Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold502
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: 762056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 6
Found at i:493063 original size:13 final size:13
Alignment explanation
Indices: 493041--493092 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
493031 TTGAATATTT
*
493041 ATATTATATTTAA
1 ATATTTTATTTAA
*
493054 ATATTTTATTAAA
1 ATATTTTATTTAA
493067 TGATAATTTTATTTAAA
1 --AT-ATTTTATTT-AA
493084 ATATTTTAT
1 ATATTTTAT
493093 ATTTATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.34
14 7 0.22
15 4 0.12
16 8 0.25
17 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTTATTTAA
Found at i:499915 original size:6 final size:6
Alignment explanation
Indices: 499904--499929 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
499894 CCGACAAGAT
499904 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
499930 TGTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:500411 original size:18 final size:18
Alignment explanation
Indices: 500388--500422 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
500378 TTTATTTATT
*
500388 AAAATTTAAAA-AATATA
1 AAAAATTAAAATAATATA
500405 AAAAATTAAAATAATATA
1 AAAAATTAAAATAATATA
500423 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTAAAATAATATA
Found at i:501012 original size:14 final size:14
Alignment explanation
Indices: 500993--501026 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
500983 AATAAAATAT
*
500993 TTTTAAGATTTAAA
1 TTTTAAAATTTAAA
501007 TTTTAAAATTTAAA
1 TTTTAAAATTTAAA
501021 TTTTAA
1 TTTTAA
501027 TTTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTTAAAATTTAAA
Found at i:502066 original size:2 final size:2
Alignment explanation
Indices: 502059--502098 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
502049 GCACCGTCTG
502059 AT AT 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 AT AT
502099 GGTTCAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502436 original size:2 final size:2
Alignment explanation
Indices: 502429--502463 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
502419 CCCACAGAAT
* *
502429 TC TC TC TC TC TC TC GC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
502464 TTCGATTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:505101 original size:17 final size:17
Alignment explanation
Indices: 505079--505132 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
505069 TTGAATTTAA
505079 ATATAAATATATATTTT
1 ATATAAATATATATTTT
505096 ATATAAATATATA-TTT
1 ATATAAATATATATTTT
*
505112 A-AAAAAT-TATATTTAT
1 ATATAAATATATATTT-T
505128 ATATA
1 ATATA
505133 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 7 0.22
16 6 0.19
17 15 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAAATATATATTTT
Found at i:505129 original size:24 final size:24
Alignment explanation
Indices: 505102--505148 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
505092 TTTTATATAA
505102 ATATATAT-TTAAAAAATTATATTT
1 ATATATATATTAAAAAA-TATATTT
*
505126 ATATATATATTTAAAAATATATT
1 ATATATATATTAAAAAATATATT
505149 AAATACAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATATATATTAAAAAATATATTT
Found at i:505136 original size:12 final size:12
Alignment explanation
Indices: 505099--505148 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
505089 ATATTTTATA
*
505099 TAAATATATATT
1 TAAAAATATATT
505111 TAAAAAATTATATT
1 T-AAAAA-TATATT
* *
505125 TATATATATATT
1 TAAAAATATATT
505137 TAAAAATATATT
1 TAAAAATATATT
505149 AAATACAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 17 0.55
13 7 0.23
14 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:507322 original size:32 final size:32
Alignment explanation
Indices: 507285--507350 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
507275 AAATTGATAA
* *
507285 AAATAAATATTTA-TAATATTTAATTTGATTTT
1 AAATAAATATTTATTAA-ATTAAATTTAATTTT
*
507317 AAATAAATTTTTATTAAATTAAATTTAATTTT
1 AAATAAATATTTATTAAATTAAATTTAATTTT
507349 AA
1 AA
507351 TTTAGATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATAAATATTTATTAAATTAAATTTAATTTT
Found at i:507362 original size:12 final size:12
Alignment explanation
Indices: 507338--507372 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
507328 TATTAAATTA
*
507338 AATTTA-ATTTT
1 AATTTAGATATT
507349 AATTTAGATATT
1 AATTTAGATATT
507361 AATTTAGATATT
1 AATTTAGATATT
507373 GTTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (12 bp):
AATTTAGATATT
Found at i:507445 original size:11 final size:11
Alignment explanation
Indices: 507429--507466 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
507419 ATTAAATGAA
507429 ATTTTATTTTT
1 ATTTTATTTTT
507440 ATTTTATTTTT
1 ATTTTATTTTT
* *
507451 AATTAATTTTT
1 ATTTTATTTTT
507462 ATTTT
1 ATTTT
507467 TTATAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:507517 original size:10 final size:11
Alignment explanation
Indices: 507502--507553 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 11
507492 TATAAATTAG
507502 TAAAAA-ATTT
1 TAAAAATATTT
507512 TAAAAATATTAT
1 TAAAAATATT-T
*
507524 AAAAATATATTTT
1 TAAAA-ATA-TTT
507537 TAAAAATA-TT
1 TAAAAATATTT
507547 TAAAAAT
1 TAAAAAT
507554 CGATATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 15 0.42
11 3 0.08
12 8 0.22
13 8 0.22
14 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:507541 original size:24 final size:24
Alignment explanation
Indices: 507464--507553 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 24
507454 TAATTTTTAT
*
507464 TTTTTATAATA-TA-AAAATATATA
1 TTTTTAAAATATTATAAAA-ATATA
*
507487 TTATTTATAA-ATTAGT-AAAA-A-A
1 TT-TTTAAAATATTA-TAAAAATATA
*
507509 TTTTAAAAATATTATAAAAATATA
1 TTTTTAAAATATTATAAAAATATA
507533 TTTTTAAAAATATT-TAAAAAT
1 TTTTT-AAAATATTATAAAAAT
507554 CGATATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
21 6 0.11
22 11 0.20
23 5 0.09
24 22 0.40
25 11 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
TTTTTAAAATATTATAAAAATATA
Found at i:508197 original size:16 final size:18
Alignment explanation
Indices: 508176--508217 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
508166 AAAAATATAT
508176 TAATA-TTAATAA-AAAA
1 TAATATTTAATAATAAAA
508192 TAATATTTTAATAATAAAA
1 TAATA-TTTAATAATAAAA
508211 TAA-ATTT
1 TAATATTT
508218 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 3 0.13
18 8 0.35
19 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAATAAAA
Found at i:508221 original size:19 final size:18
Alignment explanation
Indices: 508181--508218 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
508171 TATATTAATA
508181 TTAATAAAAAATAATATT
1 TTAATAAAAAATAATATT
508199 TTAATAATAAAATAA-ATT
1 TTAATAA-AAAATAATATT
508217 TT
1 TT
508219 TAAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATAAAAAATAATATT
Found at i:508227 original size:21 final size:21
Alignment explanation
Indices: 508175--508239 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
508165 TAAAAATATA
*
508175 TTAATATTAATAAAAAATAATATT
1 TTAA-ATTAATAAAATA-AAT-TT
508199 TT-AA-TAATAAAATAAATTT
1 TTAAATTAATAAAATAAATTT
*
508218 TTAAATTAATTAAACTAAATTT
1 TTAAATTAA-TAAAATAAATTT
508240 GATAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 12 0.33
22 12 0.33
23 1 0.03
24 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATTAATAAAATAAATTT
Found at i:508737 original size:2 final size:2
Alignment explanation
Indices: 508730--508760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
508720 TCCATTAGAT
508730 TA 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 TA T
508761 CATTATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:509665 original size:16 final size:16
Alignment explanation
Indices: 509646--509685 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
509636 TTTAAATTAA
*
509646 TTAAATTCAAGTTATT
1 TTAAATTCAAATTATT
509662 TTAAATTCAAATTATT
1 TTAAATTCAAATTATT
509678 TTAAATTC
1 TTAAATTC
509686 GGATCATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATTCAAATTATT
Found at i:510588 original size:20 final size:21
Alignment explanation
Indices: 510531--510589 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 21
510521 AATTATTTTA
510531 ATATA-TTAATAATTCATATTAT
1 ATATATTTAAT-A-TCATATTAT
* *
510553 ATAAATTTTA-AT-ATATT-T
1 ATATATTTAATATCATATTAT
510571 ATATATTTAATATCATATT
1 ATATATTTAATATCATATT
510590 CGTGTTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 9 0.30
19 7 0.23
20 6 0.20
21 1 0.03
22 4 0.13
23 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTAATATCATATTAT
Found at i:511872 original size:15 final size:15
Alignment explanation
Indices: 511839--511890 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 15
511829 TATTTAAAAT
511839 TTTATATATTATATAAA
1 TTTATATATTA-AT-AA
511856 TTTATATATTAATAA
1 TTTATATATTAATAA
511871 TTTATATTATATAA-AA
1 TTTATA-TAT-TAATAA
511887 TTTA
1 TTTA
511891 ATAAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.24
16 11 0.33
17 14 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTATATATTAATAA
Found at i:511879 original size:30 final size:33
Alignment explanation
Indices: 511843--511914 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
511833 TAAAATTTTA
*
511843 TATATTATAT-AAATTT-ATATAT-TA-ATAATT
1 TATATTATATAAAATTTAATAAATATATAT-ATT
511873 TATATTATATAAAATTTAATAAATATATATATT
1 TATATTATATAAAATTTAATAAATATATATATT
511906 TATATTATA
1 TATATTATA
511915 ACATATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 10 0.27
31 6 0.16
32 5 0.14
33 14 0.38
34 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TATATTATATAAAATTTAATAAATATATATATT
Found at i:512760 original size:13 final size:13
Alignment explanation
Indices: 512744--512769 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
512734 TTATTTTTTA
512744 AAATTAATTAAAT
1 AAATTAATTAAAT
512757 AAATTAATTAAAT
1 AAATTAATTAAAT
512770 TTTAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAATTAAAT
Found at i:514639 original size:29 final size:28
Alignment explanation
Indices: 514582--514642 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
514572 GATAAATATC
*
514582 AATTATTTTAATTATAAATTTATTTGTAA
1 AATTATTTT-ATTAAAAATTTATTTGTAA
*
514611 AATTATTTT-TTAAAAATTATTTTTCGTAA
1 AATTATTTTATTAAAAATT-TATTT-GTAA
514640 AAT
1 AAT
514643 AAACCCTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.29
28 4 0.14
29 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (28 bp):
AATTATTTTATTAAAAATTTATTTGTAA
Found at i:514641 original size:15 final size:14
Alignment explanation
Indices: 514604--514642 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
514594 TATAAATTTA
514604 TTTGTAAAATTATT
1 TTTGTAAAATTATT
514618 TTT-TAAAAATTATT
1 TTTGT-AAAATTATT
514632 TTTCGTAAAAT
1 TTT-GTAAAAT
514643 AAACCCTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 15 0.68
15 5 0.23
16 1 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (14 bp):
TTTGTAAAATTATT
Found at i:519847 original size:2 final size:2
Alignment explanation
Indices: 519840--519878 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
519830 CATGTTTGGG
519840 TA TA TA TA TA 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 TA TA TA TA TA T
519879 GAGTTTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:520334 original size:17 final size:18
Alignment explanation
Indices: 520314--520355 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
520304 AAATATTTTT
520314 AATATAAAAAT-AACATA
1 AATATAAAAATAAACATA
*
520331 AATAT-AAAATAAATATA
1 AATATAAAAATAAACATA
520348 AATATAAA
1 AATATAAA
520356 TATATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAAAATAAACATA
Found at i:520337 original size:6 final size:6
Alignment explanation
Indices: 520314--520359 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
520304 AAATATTTTT
* *
520314 AATATA AAAAT- AACATA AATATA AA-ATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
520360 TTTTATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (6 bp):
AATATA
Found at i:520337 original size:11 final size:11
Alignment explanation
Indices: 520317--520359 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
520307 TATTTTTAAT
* *
520317 ATAAAAATAAC
1 ATAAATATAAA
520328 ATAAATATAAA
1 ATAAATATAAA
520339 ATAAATATAAA
1 ATAAATATAAA
520350 TATAAATATA
1 -ATAAATATA
520360 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATATAAA
Found at i:520987 original size:23 final size:23
Alignment explanation
Indices: 520961--521006 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
520951 CTTATCAACT
520961 TAAT-TTAAAAAAATTATATAATA
1 TAATATTAAAAAAA-TATATAATA
* *
520984 TAATATTAAATAAATATTTAATA
1 TAATATTAAAAAAATATATAATA
521007 AACTAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATATTAAAAAAATATATAATA
Found at i:523438 original size:19 final size:19
Alignment explanation
Indices: 523397--523442 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
523387 TAATTTTATT
523397 TAAAT-TATTATTTAATAA
1 TAAATATATTATTTAATAA
*
523415 TAAATATATT-TTTAATCA
1 TAAATATATTATTTAATAA
523433 TAAAATATAT
1 T-AAATATAT
523443 AAATATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATATATTATTTAATAA
Found at i:523836 original size:13 final size:13
Alignment explanation
Indices: 523818--523844 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
523808 TTTTTGAGTG
523818 TTTATATTTAATA
1 TTTATATTTAATA
523831 TTTATATTTAATA
1 TTTATATTTAATA
523844 T
1 T
523845 ATAATCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATATTTAATA
Found at i:523941 original size:17 final size:17
Alignment explanation
Indices: 523916--523953 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
523906 TTAAAAAAAT
523916 TAAATATAT-TT-ATAA
1 TAAATATATATTCATAA
*
523931 TAAATATATATTCATAT
1 TAAATATATATTCATAA
523948 TAAATA
1 TAAATA
523954 CCCGCATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 2 0.10
17 9 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATATATATTCATAA
Found at i:525117 original size:39 final size:36
Alignment explanation
Indices: 525056--525131 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 36
525046 ATTTAATTTT
525056 TTATTATTTTATATTTTTTAAAAAATTT-TAAAAAA
1 TTATTATTTTATATTTTTTAAAAAATTTATAAAAAA
*
525091 TTATATATTTTGATATTTATCTTAAAAAATTTATTAAAAA
1 TTAT-TATTTT-ATATTT-T-TTAAAAAATTTATAAAAAA
525131 T
1 T
525132 AAATATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
35 4 0.11
36 6 0.17
37 6 0.17
38 1 0.03
39 11 0.31
40 7 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
TTATTATTTTATATTTTTTAAAAAATTTATAAAAAA
Found at i:525584 original size:17 final size:17
Alignment explanation
Indices: 525562--525597 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
525552 ATAAGATACG
*
525562 AAGTAAATGTTAAATAT
1 AAGTAAATGTAAAATAT
525579 AAGTAAATGTAAAATAT
1 AAGTAAATGTAAAATAT
525596 AA
1 AA
525598 ATAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (17 bp):
AAGTAAATGTAAAATAT
Found at i:527405 original size:15 final size:16
Alignment explanation
Indices: 527385--527420 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
527375 TTAAAAAATA
527385 AAATATATTT-ATATT
1 AAATATATTTAATATT
527400 AAATATATTTAATATT
1 AAATATATTTAATATT
*
527416 CAATA
1 AAATA
527421 CTTATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATATTTAATATT
Found at i:529257 original size:14 final size:14
Alignment explanation
Indices: 529238--529268 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
529228 ATAATTTTTA
*
529238 TTTTTAATAATATT
1 TTTTTAAAAATATT
529252 TTTTTAAAAATATT
1 TTTTTAAAAATATT
529266 TTT
1 TTT
529269 GATAAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTAAAAATATT
Found at i:532267 original size:18 final size:18
Alignment explanation
Indices: 532244--532280 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
532234 TATCTCTGTA
532244 CCCATATTGAATATGCGT
1 CCCATATTGAATATGCGT
532262 CCCATATTGAATATGCGT
1 CCCATATTGAATATGCGT
532280 C
1 C
532281 GGATACGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
CCCATATTGAATATGCGT
Found at i:532536 original size:25 final size:25
Alignment explanation
Indices: 532508--532555 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
532498 AAAATTAAAA
532508 AAAAATCT-CAATAACATAGATGAGT
1 AAAAAT-TACAATAACATAGATGAGT
* *
532533 AAAACTTACAATGACATAGATGA
1 AAAAATTACAATAACATAGATGA
532556 CTGAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (25 bp):
AAAAATTACAATAACATAGATGAGT
Found at i:534039 original size:21 final size:21
Alignment explanation
Indices: 533993--534040 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
533983 ACGTTTTTTT
*
533993 TAAATAAAAAAATCATAATTTA
1 TAAAT-AAAAAATCATAAATTA
*
534015 -AAATAAAAAATTATAAATTA
1 TAAATAAAAAATCATAAATTA
534035 TAAATA
1 TAAATA
534041 TTATGATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATAAAAAATCATAAATTA
Found at i:534368 original size:24 final size:23
Alignment explanation
Indices: 534309--534371 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
534299 CATTTAAATT
* * *
534309 AAATGAATTTATTTACAAACATC
1 AAATAAATATATTTATAAACATC
534332 AAATAAATATATTTATAAACAT-
1 AAATAAATATATTTATAAACATC
534354 ATAATCAAATATATTTAT
1 A-AAT-AAATATATTTAT
534372 GGATAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 22 0.63
24 12 0.34
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATAAATATATTTATAAACATC
Found at i:535666 original size:19 final size:20
Alignment explanation
Indices: 535651--535690 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
535641 TTAAATATGA
535651 TTAATATA-ATATAATATAT
1 TTAATATATATATAATATAT
535670 TTAATATATATATATATATAT
1 TTAATATATATATA-ATATAT
535691 CATAATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATATATATATAATATAT
Found at i:536115 original size:6 final size:6
Alignment explanation
Indices: 536091--536126 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
536081 TATAACTCTT
536091 TTTATAA TTTATA -TTATA TTTATA TTTATA TTTATA
1 TTTAT-A TTTATA TTTATA TTTATA TTTATA TTTATA
536127 CGACTTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTATA
Found at i:543448 original size:17 final size:17
Alignment explanation
Indices: 543426--543458 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
543416 TTTTAGTATT
*
543426 TTTTAAATAAATTAAAA
1 TTTTAAAAAAATTAAAA
543443 TTTTAAAAAAATTAAA
1 TTTTAAAAAAATTAAA
543459 TATATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAATTAAAA
Found at i:543737 original size:28 final size:30
Alignment explanation
Indices: 543709--543764 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
543699 TAATTAATAA
*
543709 TAAAAATAATATTTAAAT-TTAA-ATTTAAT
1 TAAAAA-AATATATAAATATTAATATTTAAT
*
543738 TATAAAAATATATAAATATTAATATTT
1 TAAAAAAATATATAAATATTAATATTT
543765 TTAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 9 0.39
30 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAAAAATATATAAATATTAATATTTAAT
Found at i:543974 original size:14 final size:14
Alignment explanation
Indices: 543957--544004 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
543947 TATTTATATT
543957 TATATATATTTAAA
1 TATATATATTTAAA
* *
543971 TATAAATATTAAAA
1 TATATATATTTAAA
*
543985 TATA-ATTTTATAAA
1 TATATATATT-TAAA
543999 TATATA
1 TATATA
544005 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 4 0.14
14 23 0.82
15 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATATATTTAAA
Found at i:544117 original size:2 final size:2
Alignment explanation
Indices: 544110--544134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
544100 AGAGTTGCAC
544110 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
544135 AAATAAAAAG
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:544463 original size:21 final size:22
Alignment explanation
Indices: 544425--544465 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
544415 CTCACTTCAC
*
544425 TTTCCTTCTTCTCATCCTCCCT
1 TTTCCTTCTCCTCATCCTCCCT
*
544447 TTTCCTT-TCCTCTTCCTCC
1 TTTCCTTCTCCTCATCCTCC
544466 ACCAAGCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTCCTTCTCCTCATCCTCCCT
Found at i:548188 original size:3 final size:3
Alignment explanation
Indices: 548182--548219 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
548172 TATTCATCAT
548182 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
548220 TAAGGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:549634 original size:2 final size:2
Alignment explanation
Indices: 549622--549660 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
549612 ATAATACATT
* * *
549622 TA TA TA AA TA TA TA TA CA TA TA TG 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 TA TA TA T
549661 GTAAAGAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:551830 original size:2 final size:2
Alignment explanation
Indices: 551812--551845 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
551802 AAATAATTAA
*
551812 AT AT AA AT AT CAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
551846 AATACTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:555199 original size:13 final size:13
Alignment explanation
Indices: 555181--555219 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
555171 ATTTAAATAA
555181 TTATATTATATTT
1 TTATATTATATTT
555194 TTATATTATA-TT
1 TTATATTATATTT
555206 TTA-ATTATTATTT
1 TTATATTA-TATTT
555219 T
1 T
555220 GCTGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:555217 original size:12 final size:12
Alignment explanation
Indices: 555181--555219 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
555171 ATTTAAATAA
555181 TTATATTATATTT
1 TTATATTATA-TT
555194 TTATATTATATT
1 TTATATTATATT
555206 TTA-ATTATTATT
1 TTATATTA-TATT
555218 TT
1 TT
555220 GCTGTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.16
12 11 0.44
13 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTATATT
Found at i:557965 original size:17 final size:16
Alignment explanation
Indices: 557933--557988 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
557923 AATTTTTTTC
*
557933 ATATTAATA-GTATAA
1 ATATTAATATATATAA
557948 ATATTAATATAATATAA
1 ATATTAATAT-ATATAA
557965 ATTATTGAATATAT-TAA
1 A-TATT-AATATATATAA
557982 A-ATTAAT
1 ATATTAAT
557989 TTTAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.08
15 12 0.33
17 10 0.28
18 6 0.17
19 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
ATATTAATATATATAA
Found at i:557984 original size:18 final size:18
Alignment explanation
Indices: 557943--557986 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
557933 ATATTAATAG
557943 TATAAA-TATTAATATAA
1 TATAAATTATTAATATAA
*
557960 TATAAATTATTGAATATAT
1 TATAAATTATT-AATATAA
557979 TA-AAATTA
1 TATAAATTA
557987 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TATAAATTATTAATATAA
Found at i:558332 original size:18 final size:18
Alignment explanation
Indices: 558301--558339 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
558291 AAATTTTATT
** *
558301 TTTAAAATTTAAATTTAA
1 TTTAAAATAAAAATTAAA
558319 TTTAAAATAAAAATTAAA
1 TTTAAAATAAAAATTAAA
558337 TTT
1 TTT
558340 TTTAAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAAATAAAAATTAAA
Found at i:558385 original size:34 final size:39
Alignment explanation
Indices: 558299--558392 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
558289 TTAAATTTTA
* *
558299 TTTTTAA-AATTTAAATTTAATTTAAAATAAAAATTAAAT
1 TTTTTAATTATTT-AATTTTATTTAAAATAAAAATTAAAT
*
558338 TTTTTAAATTATTTATTTTTATTTAAAAT-AAAA-TAAA-
1 TTTTT-AATTATTTAATTTTATTTAAAATAAAAATTAAAT
558375 TTTTT-A-TATTTAATTTTA
1 TTTTTAATTATTTAATTTTA
558393 AATTTAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
34 11 0.22
35 1 0.02
37 5 0.10
38 4 0.08
39 9 0.18
40 15 0.31
41 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
TTTTTAATTATTTAATTTTATTTAAAATAAAAATTAAAT
Found at i:558396 original size:20 final size:21
Alignment explanation
Indices: 558371--558417 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
558361 TAAAATAAAA
*
558371 TAAATTTTTA-TATTTAATTT
1 TAAATTTTAATTATTTAATTT
558391 TAAA-TTTAATTATTTAATTT
1 TAAATTTTAATTATTTAATTT
558411 TAAATTT
1 TAAATTT
558418 GAGTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAATTTTAATTATTTAATTT
Found at i:558397 original size:12 final size:12
Alignment explanation
Indices: 558376--558428 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
558366 TAAAATAAAT
*
558376 TTTTATATTTAA
1 TTTTAAATTTAA
558388 TTTTAAATTTAA
1 TTTTAAATTTAA
558400 --TT--ATTTAA
1 TTTTAAATTTAA
*
558408 TTTTAAATTTGA
1 TTTTAAATTTAA
*
558420 GTTTAAATT
1 TTTTAAATT
558429 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 6 0.18
10 4 0.12
12 24 0.71
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (12 bp):
TTTTAAATTTAA
Found at i:558546 original size:35 final size:34
Alignment explanation
Indices: 558481--558546 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
558471 ATTATTCAAA
*
558481 TTAAACTTCAAAATATTTAACTTAACTTAATAAC
1 TTAAACTTCAAAATATTAAACTTAACTTAATAAC
* *
558515 TTAAA-TTCAATAATAATTAAATTTAATTTAAT
1 TTAAACTTCAA-AAT-ATTAAACTTAACTTAAT
558547 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.19
34 8 0.30
35 14 0.52
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (34 bp):
TTAAACTTCAAAATATTAAACTTAACTTAATAAC
Found at i:559013 original size:23 final size:23
Alignment explanation
Indices: 558965--559018 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
558955 TTTTTTTTAT
** *
558965 TATTTATATTAATTTATTAATTA
1 TATTTATATTAAAATATTAATCA
558988 TATTTATATTAAAAT-TTAATACA
1 TATTTATATTAAAATATTAAT-CA
559011 TATTTATA
1 TATTTATA
559019 AAATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTATATTAAAATATTAATCA
Found at i:559734 original size:19 final size:23
Alignment explanation
Indices: 559698--559740 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 23
559688 TAAATTTATT
559698 AAATAAATATATATATTTT-TAA
1 AAATAAATATATATATTTTATAA
559720 AAAT-AATAT-TA-ATTTTATAA
1 AAATAAATATATATATTTTATAA
559740 A
1 A
559741 TAAGCAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 5 0.25
22 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAAATATATATATTTTATAA
Found at i:560267 original size:2 final size:2
Alignment explanation
Indices: 560254--560283 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
560244 CCATCCTCAC
*
560254 CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
560284 AGACTTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:562561 original size:23 final size:22
Alignment explanation
Indices: 562521--562564 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
562511 TATTAATATT
*
562521 AATATTTTTATAATTAAATAAA
1 AATATTTTTATAAGTAAATAAA
*
562543 AATATTTTTTATTAGTAAATAA
1 AATA-TTTTTATAAGTAAATAA
562565 TAATTCATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATATTTTTATAAGTAAATAAA
Found at i:562566 original size:20 final size:23
Alignment explanation
Indices: 562520--562568 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
562510 TTATTAATAT
562520 TAATATTTTTATAATTAAATAAA
1 TAATATTTTTATAATTAAATAAA
* *
562543 -AATATTTTTTATTAGTAAAT-AA
1 TAATA-TTTTTATAATTAAATAAA
562565 TAAT
1 TAAT
562569 TCATCTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATATTTTTATAATTAAATAAA
Found at i:563339 original size:2 final size:2
Alignment explanation
Indices: 563332--563357 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
563322 AACGTACGCT
563332 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
563358 GAAGTTACTT
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):
TA
Found at i:564318 original size:27 final size:30
Alignment explanation
Indices: 564271--564332 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 30
564261 TTGTATTTAT
564271 ATATTTTATCATATTATTAT-AATGTTTAAA
1 ATATTTTATCATATTATTATAAAT-TTTAAA
*
564301 ATATTTTAT-AT-TTA-TATAAATTTTAAT
1 ATATTTTATCATATTATTATAAATTTTAAA
564328 ATATT
1 ATATT
564333 AACAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 13 0.43
28 6 0.20
29 2 0.07
30 9 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATTTTATCATATTATTATAAATTTTAAA
Found at i:567128 original size:17 final size:17
Alignment explanation
Indices: 567088--567135 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
567078 TATATTAATC
567088 ATATTT-ATATAAA-AT
1 ATATTTAATATAAATAT
567103 ATA---AATATAAATAT
1 ATATTTAATATAAATAT
567117 ATATTTAATATAAATAT
1 ATATTTAATATAAATAT
567134 AT
1 AT
567136 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 3 0.11
17 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTTAATATAAATAT
Found at i:567136 original size:15 final size:15
Alignment explanation
Indices: 567088--567140 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
567078 TATATTAATC
567088 ATATTT-ATATAAA-
1 ATATTTAATATAAAT
*
567101 ATA-TAAATATAAATAT
1 ATATTTAATAT-AA-AT
567117 ATATTTAATATAAAT
1 ATATTTAATATAAAT
567132 ATATTTAAT
1 ATATTTAAT
567141 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 1 0.03
13 7 0.21
14 2 0.06
15 12 0.36
16 5 0.15
17 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTAATATAAAT
Found at i:567147 original size:17 final size:16
Alignment explanation
Indices: 567115--567174 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 16
567105 AAATATAAAT
*
567115 ATATATTTAA-TATAA
1 ATATATTTAATTTTAA
567130 ATATATTTAATTTTTAA
1 ATATATTTAA-TTTTAA
* *
567147 AAAT-TTTTATATTTAA
1 ATATATTTAAT-TTTAA
567163 ATAATATTTAAT
1 AT-ATATTTAAT
567175 AAGTCATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 9 0.26
18 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTAATTTTAA
Found at i:567167 original size:27 final size:29
Alignment explanation
Indices: 567137--567205 Score: 70
Period size: 33 Copynumber: 2.3 Consensus size: 29
567127 TAAATATATT
567137 TAATTTTTAA-AAATTTTTATA-TTTAAA
1 TAATTTTTAACAAATTTTTATATTTTAAA
*
567164 TAATATTTAATAAGTCATATTTTTATATTTTAAA
1 TAAT-TTT--TAA--CAAATTTTTATATTTTAAA
567198 TAATTTTT
1 TAATTTTT
567206 TATTTCGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
27 4 0.12
28 3 0.09
30 3 0.09
31 1 0.03
33 13 0.38
34 10 0.29
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TAATTTTTAACAAATTTTTATATTTTAAA
Found at i:568030 original size:41 final size:41
Alignment explanation
Indices: 567985--568141 Score: 199
Period size: 41 Copynumber: 3.8 Consensus size: 41
567975 TTTCTACACT
* * * **
567985 AAACGCCACTAAA-TATTTCTTACTAGCGATATTTGTATTAA
1 AAACGCCGCTAAATTTTTTC-TATTAGCGACGTTTGTATTAA
* *
568026 AAACGTCGCTAAATTTTTTCTATTAGCGGCGTTTGTATTAA
1 AAACGCCGCTAAATTTTTTCTATTAGCGACGTTTGTATTAA
*
568067 AAACACCGCTAAATTTTTTCTATTAGCGACGTTTGTATTAA
1 AAACGCCGCTAAATTTTTTCTATTAGCGACGTTTGTATTAA
* * *
568108 AAACGCTGCTAAATTTTTTTTATTAACGACGTTT
1 AAACGCCGCTAAATTTTTTCTATTAGCGACGTTT
568142 ATTTTTAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 96 0.95
42 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (41 bp):
AAACGCCGCTAAATTTTTTCTATTAGCGACGTTTGTATTAA
Found at i:568052 original size:82 final size:82
Alignment explanation
Indices: 567953--568132 Score: 213
Period size: 82 Copynumber: 2.2 Consensus size: 82
567943 TGAACGCCGT
* * *
567953 TAAATTTTTTTTATTAGCAGCGTTTCTA-CACTAAACGCCACTAAATATTTCT-TACTAGCGATA
1 TAAATTTTTTTTATTAGCAGCGTTTCTATCA-AAAACACCACTAAAT-TTTCTCTACTAGCGACA
568016 TTTGTATTAAAAACG-TCGC
64 TTTGTATTAAAAACGCT-GC
* * * * * * * *
568035 TAAATTTTTTCTATTAGCGGCGTTTGTATTAAAAACACCGCTAAATTTTTTCTATTAGCGACGTT
1 TAAATTTTTTTTATTAGCAGCGTTTCTATCAAAAACACCACTAAATTTTCTCTACTAGCGACATT
568100 TGTATTAAAAACGCTGC
66 TGTATTAAAAACGCTGC
568117 TAAATTTTTTTTATTA
1 TAAATTTTTTTTATTA
568133 ACGACGTTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
81 4 0.05
82 77 0.93
83 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (82 bp):
TAAATTTTTTTTATTAGCAGCGTTTCTATCAAAAACACCACTAAATTTTCTCTACTAGCGACATT
TGTATTAAAAACGCTGC
Found at i:570450 original size:2 final size:2
Alignment explanation
Indices: 570443--570508 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
570433 GCGTCCGATA
* * * *
570443 AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT GT AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
570484 AT AT AT AT -T A- AT -T AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
570509 TTTTTAAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:570516 original size:15 final size:16
Alignment explanation
Indices: 570448--570531 Score: 59
Period size: 15 Copynumber: 5.4 Consensus size: 16
570438 CGATAATATA
*
570448 TATATATATATATATAT
1 TATAAATATATAT-TAT
*
570465 T-TAAATATGTATTA-
1 TATAAATATATATTAT
* *
570479 AATATATATATATTAAT
1 TATAAATATATATT-AT
570496 TATAAATATATATT-T
1 TATAAATATATATTAT
* * *
570511 TTTAAA-ATTTATTAA
1 TATAAATATATATTAT
570526 TATAAA
1 TATAAA
570532 ATAAAATATA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
14 6 0.12
15 23 0.44
16 10 0.19
17 13 0.25
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
TATAAATATATATTAT
Found at i:570928 original size:31 final size:31
Alignment explanation
Indices: 570867--570928 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
570857 TTATATAATT
* * * *
570867 TTATTTATTTAATTTGATAATTATATTTTTA
1 TTATTTATTTAATATAAAAATTATAATTTTA
*
570898 TTATTTATTTAATATAAAAATTTTAATTTTA
1 TTATTTATTTAATATAAAAATTATAATTTTA
570929 AATGTGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
TTATTTATTTAATATAAAAATTATAATTTTA
Found at i:571243 original size:24 final size:22
Alignment explanation
Indices: 571216--571265 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
571206 TATAAATGAT
*
571216 ATTAAAATTTAATTTTTAAAATTA
1 ATTAAAA-TCAATTTTTAAAA-TA
* *
571240 ATTAATATCATTTTTTAAAATA
1 ATTAAAATCAATTTTTAAAATA
571262 ATTA
1 ATTA
571266 TATAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 11 0.48
24 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAAATCAATTTTTAAAATA
Found at i:571453 original size:11 final size:10
Alignment explanation
Indices: 571416--571498 Score: 55
Period size: 10 Copynumber: 8.0 Consensus size: 10
571406 TATGTCAAGT
571416 ATTATATAAA
1 ATTATATAAA
* *
571426 TAGATATATAAT
1 -A-TTATATAAA
571438 ATTATATAAA
1 ATTATATAAA
571448 ACTTATAT-AA
1 A-TTATATAAA
* *
571458 ATATATTTAAT
1 AT-TATATAAA
571469 ATTATATAAA
1 ATTATATAAA
571479 TATT-T-TAAA
1 -ATTATATAAA
571488 ATTTATATAAA
1 A-TTATATAAA
571499 TATAAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
8 1 0.02
9 7 0.12
10 23 0.41
11 18 0.32
12 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (10 bp):
ATTATATAAA
Found at i:571472 original size:31 final size:32
Alignment explanation
Indices: 571417--571478 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 32
571407 ATGTCAAGTA
571417 TTATATAAATAGATATATAATATTATATAAAAC
1 TTATATAAATA-ATATATAATATTATATAAAAC
*
571450 TTATATAAAT-ATATTTAATATTATATAAA
1 TTATATAAATAATATATAATATTATATAAA
571479 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 18 0.64
33 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
TTATATAAATAATATATAATATTATATAAAAC
Found at i:571475 original size:20 final size:21
Alignment explanation
Indices: 571429--571502 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 21
571419 ATATAAATAG
* *
571429 ATATATAATATTATATAAAACTT
1 ATATA-AATA-TATTTAAAATTT
*
571452 ATATAAATATATTTAATA-TT
1 ATATAAATATATTTAAAATTT
571472 ATATAAATAT-TTTAAAATTT
1 ATATAAATATATTTAAAATTT
571492 ATATAAATATA
1 ATATAAATATA
571503 AAATAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.13
20 24 0.52
21 7 0.15
22 4 0.09
23 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATAAATATATTTAAAATTT
Found at i:571510 original size:20 final size:19
Alignment explanation
Indices: 571450--571558 Score: 59
Period size: 20 Copynumber: 5.7 Consensus size: 19
571440 TATATAAAAC
**
571450 TTATATAAATATATTTAAT
1 TTATATAAATATAAATAAT
*
571469 ATTATATAAATATTTTAA-AAT
1 -TTATATAAATA--TAAATAAT
571490 TTATATAAATATAAAATAAT
1 TTATATAAATAT-AAATAAT
*
571510 TTATTTATAATTATAATATAA-
1 TTA--TATAAATATAA-ATAAT
*
571531 -TA-AAAAATATAAAT-A-
1 TTATATAAATATAAATAAT
*
571546 TAATATAAATATA
1 TTATATAAATATA
571559 TGAAATAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
17 16 0.23
18 1 0.01
19 2 0.03
20 30 0.42
21 5 0.07
22 13 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATATAAATATAAATAAT
Found at i:571529 original size:11 final size:11
Alignment explanation
Indices: 571515--571558 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
571505 ATAATTTATT
*
571515 TATAATTATAA
1 TATAAATATAA
* *
571526 TATAATAAAAAA
1 TATAA-ATATAA
571538 TATAAATATAA
1 TATAAATATAA
571549 TATAAATATA
1 TATAAATATA
571559 TGAAATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAATATAA
Found at i:571556 original size:29 final size:28
Alignment explanation
Indices: 571515--571575 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
571505 ATAATTTATT
571515 TATAATTATAATATAAT-AAAAAATATAAA
1 TATAATTATAATAT-ATGAAAAAATA-AAA
*
571544 TATAA-TATAAATATATGAAATAATAAAA
1 TATAATTAT-AATATATGAAAAAATAAAA
571572 TATA
1 TATA
571576 CTGATAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
TATAATTATAATATATGAAAAAATAAAA
Found at i:571564 original size:20 final size:18
Alignment explanation
Indices: 571524--571571 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
571514 TTATAATTAT
571524 AATATAATAAAAAATATA
1 AATATAATAAAAAATATA
* *
571542 AATATAATATAAATATATG
1 AATATAATA-AAAAATATA
571561 AA-ATAATAAAA
1 AATATAATAAAA
571572 TATACTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 15 0.56
19 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AATATAATAAAAAATATA
Found at i:576775 original size:32 final size:32
Alignment explanation
Indices: 576736--576796 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
576726 TATGATCAAG
*
576736 TTTAAA-TT-ATTACTAAATAATAAATATTTTTA
1 TTTAAATTTAATTA-TAAAAAATAAA-ATTTTTA
576768 TTTAAATTTAATTATAAAAAATAAAATTT
1 TTTAAATTTAATTATAAAAAATAAAATTT
576797 ATAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 10 0.38
33 12 0.46
34 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTAAATTTAATTATAAAAAATAAAATTTTTA
Found at i:577372 original size:20 final size:19
Alignment explanation
Indices: 577347--577402 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
577337 ATATATATAT
577347 ATATAATT-TGATAATATAAA
1 ATATAATTAT-ATAA-ATAAA
*
577367 ATATAATTATATAAATATA
1 ATATAATTATATAAATAAA
* *
577386 ATATAAATATGTAAATA
1 ATATAATTATATAAATA
577403 TATTTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.59
20 12 0.38
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
ATATAATTATATAAATAAA
Found at i:577447 original size:11 final size:11
Alignment explanation
Indices: 577366--577447 Score: 50
Period size: 11 Copynumber: 7.7 Consensus size: 11
577356 GATAATATAA
577366 AATATAATTAT
1 AATATAATTAT
577377 -ATA-AA-TAT
1 AATATAATTAT
*
577385 AATATAAATATGT
1 AATAT-AAT-TAT
577398 AA-ATATATT-T
1 AATATA-ATTAT
*
577408 AA-ATAAATAT
1 AATATAATTAT
* *
577418 AAAATAATTAA
1 AATATAATTAT
*
577429 AACATAATTAT
1 AATATAATTAT
577440 AATATAAT
1 AATATAAT
577448 GAAATATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.05
9 7 0.12
10 12 0.21
11 26 0.46
12 4 0.07
13 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
AATATAATTAT
Found at i:578215 original size:2 final size:2
Alignment explanation
Indices: 578208--578243 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
578198 TTACTTGCTT
578208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
578244 TAATAAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:579734 original size:22 final size:22
Alignment explanation
Indices: 579692--579746 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
579682 AAAATTTATA
* *
579692 TTTAT-ATTAATATTTATATATT
1 TTTATAATTAA-AATTAAATATT
579714 TTTATAATTAAAATTAAATATT
1 TTTATAATTAAAATTAAATATT
*
579736 ATT-TAATTAAA
1 TTTATAATTAAA
579747 TAAATAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 16 0.55
23 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATAATTAAAATTAAATATT
Found at i:581170 original size:2 final size:2
Alignment explanation
Indices: 581163--581194 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
581153 ACATAGATGA
581163 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
581195 GTGAGTTTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:581376 original size:21 final size:21
Alignment explanation
Indices: 581311--581378 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 21
581301 TTTATATTAT
*
581311 TATTTTATTATATTAATAA-AA
1 TATTTTATTAT-TAAATAATAA
*
581332 TATTTTTATAATTAAATTTAAATAA
1 TA-TTTTATTATTAAA--T-AATAA
581357 TATTTTATTATTAAATAATAA
1 TATTTTATTATTAAATAATAA
581378 T
1 T
581379 TTGAAAAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 11 0.28
22 9 0.23
23 1 0.03
24 14 0.36
25 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTTATTATTAAATAATAA
Found at i:582373 original size:25 final size:24
Alignment explanation
Indices: 582324--582373 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
582314 ATTTATTATT
* *
582324 TTTAATATATTTATAATATTATCA
1 TTTAATATATATATAATAATATCA
582348 TTTATATATATATATAATTAAT-TCA
1 TTTA-ATATATATATAA-TAATATCA
582373 T
1 T
582374 AAATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 15 0.68
26 3 0.14
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAATATATATATAATAATATCA
Found at i:582817 original size:24 final size:24
Alignment explanation
Indices: 582790--582835 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
582780 TAATCAATTT
*
582790 TAAGGTATTATATATTTATATATA
1 TAAGATATTATATATTTATATATA
582814 TAAGATATTATATATTTATATA
1 TAAGATATTATATATTTATATA
582836 CGTTTTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
TAAGATATTATATATTTATATATA
Found at i:583514 original size:2 final size:2
Alignment explanation
Indices: 583507--583537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
583497 TATCTCAATG
583507 AT AT AT 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 AT AT AT A
583538 CACACTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:586866 original size:467 final size:467
Alignment explanation
Indices: 585993--586926 Score: 1769
Period size: 467 Copynumber: 2.0 Consensus size: 467
585983 TTTTCCTTAA
585993 ATGGAAAAATATGATTGAGAACCAGACTAATAAGAAGATCAAACGACTTAGGACGGAAAATGAAG
1 ATGGAAAAATATGATTGAGAACCAGACTAATAAGAAGATCAAACGACTTAGGACGGAAAATGAAG
*
586058 GGGAGTATAAAAGTGATCCATTCTTCGATATTTGCCAGGAGCATGGTATTGTTTGACACTTCACC
66 GGGAGTATAAAAGTGATCCATTCTTCGATATTTGCCAAGAGCATGGTATTGTTTGACACTTCACC
* *
586123 GTTAGAGATACACCACAACAGAATGGGGTGGCAGAACGTATGGATCGAATACTACTGGAGAAAGT
131 GTTAGAGATACACCACAACAGAATGGGGTGGCAGAACGTATGAATCGAATACTACTAGAGAAAGT
586188 TCGATGTATGTTGTCCAATGCTGGGTTGAGCAAACCATTTTGGGCTGAGGCTGTGACATATGCTG
196 TCGATGTATGTTGTCCAATGCTGGGTTGAGCAAACCATTTTGGGCTGAGGCTGTGACATATGCTG
* *
586253 GCCATCTCATCAATCGTCTACCATCATCAGCAATAAGAGGAAAAACACCATTCGAGGTATGGTCT
261 GCCATCTCATCAATCATCTACCATCATCAGCAATAAGAGAAAAAACACCATTCGAGGTATGGTCT
*
586318 GAAAAACCTGCTACTGATTATGATTCCTTACATATATTTGGATCCACTGCCTATTATCATGTGAA
326 GAAAAACCTGCTACTGATTATGATTCCTCACATATATTTGGATCCACTGCCTATTATCATGTGAA
586383 GGAATCAAAGCTTGATCTGAGAGCAAAGAAAGCTCTCTTTATGAGAATCACACGTGGAGTGAAGG
391 GGAATCAAAGCTTGATCTGAGAGCAAAGAAAGCTCTCTTTATGAGAATCACACGTGGAGTGAAGG
*
586448 GATTTCGACTTT
456 GATTCCGACTTT
* * *
586460 ATGGAAAAATATGATTGAGAACCAGACTAATAGGAAGATCAAACGACTTAGGACGGACAATGGAG
1 ATGGAAAAATATGATTGAGAACCAGACTAATAAGAAGATCAAACGACTTAGGACGGAAAATGAAG
586525 GGGAGTATAAAAGTGATCCATTCTTCGATATTTGCCAAGAGCATGGTATTGTTTGACACTTCACC
66 GGGAGTATAAAAGTGATCCATTCTTCGATATTTGCCAAGAGCATGGTATTGTTTGACACTTCACC
586590 GTTAGAGATACACCACAACAGAATGGGGTGGCAGAACGTATGAATCGAATACTACTAGAGAAAGT
131 GTTAGAGATACACCACAACAGAATGGGGTGGCAGAACGTATGAATCGAATACTACTAGAGAAAGT
*
586655 TCGATGTATGTTGTCCAATGTTGGGTTGAGCAAACCATTTTGGGCTGAGGCTGTGACATATGCTG
196 TCGATGTATGTTGTCCAATGCTGGGTTGAGCAAACCATTTTGGGCTGAGGCTGTGACATATGCTG
586720 GCCATCTCATCAATCATCTACCATCATCAGCAATAAGAGAAAAAACACCATTCGAGGTATGGTCT
261 GCCATCTCATCAATCATCTACCATCATCAGCAATAAGAGAAAAAACACCATTCGAGGTATGGTCT
586785 GAAAAACCTGCTACTGATTATGATTCCTCACATATATTTGGATCCACTGCCTATTATCATGTGAA
326 GAAAAACCTGCTACTGATTATGATTCCTCACATATATTTGGATCCACTGCCTATTATCATGTGAA
586850 GGAATCAAAGCTTGATCTGAGAGCAAAGAAAGCTCTCTTTATGAGAATCACACGTGGAGTGAAGG
391 GGAATCAAAGCTTGATCTGAGAGCAAAGAAAGCTCTCTTTATGAGAATCACACGTGGAGTGAAGG
586915 GATTCCGACTTT
456 GATTCCGACTTT
586927 GGTGCTTAGA
Statistics
Matches: 456, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
467 456 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (467 bp):
ATGGAAAAATATGATTGAGAACCAGACTAATAAGAAGATCAAACGACTTAGGACGGAAAATGAAG
GGGAGTATAAAAGTGATCCATTCTTCGATATTTGCCAAGAGCATGGTATTGTTTGACACTTCACC
GTTAGAGATACACCACAACAGAATGGGGTGGCAGAACGTATGAATCGAATACTACTAGAGAAAGT
TCGATGTATGTTGTCCAATGCTGGGTTGAGCAAACCATTTTGGGCTGAGGCTGTGACATATGCTG
GCCATCTCATCAATCATCTACCATCATCAGCAATAAGAGAAAAAACACCATTCGAGGTATGGTCT
GAAAAACCTGCTACTGATTATGATTCCTCACATATATTTGGATCCACTGCCTATTATCATGTGAA
GGAATCAAAGCTTGATCTGAGAGCAAAGAAAGCTCTCTTTATGAGAATCACACGTGGAGTGAAGG
GATTCCGACTTT
Found at i:589014 original size:27 final size:26
Alignment explanation
Indices: 588946--589023 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
588936 AAAGCCACCA
**
588946 TTTGTGTTTGTCAAAAATAATGGTTCC
1 TTTGTG-TTGTCAAAAATGGTGGTTCC
* * *
588973 TTTATATTTGTAAAAAATGGTGGTTCC
1 TTTGT-GTTGTCAAAAATGGTGGTTCC
*
589000 TTTGTGTTGTCAAAATTGGTGGTT
1 TTTGTGTTGTCAAAAATGGTGGTT
589024 AATTTTTATT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 16 0.39
27 25 0.61
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (26 bp):
TTTGTGTTGTCAAAAATGGTGGTTCC
Found at i:590793 original size:28 final size:28
Alignment explanation
Indices: 590745--590844 Score: 69
Period size: 28 Copynumber: 3.5 Consensus size: 28
590735 ATAAATCATA
* **
590745 TTATGT-AAATTTTAAAAATTTATATAT
1 TTATGTCATATTTTAATTATTTATATAT
*
590772 TTATGTCATATTTTAATTATTT-TTTAT
1 TTATGTCATATTTTAATTATTTATATAT
** * *
590799 ACCATATCATATTTTAATTTTTTTATATTATAT
1 -TTATGTCATATTTTAA--TTATT-TA-TATAT
590832 TTATGTCATATTT
1 TTATGTCATATTT
590845 AATATTATCA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
27 10 0.19
28 25 0.46
30 4 0.07
31 1 0.02
32 10 0.19
33 4 0.07
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (28 bp):
TTATGTCATATTTTAATTATTTATATAT
Found at i:591416 original size:11 final size:11
Alignment explanation
Indices: 591402--591435 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
591392 ATTAATTTGA
591402 ATTTTATTTTT
1 ATTTTATTTTT
591413 ATTTTATTTTT
1 ATTTTATTTTT
* *
591424 AATTAATTTTT
1 ATTTTATTTTT
591435 A
1 A
591436 ACGTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:595482 original size:2 final size:2
Alignment explanation
Indices: 595469--595510 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
595459 AAACTTACAG
*
595469 AT AT AG 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 AT AT AT
595511 TTAATCAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:595754 original size:9 final size:9
Alignment explanation
Indices: 595740--595777 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
595730 CTATCGATTT
595740 AATTAATTA
1 AATTAATTA
595749 AATTAATTA
1 AATTAATTA
*
595758 AATCAA-TA
1 AATTAATTA
595766 AATTATATTA
1 AATTA-ATTA
595776 AA
1 AA
595778 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 6 0.24
9 15 0.60
10 4 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTAATTA
Found at i:596407 original size:2 final size:2
Alignment explanation
Indices: 596400--596426 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
596390 ATCTGATCTA
596400 AT 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 AT A
596427 AACTGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:597366 original size:38 final size:38
Alignment explanation
Indices: 597331--597405 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
597321 TTAATTATGT
*
597331 TATATTTGTTATAATTAAAAATATAATAAATATTATTA
1 TATATTTATTATAATTAAAAATATAATAAATATTATTA
* * *
597369 TATATTTATTATGATTATAGATATAATAAATATTATT
1 TATATTTATTATAATTAAAAATATAATAAATATTATT
597406 GTAATCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (38 bp):
TATATTTATTATAATTAAAAATATAATAAATATTATTA
Found at i:597699 original size:25 final size:25
Alignment explanation
Indices: 597671--597724 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
597661 GGAGTATTAA
597671 ATATT-AATTTATATTTAATA-TAAAT
1 ATATTAAATTT-T-TTTAATATTAAAT
597696 ATATTAAATTTTTTTAATATTAAAT
1 ATATTAAATTTTTTTAATATTAAAT
597721 ATAT
1 ATAT
597725 ATATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 7 0.26
25 15 0.56
26 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATTAAATTTTTTTAATATTAAAT
Found at i:600003 original size:36 final size:36
Alignment explanation
Indices: 599931--600005 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
599921 TTATAAAAAT
*
599931 AATAAAAATATTTATATATTTTTATAATTAAATTTA
1 AATAAAAATATTTATATATTATTATAATTAAATTTA
599967 AATAAAAATA-TTATCATAATTATTA-AA-TAATATTTA
1 AATAAAAATATTTAT-AT-ATTATTATAATTAA-ATTTA
600003 AAT
1 AAT
600006 TAATTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 7 0.20
36 22 0.63
37 6 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
AATAAAAATATTTATATATTATTATAATTAAATTTA
Found at i:600425 original size:18 final size:19
Alignment explanation
Indices: 600410--600450 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
600400 AAATTTTATT
600410 TTTAA-TAATTATTTTAAA
1 TTTAATTAATTATTTTAAA
600428 TTTAATTAATT-TTTTAAA
1 TTTAATTAATTATTTTAAA
600446 TTTAA
1 TTTAA
600451 ATTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAATTAATTATTTTAAA
Found at i:600453 original size:19 final size:19
Alignment explanation
Indices: 600415--600459 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 19
600405 TTATTTTTAA
600415 TAATTATTTTAAATTTAA-T
1 TAATT-TTTTAAATTTAATT
600434 TAATTTTTTAAATTTAAATT
1 TAATTTTTTAAATTT-AATT
600454 TAATTT
1 TAATTT
600460 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTTTTTAAATTTAATT
Found at i:602893 original size:9 final size:9
Alignment explanation
Indices: 602879--602944 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
602869 ACGATATATT
602879 TAATAAATA
1 TAATAAATA
602888 TAATAAATA
1 TAATAAATA
602897 TAATAAA-A
1 TAATAAATA
*
602905 AAATTTTAAATA
1 TAA---TAAATA
*
602917 TAATTAATA
1 TAATAAATA
*
602926 TTATAAA-A
1 TAATAAATA
*
602934 TAATTAATA
1 TAATAAATA
602943 TA
1 TA
602945 TTTATCATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 9 0.20
9 29 0.64
11 4 0.09
12 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATAAATA
Found at i:602925 original size:29 final size:29
Alignment explanation
Indices: 602882--602938 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
602872 ATATATTTAA
602882 TAAATATAATAAATATAATAAAAAAATTT
1 TAAATATAATAAATATAATAAAAAAATTT
* * *
602911 TAAATATAATTAATATTATAAAATAATT
1 TAAATATAATAAATATAATAAAAAAATT
602939 AATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAATATAATAAATATAATAAAAAAATTT
Found at i:602933 original size:26 final size:24
Alignment explanation
Indices: 602888--602975 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 24
602878 TTAATAAATA
*
602888 TAATA-AATATAATA-AAAAAATTT
1 TAATATAAT-TAATATATAAAATTT
*
602911 TAAATATAATTAATATTATAAAATAAT
1 T-AATATAATTAATA-TATAAAAT-TT
*
602938 TAATAT-ATTTATCATATAAAATTT
1 TAATATAATTAAT-ATATAAAATTT
* *
602962 TGATATATTTAATA
1 TAATATAATTAATA
602976 ATTTAATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
23 1 0.02
24 16 0.31
25 20 0.39
26 12 0.24
27 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
TAATATAATTAATATATAAAATTT
Found at i:602946 original size:19 final size:18
Alignment explanation
Indices: 602879--602943 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 18
602869 ACGATATATT
* *
602879 TAATAAATATAATAAATA
1 TAATTAATATTATAAATA
* * *
602897 TAATAAAAAAATTTTAAATA
1 TAAT--TAATATTATAAATA
602917 TAATTAATATTATAAA-A
1 TAATTAATATTATAAATA
602934 TAATTAATAT
1 TAATTAATAT
602944 ATTTATCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 11 0.28
18 13 0.33
20 15 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATTAATATTATAAATA
Found at i:604478 original size:14 final size:15
Alignment explanation
Indices: 604450--604478 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
604440 TTTTTAACCC
604450 ATTTTTTAACTCAAA
1 ATTTTTTAACTCAAA
604465 ATTTTTTAAC-CAAA
1 ATTTTTTAACTCAAA
604479 TGGCCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTTTAACTCAAA
Found at i:604756 original size:22 final size:23
Alignment explanation
Indices: 604731--604774 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
604721 TTATTTCTTT
*
604731 ATTTTTATTTTTT-TGATTTTTG
1 ATTTTGATTTTTTATGATTTTTG
*
604753 ATTTTGATTTTTTATGTTTTTT
1 ATTTTGATTTTTTATGATTTTT
604775 TTAGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (23 bp):
ATTTTGATTTTTTATGATTTTTG
Found at i:609475 original size:19 final size:17
Alignment explanation
Indices: 609415--609463 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
609405 AAATATATTT
* *
609415 ATATTTAATATACACCA
1 ATATTAAATATTCACCA
609432 ATATTAAATATTCACCA
1 ATATTAAATATTCACCA
609449 ATATTAAATATTCAC
1 ATATTAAATATTCAC
609464 AATCGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTAAATATTCACCA
Found at i:609977 original size:20 final size:20
Alignment explanation
Indices: 609934--609977 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
609924 AATATAATTT
* * *
609934 TTAAAAAAATTTTAAATATA
1 TTAAAAAAAATTTAAAAAAA
609954 -TAAAAAAAATTTAAAAAAA
1 TTAAAAAAAATTTAAAAAAA
609973 TTAAA
1 TTAAA
609978 TATAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAAAAAATTTAAAAAAA
Found at i:610549 original size:16 final size:16
Alignment explanation
Indices: 610530--610564 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
610520 TAAGTTATAA
610530 TTATATTTAAAATATT
1 TTATATTTAAAATATT
* *
610546 TTATATTTATATTATT
1 TTATATTTAAAATATT
610562 TTA
1 TTA
610565 ATACATTAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:610667 original size:21 final size:25
Alignment explanation
Indices: 610635--610687 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 25
610625 TATATTATTT
610635 TATATATATAAT-TTTC-ATATA-A
1 TATATATATAATATTTCTATATATA
*
610657 T-TATATTTAATATTTCTATATATA
1 TATATATATAATATTTCTATATATA
610681 TATATAT
1 TATATAT
610688 GGACCCGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.35
22 5 0.19
23 5 0.19
24 2 0.08
25 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATATAATATTTCTATATATA
Found at i:612319 original size:5 final size:5
Alignment explanation
Indices: 612309--612338 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
612299 TATAGTGTTC
612309 AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
612339 TTATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:612409 original size:2 final size:2
Alignment explanation
Indices: 612402--612437 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
612392 TGTAAATAAG
612402 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
612438 CCCTTGAAAG
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:614083 original size:21 final size:22
Alignment explanation
Indices: 614044--614088 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
614034 CTTTGTTTCT
*
614044 TTTAGTTAAAGAAATACTT-TG
1 TTTAGTTAAAGAAAAACTTATG
614065 TTTAGTTAATA-AAAAACTTATG
1 TTTAGTTAA-AGAAAAACTTATG
614087 TT
1 TT
614089 ACACGGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.44
Consensus pattern (22 bp):
TTTAGTTAAAGAAAAACTTATG
Found at i:614944 original size:17 final size:17
Alignment explanation
Indices: 614909--614954 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
614899 CTGTAATTAC
* **
614909 AAAAATTTATAATTTTT
1 AAAAATTTATGATCCTT
614926 AAAAATTTATGATCCTT
1 AAAAATTTATGATCCTT
614943 -AAAATTTATGAT
1 AAAAATTTATGAT
614955 TAATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
AAAAATTTATGATCCTT
Done.