18
Alignment explanation
Indices: 666569--666618 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
666559 CATTTTAAAA
666569 TAAAATAATACAAATTTGT
1 TAAAATAATAC-AATTTGT
*
666588 TAAAAGCAAT--AATTT-T
1 TAAAA-TAATACAATTTGT
666604 TAAAATAATACAATT
1 TAAAATAATACAATT
666619 GTGTCAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 3 0.12
16 6 0.23
17 9 0.35
19 5 0.19
20 3 0.12
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (18 bp):
TAAAATAATACAATTTGT
Found at i:666945 original size:13 final size:13
Alignment explanation
Indices: 666924--666984 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
666914 ACACTCAAAA
666924 TTTTCAAAAACAC
1 TTTTCAAAAACAC
* *
666937 TTCTCAAAAGCAC
1 TTTTCAAAAACAC
* *
666950 TTTTCCACAACAC
1 TTTTCAAAAACAC
666963 TTTTCAAAAACAC
1 TTTTCAAAAACAC
666976 TTTTCAAAA
1 TTTTCAAAA
666985 GCAATTAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:667203 original size:17 final size:17
Alignment explanation
Indices: 667181--667213 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
667171 AATTCACATA
667181 TTTAAAACAT-ATATATG
1 TTTAAAA-ATAATATATG
667198 TTTAAAAATAATATAT
1 TTTAAAAATAATATAT
667214 AATAAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAAAATAATATATG
Found at i:672346 original size:18 final size:18
Alignment explanation
Indices: 672323--672357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
672313 CAACTTTTTC
672323 TTTTTTTGAAAACACAAA
1 TTTTTTTGAAAACACAAA
* *
672341 TTTTTTTTAAAATACAA
1 TTTTTTTGAAAACACAA
672358 GAATTTTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTTTTTGAAAACACAAA
Found at i:672380 original size:35 final size:34
Alignment explanation
Indices: 672326--672417 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 34
672316 CTTTTTCTTT
* *
672326 TTTTGAAAACACAAATTTTTTTTAAAATAC-AAGAA
1 TTTTG-AAACACGAATTTTTTTTAAAACACGAA-AA
672361 TTTTAGAAACACG-ATTTTTTTTAAAAACACGAAAA
1 TTTT-GAAACACGAATTTTTTTT-AAAACACGAAAA
672396 TTTTGAAACACGAGATTTTTTT
1 TTTTGAAACACGA-ATTTTTTT
672418 CTTTTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
34 17 0.34
35 22 0.44
36 11 0.22
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (34 bp):
TTTTGAAACACGAATTTTTTTTAAAACACGAAAA
Done.