Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397287.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_302.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 796134
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1883 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:391525 original size:25 final size:26
Alignment explanation
Indices: 391479--391535 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
391469 ACCTAAAATG
*
391479 ATAAA-TAAAAATTTATTTATTA-AA
1 ATAAATTAAAAATTTATTAATTATAA
391503 ATAAATTAATAAA-TTATTAATTATAA
1 ATAAATTAA-AAATTTATTAATTATAA
391529 A-AAATTA
1 ATAAATTA
391536 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.17
25 18 0.62
26 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAATTAAAAATTTATTAATTATAA
Found at i:391535 original size:17 final size:18
Alignment explanation
Indices: 391513--391568 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
391503 ATAAATTAAT
391513 AAATTA-TTAATTATAAA
1 AAATTACTTAATTATAAA
*
391530 AAATTATTTAATT-TAAA
1 AAATTACTTAATTATAAA
*
391547 ATAA-AACTTAATTA-AAA
1 A-AATTACTTAATTATAAA
391564 AAATT
1 AAATT
391569 GAACAAGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 22 0.69
18 8 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTACTTAATTATAAA
Found at i:393759 original size:18 final size:19
Alignment explanation
Indices: 393730--393766 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
393720 TAAAGTGTAA
*
393730 TATTTAAAAAAAATTAAAT
1 TATTTAAAAAAAATCAAAT
393749 TATTT-AAAAAAATCAAAT
1 TATTTAAAAAAAATCAAAT
393767 AAACCCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TATTTAAAAAAAATCAAAT
Found at i:409875 original size:29 final size:30
Alignment explanation
Indices: 409843--409906 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
409833 TTACTTATTA
* *
409843 TTTTTAT-TTTTTATTTT-ATTTAATTAAG
1 TTTTTATATTTTTATTTTGAGTTAAGTAAG
*
409871 GTTTTATATTTTTATTTTGAGTTAAGTAAG
1 TTTTTATATTTTTATTTTGAGTTAAGTAAG
409901 TTTTTA
1 TTTTTA
409907 GTTCATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.20
29 10 0.33
30 14 0.47
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (30 bp):
TTTTTATATTTTTATTTTGAGTTAAGTAAG
Found at i:410344 original size:17 final size:17
Alignment explanation
Indices: 410324--410361 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
410314 TTAAGTTTAG
410324 TATTAA-AAGATTAAAAA
1 TATTAATAA-ATTAAAAA
*
410341 TATTAATAACTTAAAAA
1 TATTAATAAATTAAAAA
410358 TATT
1 TATT
410362 TTGGAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TATTAATAAATTAAAAA
Found at i:413270 original size:2 final size:2
Alignment explanation
Indices: 413263--413294 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
413253 TGCAATGGAG
413263 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
413295 GCTACCCCTT
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:422386 original size:15 final size:14
Alignment explanation
Indices: 422366--422439 Score: 55
Period size: 14 Copynumber: 5.0 Consensus size: 14
422356 TTTATTATTT
422366 TATTATATTTAATTA
1 TATTAT-TTTAATTA
422381 TATTATTTTAATT-
1 TATTATTTTAATTA
422394 T-TTATTTTGAATTAA
1 TATTATTTT-AATT-A
*
422409 GTATGTTTTTATAATTA
1 -TAT-TATTT-TAATTA
422426 -ATTATTATTAATTA
1 TATTATT-TTAATTA
422440 AAATATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
12 7 0.14
13 5 0.10
14 16 0.33
15 9 0.18
16 1 0.02
17 2 0.04
18 8 0.16
19 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (14 bp):
TATTATTTTAATTA
Found at i:422662 original size:23 final size:25
Alignment explanation
Indices: 422636--422701 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
422626 TAATTAATTA
422636 TTAATAATAAAAAT-AT-ATTTAAT
1 TTAATAATAAAAATAATAATTTAAT
422659 TTAA-AATAAAAATAATAATTTAAT
1 TTAATAATAAAAATAATAATTTAAT
*
422683 TAAAT-ATAATAAAATAATA
1 TTAATAAT-A-AAAATAATA
422702 TTTTTTCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 9 0.24
23 6 0.16
24 12 0.32
25 1 0.03
26 9 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAATAATAAAAATAATAATTTAAT
Found at i:422669 original size:22 final size:23
Alignment explanation
Indices: 422582--422701 Score: 77
Period size: 23 Copynumber: 5.0 Consensus size: 23
422572 AAATATAAAT
*
422582 TTTAATTAATAATAAATAATTAATTA
1 TTTAATTAA-AATAAA-AA-TAATAA
** * *
422608 TTTTTTTACATTAATAAATAATTAA
1 TTTAATTAAAATAA-AAATAA-TAA
422633 -TT-ATTAATAATAAAAAT-AT-A
1 TTTAATTAA-AATAAAAATAATAA
422653 TTTAATTTAAAATAAAAATAATAA
1 TTTAA-TTAAAATAAAAATAATAA
422677 TTTAATTAAATATAATAAAATAATA
1 TTTAATTAAA-AT-A-AAAATAATA
422702 TTTTTTCAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 11 0.15
23 18 0.24
24 17 0.23
25 9 0.12
26 16 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAATTAAAATAAAAATAATAA
Found at i:422691 original size:18 final size:19
Alignment explanation
Indices: 422636--422694 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 19
422626 TAATTAATTA
422636 TTAATAATAAAAATATATTTAAT
1 TTAA-AATAAAAATA-A--TAAT
422659 TTAAAATAAAAATAATAAT
1 TTAAAATAAAAATAATAAT
* *
422678 TT-AATTAAATATAATAA
1 TTAAAATAAAAATAATAA
422695 AATAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.38
19 6 0.18
21 1 0.03
22 10 0.29
23 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATAAAAATAATAAT
Found at i:422741 original size:20 final size:20
Alignment explanation
Indices: 422709--422751 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
422699 ATATTTTTTC
422709 AATTTTTTAAAATAATTA-AA
1 AATTTTTTAAAAT-ATTATAA
422729 AATTTTATT-AAATATTATAA
1 AATTTT-TTAAAATATTATAA
422749 AAT
1 AAT
422752 AAACACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTTTAAAATATTATAA
Found at i:451450 original size:18 final size:18
Alignment explanation
Indices: 451427--451462 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
451417 TCAAAAGCTA
451427 AAGCAGTCTGACTCCTTT
1 AAGCAGTCTGACTCCTTT
*
451445 AAGCAGTGTGACTCCTTT
1 AAGCAGTCTGACTCCTTT
451463 CATATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (18 bp):
AAGCAGTCTGACTCCTTT
Found at i:461111 original size:116 final size:116
Alignment explanation
Indices: 460956--461185 Score: 397
Period size: 116 Copynumber: 2.0 Consensus size: 116
460946 CTAGCAAGGC
*
460956 TGTTGGGCCATAGTTCCTCTGATGCACTGTGTAGGGTTTGTAGGAAAATCATAGTGCATGAATAA
1 TGTTGGGCCATAGGTCCTCTGATGCACTGTGTAGGGTTTGTAGGAAAATCATAGTGCATGAATAA
*
461021 ACATATTCCTCTCCTTTCATACATCCAACATGCTTGTGATTCTAGCATGAT
66 ACATATTCCTCTCCCTTCATACATCCAACATGCTTGTGATTCTAGCATGAT
*
461072 TGTTGGGCCATAGGTCTTCTGATGCACTGTGTAGGGTTTGTAGGAAAATCATAGTGCATGAATAA
1 TGTTGGGCCATAGGTCCTCTGATGCACTGTGTAGGGTTTGTAGGAAAATCATAGTGCATGAATAA
* * * *
461137 ACTTATTCTTCTCCCTTCATACATCCTACATGCTTGTGATTGTAGCATG
66 ACATATTCCTCTCCCTTCATACATCCAACATGCTTGTGATTCTAGCATG
461186 GTCAGAGTCA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 107 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (116 bp):
TGTTGGGCCATAGGTCCTCTGATGCACTGTGTAGGGTTTGTAGGAAAATCATAGTGCATGAATAA
ACATATTCCTCTCCCTTCATACATCCAACATGCTTGTGATTCTAGCATGAT
Found at i:465218 original size:23 final size:22
Alignment explanation
Indices: 465185--465235 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
465175 CTCTTAATTA
*
465185 TATTTTTAATAT-ATTTTATTTT
1 TATTTTTAATATAATTTT-TTCT
465207 TATTTTTGAATATAATTTTTTCT
1 TATTTTT-AATATAATTTTTTCT
465230 TATTTT
1 TATTTT
465236 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 14 0.54
24 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTTAATATAATTTTTTCT
Found at i:465382 original size:15 final size:16
Alignment explanation
Indices: 465341--465382 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
465331 TAAAAGAAAT
*
465341 ATTATAATATAATATA
1 ATTATAATATATTATA
465357 ATTA-AATATATTATA
1 ATTATAATATATTATA
465372 ATTATAA-ATAT
1 ATTATAATATAT
465383 GTACTCTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATAATATATTATA
Found at i:474631 original size:29 final size:28
Alignment explanation
Indices: 474576--474637 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
474566 ATTAAAGAAA
474576 TTTTAAATAAATCATTATTGTTCTATTT
1 TTTTAAATAAATCATTATTGTTCTATTT
*
474604 TATTTAATTAAATTCATATATT-TT-TATTT
1 T-TTTAAATAAA-TCAT-TATTGTTCTATTT
474633 TTTTA
1 TTTTA
474638 CATCAAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 5 0.17
29 15 0.50
30 6 0.20
31 4 0.13
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAATAAATCATTATTGTTCTATTT
Found at i:482722 original size:29 final size:29
Alignment explanation
Indices: 482663--482735 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
482653 TTAAGAAAAT
482663 TTAAAT-AAATATTTAT--TTTTATTAC-A
1 TTAAATAAAAT-TTTATACTTTTATTACAA
* *
482689 TTTAATAAAATCTTTATACTTTTATTTCAA
1 TTAAATAAAAT-TTTATACTTTTATTACAA
482719 TTAAATAAAATTTTATA
1 TTAAATAAAATTTTATA
482736 ACTAATGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 5 0.13
27 9 0.23
29 14 0.36
30 11 0.28
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAAATAAAATTTTATACTTTTATTACAA
Found at i:496124 original size:2 final size:2
Alignment explanation
Indices: 496119--496148 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
496109 TGTCTTCATC
496119 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
496149 TATCAGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:501672 original size:15 final size:15
Alignment explanation
Indices: 501652--501686 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
501642 TGTAATTGTT
501652 CATCTAATTGACTCG
1 CATCTAATTGACTCG
501667 CATCTAATTGACTCG
1 CATCTAATTGACTCG
501682 CATCT
1 CATCT
501687 TTTCTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (15 bp):
CATCTAATTGACTCG
Found at i:502808 original size:2 final size:2
Alignment explanation
Indices: 502801--502833 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
502791 TTCAACTTCT
502801 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 T
502834 TATCCATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:512424 original size:6 final size:6
Alignment explanation
Indices: 512418--512449 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
512408 GCTACTGCTG
*
512418 CCACTG CCACTA CCACTA CCACTA CCACTA CC
1 CCACTA CCACTA CCACTA CCACTA CCACTA CC
512450 GCCCTCATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.53, G:0.03, T:0.16
Consensus pattern (6 bp):
CCACTA
Found at i:515875 original size:16 final size:17
Alignment explanation
Indices: 515854--515886 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
515844 TTGTTCAACA
515854 CTTCATTCTTT-ATTTT
1 CTTCATTCTTTCATTTT
515870 CTTCATTCTTTCATTTT
1 CTTCATTCTTTCATTTT
515887 TTCTTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTCATTCTTTCATTTT
Found at i:516651 original size:15 final size:16
Alignment explanation
Indices: 516631--516660 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
516621 CTTTAATGTG
516631 AAAAGATAAA-AAAAA
1 AAAAGATAAAGAAAAA
516646 AAAAGATAAAGAAAA
1 AAAAGATAAAGAAAA
516661 TCAACTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (16 bp):
AAAAGATAAAGAAAAA
Found at i:518009 original size:12 final size:12
Alignment explanation
Indices: 517992--518017 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
517982 AGGCTGCAAC
517992 TTTGAGTATTTA
1 TTTGAGTATTTA
518004 TTTGAGTATTTA
1 TTTGAGTATTTA
518016 TT
1 TT
518018 ATTTTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTGAGTATTTA
Found at i:519606 original size:2 final size:2
Alignment explanation
Indices: 519594--519625 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
519584 TTATTGACAA
519594 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
519626 ATATATATAT
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:519811 original size:12 final size:12
Alignment explanation
Indices: 519794--519834 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
519784 TCTTTCACAA
*
519794 AATAACAATAAC
1 AATAACAATAAT
519806 AATAACAATAAT
1 AATAACAATAAT
*
519818 AATAATAATAAT
1 AATAACAATAAT
519830 AATAA
1 AATAA
519835 GATATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAACAATAAT
Found at i:519820 original size:3 final size:3
Alignment explanation
Indices: 519794--519834 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
519784 TCTTTCACAA
* * *
519794 AAT AAC AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
519835 GATATAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:532926 original size:2 final size:2
Alignment explanation
Indices: 532919--532949 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
532909 TCATGTTTGG
532919 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
532950 TCTTTTTATC
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:537918 original size:20 final size:19
Alignment explanation
Indices: 537873--537922 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
537863 GTATTATACA
537873 TTTTTATTGTTATTATTTAG
1 TTTTTATT-TTATTATTTAG
537893 TATTTTATTTTA-TATTTTATG
1 T-TTTTATTTTATTA-TTTA-G
537914 TTTTT-TTTT
1 TTTTTATTTT
537923 CATTTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.22
20 12 0.44
21 9 0.33
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTATTATTTAG
Found at i:538711 original size:20 final size:20
Alignment explanation
Indices: 538679--538733 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
538669 TATTACCTGC
538679 TTTCTCTTCTCTCTTTCTTT
1 TTTCTCTTCTCTCTTTCTTT
*
538699 TTTCT-TTCTTCTCTTTCTTC
1 TTTCTCTTC-TCTCTTTCTTT
* *
538719 TTCCTCTTCTTTCTT
1 TTTCTCTTCTCTCTT
538734 CCTTGCCGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTCTCTTCTCTCTTTCTTT
Found at i:538719 original size:16 final size:16
Alignment explanation
Indices: 538683--538734 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
538673 ACCTGCTTTC
*
538683 TCTTCTCTCTT-TCTT
1 TCTTCTTTCTTCTCTT
*
538698 TTTTCTTTCTTCTCTT
1 TCTTCTTTCTTCTCTT
*
538714 TCTTC-TTCCTCTTCTT
1 TCTTCTTTCTTC-TCTT
538730 TCTTC
1 TCTTC
538735 CTTGCCGCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTCTTTCTTCTCTT
Found at i:538734 original size:13 final size:13
Alignment explanation
Indices: 538700--538736 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
538690 TCTTTCTTTT
538700 TTCTTTCTT-CTC
1 TTCTTTCTTCCTC
538712 TT-TCTTCTTCCTC
1 TTCT-TTCTTCCTC
538725 TTCTTTCTTCCT
1 TTCTTTCTTCCT
538737 TGCCGCCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 7 0.32
13 13 0.59
14 1 0.05
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTCTTTCTTCCTC
Found at i:538780 original size:21 final size:21
Alignment explanation
Indices: 538748--538809 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
538738 GCCGCCGGCC
538748 TCTTCTTTTTCTCTCCTTTTTCT
1 TCTTC-TTTTCTCT-CTTTTTCT
538771 T-TTCTTTTCT-TCTTTTT-T
1 TCTTCTTTTCTCTCTTTTTCT
*
538789 TCTTCTTTCCTACTCTTTTTC
1 TCTTCTTTTCT-CTCTTTTTC
538810 CACTAGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 14 0.41
20 1 0.03
21 13 0.38
22 3 0.09
23 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTCTTTTCTCTCTTTTTCT
Found at i:538793 original size:11 final size:11
Alignment explanation
Indices: 538764--538796 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
538754 TTTTCTCTCC
538764 TTTTTCTT-TT
1 TTTTTCTTCTT
*
538774 CTTTTCTTCTT
1 TTTTTCTTCTT
538785 TTTTTCTTCTT
1 TTTTTCTTCTT
538796 T
1 T
538797 CCTACTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:547611 original size:15 final size:15
Alignment explanation
Indices: 547562--547603 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
547552 TTTACAATGC
* *
547562 AATGTGATTACAGGT
1 AATGTGATTGCAGAT
547577 AATGTGATTGCAGAT
1 AATGTGATTGCAGAT
547592 AATGTGATTGCA
1 AATGTGATTGCA
547604 AGCTATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAGAT
Found at i:547928 original size:15 final size:15
Alignment explanation
Indices: 547910--548026 Score: 79
Period size: 15 Copynumber: 8.0 Consensus size: 15
547900 TTATATTATA
*
547910 TATTTTATGTTAATT
1 TATTTTATTTTAATT
547925 TATTTTA-TTT-ATAT
1 TATTTTATTTTAAT-T
*
547939 TATATATATTTTAATT
1 TAT-TTTATTTTAATT
*
547955 T-TTTATATTTTATTT
1 TATTT-TATTTTAATT
*
547970 TATTTTAATTT--TT
1 TATTTTATTTTAATT
* *
547983 TATTCTTATGTT-ATA
1 TATT-TTATTTTAATT
547998 TATTTTATTTTAA--
1 TATTTTATTTTAATT
548011 TATTTTAATTTTAATT
1 TATTTT-ATTTTAATT
548027 ATAACATTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
13 14 0.17
14 25 0.31
15 32 0.40
16 8 0.10
17 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTTATTTTAATT
Found at i:547932 original size:24 final size:24
Alignment explanation
Indices: 547899--548005 Score: 76
Period size: 24 Copynumber: 4.4 Consensus size: 24
547889 AATATAAATT
*
547899 TTTATATTATATATTTTATGTTAA
1 TTTATTTTATATATTTTATGTTAA
* * * *
547923 TTTATTTTATTTATATTATATATAT
1 TTTATTTTATATATTTTATGT-TAA
* * *
547948 TTTAATTTTTTATATTTTATTTTAT
1 TTT-ATTTTATATATTTTATGTTAA
547973 TTTAATTTT-T-TATTCTTATGTT-A
1 TTT-ATTTTATATATT-TTATGTTAA
*
547996 TATATTTTAT
1 TTTATTTTAT
548006 TTTAATATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
22 5 0.07
23 7 0.10
24 24 0.36
25 17 0.25
26 14 0.21
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTATTTTATATATTTTATGTTAA
Found at i:547944 original size:50 final size:50
Alignment explanation
Indices: 547872--547986 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
547862 TCTTATATAT
* *
547872 TTTATTTTCATTTCTTTAATATAAATTTTTATATTATATATTTTATGTTAA
1 TTTATTTT-ATTTATTTAATATAAATTTTAATATTATATATTTTATGTTAA
* * * * *
547923 TTTATTTTATTTATATT-ATATATATTTTAATTTTTTATATTTTATTTTAT
1 TTTATTTTATTTAT-TTAATATAAATTTTAATATTATATATTTTATGTTAA
*
547973 TTTAATTT-TTTATT
1 TTTATTTTATTTATT
547987 CTTATGTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.02
49 5 0.09
50 39 0.71
51 10 0.18
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.69
Consensus pattern (50 bp):
TTTATTTTATTTATTTAATATAAATTTTAATATTATATATTTTATGTTAA
Found at i:547960 original size:33 final size:31
Alignment explanation
Indices: 547899--548029 Score: 89
Period size: 33 Copynumber: 4.2 Consensus size: 31
547889 AATATAAATT
*
547899 TTTATATTATATATTTT-ATGTTAATTTATTTTA
1 TTTATATT-TATATTTTAATATT--TTTATTTTA
547932 TTTATATTATATATATTTTAAT-TTTTTA---TA
1 TTTATA-T-T-TATATTTTAATATTTTTATTTTA
547962 TTT-TATTT-TATTTTAAT-TTTTTATTCTTA
1 TTTATATTTATATTTTAATATTTTTATT-TTA
* *
547991 TGTTATATATTTTATTTTAATATTTTAATTTTA
1 T-TTATAT-TTATATTTTAATATTTTTATTTTA
*
548024 ATTATA
1 TTTATA
548030 ACATTATAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 25
0.76 0.02 0.23
Matches are distributed among these distances:
25 15 0.18
26 1 0.01
27 1 0.01
28 1 0.01
29 5 0.06
30 7 0.08
31 3 0.04
32 7 0.08
33 22 0.26
34 8 0.10
35 12 0.14
36 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTATATTTATATTTTAATATTTTTATTTTA
Found at i:547970 original size:5 final size:5
Alignment explanation
Indices: 547910--548009 Score: 66
Period size: 5 Copynumber: 20.4 Consensus size: 5
547900 TTATATTATA
* * * * *
547910 TATTT TATGT TAATT TATTT TA-TT TATAT TATATA TATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT
* * *
547960 TATTT TATTT TATTT TA-AT T-TTT TATTCT TATGT TA-TA TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT
548008 TA
1 TA
548010 ATATTTTAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
4 13 0.18
5 46 0.65
6 12 0.17
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:564438 original size:69 final size:69
Alignment explanation
Indices: 564277--564438 Score: 152
Period size: 69 Copynumber: 2.3 Consensus size: 69
564267 CCAACTCATC
* * * * * *
564277 CCTATGGTCTTCTTACCCCCATA-CTAAGATTCATAAAAAAGGAAAAAGTGGTATTATGCCCAAC
1 CCTATGGTATTCTTACCCCCACATCTAAGAATCATAAAAAAGGAAAAAGCGGTATGACGCCCAAC
564341 TTAA
66 TTAA
* ** * *
564345 CCT-TGCAGTGTTCTTACCTTCACATC-GAGAATCATAAAGAGAGGAAAAA-CGGTATGACGCCC
1 CCTATG--GTATTCTTACCCCCACATCTAAGAATCATAAA-AAAGGAAAAAGCGGTATGACGCCC
*
564407 AACTTGA
63 AACTTAA
564414 CTCTATGGTATTCTTACCCCCACAT
1 C-CTATGGTATTCTTACCCCCACAT
564439 GGGACTAGAG
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
67 2 0.03
68 3 0.04
69 55 0.74
70 12 0.16
71 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (69 bp):
CCTATGGTATTCTTACCCCCACATCTAAGAATCATAAAAAAGGAAAAAGCGGTATGACGCCCAAC
TTAA
Found at i:565029 original size:16 final size:18
Alignment explanation
Indices: 564989--565034 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
564979 ATTTGATTTC
*
564989 AAATGATTAATTAACCTAA
1 AAATAATTAATTAACCT-A
565008 AAATAATTAATTAA-CT-
1 AAATAATTAATTAACCTA
565024 AAATAATTAAT
1 AAATAATTAAT
565035 GAAGTATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
18 2 0.08
19 13 0.50
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (18 bp):
AAATAATTAATTAACCTA
Found at i:566182 original size:24 final size:24
Alignment explanation
Indices: 566155--566201 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
566145 GAAAATTAGT
566155 CATTAATCCAAGTAAAAAAAAATC
1 CATTAATCCAAGTAAAAAAAAATC
* *
566179 CATTAATCCAAGTCAAAGAAAAT
1 CATTAATCCAAGTAAAAAAAAAT
566202 AAAAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.21
Consensus pattern (24 bp):
CATTAATCCAAGTAAAAAAAAATC
Found at i:566398 original size:17 final size:16
Alignment explanation
Indices: 566359--566398 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
566349 GGCCTCTTAA
*
566359 ATAATCTCCAAAATCC
1 ATAATTTCCAAAATCC
*
566375 TTAATTTCCAAAATCTC
1 ATAATTTCCAAAATC-C
566392 ATAATTT
1 ATAATTT
566399 GTTAGTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATTTCCAAAATCC
Found at i:569062 original size:2 final size:2
Alignment explanation
Indices: 569055--569080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
569045 GAATAATCAC
569055 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
569081 TGTGTGTGTG
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:573928 original size:2 final size:2
Alignment explanation
Indices: 573921--573950 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
573911 TGAACTTCCA
573921 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
573951 CAATCTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:574967 original size:15 final size:15
Alignment explanation
Indices: 574949--574991 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
574939 GACTAACTTA
574949 AAATATCATAAAAAC
1 AAATATCATAAAAAC
* *
574964 AAATAACA-ATAAA-
1 AAATATCATAAAAAC
574977 AAATATCATAAAAAC
1 AAATATCATAAAAAC
574992 TACAAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 7 0.32
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATATCATAAAAAC
Found at i:580750 original size:68 final size:67
Alignment explanation
Indices: 580641--580772 Score: 167
Period size: 68 Copynumber: 2.0 Consensus size: 67
580631 CATGTTTTAA
** *
580641 ATGGGAATAATAATACATGACTTAGCTGGAAACATTTGTCTTTTGGTACTGGAATAACAATGTAT
1 ATGGGAATAATAATACATGACTTAGCTGGAAACAAATGTCTTTTGCTACTGGAATAACAATGTAT
580706 GG
66 GG
* * * * *
580708 ATGGGAATAATAGTATATGATTTGAGCTGGGAAA-AAATGTCTTTTGCTGCTGGATTAACAATGT
1 ATGGGAATAATAATACATGACTT-AGCT-GGAAACAAATGTCTTTTGCTACTGGAATAACAATGT
580772 A
64 A
580773 GGAATTAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 20 0.36
68 30 0.55
69 5 0.09
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (67 bp):
ATGGGAATAATAATACATGACTTAGCTGGAAACAAATGTCTTTTGCTACTGGAATAACAATGTAT
GG
Found at i:596672 original size:16 final size:16
Alignment explanation
Indices: 596653--596727 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
596643 TAAAAACTCC
*
596653 TTTTTTTTAAATTTTA
1 TTTTTTTAAAATTTTA
* **
596669 TTTTTTAAAAAAGTTA
1 TTTTTTTAAAATTTTA
596685 -TTTTTTAAAATTTTA
1 TTTTTTTAAAATTTTA
* **
596700 TTTTTTAAAAAAAGTTA
1 TTTTTT-TAAAATTTTA
596717 TTTTTTTAAAA
1 TTTTTTTAAAA
596728 AAAATTTAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.26
16 21 0.46
17 13 0.28
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTTTAAAATTTTA
Found at i:596676 original size:31 final size:30
Alignment explanation
Indices: 596638--596710 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
596628 TCATAGAAAC
*
596638 TTTTTTAAAAACTCCT-TTTTTTTAAATTTTA
1 TTTTTTAAAAACT--TATTTTTTAAAATTTTA
*
596669 TTTTTTAAAAAAGTTATTTTTTAAAATTTTA
1 TTTTTT-AAAAACTTATTTTTTAAAATTTTA
596700 TTTTTTAAAAA
1 TTTTTTAAAAA
596711 AAGTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 6 0.16
31 26 0.68
32 6 0.16
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTTTTAAAAACTTATTTTTTAAAATTTTA
Found at i:596689 original size:17 final size:17
Alignment explanation
Indices: 596669--596729 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
596659 TTAAATTTTA
596669 TTTTTTAAAAAAGTTA-
1 TTTTTTAAAAAAGTTAT
**
596685 TTTTTT-AAAATTTTAT
1 TTTTTTAAAAAAGTTAT
*
596701 TTTTTAAAAAAAGTTAT
1 TTTTTTAAAAAAGTTAT
596718 TTTTTTAAAAAA
1 TTTTTTAAAAAA
596730 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 7 0.19
16 11 0.30
17 19 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTTTAAAAAAGTTAT
Found at i:596706 original size:15 final size:15
Alignment explanation
Indices: 596654--596709 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
596644 AAAAACTCCT
*
596654 TTTTTTTAAATTTTA
1 TTTTTTAAAATTTTA
**
596669 TTTTTTAAAAAAGTTA
1 TTTTTT-AAAATTTTA
596685 TTTTTTAAAATTTTA
1 TTTTTTAAAATTTTA
596700 TTTTTTAAAA
1 TTTTTTAAAA
596710 AAAGTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 23 0.66
16 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTTTAAAATTTTA
Found at i:596711 original size:31 final size:33
Alignment explanation
Indices: 596653--596727 Score: 127
Period size: 31 Copynumber: 2.3 Consensus size: 33
596643 TAAAAACTCC
*
596653 TTTTTTTTAAATTTTATTTTTT-AAAAAAGTTA
1 TTTTTTTAAAATTTTATTTTTTAAAAAAAGTTA
596685 -TTTTTTAAAATTTTATTTTTTAAAAAAAGTTA
1 TTTTTTTAAAATTTTATTTTTTAAAAAAAGTTA
596717 TTTTTTTAAAA
1 TTTTTTTAAAA
596728 AAAATTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 20 0.50
32 10 0.25
33 10 0.25
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (33 bp):
TTTTTTTAAAATTTTATTTTTTAAAAAAAGTTA
Found at i:596720 original size:15 final size:15
Alignment explanation
Indices: 596670--596721 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
596660 TAAATTTTAT
596670 TTTTTAAAAAAGTTA
1 TTTTTAAAAAAGTTA
* **
596685 TTTTTTAAAATTTTA
1 TTTTTAAAAAAGTTA
596700 TTTTTTAAAAAAAGTTA
1 -TTTTT-AAAAAAGTTA
596717 TTTTT
1 TTTTT
596722 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 12 0.41
16 10 0.34
17 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAAAGTTA
Found at i:596853 original size:14 final size:13
Alignment explanation
Indices: 596810--596855 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
596800 AGGAGTACTT
*
596810 AAAT-AACACTTA
1 AAATAAACATTTA
596822 AAATAAACATTTA
1 AAATAAACATTTA
596835 AAATAAAC-TTCTAA
1 AAATAAACATT-T-A
596849 AAATAAA
1 AAATAAA
596856 AATAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.20
13 16 0.53
14 8 0.27
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATAAACATTTA
Found at i:603441 original size:63 final size:61
Alignment explanation
Indices: 603331--603450 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 61
603321 ATAAACGGAA
* *
603331 TAAATCTTACTAATAATTATAATAAAAATATTTCAATGATCATCATTTGATAAATACGCTT
1 TAAATCTTACTAATAATTATAATAAAAATATTTCAATGATCACCATTTAATAAATACGCTT
*
603392 TAAATCTTACTAATAATTATAATCAAAAAATATTTCAATGATCACCATTTAATGAATAC
1 TAAATCTTACTAATAATTATAAT--AAAAATATTTCAATGATCACCATTTAATAAATAC
603451 ATATTTACAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 23 0.43
63 31 0.57
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (61 bp):
TAAATCTTACTAATAATTATAATAAAAATATTTCAATGATCACCATTTAATAAATACGCTT
Found at i:606887 original size:18 final size:18
Alignment explanation
Indices: 606864--606918 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 18
606854 CACAGAAAAA
606864 ATTTTCC-TCTAGCAAATC
1 ATTTTCCGT-TAGCAAATC
606882 ATTTTCCGGTTAGCAAATC
1 ATTTTCC-GTTAGCAAATC
606901 ATTTTCCGGTTAGCAAAT
1 ATTTTCC-GTTAGCAAAT
606919 GGGCTCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.20
19 27 0.77
20 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTTTCCGTTAGCAAATC
Found at i:606897 original size:19 final size:19
Alignment explanation
Indices: 606873--606918 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
606863 AATTTTCCTC
606873 TAGCAAATCATTTTCCGGT
1 TAGCAAATCATTTTCCGGT
606892 TAGCAAATCATTTTCCGGT
1 TAGCAAATCATTTTCCGGT
606911 TAGCAAAT
1 TAGCAAAT
606919 GGGCTCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (19 bp):
TAGCAAATCATTTTCCGGT
Found at i:610330 original size:2 final size:2
Alignment explanation
Indices: 610323--610350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
610313 AAGAAATTCT
610323 TA 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 TA
610351 AAAGATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:625972 original size:21 final size:21
Alignment explanation
Indices: 625946--625986 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
625936 ATGGTGAAAA
* *
625946 ATGTCACATGACTATGTTATC
1 ATGTCACATCAATATGTTATC
625967 ATGTCACATCAATATGTTAT
1 ATGTCACATCAATATGTTAT
625987 GTCATCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (21 bp):
ATGTCACATCAATATGTTATC
Found at i:626147 original size:30 final size:30
Alignment explanation
Indices: 626084--626148 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
626074 TAGTCATAAG
* * *
626084 GGCTTATTTGGCTCAAAATAGAAGTGTGAA
1 GGCTTATTTGACTCAAAATAAAAATGTGAA
*
626114 GGCTTATTTGATTCAAAATAAAAATGT-AGA
1 GGCTTATTTGACTCAAAATAAAAATGTGA-A
626144 GGCTT
1 GGCTT
626149 GATTGAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (30 bp):
GGCTTATTTGACTCAAAATAAAAATGTGAA
Found at i:627256 original size:39 final size:40
Alignment explanation
Indices: 627184--627269 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
627174 AATTATAAAT
*
627184 AAAAATATTAATATTTCAAAATATTAATGATTAA-ATTGTA
1 AAAAATATTAATATTTCAAAATATCAATGATTAATATT-TA
* *
627224 AAAAATATTAAT-TTGT-AAATTATCAATTATTAATATTTA
1 AAAAATATTAATATT-TCAAAATATCAATGATTAATATTTA
627263 AAAAATA
1 AAAAATA
627270 AAATAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 25 0.61
40 16 0.39
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (40 bp):
AAAAATATTAATATTTCAAAATATCAATGATTAATATTTA
Found at i:627410 original size:89 final size:90
Alignment explanation
Indices: 627248--627417 Score: 197
Period size: 93 Copynumber: 1.9 Consensus size: 90
627238 GTAAATTATC
* *
627248 AATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAAATTTTAATTATATATTAAAAAATAA
1 AATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAAATGTTAACTATATATTAAAAAATAA
*
627313 TGTTTTAAATT-TAAAAATTAATTA
66 TGTATTAAATTATAAAAATTAATTA
* * **
627337 AATTATTAATATTTTAATAATAATAAAATTTAAATATAAATAAAATGTTAACT-T-T-TTAAATT
1 AATTATTAATA-TTTAA-AA-AATAAAA-TAAAATAAAAATAAAATGTTAACTATATATTAAAAA
*
627399 TTAATG-ATTAAATTATAAA
62 ATAATGTATTAAATTATAAA
627418 TAAAATATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
89 18 0.26
90 19 0.28
91 3 0.04
92 8 0.12
93 20 0.29
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (90 bp):
AATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAAATGTTAACTATATATTAAAAAATAA
TGTATTAAATTATAAAAATTAATTA
Found at i:646997 original size:112 final size:111
Alignment explanation
Indices: 646850--647124 Score: 279
Period size: 110 Copynumber: 2.5 Consensus size: 111
646840 TTTTCGATGA
* * *** *
646850 ATTTTCAACAGAATTTTTTCAACTGAAAAAT--TCCGTTGGAAATCCGTCGAAATTTTTTTTGGT
1 ATTTTCAA-AGAAATTTTCCAAC-GAAAAATAATCCGTTGGAAATCCGTCGAAAAAATTTATGG-
* * * *
646913 GCAAAAAAAAAATTACTCTCGCCAAACTTTCCAATGGAATTTC-CAACGG
63 CCAAAAAAAAAATTACTCCCACCAAACTTTCCAATGGAATTTCTC-ACAG
*** * *
646962 ATTTTCGTTGGAATTTTCCAACGAAAAATAATCCGTTGGAAATCCGTC-AAAAAATTTATGGCCT
1 ATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGAAATCCGTCGAAAAAATTTATGGCCA
* * * * *
647026 CAAAAAAATTTACTCCCATCAGACTTTTCAATGGAATTTCTCACAG
66 AAAAAAAAATTACTCCCACCAAACTTTCCAATGGAATTTCTCACAG
* * *
647072 ATTTTCAAAGAAATTTTCGAACGGACAATAATCCGTTGGAAATCCGTCGAAAA
1 ATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGAAATCCGTCGAAAA
647125 GTTTAGAGGC
Statistics
Matches: 132, Mismatches: 27, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
110 85 0.64
111 24 0.18
112 23 0.17
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (111 bp):
ATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGAAATCCGTCGAAAAAATTTATGGCCA
AAAAAAAAATTACTCCCACCAAACTTTCCAATGGAATTTCTCACAG
Found at i:647061 original size:110 final size:109
Alignment explanation
Indices: 646938--647146 Score: 269
Period size: 110 Copynumber: 1.9 Consensus size: 109
646928 CTCTCGCCAA
* *** *
646938 ACTTTCCAATGGAATTTC-CAACGGATTTTCGTTGGAATTTTCCAACGAAAAATAATCCGTTGGA
1 ACTTTCCAATGGAATTTCTC-ACAGATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGA
647002 AATCCGTCAAAAAATTTATG-GCCTCAAAAAAATTTACTCCCATCAG
65 AATCCGTCAAAAAATTTA-GAGCCT-AAAAAAATTTACTCCCATCAG
* * * *
647048 ACTTTTCAATGGAATTTCTCACAGATTTTCAAAGAAATTTTCGAACGGACAATAATCCGTTGGAA
1 ACTTTCCAATGGAATTTCTCACAGATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGAA
* * *
647113 ATCCGTCGAAAAGTTTAGAGGCTAAAAAAATTTA
66 ATCCGTCAAAAAATTTAGAGCCTAAAAAAATTTA
647147 AAACTCTCAA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
109 12 0.14
110 72 0.85
111 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (109 bp):
ACTTTCCAATGGAATTTCTCACAGATTTTCAAAGAAATTTTCCAACGAAAAATAATCCGTTGGAA
ATCCGTCAAAAAATTTAGAGCCTAAAAAAATTTACTCCCATCAG
Found at i:648053 original size:14 final size:14
Alignment explanation
Indices: 648034--648074 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
648024 TCTCTCTACT
*
648034 TTTCTTTTTTCTTC
1 TTTCTTTCTTCTTC
*
648048 TTTCTTTCTTCTCC
1 TTTCTTTCTTCTTC
*
648062 CTTCTTTCTTCTT
1 TTTCTTTCTTCTT
648075 TTCTACGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCTTTCTTCTTC
Found at i:648057 original size:18 final size:18
Alignment explanation
Indices: 648034--648077 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
648024 TCTCTCTACT
**
648034 TTTCTTTTTTCTTCTTTC
1 TTTCTTTTCCCTTCTTTC
*
648052 TTTCTTCTCCCTTCTTTC
1 TTTCTTTTCCCTTCTTTC
648070 -TTCTTTTC
1 TTTCTTTTC
648078 TACGTTGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCCCTTCTTTC
Found at i:648149 original size:53 final size:53
Alignment explanation
Indices: 648084--648190 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
648074 TTTCTACGTT
*
648084 GACAGCCTTTCTTTTTCCTCCCTATTACCGACGTCTCTCCCTATCCTCTCACC
1 GACAGCCCTTCTTTTTCCTCCCTATTACCGACGTCTCTCCCTATCCTCTCACC
* * *
648137 GACAGCCCTTCTTTTTCCTCCCTATTATCGGCGTCTCTCCCTTTCCTCTCACC
1 GACAGCCCTTCTTTTTCCTCCCTATTACCGACGTCTCTCCCTATCCTCTCACC
648190 G
1 G
648191 GCAACAACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.11, C:0.43, G:0.09, T:0.36
Consensus pattern (53 bp):
GACAGCCCTTCTTTTTCCTCCCTATTACCGACGTCTCTCCCTATCCTCTCACC
Found at i:653472 original size:41 final size:42
Alignment explanation
Indices: 653413--653503 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 42
653403 TCCAACTTCT
* * *
653413 AATAAAATATTAATATTTTCAAATATT-AATATTAAATTATA
1 AATAAAATATTAACATTTTAAAATATTAAAAATTAAATTATA
653454 AATAAAATATTAACATTTTAAAATATTAAAAATTAAATTATA
1 AATAAAATATTAACATTTTAAAATATTAAAAATTAAATTATA
653496 AATAAAAT
1 AATAAAAT
653504 TAAAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 25 0.54
42 21 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (42 bp):
AATAAAATATTAACATTTTAAAATATTAAAAATTAAATTATA
Found at i:653490 original size:7 final size:8
Alignment explanation
Indices: 653415--653517 Score: 59
Period size: 8 Copynumber: 12.8 Consensus size: 8
653405 CAACTTCTAA
653415 TAAAATAT
1 TAAAATAT
* *
653423 TAATATTT
1 TAAAATAT
*
653431 TCAAATAT
1 TAAAATAT
653439 T--AATAT
1 TAAAATAT
*
653445 TAAATTATAAA
1 TAAA--AT-AT
653456 TAAAATAT
1 TAAAATAT
* *
653464 TAACATTT
1 TAAAATAT
653472 TAAAATAT
1 TAAAATAT
653480 TAAAA-AT
1 TAAAATAT
*
653487 TAAATTAT
1 TAAAATAT
* *
653495 AAATAAAAT
1 TAA-AATAT
653504 TAAAATAT
1 TAAAATAT
*
653512 TTAAAT
1 TAAAAT
653518 TATCAATTAT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
6 6 0.09
7 6 0.09
8 44 0.63
9 7 0.10
10 2 0.03
11 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAAATAT
Found at i:653515 original size:41 final size:42
Alignment explanation
Indices: 653413--653516 Score: 135
Period size: 41 Copynumber: 2.5 Consensus size: 42
653403 TCCAACTTCT
* * *
653413 AATAAAATATTAATAT-TTTCAAATATTAATATTAAATTATA
1 AATAAAATATTAAAATATTTAAAATATTAAAATTAAATTATA
*
653454 AATAAAATATTAACAT-TTTAAAATATTAAAAATTAAATTATA
1 AATAAAATATTAAAATATTTAAAATATT-AAAATTAAATTATA
653496 AAT-AAA-ATTAAAATATTTAAA
1 AATAAAATATTAAAATATTTAAA
653517 TTATCAATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 7 0.12
41 34 0.60
42 16 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (42 bp):
AATAAAATATTAAAATATTTAAAATATTAAAATTAAATTATA
Found at i:653546 original size:27 final size:28
Alignment explanation
Indices: 653513--653571 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
653503 TTAAAATATT
*
653513 TAAATTATCAA-TTATTAATATTT-CAAA
1 TAAATTAT-AATTTATTAATATTTAAAAA
*
653540 TAAATTATAATTTATTACTATTTAAAAA
1 TAAATTATAATTTATTAATATTTAAAAA
653568 TAAA
1 TAAA
653572 ATAAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 19 0.68
28 7 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAATTATAATTTATTAATATTTAAAAA
Found at i:653578 original size:27 final size:27
Alignment explanation
Indices: 653524--653578 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
653514 AAATTATCAA
* *
653524 TTATTAATATTTCAAATAAATTATAAT
1 TTATTAATATTTAAAATAAAATATAAT
*
653551 TTATTACTATTTAAAAATAAAATA-AAT
1 TTATTAATATTT-AAAATAAAATATAAT
653578 T
1 T
653579 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TTATTAATATTTAAAATAAAATATAAT
Found at i:653671 original size:88 final size:88
Alignment explanation
Indices: 653505--653671 Score: 207
Period size: 88 Copynumber: 1.9 Consensus size: 88
653495 AAATAAAATT
* * *
653505 AAAATATTTAAATTATCAATTATTAATATTTCAAATAAATTATAATTTATTACTATTTAAAAATA
1 AAAATATTTAAATTATCAAATATAAATATTTCAAATAAATTATAATTTATTAATATTTAAAAATA
**
653570 AAATAAATTAAAAATAAAAAAGA
66 AAATAAAACAAAAATAAAAAAGA
*
653593 AAAATATTTAAATTAT-AAATA-AAATATTAAT-AATTAAATTATCAA-TTATTAATATTTAAAA
1 AAAATATTTAAATTATCAAATATAAATATT--TCAAATAAATTAT-AATTTATTAATATTT-AAA
*
653654 AATATAATAAAACAAAAA
62 AATAAAATAAAACAAAAA
653672 ATTAATAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
86 6 0.09
87 25 0.37
88 37 0.54
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.37
Consensus pattern (88 bp):
AAAATATTTAAATTATCAAATATAAATATTTCAAATAAATTATAATTTATTAATATTTAAAAATA
AAATAAAACAAAAATAAAAAAGA
Found at i:653856 original size:154 final size:154
Alignment explanation
Indices: 653633--654042 Score: 522
Period size: 154 Copynumber: 2.6 Consensus size: 154
653623 TAATTAAATT
* * *
653633 ATCAATTATTAATATTTAAAAAATATAATAAAACAAAAAATTA--ATAATAATATTTAAATTAAA
1 ATCAATTATTAATATTT-AAAAATAAAATAAAATAAATAATTATCATAATAATATTTAAATTAAA
** * * *
653696 CCAAATATTAATATTTTCAAATACTAATGATTAAATTATAAATAAAATATTAATATTCAACTATA
65 TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTCAAAT-TA
653761 T-A-TTACTAATATTTTAAATAAACA
129 TCAGTTACTAATATTTTAAATAAACA
* * *
653785 ATCAATTATTAATATTTAAAAATAAAATAAAATAAATAATTGATCATAATATTCTTTAAAATAAA
1 ATCAATTATTAATATTTAAAAATAAAATAAAATAAATAATT-ATCATAATAATATTTAAATTAAA
* * *
653850 TAAAATATTAATATTTTAAAATATTAATTATTAAGTTATAAATAAAATATTAATATTTAAATTAT
65 TAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTCAAATTAT
* **
653915 CAGTTATTAATATTTTAAATAAATT
130 CAGTTACTAATATTTTAAATAAACA
* *
653940 ATCAATTATTAATTGATAATAATAAAATAAAATAAGATAAAATAATTAGTCATAATAATATTTAA
1 ATCAATTATTAA-T-AT--TTA-AAAATAAAATAAAAT-AAATAATTA-TCATAATAATATTTAA
*
654005 ATTAAATAAATTATTAATATTTTAAAATATTAATGATT
59 ATTAAATAAAATATTAATATTTTAAAATATTAATGATT
654043 NNNNNNNNNN
Statistics
Matches: 222, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
151 21 0.09
152 18 0.08
153 3 0.01
154 72 0.32
155 31 0.14
156 1 0.00
157 2 0.01
159 2 0.01
160 15 0.07
161 57 0.26
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (154 bp):
ATCAATTATTAATATTTAAAAATAAAATAAAATAAATAATTATCATAATAATATTTAAATTAAAT
AAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTCAAATTATC
AGTTACTAATATTTTAAATAAACA
Found at i:653922 original size:41 final size:42
Alignment explanation
Indices: 653845--653924 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
653835 ATTCTTTAAA
*
653845 ATAAATAAAATATTAATATTTTAAAATATTAATTATTAAGTT
1 ATAAATAAAATATTAATATTTTAAAATATCAATTATTAAGTT
* *
653887 ATAAATAAAATATTAATA-TTTAAATTATCAGTTATTAA
1 ATAAATAAAATATTAATATTTTAAAATATCAATTATTAA
653925 TATTTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 17 0.49
42 18 0.51
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (42 bp):
ATAAATAAAATATTAATATTTTAAAATATCAATTATTAAGTT
Found at i:653934 original size:42 final size:42
Alignment explanation
Indices: 653845--653937 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
653835 ATTCTTTAAA
* *
653845 ATAAATAAAATATTAATATTTTAAAATATTAATTATTAAGTT
1 ATAAATAAAATATTAATATTTTAAAATATCAATTATTAAATT
* *
653887 ATAAATAAAATATTAATA-TTTAAATTATCAGTTATTAATATT
1 ATAAATAAAATATTAATATTTTAAAATATCAATTATTAA-ATT
*
653929 TTAAATAAA
1 ATAAATAAA
653938 TTATCAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 17 0.38
42 28 0.62
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (42 bp):
ATAAATAAAATATTAATATTTTAAAATATCAATTATTAAATT
Found at i:655271 original size:36 final size:34
Alignment explanation
Indices: 655224--655309 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 34
655214 AAGTTTGATG
655224 AATATTAATATTTAACTTAAAAT-ATTAAAAAGTAAA
1 AATATTAATATTTAACTTAAAATAATT---AAGTAAA
* * *
655260 AATATTAATATTTACATTTAAAATAATTAATTTAA
1 AATATTAATATTTA-ACTTAAAATAATTAAGTAAA
655295 AATATTAATATTTAA
1 AATATTAATATTTAA
655310 ATTATACAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.02
35 19 0.42
36 14 0.31
37 8 0.18
38 3 0.07
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (34 bp):
AATATTAATATTTAACTTAAAATAATTAAGTAAA
Found at i:655310 original size:15 final size:14
Alignment explanation
Indices: 655275--655303 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
655265 TAATATTTAC
655275 ATTTAAAATAATTA
1 ATTTAAAATAATTA
655289 ATTTAAAAT-ATTA
1 ATTTAAAATAATTA
655302 AT
1 AT
655304 ATTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAAAATAATTA
Found at i:655470 original size:74 final size:74
Alignment explanation
Indices: 655392--655533 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
655382 ATAAATGGAA
* * *
655392 TAAATCTTACTAAAAATTATGACAAAAAATATTTCAATGATCATCATTTGATGAATACACATTTA
1 TAAATCTTACTAAAAATTATAACAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
655457 TAATATGCT
66 TAATATGCT
* * ** * *
655466 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATTTTTATTTAATGAATACATATTTA
1 TAAATCTTACTAAAAATTATAACAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
655531 TAA
66 TAA
655534 GTATAAGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (74 bp):
TAAATCTTACTAAAAATTATAACAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
TAATATGCT
Found at i:663535 original size:2 final size:2
Alignment explanation
Indices: 663528--663555 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
663518 TGTGCTCCTT
663528 TA 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 TA
663556 GATCATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:664617 original size:15 final size:15
Alignment explanation
Indices: 664593--664626 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
664583 TATCTTACTT
*
664593 TTATATATATATATA
1 TTATAGATATATATA
*
664608 TTATAGATATATATG
1 TTATAGATATATATA
664623 TTAT
1 TTAT
664627 TGGTTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTATAGATATATATA
Found at i:668104 original size:72 final size:72
Alignment explanation
Indices: 667969--668114 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 72
667959 ACCAAGAGCG
* * *
667969 TGATAAAATGATTTCAGCATCAGAACAGAGCAAGCACCTGACTGAAACGATGTCTGTTGTTGTG-
1 TGATAAAATGATTTCAGCATCAGAACAGAACAAGCACCTGACTGAAACAATGCCTGTTGTTGTGC
668033 CCACGTGC
66 CCA-GTGC
* ** * *
668041 TGATAAAATGGTTTCAGCATCAGAACAGAATGAGCATCTGACTGAAGCAATGCCTGATT-TTGTG
1 TGATAAAATGATTTCAGCATCAGAACAGAACAAGCACCTGACTGAAACAATGCCTG-TTGTTGTG
668105 CCCAGTGC
65 CCCAGTGC
668113 TG
1 TG
668115 CTCAAGTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 59 0.92
73 5 0.08
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (72 bp):
TGATAAAATGATTTCAGCATCAGAACAGAACAAGCACCTGACTGAAACAATGCCTGTTGTTGTGC
CCAGTGC
Found at i:677334 original size:41 final size:41
Alignment explanation
Indices: 677289--677371 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
677279 AATAAACTAG
677289 TTTGAAGATAACACATTTAACCT-TCTACAATAATAACACTT
1 TTTGAAGATAACACATTTAACCTCT-TACAATAATAACACTT
** * *
677330 TTTGAAGATAACATGTTTTACCTCTTACTATAATAACACTT
1 TTTGAAGATAACACATTTAACCTCTTACAATAATAACACTT
677371 T
1 T
677372 CTATCTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (41 bp):
TTTGAAGATAACACATTTAACCTCTTACAATAATAACACTT
Found at i:679897 original size:28 final size:28
Alignment explanation
Indices: 679865--679928 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
679855 ACATATTTCT
*
679865 TTTTGTTACATGCAC-TATATAATCTCTA
1 TTTTGTTACACGCACTTA-ATAATCTCTA
*
679893 TTTTGTTACACGCACTTAATAATTTCTA
1 TTTTGTTACACGCACTTAATAATCTCTA
679921 TTTTGTTA
1 TTTTGTTA
679929 TACACCTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.50
Consensus pattern (28 bp):
TTTTGTTACACGCACTTAATAATCTCTA
Found at i:696995 original size:17 final size:17
Alignment explanation
Indices: 696973--697005 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
696963 ACAAAGATAG
696973 AAAATA-AAATGAAAAAC
1 AAAATAGAAA-GAAAAAC
696990 AAAATAGAAAGAAAAA
1 AAAATAGAAAGAAAAA
697006 GAAGAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAGAAAAAC
Found at i:708384 original size:20 final size:21
Alignment explanation
Indices: 708361--708400 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
708351 AAGTAAGTTA
*
708361 TTTTAATTTTA-TGTTATTTC
1 TTTTAATTTGATTGTTATTTC
708381 TTTTAATTTGATTGTTATTT
1 TTTTAATTTGATTGTTATTT
708401 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTAATTTGATTGTTATTTC
Found at i:711010 original size:118 final size:119
Alignment explanation
Indices: 710782--711014 Score: 360
Period size: 118 Copynumber: 2.0 Consensus size: 119
710772 CATATTGTAA
* * * *
710782 AGTGGTCTTCCATGGACATAACTTAGTCATGTACAATGGCCAACTAATGGACAACATACATCATC
1 AGTGGTCCTCCATGGACATAACATAGTCATGTACAATGGCCAACCAACGGACAACATACATCATC
*
710847 ATGTCACACCCCATTATCGAAGCAAATGGCAGAGTCTGTAATCATCATCCATCG
66 ATGTCACACCCCATTATCGAAGCAAATGGCAGAGTCTATAATCATCATCCATCG
* * *
710901 AGTGGTCCTCCTTGGACATAACATAGTCATGTCCAGTGGCCAACCAACGGACAACATA-ATCATC
1 AGTGGTCCTCCATGGACATAACATAGTCATGTACAATGGCCAACCAACGGACAACATACATCATC
* * *
710965 ATGTCACACCTCATTGTCGAAGCAAATGGCGGAGTCTATAATCATCATCC
66 ATGTCACACCCCATTATCGAAGCAAATGGCAGAGTCTATAATCATCATCC
711015 GAAGTATTCT
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
118 52 0.50
119 51 0.50
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (119 bp):
AGTGGTCCTCCATGGACATAACATAGTCATGTACAATGGCCAACCAACGGACAACATACATCATC
ATGTCACACCCCATTATCGAAGCAAATGGCAGAGTCTATAATCATCATCCATCG
Found at i:712874 original size:27 final size:30
Alignment explanation
Indices: 712820--712875 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 30
712810 GTCAAGTATA
712820 TTTAATTTATGTTGATTAATTTAGTGTTTAT
1 TTTAATTTATGTT-ATTAATTTAGTGTTTAT
712851 TTTAATTT-TGTT-TTAA-TTAGTGTTT
1 TTTAATTTATGTTATTAATTTAGTGTTT
712876 TTCCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 4 0.16
30 4 0.16
31 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.64
Consensus pattern (30 bp):
TTTAATTTATGTTATTAATTTAGTGTTTAT
Found at i:714677 original size:32 final size:32
Alignment explanation
Indices: 714636--714696 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
714626 CATTATGTCA
*
714636 TTATGTGCCAAACTTATGCACAACATCATCAT
1 TTATGTGCCAAACGTATGCACAACATCATCAT
* *
714668 TTATGTGCCATACGTATGCACAATATCAT
1 TTATGTGCCAAACGTATGCACAACATCAT
714697 TTTAACATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (32 bp):
TTATGTGCCAAACGTATGCACAACATCATCAT
Found at i:720341 original size:16 final size:16
Alignment explanation
Indices: 720320--720353 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
720310 TCTTCTAAAT
*
720320 TTGTTTTTATTTGGAC
1 TTGTTTTAATTTGGAC
720336 TTGTTTTAATTTGGAC
1 TTGTTTTAATTTGGAC
720352 TT
1 TT
720354 CCGACTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.62
Consensus pattern (16 bp):
TTGTTTTAATTTGGAC
Found at i:724414 original size:74 final size:74
Alignment explanation
Indices: 724226--724422 Score: 224
Period size: 74 Copynumber: 2.7 Consensus size: 74
724216 GGTCGGTTCA
* ** * *
724226 AAGATAGAGAAGGTTTAATCGACTAAGAAGCATGGTTAGCCAACTAAGAGCTTACTACCAGAGAC
1 AAGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAATTAAGAGCTTACTACCAGAGAC
*
724291 TTCAATTAC
66 TCCAATTAC
* *
724300 AAGACAGAG-AGAACTTAATCGATTGAA-AAGCATGGTTAGTCAATTAAGA-TTTCACTACCAGA
1 AAGACAGAGAAG-ACTTAATCGACT-AAGAAGCATGGTTAGTCAATTAAGAGCTT-ACTACCAGA
724362 GGA-TCCAATTAC
63 -GACTCCAATTAC
* *
724374 AAGACAGAGAAGACTTAATCAACTAAGAAGTATAGG-TAGTCAATTAAGA
1 AAGACAGAGAAGACTTAATCGACTAAGAAGCAT-GGTTAGTCAATTAAGA
724423 ACACTCTATT
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
73 6 0.06
74 91 0.87
75 8 0.08
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (74 bp):
AAGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAATTAAGAGCTTACTACCAGAGAC
TCCAATTAC
Found at i:726903 original size:21 final size:20
Alignment explanation
Indices: 726879--726935 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
726869 TTTGCTGATA
726879 TATTAATTTTAATTATTAATT
1 TATTAATTTTAATTATT-ATT
* * *
726900 TATTGATTTAAAATT-TTCTT
1 TATTAATTT-TAATTATTATT
726920 T-TTAATTTTAATTATT
1 TATTAATTTTAATTATT
726936 TAGATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
20 3 0.10
21 10 0.34
22 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTAATTTTAATTATTATT
Found at i:729197 original size:28 final size:28
Alignment explanation
Indices: 729090--729363 Score: 273
Period size: 29 Copynumber: 9.6 Consensus size: 28
729080 AAAAACTTTT
*
729090 ACATATTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
729118 ACATGTTATGTCTTAATTTAGACAAGAAA
1 ACATGTT-TGTCTTAATTTAGACAAGAAA
* * *
729147 ACAAGTTATTTCTTAATTTAGATAAGAAA
1 ACATGTT-TGTCTTAATTTAGACAAGAAA
* * *
729176 ACATGTTTGTTTTAATTTAGATAAGGAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
729204 ACATGTTTTGTATTAATTTAGACAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAGAAA
*** ** *
729233 ATGGGTTCATCTTAATTTAAAC-AGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
729260 ACATGTTTTGTCTTAATTTAGACATA-AAA
1 ACATG-TTTGTCTTAATTTAGACA-AGAAA
*
729289 ACATGTTTGTCTTAATATAAGACAAGAAA
1 ACATGTTTGTCTTAAT-TTAGACAAGAAA
** * * * *
729318 ACAAATTTATCTCAATTTAGAGAAGATA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
729346 ACATGTTTTTTCTTAATT
1 ACATG-TTTGTCTTAATT
729364 AATGACAAAA
Statistics
Matches: 202, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
27 7 0.03
28 80 0.40
29 114 0.56
30 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:729349 original size:57 final size:57
Alignment explanation
Indices: 729090--729371 Score: 252
Period size: 57 Copynumber: 4.9 Consensus size: 57
729080 AAAAACTTTT
*
729090 ACAT-ATTTGTCTTAATTTAGACAAGAAAACATGTTATGTCTTAATTTAGACAAGAAA
1 ACATAATTTGTCTTAATTTAGACAAGAAAACATGTT-TGTCTTAATTAAGACAAGAAA
* * * * * * *
729147 ACA-AGTTATTTCTTAATTTAGATAAGAAAACATGTTTGTTTTAATTTAGATAAGGAA
1 ACATAATT-TGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTAAGACAAGAAA
** * *** **
729204 ACATGTTTTGTATTAATTTAGACAAGAAAATGGGTTCATCTTAATTTAA-AC-AGAAA
1 ACATAATTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAA-TTAAGACAAGAAA
**
729260 ACATGTTTTGTCTTAATTTAGACATA-AAAACATGTTTGTCTTAATATAAGACAAGAAA
1 ACATAATTTGTCTTAATTTAGACA-AGAAAACATGTTTGTCTTAAT-TAAGACAAGAAA
* * * * *
729318 ACA-AATTTATCTCAATTTAGAGAAGATAACATGTTTTTTCTTAATTAATGACAA
1 ACATAATTTGTCTTAATTTAGACAAGAAAACATG-TTTGTCTTAATTAA-GACAA
729372 AAGTTATCTT
Statistics
Matches: 181, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
55 1 0.01
56 44 0.24
57 82 0.45
58 54 0.30
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (57 bp):
ACATAATTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTAAGACAAGAAA
Found at i:734292 original size:20 final size:20
Alignment explanation
Indices: 734267--734341 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
734257 TTAAGTTGCT
734267 ATCTATCGATAGATATGTCC
1 ATCTATCGATAGATATGTCC
* *
734287 ATCTATCAATAGATATATCC
1 ATCTATCGATAGATATGTCC
* * * * *
734307 TTCTATAGATAAATAGGTCTG
1 ATCTATCGATAGATATGTC-C
*
734328 ATCTATTGATAGAT
1 ATCTATCGATAGAT
734342 GTTGAACATT
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
ATCTATCGATAGATATGTCC
Found at i:735435 original size:31 final size:31
Alignment explanation
Indices: 735398--735467 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
735388 GTAAAAATAC
* *
735398 TCAATTTAGTTTCTATATTATAGAA-TTTTAT
1 TCAATTTAGTTCCTATACTATA-AAGTTTTAT
* *
735429 TTAATTTAGTTCCTATACTATAAAGTTTTGT
1 TCAATTTAGTTCCTATACTATAAAGTTTTAT
735460 TCAATTTA
1 TCAATTTA
735468 ATTCTTGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (31 bp):
TCAATTTAGTTCCTATACTATAAAGTTTTAT
Found at i:736704 original size:19 final size:20
Alignment explanation
Indices: 736670--736707 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
736660 AATTCATAAA
736670 AAAATTAAGTAATATTTTTG
1 AAAATTAAGTAATATTTTTG
736690 AAAATTAAG-AATATTTTT
1 AAAATTAAGTAATATTTTT
736708 AATGTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
AAAATTAAGTAATATTTTTG
Found at i:739200 original size:300 final size:300
Alignment explanation
Indices: 738658--739255 Score: 991
Period size: 300 Copynumber: 2.0 Consensus size: 300
738648 AGGGATGTTT
* * * *
738658 CAAGACTTTCCAGTGAGCCTCACCTGCTAGAGTCAATTAACTCCACTTTTCAAGAAGATGTACTT
1 CAAGACTTTCCAGTAAGCCTCACCTGCTAGAATCAATTAACTCAACTTTTCAAGAAGATATACTT
* *
738723 TTGAATATCAAATCTCAACAAGTACATAGAGAAAACCAGAACCCGAACCCTCTTTCTACTTCGAA
66 TTGAATATCAAATCTCAACAAGTACATAAAGAAAACCAGAACCCCAACCCTCTTTCTACTTCGAA
* *
738788 ACCAATGGAGGAAAGAGGAAACAAGGAGAATGCTGCAGCATATCAACAGTCCATCTTGATGGTGA
131 ACCAATGGAGGAAAGAGGAAACAAAGAGAATGCTGCAGCAGATCAACAGTCCATCTTGATGGTGA
*
738853 ACCTAGATTCTACATGTTCTGATGGATGCAAAGACTATCTCTCTGGAAAGGTTGAGGATGCTGA-
196 ACCTAGATTCTACATGTTCTGATGGATGCAAAGACCATCTCTCTGGAAAGGTTGAGGATGCTGAG
* *
738917 AGACCAGAATCTATCAAGGAAAGACTATGAAAGTGACAATG
261 A-ACCAGAATCGATCAAGGAAAGACTATGAAAGGGACAATG
* *
738958 CAAGACTTTCCAGTAAGCCTTACCTGCTAGAATCAATTAATTCAACTTTTCAAGAAGATATACTT
1 CAAGACTTTCCAGTAAGCCTCACCTGCTAGAATCAATTAACTCAACTTTTCAAGAAGATATACTT
* *
739023 TTGAATATCAAATCTCAACAAGTACATAAAGAAAACCAGACCCCCAAGCCTCTTTCTACTTCGAA
66 TTGAATATCAAATCTCAACAAGTACATAAAGAAAACCAGAACCCCAACCCTCTTTCTACTTCGAA
* **
739088 ACCAATGGAGGAAAGAGGAACCAAAGAGAATGCTGCAGCAGATCAACAGTTGATCTTGATGGTGA
131 ACCAATGGAGGAAAGAGGAAACAAAGAGAATGCTGCAGCAGATCAACAGTCCATCTTGATGGTGA
**
739153 ACCTAGATTCTACATGTTCTGATGGATGTGAAGACCATCTCTCTGGAAAGGTTGAGGATGCTGAG
196 ACCTAGATTCTACATGTTCTGATGGATGCAAAGACCATCTCTCTGGAAAGGTTGAGGATGCTGAG
*
739218 AACGAGAATCGATCAAGGAAAGACTATGAAAGGGACAA
261 AACCAGAATCGATCAAGGAAAGACTATGAAAGGGACAA
739256 CACAAGTTTT
Statistics
Matches: 276, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
300 275 1.00
301 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (300 bp):
CAAGACTTTCCAGTAAGCCTCACCTGCTAGAATCAATTAACTCAACTTTTCAAGAAGATATACTT
TTGAATATCAAATCTCAACAAGTACATAAAGAAAACCAGAACCCCAACCCTCTTTCTACTTCGAA
ACCAATGGAGGAAAGAGGAAACAAAGAGAATGCTGCAGCAGATCAACAGTCCATCTTGATGGTGA
ACCTAGATTCTACATGTTCTGATGGATGCAAAGACCATCTCTCTGGAAAGGTTGAGGATGCTGAG
AACCAGAATCGATCAAGGAAAGACTATGAAAGGGACAATG
Found at i:742123 original size:27 final size:27
Alignment explanation
Indices: 742085--742145 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
742075 AACAATAATA
*
742085 TTTTTTTTTAACATGACGTGTAACATG
1 TTTTTATTTAACATGACGTGTAACATG
742112 TTTTTATTTAACATGACGTGTAACATG
1 TTTTTATTTAACATGACGTGTAACATG
742139 TTTTTAT
1 TTTTTAT
742146 GCATGACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (27 bp):
TTTTTATTTAACATGACGTGTAACATG
Found at i:759154 original size:66 final size:66
Alignment explanation
Indices: 759072--759234 Score: 276
Period size: 66 Copynumber: 2.5 Consensus size: 66
759062 GGTAAACTCT
*
759072 TTAAAC-AAGAAC-TAAAGAAACATAGAAATAAATTGAGAAAAATTATAATACTATATTATGGTA
1 TTAAACAAAG-ACTTAAAGAAACAAAGAAATAAATTGAGAAAAATTATAATACTATATTATGGTA
759135 AA
65 AA
*
759137 TTAAACAAAGATTTAAAGAAACAAAGAAATAAATTGAGAAAAATTATAATACTATATTATGGTAA
1 TTAAACAAAGACTTAAAGAAACAAAGAAATAAATTGAGAAAAATTATAATACTATATTATGGTAA
759202 A
66 A
*
759203 TTAAACAAAGACTTAAAGAAACAAAAAAATAA
1 TTAAACAAAGACTTAAAGAAACAAAGAAATAA
759235 TTACCGAAAT
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
65 7 0.08
66 85 0.92
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.25
Consensus pattern (66 bp):
TTAAACAAAGACTTAAAGAAACAAAGAAATAAATTGAGAAAAATTATAATACTATATTATGGTAA
A
Found at i:759203 original size:33 final size:33
Alignment explanation
Indices: 759100--759204 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
759090 AACATAGAAA
759100 TAAATTGAGAAAAATTATAATACTATATTATGG
1 TAAATTGAGAAAAATTATAATACTATATTATGG
* * * ** **
759133 TAAATT-AAACAAAGATTTAAAGAAAC-A-AAGA-AA
1 TAAATTGAGA-AAA-A-TTATA-ATACTATATTATGG
759166 TAAATTGAGAAAAATTATAATACTATATTATGG
1 TAAATTGAGAAAAATTATAATACTATATTATGG
759199 TAAATT
1 TAAATT
759205 AAACAAAGAC
Statistics
Matches: 50, Mismatches: 14, Indels: 16
0.62 0.17 0.20
Matches are distributed among these distances:
30 3 0.06
31 5 0.10
32 5 0.10
33 24 0.48
34 5 0.10
35 5 0.10
36 3 0.06
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (33 bp):
TAAATTGAGAAAAATTATAATACTATATTATGG
Found at i:762999 original size:16 final size:17
Alignment explanation
Indices: 762974--763019 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
762964 ATATTTTTAG
*
762974 TTTATGATTTT-ATTTT
1 TTTATTATTTTGATTTT
762990 TTTATTATTTTGATTTT
1 TTTATTATTTTGATTTT
763007 TATTCATTATTTT
1 T-TT-ATTATTTT
763020 TTTAACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 6 0.23
18 2 0.08
19 8 0.31
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (17 bp):
TTTATTATTTTGATTTT
Found at i:763015 original size:19 final size:17
Alignment explanation
Indices: 762965--763019 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
762955 TTTTTAAAAA
*
762965 TATTTTTAGTTTATGATTT
1 TATTTTTA--TTATTATTT
762984 TATTTTT-TTATTATTT
1 TATTTTTATTATTATTT
763000 TGATTTTTATTCATTATTT
1 T-ATTTTTATT-ATTATTT
763019 T
1 T
763020 TTTAACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.28
17 6 0.19
18 2 0.06
19 15 0.47
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (17 bp):
TATTTTTATTATTATTT
Found at i:771735 original size:61 final size:61
Alignment explanation
Indices: 771640--771757 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
771630 TAGAGTTTAG
771640 AAGGTATTAATTAATACAATATTAAGAGAAATTTAGATGATATAGAAAAATAACCAATTAC
1 AAGGTATTAATTAATACAATATTAAGAGAAATTTAGATGATATAGAAAAATAACCAATTAC
*
771701 AAGGTATTAATTAATACAATATTAAGAGAAATTTAGATGTTATAGAAAAATAACCAA
1 AAGGTATTAATTAATACAATATTAAGAGAAATTTAGATGATATAGAAAAATAACCAA
771758 ACAGAATGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.30
Consensus pattern (61 bp):
AAGGTATTAATTAATACAATATTAAGAGAAATTTAGATGATATAGAAAAATAACCAATTAC
Found at i:778195 original size:16 final size:16
Alignment explanation
Indices: 778174--778205 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
778164 TGCATCAACT
778174 AATGCCTCAAAAATCA
1 AATGCCTCAAAAATCA
*
778190 AATGCCTTAAAAATCA
1 AATGCCTCAAAAATCA
778206 TTTTCAAAGG
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:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (16 bp):
AATGCCTCAAAAATCA
Found at i:782398 original size:45 final size:45
Alignment explanation
Indices: 782349--782450 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 45
782339 ATACGCCATG
* *
782349 GTTAGGTTGTTACATATCATGTATAAAAACGTGTGACACGCAATA
1 GTTAGGTTGTTACACATCATGTACAAAAACGTGTGACACGCAATA
* * *
782394 GTTAGGTTGTTACACGTCATGTACAAAAACGTGTGACACGCCATG
1 GTTAGGTTGTTACACATCATGTACAAAAACGTGTGACACGCAATA
*
782439 GTTTGGTTGTTA
1 GTTAGGTTGTTA
782451 TACACTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (45 bp):
GTTAGGTTGTTACACATCATGTACAAAAACGTGTGACACGCAATA
Found at i:782467 original size:45 final size:46
Alignment explanation
Indices: 782341--782460 Score: 149
Period size: 45 Copynumber: 2.7 Consensus size: 46
782331 AACATGTTAT
* * *
782341 ACGCCATGGTTAGGTTGTTACATA-TCATGTATAAAAACGTGTGAC
1 ACGCCATGGTTAGGTTGTTATACACTCATGTACAAAAACGTGTGAC
* *
782386 ACGCAATAGTTAGGTTG-T-TACACGTCATGTACAAAAACGTGTGAC
1 ACGCCATGGTTAGGTTGTTATACAC-TCATGTACAAAAACGTGTGAC
*
782431 ACGCCATGGTTTGGTTGTTATACACT-ATGT
1 ACGCCATGGTTAGGTTGTTATACACTCATGT
782461 TAAAAAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 2 0.03
44 1 0.02
45 53 0.84
46 2 0.03
47 5 0.08
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (46 bp):
ACGCCATGGTTAGGTTGTTATACACTCATGTACAAAAACGTGTGAC
Found at i:782593 original size:24 final size:23
Alignment explanation
Indices: 782556--782628 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
782546 AAAAAATACT
*
782556 ATTGTTACATGCCATGTACAAAA
1 ATTGTTACACGCCATGTACAAAA
*
782579 ATATGTTACACGCCATGGTTAAAAAA
1 AT-TGTTACACGCCAT-G-TACAAAA
* * *
782605 ATTATTACACGCCATATTCAAAA
1 ATTGTTACACGCCATGTACAAAA
782628 A
1 A
782629 CATTTTGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 13 0.32
26 8 0.20
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (23 bp):
ATTGTTACACGCCATGTACAAAA
Found at i:783976 original size:18 final size:19
Alignment explanation
Indices: 783950--783990 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
783940 TAAGTCCAAG
*
783950 AAAAGAAAAAG-ATAAGGA
1 AAAAAAAAAAGAATAAGGA
783968 AAAAAAAAAAGAAATAAGGA
1 AAAAAAAAAAG-AATAAGGA
783988 AAA
1 AAA
783991 GAGGGAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAGAATAAGGA
Found at i:788752 original size:20 final size:20
Alignment explanation
Indices: 788706--788745 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
788696 ATTTAAGTCT
788706 TTTTAGTCTTCAAAATAGATA
1 TTTT-GTCTTCAAAATAGATA
788727 TTTTGTCTT-AAAATA-ATA
1 TTTTGTCTTCAAAATAGATA
788745 T
1 T
788746 AATTTGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 5 0.26
21 4 0.21
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTGTCTTCAAAATAGATA
Found at i:788913 original size:19 final size:20
Alignment explanation
Indices: 788877--788915 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
788867 ATGACTATAA
*
788877 TATTTAAAAAAACCTTCAAAC
1 TATTCAAAAAAA-CTTCAAAC
788898 TATTCAAAAAAA-TTCAAA
1 TATTCAAAAAAACTTCAAA
788916 TAAACTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
TATTCAAAAAAACTTCAAAC
Found at i:788985 original size:30 final size:30
Alignment explanation
Indices: 788951--789007 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
788941 CAATTAAATC
788951 TTTATATTTGTATTTTAAACTAAATAAGTT
1 TTTATATTTGTATTTTAAACTAAATAAGTT
* *
788981 TTTATATTTTTATTTTAAATTAAATAA
1 TTTATATTTGTATTTTAAACTAAATAA
789008 ACTCTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTATATTTGTATTTTAAACTAAATAAGTT
Found at i:789016 original size:30 final size:30
Alignment explanation
Indices: 788907--789016 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
788897 CTATTCAAAA
*
788907 AAATTCAAATAAACTCTTATACTTTTATTGCGTT
1 AAATT-AAATAAACTCTTATATTTTTATT---TT
* *
788941 CAATTAAAT---CT-TTATATTTGTATTTT
1 AAATTAAATAAACTCTTATATTTTTATTTT
* ** *
788967 AAACTAAATAAGTTTTTATATTTTTATTTT
1 AAATTAAATAAACTCTTATATTTTTATTTT
788997 AAATTAAATAAACTCTTATA
1 AAATTAAATAAACTCTTATA
789017 ACTACTTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
26 9 0.15
29 12 0.20
30 32 0.52
33 4 0.07
34 4 0.07
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (30 bp):
AAATTAAATAAACTCTTATATTTTTATTTT
Found at i:793902 original size:33 final size:34
Alignment explanation
Indices: 793863--793934 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
793853 AAATTTAAAT
*
793863 TTAAATAA-T-TAAAAAAAAATCTCAAATATCAAC
1 TTAAATAACTATAAAAAAAAATC-CAAATAACAAC
* *
793896 TTAAATAACTATAAACAAATATCCAAATAACAAC
1 TTAAATAACTATAAAAAAAAATCCAAATAACAAC
793930 TTAAA
1 TTAAA
793935 CAACATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (34 bp):
TTAAATAACTATAAAAAAAAATCCAAATAACAAC
Done.