Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 5 of 24
Found at i:605097 original size:18 final size:18
Alignment explanation
Indices: 605044--605101 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
605034 GATGATAATG
605044 ATATTGAATATTTTAAA-A
1 ATATTGAATA-TTTAAATA
* * *
605062 TTAATAAATA-TTATAATA
1 ATATTGAATATTTA-AATA
605080 ATATTGAATATTTAAAT-
1 ATATTGAATATTTAAATA
605097 ATATT
1 ATATT
605102 AAAAATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 18 0.58
19 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTGAATATTTAAATA
Found at i:613355 original size:21 final size:21
Alignment explanation
Indices: 613324--613375 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
613314 ATAATTTTGT
613324 AGTTTTTAAATAAT-TTTTAA
1 AGTTTTTAAATAATATTTTAA
*
613344 AGTTTTTGAAATTATATTTTAA
1 AGTTTTT-AAATAATATTTTAA
**
613366 TTTTTTTAAA
1 AGTTTTTAAA
613376 ATATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
AGTTTTTAAATAATATTTTAA
Found at i:613427 original size:19 final size:19
Alignment explanation
Indices: 613401--613441 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
613391 ATATTTTGAA
613401 TATATATTAAAATATAATTTT
1 TATAT-TTAAAA-ATAATTTT
*
613422 TATATTTTAAAATAATTTT
1 TATATTTAAAAATAATTTT
613441 T
1 T
613442 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTTAAAAATAATTTT
Found at i:613450 original size:21 final size:21
Alignment explanation
Indices: 613401--613448 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
613391 ATATTTTGAA
*
613401 TATATATTAAAATATAATTTT
1 TATATTTTAAAATATAATTTT
*
613422 TATATTTTAAAATA-ATTTTT
1 TATATTTTAAAATATAATTTT
613442 TA-ATTTT
1 TATATTTT
613449 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTTAAAATATAATTTT
Found at i:613482 original size:23 final size:25
Alignment explanation
Indices: 613442--613488 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
613432 AATAATTTTT
*
613442 TAATTTTTTTATAAAAATTCATATAC
1 TAATTTTTTTAT-AAAATTAATATAC
613468 TAATTTTTTT-T-AAATTAATAT
1 TAATTTTTTTATAAAATTAATAT
613489 TGCTACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
25 1 0.05
26 10 0.50
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTTTTTTATAAAATTAATATAC
Found at i:613740 original size:8 final size:8
Alignment explanation
Indices: 613718--613751 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
613708 ATTCACTACT
*
613718 TATTTAAA
1 TATTTTAA
613726 TATTTTTAA
1 TA-TTTTAA
613735 TATTTTAA
1 TATTTTAA
613743 TATTTTAA
1 TATTTTAA
613751 T
1 T
613752 TAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:614151 original size:9 final size:9
Alignment explanation
Indices: 614131--614165 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
614121 TTTTTTTTTC
614131 CCTTTCCTTT
1 CCTTT-CTTT
614141 CCTTTCTTT
1 CCTTTCTTT
614150 CCTTTCTTT
1 CCTTTCTTT
*
614159 CTTTTCT
1 CCTTTCT
614166 CGTCTCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:614164 original size:14 final size:14
Alignment explanation
Indices: 614132--614162 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
614122 TTTTTTTTCC
614132 CTTTCCTTTCCTTT
1 CTTTCCTTTCCTTT
614146 CTTTCCTTT-CTTT
1 CTTTCCTTTCCTTT
614159 CTTT
1 CTTT
614163 TCTCGTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
CTTTCCTTTCCTTT
Found at i:614164 original size:34 final size:34
Alignment explanation
Indices: 614092--614164 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
614082 TCCCATTTTT
* * *
614092 TTTTCTCTTTCCTCTCTTCTTTCACTTTTTTTTT
1 TTTTCCCTTTCCTCTCTTCTTTCACTTTTCTTTC
*
614126 TTTTCCCTTTCCTTTCCTTTCTTTC-C-TTTCTTTC
1 TTTTCCCTTTCCTCT-C-TTCTTTCACTTTTCTTTC
614160 TTTTC
1 TTTTC
614165 TCGTCTCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 24 0.73
35 2 0.06
36 7 0.21
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (34 bp):
TTTTCCCTTTCCTCTCTTCTTTCACTTTTCTTTC
Found at i:614268 original size:13 final size:13
Alignment explanation
Indices: 614250--614274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614240 TTCCATTCGT
614250 TTTCTTTCTTCTC
1 TTTCTTTCTTCTC
614263 TTTCTTTCTTCT
1 TTTCTTTCTTCT
614275 TGCTTTGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCTTCTC
Found at i:614478 original size:2 final size:2
Alignment explanation
Indices: 614471--614501 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
614461 CTCAAGTGAA
614471 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
614502 GATTTAATGT
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:615944 original size:11 final size:11
Alignment explanation
Indices: 615928--615964 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
615918 TTATAATATC
615928 AAATATATTTA
1 AAATATATTTA
615939 AAATATATTTA
1 AAATATATTTA
* *
615950 AAATAGATATA
1 AAATATATTTA
615961 AAAT
1 AAAT
615965 TCCAACGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAATATATTTA
Found at i:616781 original size:118 final size:117
Alignment explanation
Indices: 616586--616819 Score: 299
Period size: 118 Copynumber: 2.0 Consensus size: 117
616576 AACTTAATCT
* *
616586 TGATTTTAGATGAGTAATTTTATCTATTACTACTTTATCTTGATTTTAGATGAATAAAAAAATCA
1 TGATTTTAGATGAGCAATTTTAACTATTACTACTTTATCTTGATTTTAGATGAATAAAAAAATCA
* * *
616651 AAAGATTGATAATAGATAATTTAAAAAAAAATTAATTTGAAATTTTTTGAATTA
66 AAAGATTAATAATAGATAATCT-AAAAAAAATTAATTTGAAAATTTTT-AATTA
* * * ** **
616705 TGATTTTATATGTGCAATTTTAACTATTATTGGTTTATC-TGATTTTAGATGGTTAAAAAAATCA
1 TGATTTTAGATGAGCAATTTTAACTATTACTACTTTATCTTGATTTTAGATGAATAAAAAAATCA
* * * *
616769 AAAGATTAATAATAGTTTATCTAAAAAGATTTAATTTGAAAATTTTTAATT
66 AAAGATTAATAATAGATAATCTAAAAAAAATTAATTTGAAAATTTTTAATT
616820 TTGAATAATC
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
116 4 0.04
117 22 0.22
118 41 0.41
119 32 0.32
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (117 bp):
TGATTTTAGATGAGCAATTTTAACTATTACTACTTTATCTTGATTTTAGATGAATAAAAAAATCA
AAAGATTAATAATAGATAATCTAAAAAAAATTAATTTGAAAATTTTTAATTA
Found at i:618671 original size:2 final size:2
Alignment explanation
Indices: 618664--618702 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
618654 TATGTGTAAA
*
618664 AT AT AT AT AT AT AG 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 AT AT AT AT A
618703 AATTTATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:619534 original size:17 final size:18
Alignment explanation
Indices: 619512--619557 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
619502 TTTCAAAAGA
619512 AATTTGTTAAAT-AACAT
1 AATTTGTTAAATAAACAT
* *
619529 AATTTGCT-AATAAATAT
1 AATTTGTTAAATAAACAT
*
619546 AAATTGTTAAAT
1 AATTTGTTAAAT
619558 TTTTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (18 bp):
AATTTGTTAAATAAACAT
Found at i:620528 original size:19 final size:19
Alignment explanation
Indices: 620506--620543 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
620496 TATATATAAT
620506 ATTATAAAAA-ATTTCATTA
1 ATTATAAAAATA-TTCATTA
620525 ATTATAAAAATATTCATTA
1 ATTATAAAAATATTCATTA
620544 TGTAATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAAAATATTCATTA
Found at i:620621 original size:16 final size:16
Alignment explanation
Indices: 620602--620654 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
620592 TAATTGTTAA
*
620602 ATTTATAAGTAATTAT
1 ATTTATAAGTTATTAT
* *
620618 ATTTA-ATATTTATTAA
1 ATTTATA-AGTTATTAT
620634 ATTTATAAGTTATTAT
1 ATTTATAAGTTATTAT
620650 ATTTA
1 ATTTA
620655 ATATTTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTTATAAGTTATTAT
Found at i:620623 original size:32 final size:32
Alignment explanation
Indices: 620587--620666 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
620577 GCTGTAACTT
* *
620587 TTTAATAATTGTTAAATTTATAAGTAATTATA
1 TTTAATATTTATTAAATTTATAAGTAATTATA
*
620619 TTTAATATTTATTAAATTTATAAGTTATTATA
1 TTTAATATTTATTAAATTTATAAGTAATTATA
620651 TTTAATATTTATTAAA
1 TTTAATATTTATTAAA
620667 ATTAAGATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (32 bp):
TTTAATATTTATTAAATTTATAAGTAATTATA
Found at i:620662 original size:16 final size:16
Alignment explanation
Indices: 620613--620664 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
620603 TTTATAAGTA
620613 ATTATATTTAATATTT
1 ATTATATTTAATATTT
* *
620629 ATTAAATTT-ATAAGTT
1 ATTATATTTAAT-ATTT
620645 ATTATATTTAATATTT
1 ATTATATTTAATATTT
620661 ATTA
1 ATTA
620665 AAATTAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTATATTTAATATTT
Found at i:620671 original size:16 final size:16
Alignment explanation
Indices: 620620--620671 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
620610 GTAATTATAT
620620 TTAATATTTATT-AAA
1 TTAATATTTATTAAAA
* * * *
620635 TTTATAAGTTATTATAT
1 TTAAT-ATTTATTAAAA
620652 TTAATATTTATTAAAA
1 TTAATATTTATTAAAA
620668 TTAA
1 TTAA
620672 GATCAATATC
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAATATTTATTAAAA
Found at i:621389 original size:22 final size:23
Alignment explanation
Indices: 621356--621408 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
621346 TATGTAACTT
*
621356 TAAATCTTAA-TTATTTAAAA-AA
1 TAAAT-TTAATTTATTCAAAATAA
*
621378 TAAATTTCAATTTATTCAAAATAT
1 TAAATTT-AATTTATTCAAAATAA
621402 TAAATTT
1 TAAATTT
621409 TAAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 7 0.27
23 9 0.35
24 8 0.31
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTTAATTTATTCAAAATAA
Found at i:621445 original size:8 final size:8
Alignment explanation
Indices: 621432--621458 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
621422 CTTTCAAATA
621432 AAAATTTT
1 AAAATTTT
621440 AAAATTTT
1 AAAATTTT
621448 AAAATTTT
1 AAAATTTT
621456 AAA
1 AAA
621459 TTTAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:622443 original size:23 final size:23
Alignment explanation
Indices: 622374--622444 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
622364 GGAGATTGTT
622374 TTGTTTGCTCAATATGGTTTATG
1 TTGTTTGCTCAATATGGTTTATG
* * * * *
622397 TTG--TCCACAA-A-GCTATTTTT
1 TTGTTTGCTCAATATGGT-TTATG
622417 TTGTTTGCTCAATATGGTTTATG
1 TTGTTTGCTCAATATGGTTTATG
622440 TTGTT
1 TTGTT
622445 CACAAAGCTG
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 2 0.06
20 7 0.21
21 5 0.15
22 5 0.15
23 12 0.36
24 2 0.06
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (23 bp):
TTGTTTGCTCAATATGGTTTATG
Found at i:622469 original size:48 final size:43
Alignment explanation
Indices: 622372--622453 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
622362 ATGGAGATTG
622372 TTTTGTTTGCTCAATATGGTTTATGTTGTCCACAAAGCTATTT
1 TTTTGTTTGCTCAATATGGTTTATGTTGTCCACAAAGCTATTT
*
622415 TTTTGTTTGCTCAATATGGTTTATGTTGTTCACAAAGCT
1 TTTTGTTTGCTCAATATGGTTTATGTTGTCCACAAAGCT
622454 GACTTACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (43 bp):
TTTTGTTTGCTCAATATGGTTTATGTTGTCCACAAAGCTATTT
Found at i:626438 original size:30 final size:30
Alignment explanation
Indices: 626373--626441 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
626363 AGCTAATAAT
* ** * *
626373 ATTTCATTTGTATTTAAATAAATTTTTGAT
1 ATTTAATTTGTATCAAAATAAATTTTTAAC
*
626403 TTTTAATTTGTATCAAAATAAATTTTTAAC
1 ATTTAATTTGTATCAAAATAAATTTTTAAC
626433 ATTTAATTT
1 ATTTAATTT
626442 ATGCTTAAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (30 bp):
ATTTAATTTGTATCAAAATAAATTTTTAAC
Found at i:628050 original size:10 final size:11
Alignment explanation
Indices: 628032--628102 Score: 55
Period size: 10 Copynumber: 6.8 Consensus size: 11
628022 AAATTATATA
628032 AAATATAAAAT
1 AAATATAAAAT
*
628043 AAAT-TAAAAC
1 AAATATAAAAT
628053 ACAATATAAACAT
1 A-AATATAAA-AT
628066 -AATAT-AAA-
1 AAATATAAAAT
*
628074 AAATA-ATAAT
1 AAATATAAAAT
*
628084 AAATA-AAAAA
1 AAATATAAAAT
628094 AAATATAAA
1 AAATATAAA
628103 CATGCATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
9 7 0.15
10 21 0.44
11 15 0.31
12 4 0.08
13 1 0.02
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:628079 original size:12 final size:12
Alignment explanation
Indices: 628033--628086 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
628023 AATTATATAA
*
628033 AATATAAAATA-
1 AATATAAAACAT
*
628044 AAT-TAAAACAC
1 AATATAAAACAT
628055 AATAT-AAACAT
1 AATATAAAACAT
*
628066 AATATAAAAAAT
1 AATATAAAACAT
628078 AATAATAAA
1 AAT-ATAAA
628087 TAAAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.17
11 16 0.44
12 9 0.25
13 5 0.14
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
AATATAAAACAT
Found at i:628091 original size:40 final size:40
Alignment explanation
Indices: 628027--628105 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
628017 ATTATAAATT
* * *
628027 ATATAAAATATAAAATAAATTAAAACACAATATAAACATA
1 ATATAAAAAATAAAATAAATTAAAAAAAAATATAAACATA
628067 ATATAAAAAATAATAATAAA-TAAAAAAAAATATAAACAT
1 ATATAAAAAATAA-AATAAATTAAAAAAAAATATAAACAT
628106 GCATCAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (40 bp):
ATATAAAAAATAAAATAAATTAAAAAAAAATATAAACATA
Found at i:635644 original size:30 final size:30
Alignment explanation
Indices: 635608--635666 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
635598 AAATACTCAT
635608 TCTTAAGATTTATGTCCGACATGTAATTAA
1 TCTTAAGATTTATGTCCGACATGTAATTAA
635638 TCTTAAGATTTATGTCCGACATGTAATTA
1 TCTTAAGATTTATGTCCGACATGTAATTA
635667 GACGTGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (30 bp):
TCTTAAGATTTATGTCCGACATGTAATTAA
Found at i:639784 original size:3 final size:3
Alignment explanation
Indices: 639776--639820 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
639766 ATCCTTCGTA
* *
639776 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
639821 GTGAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:642312 original size:15 final size:16
Alignment explanation
Indices: 642282--642318 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
642272 TTTCAAATAT
642282 ATAAAAAACTTAAAAA
1 ATAAAAAACTTAAAAA
642298 ATAAAAAACTT-AAAA
1 ATAAAAAACTTAAAAA
642313 ATAAAA
1 ATAAAA
642319 TTGGGTGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
ATAAAAAACTTAAAAA
Found at i:643207 original size:15 final size:15
Alignment explanation
Indices: 643189--643495 Score: 95
Period size: 15 Copynumber: 20.9 Consensus size: 15
643179 ACTTTTTAGT
643189 ACAAGTACTTTTGGC
1 ACAAGTACTTTTGGC
*
643204 ACAAGAAC-TTTGGC
1 ACAAGTACTTTTGGC
* *
643218 ATAAGCACTTTTGGC
1 ACAAGTACTTTTGGC
* * *
643233 ATAGGTACCTTTGGC
1 ACAAGTACTTTTGGC
* *
643248 ATATGTAC-TTTGGC
1 ACAAGTACTTTTGGC
** *
643262 -CTAAGTTTTTTTAGC
1 AC-AAGTACTTTTGGC
* * **
643277 -CTAAATACCTTTGAT
1 AC-AAGTACTTTTGGC
*
643292 AC-AGATACTTTTGAC
1 ACAAG-TACTTTTGGC
* *
643307 CCAGGTAAC-TTTGGC
1 ACAAGT-ACTTTTGGC
* * *
643322 ATAGGTAC-CTTGGC
1 ACAAGTACTTTTGGC
* **
643336 A-ATAGCACTTTTATC
1 ACA-AGTACTTTTGGC
*
643351 ACAGGTA-TTTTGGC
1 ACAAGTACTTTTGGC
*
643365 A-ATGATACTTTTGGC
1 ACAAG-TACTTTTGGC
* *
643380 CCAAATAC-TTTGGC
1 ACAAGTACTTTTGGC
* *
643394 ATAAGTATTTTTGGTC
1 ACAAGTACTTTTGG-C
*
643410 -CAGGTAAC-TTTGGC
1 ACAAGT-ACTTTTGGC
* *
643424 ACAAATACTTTTGAC
1 ACAAGTACTTTTGGC
643439 ACAAGTA-TTTTGGC
1 ACAAGTACTTTTGGC
**
643453 ACAAGTACTTTTAAC
1 ACAAGTACTTTTGGC
* *
643468 ACAGGTGC-TTTGGC
1 ACAAGTACTTTTGGC
*
643482 ACAAATACTTTTGG
1 ACAAGTACTTTTGG
643496 TAGAGATAGT
Statistics
Matches: 210, Mismatches: 62, Indels: 40
0.67 0.20 0.13
Matches are distributed among these distances:
13 3 0.01
14 76 0.36
15 123 0.59
16 8 0.04
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
ACAAGTACTTTTGGC
Found at i:643454 original size:29 final size:29
Alignment explanation
Indices: 643416--643494 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
643406 GGTCCAGGTA
643416 ACTTTGGCACAAATACTTTTGACACAAGT
1 ACTTTGGCACAAATACTTTTGACACAAGT
* * * *
643445 ATTTTGGCACAAGTACTTTTAACACAGGT
1 ACTTTGGCACAAATACTTTTGACACAAGT
*
643474 GCTTTGGCACAAATACTTTTG
1 ACTTTGGCACAAATACTTTTG
643495 GTAGAGATAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (29 bp):
ACTTTGGCACAAATACTTTTGACACAAGT
Found at i:644065 original size:16 final size:16
Alignment explanation
Indices: 644044--644077 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
644034 AACCGCCTGC
644044 CACTACACTTACTTTT
1 CACTACACTTACTTTT
*
644060 CACTACACTTATTTTT
1 CACTACACTTACTTTT
644076 CA
1 CA
644078 GGGTCTGCTC
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:0.26, C:0.29, G:0.00, T:0.44
Consensus pattern (16 bp):
CACTACACTTACTTTT
Found at i:645541 original size:2 final size:2
Alignment explanation
Indices: 645534--645564 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
645524 AGGTAACTAC
645534 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
645565 AACGGAAAAG
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:659597 original size:2 final size:2
Alignment explanation
Indices: 659590--659625 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
659580 AAATTTGAGG
659590 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
659626 TATGTTGAGA
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:661383 original size:21 final size:21
Alignment explanation
Indices: 661345--661388 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
661335 TATAAAAAAT
661345 TAAAAAAATTATCAAATTTAAA
1 TAAAAAAATTAT-AAATTTAAA
661367 TAAAAAAATTA-ATAATTTAAA
1 TAAAAAAATTATA-AATTTAAA
661388 T
1 T
661389 TTATCAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.05
21 9 0.43
22 11 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAAATTATAAATTTAAA
Found at i:663021 original size:2 final size:2
Alignment explanation
Indices: 663014--663053 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
663004 TTGTCAAGTG
663014 TA TA TA TA TA TA 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 TA TA TA TA TA TA
663054 AATCGAAAAG
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):
TA
Found at i:664202 original size:4 final size:4
Alignment explanation
Indices: 664193--664219 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
664183 GTTTGAAAAT
664193 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
664220 TACTCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:668569 original size:15 final size:14
Alignment explanation
Indices: 668536--668587 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
668526 ATATTTAATA
* *
668536 TTTAATTTAAAAAT
1 TTTAATATAAAATT
* *
668550 ATTAATATAAATTAT
1 TTTAATATAAAAT-T
668565 TTTAATAATAAAATT
1 TTTAAT-ATAAAATT
668580 TTTAATAT
1 TTTAATAT
668588 TTATATTCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 11 0.37
15 13 0.43
16 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATATAAAATT
Found at i:668819 original size:21 final size:20
Alignment explanation
Indices: 668778--668823 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
668768 ATACTATATA
*
668778 AATATATAAAATAAAATTTT
1 AATATAAAAAATAAAATTTT
*
668798 AATATAAAAAATTAATATTTT
1 AATATAAAAAA-TAAAATTTT
668819 AATAT
1 AATAT
668824 TATAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAAAAAATAAAATTTT
Found at i:670191 original size:19 final size:19
Alignment explanation
Indices: 670169--670249 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
670159 AACTTAACCC
670169 ATAAATAAATTTATATAAT
1 ATAAATAAATTTATATAAT
*
670188 AT-AA-AAATTAATATAAAT
1 ATAAATAAATTTATAT-AAT
* * *
670206 ATATTATTAATATATA-AAT
1 ATA-AATAAATTTATATAAT
*
670225 AT-ATTATAATTTATATAAT
1 ATAAATA-AATTTATATAAT
670244 ATAAAT
1 ATAAAT
670250 TATTAACTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 13
0.66 0.15 0.19
Matches are distributed among these distances:
17 10 0.22
18 14 0.31
19 12 0.27
20 3 0.07
21 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAATAAATTTATATAAT
Found at i:670201 original size:17 final size:18
Alignment explanation
Indices: 670175--670208 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
670165 ACCCATAAAT
*
670175 AAATTTATAT-AATATAA
1 AAATTAATATAAATATAA
670192 AAATTAATATAAATATA
1 AAATTAATATAAATATA
670209 TTATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTAATATAAATATAA
Found at i:670204 original size:31 final size:30
Alignment explanation
Indices: 670172--670273 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
670162 TTAACCCATA
670172 AATAAATTTATATAATATAAAAATTAATAT
1 AATAAATTTATATAATATAAAAATTAATAT
* *
670202 AA-ATATATTAT-TAATATATAAA-T-ATAT
1 AATAAAT-TTATATAATATAAAAATTAATAT
* *
670229 TAT-AATTTATATAATATAAATTATTAACTAT
1 AATAAATTTATATAATATAAA-AATTAA-TAT
*
670260 TA-AAATTTATATAA
1 AATAAATTTATATAA
670274 AATATATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.07
27 15 0.26
28 2 0.03
29 14 0.24
30 7 0.12
31 16 0.28
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AATAAATTTATATAATATAAAAATTAATAT
Found at i:670214 original size:17 final size:19
Alignment explanation
Indices: 670198--670246 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
670188 ATAAAAATTA
670198 ATATAAATATATTATTAAT
1 ATATAAATATATTATTAAT
670217 ATATAAATATATTA-TAAT
1 ATATAAATATATTATTAAT
*
670235 TTATATAATATA
1 ATATA-AATATA
670247 AATTATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAAATATATTATTAAT
Found at i:670245 original size:25 final size:22
Alignment explanation
Indices: 670196--670254 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 22
670186 ATATAAAAAT
670196 TAATATAAATATA-T-TATTAA
1 TAATATAAATATATTATATTAA
670216 T-ATATAAATATATTATAATTTATA
1 TAATATAAATATATTAT-A-TTA-A
670240 TAATATAAAT-TATTA
1 TAATATAAATATATTA
670255 ACTATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 11 0.33
20 2 0.06
21 1 0.03
22 1 0.03
23 3 0.09
24 7 0.21
25 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATAAATATATTATATTAA
Found at i:670273 original size:40 final size:40
Alignment explanation
Indices: 670193--670270 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
670183 ATAATATAAA
* *
670193 AATTAATATAA-ATATATTATTAATATATAAATATATTAT
1 AATTTATATAATATAAATTATTAATATATAAATATATTAT
670232 AATTTATATAATATAAATTATTAACTAT-TAAA-AT-TTAT
1 AATTTATATAATATAAATTATTAA-TATATAAATATATTAT
670270 A
1 A
670271 TAAAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 5 0.14
39 12 0.34
40 15 0.43
41 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (40 bp):
AATTTATATAATATAAATTATTAATATATAAATATATTAT
Found at i:670280 original size:40 final size:40
Alignment explanation
Indices: 670198--670283 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
670188 ATAAAAATTA
* **
670198 ATATAA-ATATATTATTAATATATAAATATATTATAATTT
1 ATATAATATAAATTATTAATATATAAATATATTATAAAAT
*
670237 ATATAATATAAATTATTAACTAT-TAAA-ATTTATATAAAAT
1 ATATAATATAAATTATTAA-TATATAAATATAT-TATAAAAT
670277 ATATAAT
1 ATATAAT
670284 CAAGTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 9 0.22
40 28 0.70
41 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (40 bp):
ATATAATATAAATTATTAATATATAAATATATTATAAAAT
Found at i:670893 original size:9 final size:9
Alignment explanation
Indices: 670879--670910 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
670869 TTAAATATTT
670879 AATAAATTA
1 AATAAATTA
670888 AATAAATTA
1 AATAAATTA
670897 AATAAATTTA
1 AATAAA-TTA
670907 AATA
1 AATA
670911 TAAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAAATTA
Found at i:678596 original size:6 final size:6
Alignment explanation
Indices: 678587--678618 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
678577 ATTTTTTTTG
*
678587 AAATTA AAATTA AAATTA ATATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
678619 GATAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:678786 original size:34 final size:34
Alignment explanation
Indices: 678748--678875 Score: 112
Period size: 34 Copynumber: 3.9 Consensus size: 34
678738 AAAATACTTC
678748 TTCATTGAAGCTTTAATTTTAAATGAAAAACTCT
1 TTCATTGAAGCTTTAATTTTAAATGAAAAACTCT
* **
678782 TTCATCGAAGC-TTAA-AAT-AA--AAAAACTCCT
1 TTCATTGAAGCTTTAATTTTAAATGAAAAACT-CT
*
678812 TTGC-TT-AAG-TTTCAACTTTAAAATGAAAAACTC-
1 TT-CATTGAAGCTTT-AA-TTTTAAATGAAAAACTCT
678845 TTCGATTGAAGCTTTAATTTTAAATGAAAAA
1 TTC-ATTGAAGCTTTAATTTTAAATGAAAAA
678876 GAAAACTCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 26
0.68 0.07 0.24
Matches are distributed among these distances:
29 12 0.16
30 7 0.10
31 3 0.04
32 2 0.03
33 8 0.11
34 26 0.36
35 12 0.16
36 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36
Consensus pattern (34 bp):
TTCATTGAAGCTTTAATTTTAAATGAAAAACTCT
Found at i:678966 original size:34 final size:34
Alignment explanation
Indices: 678897--679043 Score: 86
Period size: 34 Copynumber: 4.3 Consensus size: 34
678887 TATTAAGGCT
*** *
678897 TCAACTTTAAACGGAAAACTCCTCCATTGAAGCA
1 TCAACTTTAAATAAAAAACTCCTCCACTGAAGCA
* *
678931 TCAATTTTAAATAAAAAACTCCTTCACT-AAGGCA
1 TCAACTTTAAATAAAAAACTCCTCCACTGAA-GCA
* * * *
678965 TCGACTTTAAATTAAAAATTCTTCCA-TCG-AG-A
1 TCAACTTTAAATAAAAAACTCCTCCACT-GAAGCA
* * ** * *
678997 TTTCAACTTTAAATGAAAAACTCTTCTTCTAAAGCT
1 --TCAACTTTAAATAAAAAACTCCTCCACTGAAGCA
679033 TCAACTTTAAA
1 TCAACTTTAAA
679044 AATGAAAAGC
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
32 1 0.01
33 4 0.05
34 78 0.91
35 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.32
Consensus pattern (34 bp):
TCAACTTTAAATAAAAAACTCCTCCACTGAAGCA
Found at i:680721 original size:13 final size:13
Alignment explanation
Indices: 680699--680731 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
680689 TACCTATCTT
680699 TTCA-TTTTTTTC
1 TTCATTTTTTTTC
*
680711 TTCATTTTTTTTG
1 TTCATTTTTTTTC
680724 TTCATTTT
1 TTCATTTT
680732 CCATTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (13 bp):
TTCATTTTTTTTC
Found at i:685375 original size:20 final size:20
Alignment explanation
Indices: 685350--685392 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
685340 ACACTATTTT
*
685350 TTTCAAATAAAAACATGTCA
1 TTTCAAAGAAAAACATGTCA
* *
685370 TTTCAAGGAAAAACATGTGA
1 TTTCAAAGAAAAACATGTCA
685390 TTT
1 TTT
685393 ATCATAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TTTCAAAGAAAAACATGTCA
Found at i:685411 original size:19 final size:19
Alignment explanation
Indices: 685387--685424 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
685377 GAAAAACATG
685387 TGATTTATCATAACATTCT
1 TGATTTATCATAACATTCT
685406 TGATTTATCATAACATTCT
1 TGATTTATCATAACATTCT
685425 ATCTTATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
TGATTTATCATAACATTCT
Found at i:686021 original size:9 final size:9
Alignment explanation
Indices: 686007--686031 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
685997 TGAAAGATTC
686007 TAAATTTAT
1 TAAATTTAT
686016 TAAATTTAT
1 TAAATTTAT
686025 TAAATTT
1 TAAATTT
686032 TTATACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAAATTTAT
Found at i:687515 original size:20 final size:20
Alignment explanation
Indices: 687492--687534 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
687482 TTCTTCTTAC
687492 TTTTTTCTATTTTTTTAAAT
1 TTTTTTCTATTTTTTTAAAT
*
687512 TTTTTTCTTTTTTTTTAAAT
1 TTTTTTCTATTTTTTTAAAT
687532 TTT
1 TTT
687535 GATTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTATTTTTTTAAAT
Found at i:690311 original size:17 final size:16
Alignment explanation
Indices: 690279--690316 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
690269 ATTATATAAA
690279 TATATATTTTTAATAT
1 TATATATTTTTAATAT
690295 T-TATATATTTTATATAT
1 TATATAT-TTTTA-ATAT
690312 TATAT
1 TATAT
690317 TCTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 5 0.26
18 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATATTTTTAATAT
Found at i:690630 original size:25 final size:26
Alignment explanation
Indices: 690602--690650 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
690592 TTGGTAGTTT
*
690602 ATTATATTTA-TAAATAAT-TATTTTA
1 ATTA-ATTTATTAAAAAATATATTTTA
690627 ATTAATTTATTAAAAAATATATTT
1 ATTAATTTATTAAAAAATATATTT
690651 GAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 11 0.52
26 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAATTTATTAAAAAATATATTTTA
Found at i:691982 original size:9 final size:10
Alignment explanation
Indices: 691961--691985 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
691951 AGTATATATA
691961 TTTAAATTTT
1 TTTAAATTTT
691971 TTTAAATTTT
1 TTTAAATTTT
691981 TTTAA
1 TTTAA
691986 TATATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTAAATTTT
Found at i:695254 original size:18 final size:17
Alignment explanation
Indices: 695231--695267 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
695221 TACTCTAACT
695231 ATTATTTAATTAATAAAA
1 ATTATTTAATTAA-AAAA
695249 ATTATTTAATTAAAAAA
1 ATTATTTAATTAAAAAA
695266 AT
1 AT
695268 ATAAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTATTTAATTAAAAAA
Found at i:695906 original size:39 final size:39
Alignment explanation
Indices: 695848--695935 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
695838 TGTCACTGAA
*
695848 TCGTCATAACTTGTAAAGTTCCATCACAACTTGTGATAT
1 TCGTCATAACTTGTAAAGTTCCATCACAACTTGTGACAT
* *
695887 TCGTCATAACTTGTGAAGTTCTATCACAACTTGTGACAT
1 TCGTCATAACTTGTAAAGTTCCATCACAACTTGTGACAT
695926 TCCGTCATAA
1 T-CGTCATAA
695936 TTTTCATCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 37 0.82
40 8 0.18
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (39 bp):
TCGTCATAACTTGTAAAGTTCCATCACAACTTGTGACAT
Found at i:695921 original size:20 final size:19
Alignment explanation
Indices: 695855--695922 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
695845 GAATCGTCAT
*
695855 AACTTGTAAAGTTCCATCAC
1 AACTTGTGAAGTT-CATCAC
* *
695875 AACTTGTGATA-TTCGTCAT
1 AACTTGTGA-AGTTCATCAC
695894 AACTTGTGAAGTTCTATCAC
1 AACTTGTGAAGTTC-ATCAC
695914 AACTTGTGA
1 AACTTGTGA
695923 CATTCCGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.40
20 22 0.55
21 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (19 bp):
AACTTGTGAAGTTCATCAC
Found at i:699417 original size:20 final size:19
Alignment explanation
Indices: 699389--699430 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
699379 TTATTTAATT
699389 AATAAAAATTATTTAATA-AA
1 AATAAAAA-TA-TTAATATAA
*
699409 AATATAAATATTAATATAA
1 AATAAAAATATTAATATAA
699428 AAT
1 AAT
699431 TTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAAAATATTAATATAA
Found at i:702330 original size:27 final size:26
Alignment explanation
Indices: 702296--702449 Score: 85
Period size: 28 Copynumber: 5.6 Consensus size: 26
702286 CAAATAAACC
* *
702296 TTTTAATTAAGCTTCTATATATAAAA
1 TTTTAATTAAACTTCTATACATAAAA
* *
702322 TTTTCAATTAAATTTCTATACATAGAA
1 TTTT-AATTAAACTTCTATACATAAAA
*** * *
702349 TTTGTGGCTAAACTTTTTACACATAAAA
1 TTT-TAATTAAAC-TTCTATACATAAAA
* *
702377 TATTTAATCAAACTTTTTATACATAAAA
1 T-TTTAATTAAAC-TTCTATACATAAAA
* ** *
702405 GTTTTAATTAGA-TTCTTTATGTATAGAAT
1 -TTTTAATTAAACTTC--TATACATA-AAA
702434 TTTTAATTAAACTTCT
1 TTTTAATTAAACTTCT
702450 TACGTGAATT
Statistics
Matches: 96, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
26 6 0.06
27 26 0.27
28 56 0.58
29 8 0.08
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (26 bp):
TTTTAATTAAACTTCTATACATAAAA
Found at i:702492 original size:28 final size:28
Alignment explanation
Indices: 702357--702500 Score: 93
Period size: 28 Copynumber: 5.1 Consensus size: 28
702347 AATTTGTGGC
* * *
702357 TAAACTTTTTACACATAAAATATTTAAT
1 TAAACTTTTTACTCATTAAATTTTTAAT
* * *
702385 CAAACTTTTTA-TACATAAAAGTTTTAAT
1 TAAACTTTTTACT-CATTAAATTTTTAAT
* *
702413 TAGA-TTCTTTA-T-GTATAGAATTTTTAAT
1 TAAACTT-TTTACTCAT-TA-AATTTTTAAT
* * *
702441 TAAACTTCTTACGTGAATT--TTTTTTAAT
1 TAAACTTTTTAC-T-CATTAAATTTTTAAT
702469 TAAACTTTTTACTCATTAAATTTTTAAT
1 TAAACTTTTTACTCATTAAATTTTTAAT
702497 TAAA
1 TAAA
702501 TATTCATACA
Statistics
Matches: 89, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 76 0.85
29 2 0.02
30 1 0.01
31 1 0.01
32 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (28 bp):
TAAACTTTTTACTCATTAAATTTTTAAT
Found at i:703551 original size:23 final size:23
Alignment explanation
Indices: 703520--703564 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
703510 TATATTTGCA
*
703520 TATAAATATATAGATGTATACAG
1 TATAAATATATAGATATATACAG
* *
703543 TATATATATATATATATATACA
1 TATAAATATATAGATATATACA
703565 TGTGTACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (23 bp):
TATAAATATATAGATATATACAG
Found at i:703560 original size:31 final size:29
Alignment explanation
Indices: 703519--703582 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
703509 ATATATTTGC
*
703519 ATATAAATATATAGATGTATACAGTATATAT
1 ATATAAATATATACATGTATACA-TAT-TAT
* *
703550 ATATATATATATACATGTGTACATATTAT
1 ATATAAATATATACATGTATACATATTAT
703579 ATAT
1 ATAT
703583 TTAAAATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 7 0.23
30 3 0.10
31 20 0.67
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (29 bp):
ATATAAATATATACATGTATACATATTAT
Found at i:703623 original size:16 final size:16
Alignment explanation
Indices: 703591--703625 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
703581 ATTTAAAATG
* *
703591 TATATTTATATATGTA
1 TATATTTATAAAGGTA
703607 TATATTTATAAAGGTA
1 TATATTTATAAAGGTA
703623 TAT
1 TAT
703626 TTAAATGTAC
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:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
TATATTTATAAAGGTA
Found at i:703624 original size:14 final size:14
Alignment explanation
Indices: 703578--703628 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 14
703568 GTACATATTA
*
703578 TATATTTA-AAATG
1 TATATTTATAAAGG
* *
703591 TATATTTATATATGTA
1 TATATTTATA-AAG-G
703607 TATATTTATAAAGG
1 TATATTTATAAAGG
703621 TATATTTA
1 TATATTTA
703629 AATGTACATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 8 0.27
14 9 0.30
15 3 0.10
16 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
TATATTTATAAAGG
Found at i:703640 original size:30 final size:29
Alignment explanation
Indices: 703572--703628 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
703562 ACATGTGTAC
*
703572 ATAT-TATATATTTAAAATGTATATTTAT
1 ATATGTATATATTTAAAAGGTATATTTAT
703600 ATATGTATATATTTATAAAGGTATATTTA
1 ATATGTATATATTTA-AAAGGTATATTTA
703629 AATGTACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (29 bp):
ATATGTATATATTTAAAAGGTATATTTAT
Found at i:703687 original size:2 final size:2
Alignment explanation
Indices: 703680--703717 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
703670 ATGAGATTTC
* *
703680 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
703718 AAAGTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:704635 original size:23 final size:23
Alignment explanation
Indices: 704609--704683 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
704599 TGTATTTATT
*
704609 TTATATTTATATATTTTAACATA
1 TTATATTTATAAATTTTAACATA
* *
704632 TTATA-ATATAAATTTT--GATA
1 TTATATTTATAAATTTTAACATA
*
704652 CTTATATTATATAAATTTTAACACA
1 -TTATATT-TATAAATTTTAACATA
704677 TTCATAT
1 TT-ATAT
704684 ATTCATATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 3 0.08
21 5 0.12
22 9 0.22
23 15 0.38
24 2 0.05
25 6 0.15
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (23 bp):
TTATATTTATAAATTTTAACATA
Found at i:704779 original size:2 final size:2
Alignment explanation
Indices: 704772--704796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
704762 CTAACAAGAG
704772 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 T
704797 TCAGGTTCTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:708273 original size:16 final size:17
Alignment explanation
Indices: 708252--708285 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
708242 AATTAATTTG
708252 TTATTTA-AAATTAAAT
1 TTATTTATAAATTAAAT
708268 TTATTTATAAATTAAAT
1 TTATTTATAAATTAAAT
708285 T
1 T
708286 AATAATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTATAAATTAAAT
Found at i:708282 original size:23 final size:22
Alignment explanation
Indices: 708237--708287 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
708227 TTTTCCCACT
* * *
708237 AATTAAATTAATTTGTTATTTAA
1 AATTAAATTAATTTATAAATT-A
*
708260 AATTAAATTTATTTATAAATTA
1 AATTAAATTAATTTATAAATTA
708282 AATTAA
1 AATTAA
708288 TAATTAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTAAATTAATTTATAAATTA
Found at i:708712 original size:23 final size:23
Alignment explanation
Indices: 708669--708712 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
708659 ATTATTTGAA
* *
708669 ATATTAATTATTTTAATTGTGAT
1 ATATTAATTATTTAAAATGTGAT
*
708692 ATATTTATTATTTAAAATGTG
1 ATATTAATTATTTAAAATGTG
708713 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (23 bp):
ATATTAATTATTTAAAATGTGAT
Found at i:708754 original size:19 final size:19
Alignment explanation
Indices: 708732--708769 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
708722 GAATTTAAAT
708732 AAATA-AATTTTATTATTAA
1 AAATATAATTTTA-TATTAA
*
708751 AAATATTATTTTATATTAA
1 AAATATAATTTTATATTAA
708770 TATTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATAATTTTATATTAA
Found at i:709292 original size:16 final size:16
Alignment explanation
Indices: 709265--709316 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
709255 GTAACTCATT
709265 TTTAAA-TTTGAATCA
1 TTTAAATTTTGAATCA
709280 TTTAAATTTTGAATCA
1 TTTAAATTTTGAATCA
*
709296 TTTTAATTTT-AAT--
1 TTTAAATTTTGAATCA
709309 TTTAAATT
1 TTTAAATT
709317 ATTTTTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 7 0.21
15 9 0.26
16 18 0.53
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTTTGAATCA
Found at i:709300 original size:17 final size:16
Alignment explanation
Indices: 709245--709301 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 16
709235 CAATTTAGGT
709245 TTTTAAATTTGTAACTCA
1 TTTTAAATTTG-AA-TCA
709263 TTTTTAAATTTGAATCA
1 -TTTTAAATTTGAATCA
709280 -TTTAAATTTTGAATCA
1 TTTTAAA-TTTGAATCA
709296 TTTTAA
1 TTTTAA
709302 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.17
16 9 0.25
17 8 0.22
18 2 0.06
19 11 0.31
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTGAATCA
Found at i:709304 original size:22 final size:22
Alignment explanation
Indices: 709279--709321 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
709269 AATTTGAATC
*
709279 ATTTAAATTTTGAATCATTTTA
1 ATTTAAATTTTAAATCATTTTA
* *
709301 ATTTTAATTTTAAATTATTTT
1 ATTTAAATTTTAAATCATTTT
709322 TGATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTAAATTTTAAATCATTTTA
Found at i:711401 original size:34 final size:34
Alignment explanation
Indices: 711357--711421 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
711347 ATAAGTGATA
* *
711357 TTTATAAAAATTAAACTATAATTAATGTATTATTT
1 TTTATAAAAATTAAA-TATAAATAATATATTATTT
*
711392 TTTA-AAAAATTCAATATAAATAATATATTA
1 TTTATAAAAATTAAATATAAATAATATATTA
711422 AACACAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 14 0.52
34 9 0.33
35 4 0.15
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (34 bp):
TTTATAAAAATTAAATATAAATAATATATTATTT
Found at i:712388 original size:21 final size:21
Alignment explanation
Indices: 712363--712418 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
712353 AAACATCAAA
*
712363 ATTTAATTAATTTTAAAATTA-
1 ATTTAATTAATATT-AAATTAC
* *
712384 TTTTAATTACTATTAAATTAC
1 ATTTAATTAATATTAAATTAC
712405 ATTTAATTAA-ATTA
1 ATTTAATTAATATTA
712419 TATTCTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATTAATATTAAATTAC
Found at i:712413 original size:15 final size:16
Alignment explanation
Indices: 712395--712437 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
712385 TTTAATTACT
712395 ATTAAATTACATT-TA
1 ATTAAATTACATTCTA
*
712410 ATTAAATTATATTCTA
1 ATTAAATTACATTCTA
712426 ATTTAAA-TACAT
1 A-TTAAATTACAT
712438 AATGAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.50
16 7 0.29
17 5 0.21
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATTACATTCTA
Found at i:712808 original size:15 final size:15
Alignment explanation
Indices: 712764--712810 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
712754 ACACAATAAT
* *
712764 ATTATTTTTTAAAAA
1 ATTATATTTTAAATA
*
712779 ATTATA-ATTATAATA
1 ATTATATTTTA-AATA
712794 ATTATATTTTAAATA
1 ATTATATTTTAAATA
712809 AT
1 AT
712811 CAAATTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATATTTTAAATA
Found at i:713149 original size:17 final size:18
Alignment explanation
Indices: 713122--713168 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
713112 ATAAATTTAG
*
713122 AATTAAATTTTAATATTT
1 AATTAATTTTTAATATTT
* *
713140 -ATTAATTTTTTATTTTT
1 AATTAATTTTTAATATTT
713157 AATTATATTTTT
1 AATTA-ATTTTT
713169 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.58
18 4 0.17
19 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTAATTTTTAATATTT
Found at i:722610 original size:24 final size:23
Alignment explanation
Indices: 722583--722628 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
722573 AAATTAAAAT
722583 TAAA-TATAATAATAATTTATATTA
1 TAAATTATAA-AATAATTT-TATTA
*
722607 TAAATTTTAAAATAATTTTATT
1 TAAATTATAAAATAATTTTATT
722629 TTATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTATAAAATAATTTTATTA
Found at i:722678 original size:34 final size:35
Alignment explanation
Indices: 722640--722705 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
722630 TATTTTATAT
*
722640 TTTTTA-TGTAATATTATTTTTAAAATT-TTAATTA
1 TTTTTACTGTAAT-TTATATTTAAAATTATTAATTA
**
722674 TTTTTACTGTTGTTTATATTTAAAATTATTAA
1 TTTTTACTGTAATTTATATTTAAAATTATTAA
722706 ATTTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.70
35 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (35 bp):
TTTTTACTGTAATTTATATTTAAAATTATTAATTA
Found at i:723332 original size:10 final size:10
Alignment explanation
Indices: 723264--723361 Score: 53
Period size: 10 Copynumber: 9.7 Consensus size: 10
723254 ATTTATATAT
723264 TTTATAATTAAA
1 TTTA-AATT-AA
*
723276 TTTAAATAAAA
1 TTTAAAT-TAA
**
723287 TTTTTATTAA
1 TTTAAATTAA
723297 -TTAAATAATAA
1 TTTAAAT--TAA
723308 TTTAAATTAA
1 TTTAAATTAA
* *
723318 ATTAAATTAC
1 TTTAAATTAA
723328 TTTAAATT--
1 TTTAAATTAA
723336 TTATAAA--AA
1 TT-TAAATTAA
*
723345 TTTAACTTAA
1 TTTAAATTAA
723355 TTTAAAT
1 TTTAAAT
723362 CTTATCAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
8 5 0.08
9 10 0.15
10 28 0.42
11 13 0.20
12 10 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:723702 original size:29 final size:28
Alignment explanation
Indices: 723645--723723 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
723635 CTGTTTATAT
* ** *
723645 ATATATATATATATATTAATATATTTTTTT
1 ATATA-ATAT-TATATTTATATAAATTTTA
723675 ATATAATCATTATATTTATATAAATTTTA
1 ATATAAT-ATTATATTTATATAAATTTTA
*
723704 ATATTATATTA-ATTTTATAT
1 ATATAATATTATA-TTTATAT
723724 TTATTATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 11 0.26
29 23 0.55
30 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATAATATTATATTTATATAAATTTTA
Found at i:723710 original size:17 final size:16
Alignment explanation
Indices: 723638--723724 Score: 58
Period size: 17 Copynumber: 5.5 Consensus size: 16
723628 ATCAAAGCTG
*
723638 TTTATA-TATATATAT
1 TTTATATTATATAAAT
* *
723653 ATATATATTA-ATATAT
1 -TTTATATTATATAAAT
723669 TTT-T-TTATAT-AAT
1 TTTATATTATATAAAT
*
723682 CATTATATTTATATAAAT
1 -TTTATA-TTATATAAAT
*
723700 TTTAATATTATATTAAT
1 TTT-ATATTATATAAAT
723717 TTTATATT
1 TTTATATT
723725 TATTATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 3 0.05
16 16 0.28
17 22 0.39
18 6 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATATTATATAAAT
Found at i:723727 original size:17 final size:17
Alignment explanation
Indices: 723684--723727 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
723674 TATATAATCA
723684 TTATATTTATATAAATT
1 TTATATTTATATAAATT
*
723701 TTA-ATATTATATTAATT
1 TTATAT-TTATATAAATT
723718 TTATATTTAT
1 TTATATTTAT
723728 TATTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:724097 original size:16 final size:16
Alignment explanation
Indices: 724065--724114 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
724055 TATTATTATA
*
724065 AAAATATTATCAAAAAT
1 AAAATATT-TAAAAAAT
724082 AAAATATTTAAAAAAT
1 AAAATATTTAAAAAAT
** *
724098 ATCATATTAAAAAAAT
1 AAAATATTTAAAAAAT
724114 A
1 A
724115 CTGAATGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:724822 original size:17 final size:17
Alignment explanation
Indices: 724802--724854 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
724792 TTTTTGATAA
724802 AATAATAATATATAAAT
1 AATAATAATATATAAAT
*
724819 AATAATAATTTA-AAAT
1 AATAATAATATATAAAT
*
724835 AA-AAT-ATA-ATAAAA
1 AATAATAATATATAAAT
724849 AATAAT
1 AATAAT
724855 TCAATAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 7 0.23
15 6 0.19
16 6 0.19
17 11 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATATATAAAT
Found at i:724863 original size:30 final size:28
Alignment explanation
Indices: 724798--724868 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
724788 AAATTTTTTG
*
724798 ATAAAATAATAATATATAAATAATAATA
1 ATAAAATAATAATATATAAAAAATAATA
724826 ATTTAAAATAA-AATATAATAAAAAATAATTCA
1 A--TAAAATAATAATAT-ATAAAAAATAA-T-A
724858 ATAAAACTAAT
1 ATAAAA-TAAT
724869 TATAATACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
28 1 0.03
29 5 0.14
30 23 0.66
31 4 0.11
32 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAAAATAATAATATATAAAAAATAATA
Found at i:726026 original size:4 final size:4
Alignment explanation
Indices: 726017--726047 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
726007 AGGGTTATGG
726017 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
726048 TGGTTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:727147 original size:14 final size:15
Alignment explanation
Indices: 727128--727160 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
727118 AAAATTAATT
*
727128 TTTTTAAA-AATTTA
1 TTTTTAAATAATTAA
727142 TTTTTAAATAATTAA
1 TTTTTAAATAATTAA
727157 TTTT
1 TTTT
727161 AATGTTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAAATAATTAA
Found at i:728068 original size:26 final size:26
Alignment explanation
Indices: 728039--728103 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
728029 TAGAAATAGG
728039 ATTGATAAAGTTTGACTTTATTTGAA
1 ATTGATAAAGTTTGACTTTATTTGAA
728065 ATTGATAAAGTTTGACTTTATTTGAA
1 ATTGATAAAGTTTGACTTTATTTGAA
*
728091 ATTAATAAAGTTT
1 ATTGATAAAGTTT
728104 AATTTTATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (26 bp):
ATTGATAAAGTTTGACTTTATTTGAA
Found at i:728119 original size:26 final size:26
Alignment explanation
Indices: 728043--728117 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
728033 AATAGGATTG
* * *
728043 ATAAAGTTTGACTTTATTTGAAATTG
1 ATAAAGTTTAACTTTATTCGAAATTA
* *
728069 ATAAAGTTTGACTTTATTTGAAATTA
1 ATAAAGTTTAACTTTATTCGAAATTA
*
728095 ATAAAGTTTAATTTTATCTCGAA
1 ATAAAGTTTAACTTTAT-TCGAA
728118 TTTTAGTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 40 0.91
27 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.45
Consensus pattern (26 bp):
ATAAAGTTTAACTTTATTCGAAATTA
Found at i:730695 original size:31 final size:31
Alignment explanation
Indices: 730660--730748 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 31
730650 TAATTTTTAA
730660 TTATTAATATAAAATAATATAAAATTTAATT
1 TTATTAATATAAAATAATATAAAATTTAATT
* *
730691 TTATTAAGTA-ATAATAATAT--ATTTTAATT
1 TTATTAA-TATAAAATAATATAAAATTTAATT
* *
730720 TT-TT-ATTTCAAATAAAATATAAAATTTAA
1 TTATTAATAT-AAA-ATAATATAAAATTTAA
730749 ATCAATTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 4 0.09
29 16 0.35
31 22 0.48
32 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
TTATTAATATAAAATAATATAAAATTTAATT
Found at i:730881 original size:4 final size:4
Alignment explanation
Indices: 730872--730899 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
730862 TATCATTTGA
730872 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
730900 TTATTGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:731496 original size:36 final size:35
Alignment explanation
Indices: 731390--731489 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 35
731380 TAAATACATA
*
731390 TATATATATAAATATATAAA-ATAAAATA-AAT-TATT
1 TATATATA-AAAAATATAAATA-AAAATACAATAT-TT
* * * *
731425 AATATATAAAAAATTTATATAAAAATATAATATTT
1 TATATATAAAAAATATAAATAAAAATACAATATTT
731460 TATATATCAAAAAATATAAATAAAAATACA
1 TATATAT-AAAAAATATAAATAAAAATACA
731490 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
34 14 0.26
35 19 0.36
36 20 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (35 bp):
TATATATAAAAAATATAAATAAAAATACAATATTT
Found at i:731519 original size:16 final size:17
Alignment explanation
Indices: 731500--731533 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
731490 TAATTTTTTT
*
731500 CTTTCTTT-TTTTTCTC
1 CTTTCTTTCTTTCTCTC
731516 CTTTCTTTCTTTCTCTC
1 CTTTCTTTCTTTCTCTC
731533 C
1 C
731534 CATGTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTCTTTCTCTC
Found at i:731714 original size:23 final size:22
Alignment explanation
Indices: 731691--731748 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
731681 TATAAAATAT
731691 AATATTTTATATATAATTATTATA
1 AATATTTTATATAT-ATT-TTATA
*
731715 AAAATTTT-TATATATTTTATA
1 AATATTTTATATATATTTTATA
731736 AATATATTTATAT
1 AATAT-TTTATAT
731749 TTCATGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.30
22 6 0.20
23 8 0.27
24 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTTTATATATATTTTATA
Found at i:733986 original size:28 final size:27
Alignment explanation
Indices: 733929--733985 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
733919 AAATATATTA
733929 TTTAAAAATAAAATTAAAATTAAAATT
1 TTTAAAAATAAAATTAAAATTAAAATT
733956 TTTAAAAATAATTAA-TAAAA-TAAAATT
1 TTTAAAAATAA--AATTAAAATTAAAATT
733983 TTT
1 TTT
733986 TTATATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 21 0.75
28 5 0.18
29 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTAAAAATAAAATTAAAATTAAAATT
Found at i:734076 original size:25 final size:25
Alignment explanation
Indices: 734048--734096 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
734038 ATTTAAGAAG
734048 TAAATAAAAAATTAAAA-TTAAAAAT
1 TAAAT-AAAAATTAAAACTTAAAAAT
**
734073 TAAATAATTATTAAAACTTAAAAA
1 TAAATAAAAATTAAAACTTAAAAA
734097 AACTCTGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAATAAAAATTAAAACTTAAAAAT
Found at i:736360 original size:15 final size:14
Alignment explanation
Indices: 736316--736351 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
736306 TTTTTCAGAT
*
736316 TATTTTTTATAA-A
1 TATTTTTTAAAATA
736329 TATTTTTTAAAATA
1 TATTTTTTAAAATA
736343 TATTTTTTA
1 TATTTTTTA
736352 CAGTTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTTTTAAAATA
Found at i:736606 original size:40 final size:40
Alignment explanation
Indices: 736524--736609 Score: 115
Period size: 38 Copynumber: 2.2 Consensus size: 40
736514 ATTATATTAT
*
736524 AAAAATTATATTAAATTATCGATTTTTTAATATACATAAA
1 AAAAATTATATTAAATTATCGATTTTTTAATATAAATAAA
*
736564 AAAAATTATGTT-AA-TATCGATTTTTTAATA-AAATTAATA
1 AAAAATTATATTAAATTATCGATTTTTTAATATAAA-TAA-A
736603 AAAAATT
1 AAAAATT
736610 TTAAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
37 2 0.05
38 19 0.45
39 10 0.24
40 11 0.26
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (40 bp):
AAAAATTATATTAAATTATCGATTTTTTAATATAAATAAA
Found at i:737147 original size:70 final size:71
Alignment explanation
Indices: 736965--737154 Score: 174
Period size: 72 Copynumber: 2.7 Consensus size: 71
736955 TATATGAGTT
* * * * * * * *
736965 TAAATTTTATACGATATAATTTATTTTTATTTATATATTTTAAATTTAATCTTTTATTTGATTAT
1 TAAATTTTTTAAGATATGATCTATTTTTATTTATAAAATTTAAATTTAA-CTTTGAGTTGATTAT
* *
737030 ATGAATT
65 AAGAATA
* * *
737037 TAAATTTTTTAAGATGTGATTTATTTTTATTTATCGAAATTTAAATTT-A-TTTGAGTTGATTAT
1 TAAATTTTTTAAGATATGATCTATTTTTATTTAT-AAAATTTAAATTTAACTTTGAGTTGATTAT
*
737100 AAGAGTA
65 AAGAATA
*
737107 TAAATTATTTTAA-AGTATGATCTATTTTTATTTGTAAAA-TT-AATTTAA
1 TAAATT-TTTTAAGA-TATGATCTATTTTTATTTATAAAATTTAAATTTAA
737155 TTTTTGAGAT
Statistics
Matches: 98, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
68 5 0.05
69 3 0.03
70 26 0.27
71 23 0.23
72 31 0.32
73 10 0.10
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (71 bp):
TAAATTTTTTAAGATATGATCTATTTTTATTTATAAAATTTAAATTTAACTTTGAGTTGATTATA
AGAATA
Found at i:737959 original size:11 final size:12
Alignment explanation
Indices: 737936--737982 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
737926 CAAATACATA
737936 AAAAAATATTTT
1 AAAAAATATTTT
737948 AAAAAATATTTAT
1 AAAAAATATTT-T
*
737961 AAAAGAAATAATTT
1 -AAA-AAATATTTT
737975 AAAAAATA
1 AAAAAATA
737983 AAAAAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 16 0.52
13 4 0.13
14 4 0.13
15 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:738205 original size:15 final size:15
Alignment explanation
Indices: 738181--738220 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
738171 GTTTGAGTTA
738181 ATTTTGAGTTAAATT
1 ATTTTGAGTTAAATT
*
738196 ATTTTAAGTTAAATT
1 ATTTTGAGTTAAATT
738211 ATTTTGAGTT
1 ATTTTGAGTT
738221 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (15 bp):
ATTTTGAGTTAAATT
Found at i:738284 original size:16 final size:16
Alignment explanation
Indices: 738265--738312 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
738255 TTTTAGGTAT
738265 AGATTATTTCAGATTC
1 AGATTATTTCAGATTC
* *
738281 AGATCATTTC-GAATTT
1 AGATTATTTCAG-ATTC
738297 AGATTATTTCAGATTC
1 AGATTATTTCAGATTC
738313 GGGTTAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
AGATTATTTCAGATTC
Found at i:746946 original size:28 final size:29
Alignment explanation
Indices: 746909--746964 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
746899 TTGTATATAT
746909 AATTATTTTT-TAAGAGTTTTAAATATTAC
1 AATTATTTTTATAA-AGTTTTAAATATTAC
* *
746938 AATT-TTTTTATAAATTTTTATATATTA
1 AATTATTTTTATAAAGTTTTAAATATTA
746965 ATAATTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
AATTATTTTTATAAAGTTTTAAATATTAC
Found at i:747035 original size:11 final size:11
Alignment explanation
Indices: 747007--747058 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
746997 TTTTTGTACA
747007 TTTATATTATT
1 TTTATATTATT
**
747018 TACATATTATT
1 TTTATATTATT
747029 TTTATATTATGT
1 TTTATATTAT-T
747041 TTTAAATATT-TT
1 TTT--ATATTATT
747053 TTTATA
1 TTTATA
747059 AACATTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 3 0.09
11 17 0.50
12 8 0.24
13 1 0.03
14 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTATATTATT
Found at i:747751 original size:57 final size:59
Alignment explanation
Indices: 747628--747745 Score: 141
Period size: 58 Copynumber: 2.0 Consensus size: 59
747618 TATATTCATG
* * *
747628 TCATATCTCTATTCATGATATATTTTATACAATTTATCATAATAATTTAATTTAAAATA
1 TCATATCTCAATTCATGATATATTTTATACAATTTATCATAATAATTTAATTAAAAAAA
* * * * *
747687 TCATATCTCAATTCATGATAT-TTTT-TCATAATTTGTTATAGTGATTTAATTAAAAAAA
1 TCATATCTCAATTCATGATATATTTTAT-ACAATTTATCATAATAATTTAATTAAAAAAA
747745 T
1 T
747746 TTATCTTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.02
58 29 0.58
59 20 0.40
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (59 bp):
TCATATCTCAATTCATGATATATTTTATACAATTTATCATAATAATTTAATTAAAAAAA
Found at i:748013 original size:29 final size:32
Alignment explanation
Indices: 747981--748048 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 32
747971 TTTTAACTTT
*
747981 AATTTTATTTACTA-AATATT-TTTAAAT-AA
1 AATTTTATTAACTATAATATTATTTAAATAAA
* *
748010 AA-TTTATTAATTATAATATTATTTAATTAAA
1 AATTTTATTAACTATAATATTATTTAAATAAA
748041 AATTTTAT
1 AATTTTAT
748049 AAATATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.28
29 8 0.25
30 6 0.19
31 4 0.12
32 5 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
AATTTTATTAACTATAATATTATTTAAATAAA
Found at i:748019 original size:14 final size:14
Alignment explanation
Indices: 747993--748053 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
747983 TTTTATTTAC
747993 TAAATATTTTTAAA
1 TAAATATTTTTAAA
*
748007 TAAA-ATTTATTAAT
1 TAAATATTT-TTAAA
*
748021 TATAATATTATTTAAT
1 TA-AATATT-TTTAAA
*
748037 TAAAAATTTTATAAA
1 TAAATATTTT-TAAA
748052 TA
1 TA
748054 TTAAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.10
14 12 0.31
15 12 0.31
16 10 0.26
17 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATATTTTTAAA
Found at i:748035 original size:16 final size:16
Alignment explanation
Indices: 747994--748041 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 16
747984 TTTATTTACT
*
747994 AAATATT-TTTAAATA
1 AAATATTATTTAATTA
748009 AAAT-TTA-TTAATTA
1 AAATATTATTTAATTA
*
748023 TAATATTATTTAATTA
1 AAATATTATTTAATTA
748039 AAA
1 AAA
748042 ATTTTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.41
15 7 0.26
16 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATATTATTTAATTA
Found at i:749648 original size:21 final size:20
Alignment explanation
Indices: 749571--749653 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 20
749561 AAAGGTAAAT
749571 AAATATCATTTTTT-ATG-AA
1 AAATAT-ATTTTTTAATGAAA
*
749590 AAA-ATATTTTTGAATGAAA
1 AAATATATTTTTTAATGAAA
* ** **
749609 AGATGCATTGGTTAGATGAAA
1 AAATATATTTTTTA-ATGAAA
749630 AAATATATTTTTTGAATGAAA
1 AAATATATTTTTT-AATGAAA
749651 AAA
1 AAA
749654 ATGTAACTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
17 6 0.13
18 5 0.11
19 7 0.15
20 5 0.11
21 23 0.49
22 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.37
Consensus pattern (20 bp):
AAATATATTTTTTAATGAAA
Found at i:754503 original size:25 final size:25
Alignment explanation
Indices: 754475--754533 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
754465 TATATTATTT
* *
754475 AAAAATAAATGAAAATTAAAAACTA
1 AAAAATAAATAAAAAATAAAAACTA
* *
754500 AAAATTAAATAAAAAATGAAAACTA
1 AAAAATAAATAAAAAATAAAAACTA
754525 AAAAATAAA
1 AAAAATAAA
754534 GCTTTGCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAAATAAATAAAAAATAAAAACTA
Done.