Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:393857 original size:21 final size:22
Alignment explanation
Indices: 393831--393876 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
393821 ATCTGTTGAA
* *
393831 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
393852 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
393874 ACT
1 ACT
393877 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:396363 original size:20 final size:19
Alignment explanation
Indices: 396340--396378 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
396330 AGGGATACAA
*
396340 GAGAAGGATGAGGGATGCTT
1 GAGAAGGAGGAGGGA-GCTT
*
396360 GAGAGGGAGGAGGGAGCTT
1 GAGAAGGAGGAGGGAGCTT
396379 CCTTTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.51, T:0.15
Consensus pattern (19 bp):
GAGAAGGAGGAGGGAGCTT
Found at i:396448 original size:24 final size:25
Alignment explanation
Indices: 396421--396490 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
396411 AATAAAAATT
*
396421 AGCCACCAATTTTGACAAAC-AACA
1 AGCCACCAATTTTGACAAACAAAAA
*
396445 AGCCA-TAATTTTTGACAAACAAAAA
1 AGCCACCAA-TTTTGACAAACAAAAA
*
396470 AGAACCACCATTTTTGACAAA
1 AG--CCACCAATTTTGACAAA
396491 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 5 0.14
27 13 0.35
28 1 0.03
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAACAAAAA
Found at i:396490 original size:27 final size:27
Alignment explanation
Indices: 396423--396519 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
396413 TAAAAATTAG
* *
396423 CCACCAATTTTGACAAAC-AACAAG--
1 CCACCATTTTTGACAAACAAAAAAGAA
**
396447 CCATAATTTTTGACAAACAAAAAAGAA
1 CCACCATTTTTGACAAACAAAAAAGAA
* *
396474 CCACCATTTTTGACAAA-TACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAAG-AA
*
396501 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
396520 CATGGTGGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.26
25 5 0.09
26 5 0.09
27 33 0.57
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAAGAA
Found at i:396538 original size:24 final size:25
Alignment explanation
Indices: 396507--396564 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
396497 GTAACCACCA
*
396507 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
396531 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
396557 TTGTTGAC
1 TTGTTGAC
396565 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:396978 original size:3 final size:3
Alignment explanation
Indices: 396970--397024 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
396960 AACATTGTTG
*
396970 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
397018 ATT -TT AT
1 ATT ATT AT
397025 CCCCTATTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:397660 original size:2 final size:2
Alignment explanation
Indices: 397653--397677 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
397643 GGATTCAAAT
397653 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
397678 TGAATATTAT
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:399669 original size:20 final size:23
Alignment explanation
Indices: 399621--399681 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 23
399611 CATGTTATAA
399621 TATATTTAAATATTATTAACATGT
1 TATATTT-AATATTATTAACATGT
399645 TATATTTAATA-TATTAA-AT-T
1 TATATTTAATATTATTAACATGT
*
399665 TATATTTAAAATT-TTAA
1 TATATTTAATATTATTAA
399682 TACGTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 15 0.43
21 3 0.09
22 6 0.17
23 4 0.11
24 7 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTTAATATTATTAACATGT
Found at i:400608 original size:3 final size:3
Alignment explanation
Indices: 400602--400636 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
400592 ATCATCATCG
400602 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
400637 AACAGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:405175 original size:47 final size:48
Alignment explanation
Indices: 405069--405207 Score: 271
Period size: 48 Copynumber: 2.9 Consensus size: 48
405059 AGTTTTAATG
405069 AATTGGG-AAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTACTTTA
1 AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTACTTTA
405116 AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTACTTTA
1 AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTACTTTA
405164 AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTAC
1 AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTAC
405208 CTTCTGCAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
47 7 0.08
48 84 0.92
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.28
Consensus pattern (48 bp):
AATTGGGAAAAAAAATGGAAGTAAAATTTAGTGAAGCAATTTACTTTA
Found at i:410742 original size:24 final size:27
Alignment explanation
Indices: 410687--410755 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 27
410677 TAAATAGGAG
*
410687 TTTAATTAAA-AAATAATATTTAAAGAA
1 TTTAATTAAATAAA-AATATATAAAGAA
410714 TTTAATTAAATAAAAATA-ATAAA-AA
1 TTTAATTAAATAAAAATATATAAAGAA
*
410739 -TTAATTAGATAAAAATA
1 TTTAATTAAATAAAAATA
410756 GTAATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 16 0.41
25 2 0.05
26 4 0.10
27 14 0.36
28 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
TTTAATTAAATAAAAATATATAAAGAA
Found at i:412493 original size:30 final size:30
Alignment explanation
Indices: 412457--412534 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
412447 TAGGAGTTTA
* *
412457 AATTAAATAAAAATAATATTTTAAGGA-TT
1 AATTAAATAAAAATAATAGTTTAAGAACTT
412486 CAATTAAATAAAAATAATAGTTTAAGAACTT
1 -AATTAAATAAAAATAATAGTTTAAGAACTT
*
412517 AATTAGATAAAAATAATA
1 AATTAAATAAAAATAATA
412535 ATGATTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 42 0.95
31 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (30 bp):
AATTAAATAAAAATAATAGTTTAAGAACTT
Found at i:412543 original size:33 final size:31
Alignment explanation
Indices: 412457--412543 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 31
412447 TAGGAGTTTA
*
412457 AATTAAATAAAAATAATAT-TTTAAGGATTC
1 AATTAAATAAAAATAATATGTTTAAGAATTC
412487 AATTAAATAAAAATAATA-GTTTAAGAACTT-
1 AATTAAATAAAAATAATATGTTTAAGAA-TTC
*
412517 AATTAGATAAAAATAATAATGATTTAA
1 AATTAAATAAAAATAAT-ATG-TTTAA
412544 TTAGGTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
30 41 0.82
31 3 0.06
32 1 0.02
33 5 0.10
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (31 bp):
AATTAAATAAAAATAATATGTTTAAGAATTC
Found at i:413882 original size:30 final size:30
Alignment explanation
Indices: 413848--413904 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
413838 CAAATTGGAC
*
413848 TTTAATTAAACAAAAACAATATTTTAAAGG
1 TTTAATTAAACAAAAACAATAGTTTAAAGG
* * *
413878 TTTAATTGAATAAAAATAATAGTTTAA
1 TTTAATTAAACAAAAACAATAGTTTAA
413905 GAACTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTAATTAAACAAAAACAATAGTTTAAAGG
Found at i:419756 original size:14 final size:13
Alignment explanation
Indices: 419732--419771 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
419722 TAAATTCCAT
419732 TAATTATAAATAA
1 TAATTATAAATAA
*
419745 TTATTATCAAATAA
1 TAATTAT-AAATAA
*
419759 TAATTAAAAATAA
1 TAATTATAAATAA
419772 AAATAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTATAAATAA
Found at i:425243 original size:27 final size:27
Alignment explanation
Indices: 425190--425246 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
425180 CAATGCCTCA
*
425190 TCAACATAGTCGAGATGAATGGACCAT
1 TCAACATAGTCGAGATGAACGGACCAT
* *
425217 TCAACATAGTTGAGATTAAC-GAGCCAT
1 TCAACATAGTCGAGATGAACGGA-CCAT
425244 TCA
1 TCA
425247 GAAAAAGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
TCAACATAGTCGAGATGAACGGACCAT
Found at i:429583 original size:23 final size:23
Alignment explanation
Indices: 429557--429629 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
429547 TTACTTCGAT
429557 TTTAATTGGGCTTTTAGTTTAGG
1 TTTAATTGGGCTTTTAGTTTAGG
* *
429580 TTT-ATATGAGC-TTAAGTTTAGG
1 TTTAAT-TGGGCTTTTAGTTTAGG
*
429602 TTTAGA-TAGGCTTTTAGTTTAGG
1 TTTA-ATTGGGCTTTTAGTTTAGG
429625 TTTAA
1 TTTAA
429630 ATAAGTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 19 0.46
23 21 0.51
24 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.49
Consensus pattern (23 bp):
TTTAATTGGGCTTTTAGTTTAGG
Found at i:429600 original size:22 final size:21
Alignment explanation
Indices: 429572--429653 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
429562 TTGGGCTTTT
429572 AGTTTAGGTTTATATGAGCTTA
1 AGTTTAGGTTTATAT-AGCTTA
* *
429594 AGTTTAGGTTTAGATAGGCTTTT
1 AGTTTAGGTTTATATA-GC-TTA
* *
429617 AGTTTAGGTTTAAATAAGTTTA
1 AGTTTAGGTTTATAT-AGCTTA
**
429639 AGTTTAAATTTATAT
1 AGTTTAGGTTTATAT
429654 TTTATTAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
21 1 0.02
22 30 0.61
23 17 0.35
24 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (21 bp):
AGTTTAGGTTTATATAGCTTA
Found at i:429638 original size:16 final size:16
Alignment explanation
Indices: 429617--429647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
429607 ATAGGCTTTT
*
429617 AGTTTAGGTTTAAATA
1 AGTTTAAGTTTAAATA
429633 AGTTTAAGTTTAAAT
1 AGTTTAAGTTTAAAT
429648 TTATATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
AGTTTAAGTTTAAATA
Found at i:430052 original size:28 final size:27
Alignment explanation
Indices: 430003--430067 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
429993 AATAATTTTA
430003 AATACAATACAAAGATAAGATATGATT
1 AATACAATACAAAGATAAGATATGATT
*
430030 AATA-AATACAATATGATTAGATATGATT
1 AATACAATACAA-A-GATAAGATATGATT
* *
430058 ATTATAATAC
1 AATACAATAC
430068 TTTTATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 5 0.15
28 16 0.48
29 5 0.15
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.32
Consensus pattern (27 bp):
AATACAATACAAAGATAAGATATGATT
Found at i:430660 original size:23 final size:22
Alignment explanation
Indices: 430616--430660 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
430606 AATCTAATAT
* **
430616 TACAAAATAAAAAATTTTTAAA
1 TACAAAATAAAAAAATAATAAA
430638 TACAAAATTAAAAAAATAATAAA
1 TACAAAA-TAAAAAAATAATAAA
430661 ATTAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TACAAAATAAAAAAATAATAAA
Found at i:430717 original size:33 final size:34
Alignment explanation
Indices: 430680--430744 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 34
430670 TTTTATCTTA
430680 AATTTAA-TAATATTATAAA-TAAATATT-ATTTTT
1 AATTTAACT-ATATTA-AAAGTAAATATTGATTTTT
430713 AATTTAACTATATTAAAAGTAAATATTGATTT
1 AATTTAACTATATTAAAAGTAAATATTGATTT
430745 AAAATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 3 0.10
33 21 0.72
34 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (34 bp):
AATTTAACTATATTAAAAGTAAATATTGATTTTT
Found at i:430797 original size:13 final size:13
Alignment explanation
Indices: 430750--430797 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
430740 GATTTAAAAT
430750 TTTTTAAAAATATA
1 TTTTTAAAAATA-A
430764 TTTTTAAAAGATAA
1 TTTTTAAAA-ATAA
*
430778 TTATTAAAAATAA
1 TTTTTAAAAATAA
430791 TTTTTAA
1 TTTTTAA
430798 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 10 0.32
14 18 0.58
15 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:430804 original size:20 final size:21
Alignment explanation
Indices: 430775--430813 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
430765 TTTTAAAAGA
430775 TAATTATT-AAAAATAATTTT
1 TAATTATTAAAAAATAATTTT
*
430795 TAATTTTTAAAAAATAATT
1 TAATTATTAAAAAATAATT
430814 ATTGATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTATTAAAAAATAATTTT
Found at i:433542 original size:30 final size:29
Alignment explanation
Indices: 433459--433549 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 29
433449 TAATTAAACA
* * *
433459 AAAAATAAT-ATTTAAAGGATTTAACTAAAT
1 AAAAATAATAATTCAAA--ATTTAATTAGAT
*
433489 AAAAATAATACTTCAAAATTTTAATTAGAT
1 AAAAATAATAATTCAAAA-TTTAATTAGAT
* *
433519 AAAAATAGTAATTTAATAATTTAATTAGAT
1 AAAAATAATAATTCAA-AATTTAATTAGAT
433549 A
1 A
433550 TAATAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.02
30 43 0.84
31 7 0.14
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATAATAATTCAAAATTTAATTAGAT
Found at i:434252 original size:21 final size:22
Alignment explanation
Indices: 434226--434266 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
434216 ATGAATAAAA
434226 ATTAAATCA-AATTT-ATTAATC
1 ATTAAAT-ATAATTTAATTAATC
434247 ATTAAATATAATTTAATTAA
1 ATTAAATATAATTTAATTAA
434267 GATATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 12 0.67
22 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAATATAATTTAATTAATC
Found at i:434949 original size:18 final size:18
Alignment explanation
Indices: 434926--434961 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
434916 TAAATAATTT
* *
434926 TAAATATGATATAATTAA
1 TAAATATAATAAAATTAA
434944 TAAATATAATAAAATTAA
1 TAAATATAATAAAATTAA
434962 AATATTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAATATAATAAAATTAA
Found at i:434953 original size:30 final size:31
Alignment explanation
Indices: 434894--434953 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
434884 TGATCCTGAA
*
434894 TTAAGATATATATTAATTATATTAAATAATT
1 TTAAGATATATATTAATTATATAAAATAATT
434925 TTAA-ATATGATA-TAATTA-ATAAATATAAT
1 TTAAGATAT-ATATTAATTATATAAA-ATAAT
434954 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 4 0.15
30 15 0.58
31 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
TTAAGATATATATTAATTATATAAAATAATT
Found at i:436023 original size:39 final size:38
Alignment explanation
Indices: 435896--436056 Score: 216
Period size: 38 Copynumber: 4.2 Consensus size: 38
435886 TTGAATTAGT
** *
435896 TGATGGTTAGAGAATTCAATTTGAAATTGG-CTGACGGT
1 TGATGGTTAGAGAATTCAATTTGAAATTGGTC-GGTGGC
*
435934 TGATGGTTAGAGAATTCAATTTGAAATTAGTCGGTGGC
1 TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGTGGC
435972 TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGTAGGC
1 TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGT-GGC
* ** *
436011 TGACGACTAGAGAATTCAATTTGGAATTGGTCGGTGGC
1 TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGTGGC
*
436049 TGGTGGTT
1 TGATGGTT
436057 GGTGGCTAGA
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
38 73 0.68
39 35 0.32
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.34
Consensus pattern (38 bp):
TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGTGGC
Found at i:436056 original size:77 final size:76
Alignment explanation
Indices: 435896--436056 Score: 225
Period size: 77 Copynumber: 2.1 Consensus size: 76
435886 TTGAATTAGT
* * * **
435896 TGATGGTTAGAGAATTCAATTTGAAATTGGCTGACGGTTGATGGTTAGAGAATTCAATTTGAAAT
1 TGATGGTTAGAGAATTCAATTTGAAATTGGCGGACGGCTGACGACTAGAGAATTCAATTTGAAAT
435961 TAGTCGGTGGC
66 TAGTCGGTGGC
*
435972 TGATGGTTAGAGAATTCAATTTGAAATTGGTCGGTA-GGCTGACGACTAGAGAATTCAATTTGGA
1 TGATGGTTAGAGAATTCAATTTGAAATTGG-CGG-ACGGCTGACGACTAGAGAATTCAATTTGAA
*
436036 ATTGGTCGGTGGC
64 ATTAGTCGGTGGC
*
436049 TGGTGGTT
1 TGATGGTT
436057 GGTGGCTAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
76 30 0.40
77 44 0.59
78 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.34
Consensus pattern (76 bp):
TGATGGTTAGAGAATTCAATTTGAAATTGGCGGACGGCTGACGACTAGAGAATTCAATTTGAAAT
TAGTCGGTGGC
Found at i:440754 original size:18 final size:18
Alignment explanation
Indices: 440733--440768 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
440723 GGCAATAGGA
440733 ATGAATAAGATATTTGCT
1 ATGAATAAGATATTTGCT
440751 ATGAATAAGATATTTGCT
1 ATGAATAAGATATTTGCT
440769 TTGATAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
ATGAATAAGATATTTGCT
Found at i:447313 original size:13 final size:13
Alignment explanation
Indices: 447292--447337 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
447282 TTTAGGAGCA
447292 AAAAATTATTTTT
1 AAAAATTATTTTT
*
447305 AATAATTATTTTTT
1 AAAAATTA-TTTTT
447319 AAAAATATATTTTT
1 AAAAAT-TATTTTT
447333 AAAAA
1 AAAAA
447338 AATTTAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 7 0.24
14 20 0.69
15 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:447382 original size:33 final size:33
Alignment explanation
Indices: 447345--447415 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
447335 AAAAATTTAG
*
447345 AATAATATTTATCT-TTAATATAATTAAATTAAA
1 AATAATATTTAT-TACTAATATAATTAAATTAAA
* *
447378 AATAATATTTATTACTAATATTATTAAATTTAA
1 AATAATATTTATTACTAATATAATTAAATTAAA
447411 AATAA
1 AATAA
447416 AAATTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
AATAATATTTATTACTAATATAATTAAATTAAA
Found at i:447423 original size:33 final size:33
Alignment explanation
Indices: 447360--447423 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
447350 TATTTATCTT
* *
447360 TAATATAATTAAATTAAAAATAATATTTATTAC
1 TAATATAATTAAATTAAAAATAAAAATTATTAC
* *
447393 TAATATTATTAAATTTAAAATAAAAATTATT
1 TAATATAATTAAATTAAAAATAAAAATTATT
447424 TTTTAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (33 bp):
TAATATAATTAAATTAAAAATAAAAATTATTAC
Found at i:453994 original size:32 final size:33
Alignment explanation
Indices: 453950--454011 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
453940 GATTATAACA
*
453950 TTTAAAACAATAAAAAATAATTA-ATAATTATT
1 TTTAAAAAAATAAAAAATAATTATATAATTATT
*
453982 TTTAAAAAAATAAAAAATTATTATATAATT
1 TTTAAAAAAATAAAAAATAATTATATAATT
454012 TTTAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (33 bp):
TTTAAAAAAATAAAAAATAATTATATAATTATT
Found at i:454082 original size:27 final size:28
Alignment explanation
Indices: 454052--454120 Score: 68
Period size: 33 Copynumber: 2.3 Consensus size: 28
454042 TTTAAAAATA
* *
454052 TATTTTAAAA-AATTTAAAATTAATATT
1 TATTTTAAAATAAATTAAAAATAATATT
454079 TATTTTTAATATAATTAAATTAAAAATAATATT
1 TA-TTTT-A-A-AA-TAAATTAAAAATAATATT
454112 TATTTTAAA
1 TATTTTAAA
454121 TATTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
27 2 0.06
28 4 0.12
29 2 0.06
30 2 0.06
31 3 0.09
32 4 0.12
33 17 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTTTAAAATAAATTAAAAATAATATT
Found at i:454102 original size:33 final size:33
Alignment explanation
Indices: 454061--454164 Score: 131
Period size: 33 Copynumber: 3.1 Consensus size: 33
454051 ATATTTTAAA
454061 AAATTTAAAATTAATATTTATTTTTAATATAATT
1 AAATTTAAAA-TAATATTTATTTTTAATATAATT
* * *
454095 AAATTAAAAATAATATTTATTTTAAATATTATT
1 AAATTTAAAATAATATTTATTTTTAATATAATT
454128 AAATTTAAAATAA-ATTT-TTTATTAATATTAAATT
1 AAATTTAAAATAATATTTATTT-TTAATA-T-AATT
454162 AAA
1 AAA
454165 AAAATTGAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.05
32 9 0.15
33 34 0.56
34 15 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
AAATTTAAAATAATATTTATTTTTAATATAATT
Found at i:454138 original size:17 final size:17
Alignment explanation
Indices: 454086--454139 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
454076 ATTTATTTTT
* *
454086 AATATAATTAAATTAAA
1 AATATTATTAAATTTAA
* * *
454103 AATAATATT-TATTTTA
1 AATATTATTAAATTTAA
454119 AATATTATTAAATTTAA
1 AATATTATTAAATTTAA
454136 AATA
1 AATA
454140 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATTAAATTTAA
Found at i:454144 original size:28 final size:26
Alignment explanation
Indices: 454113--454170 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 26
454103 AATAATATTT
*
454113 ATTTTAAATATTATTAAATTTAAAATAA
1 ATTTTAAATAATATTAAA-TTAAAA-AA
* *
454141 ATTTTTTATTAATATTAAATTAAAAAA
1 A-TTTTAAATAATATTAAATTAAAAAA
454168 ATT
1 ATT
454171 GAGTTATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.08
27 3 0.12
28 7 0.27
29 14 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTAAATAATATTAAATTAAAAAA
Found at i:455238 original size:13 final size:15
Alignment explanation
Indices: 455209--455252 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 15
455199 TAAGTAAAAG
455209 AATTATAAATATTAA
1 AATTATAAATATTAA
455224 AATT-TAAAT-TTAA
1 AATTATAAATATTAA
455237 AATTAATTAAATATTA
1 AATT-A-TAAATATTA
455253 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 4 0.16
16 5 0.20
17 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:455761 original size:20 final size:21
Alignment explanation
Indices: 455736--455778 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
455726 GCTCACCAAA
*
455736 AATTTATATATGA-TAAATTT
1 AATTTATATATAATTAAATTT
*
455756 AATTTATATTTAATTAAATTT
1 AATTTATATATAATTAAATTT
455777 AA
1 AA
455779 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTATATATAATTAAATTT
Found at i:455787 original size:21 final size:21
Alignment explanation
Indices: 455749--455823 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
455739 TTATATATGA
* *
455749 TAAATTTAATTTATATTTAAT
1 TAAATTTAAATTAAATTTAAT
* *
455770 TAAATTTAAATAAAATTT-TT
1 TAAATTTAAATTAAATTTAAT
*
455790 TATATTTTAAATTAAA-TTAAT
1 TA-AATTTAAATTAAATTTAAT
*
455811 TTAATTTAAATTA
1 TAAATTTAAATTA
455824 TTATTTATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATTTAAATTAAATTTAAT
Found at i:458645 original size:23 final size:23
Alignment explanation
Indices: 458614--458663 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
458604 TGGAAATTCA
* *
458614 TTTTGTTCA-TTTGATTTTTATAT
1 TTTTCTTCACTTT-ATTTTCATAT
*
458637 TTTTCTTCACTTTATTTTCATCT
1 TTTTCTTCACTTTATTTTCATAT
458660 TTTT
1 TTTT
458664 TCAACTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.14, C:0.12, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTCTTCACTTTATTTTCATAT
Found at i:462563 original size:27 final size:26
Alignment explanation
Indices: 462512--462601 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 26
462502 CACCCATCTG
*
462512 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTC-AAAATGGTGATTATTTTGTA
462539 TTTGTCAAAATGGTGATT-TCCTTTGTA
1 TTTGTCAAAATGGTGATTAT--TTTGTA
* * *
462566 TTTGTCAAATATGGAGACT-TGTT-TA
1 TTTGTCAAA-ATGGTGATTATTTTGTA
462591 TTTGTCAAAAT
1 TTTGTCAAAAT
462602 TTATGGCTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.04
25 12 0.21
26 13 0.23
27 21 0.38
28 8 0.14
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (26 bp):
TTTGTCAAAATGGTGATTATTTTGTA
Found at i:464666 original size:2 final size:2
Alignment explanation
Indices: 464659--464684 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
464649 AACCTTAGAC
464659 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
464685 CTAAGAAACA
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:464948 original size:19 final size:19
Alignment explanation
Indices: 464915--464973 Score: 77
Period size: 17 Copynumber: 3.2 Consensus size: 19
464905 TTAAATCTAT
464915 ATTAAATATTATACTATTTA
1 ATTAAATA-TATACTATTTA
464935 ATTAAATATATACT-TTT-
1 ATTAAATATATACTATTTA
* *
464952 ATTAAATATTTATTATTTA
1 ATTAAATATATACTATTTA
464971 ATT
1 ATT
464974 TTAAATTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 12 0.34
18 6 0.17
19 9 0.26
20 8 0.23
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAAATATATACTATTTA
Found at i:465352 original size:98 final size:98
Alignment explanation
Indices: 465183--465380 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
465173 TGTGGATGGC
465183 AACATATAGGAGCCTATGTAAATCTTAGAGCATTTTGTGGTGGAACCAGTGGATATTCCACCTAC
1 AACATATAGGAGCCTATGTAAATCTTAGAGCATTTTGTGGTGGAACCAGTGGATATTCCACCTAC
465248 AAGCTATTAGAAAAATAAAGACAATAAAAGAAG
66 AAGCTATTAGAAAAATAAAGACAATAAAAGAAG
465281 AACATATAGGAGCCTATGTAAATCTTAGAGCATTTTGTGGTGGAACCAGTGGATATTCCACCTAC
1 AACATATAGGAGCCTATGTAAATCTTAGAGCATTTTGTGGTGGAACCAGTGGATATTCCACCTAC
465346 AAGCTATTAGAAAAATAAAGACAATAAAAGAAG
66 AAGCTATTAGAAAAATAAAGACAATAAAAGAAG
465379 AA
1 AA
465381 ACAGAACATC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.24
Consensus pattern (98 bp):
AACATATAGGAGCCTATGTAAATCTTAGAGCATTTTGTGGTGGAACCAGTGGATATTCCACCTAC
AAGCTATTAGAAAAATAAAGACAATAAAAGAAG
Found at i:465662 original size:24 final size:27
Alignment explanation
Indices: 465589--465659 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
465579 AAACAAGCCT
* *
465589 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
465617 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
465644 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
465660 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:470236 original size:24 final size:27
Alignment explanation
Indices: 470163--470233 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
470153 AAACAAGCCT
* *
470163 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
470191 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
470218 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
470234 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:470607 original size:21 final size:20
Alignment explanation
Indices: 470570--470608 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
470560 TAATTAAATT
**
470570 TAAATAAAATTTTTATTATA
1 TAAATAAAATTCATATTATA
470590 TAAATAATAATTCATATTA
1 TAAATAA-AATTCATATTA
470609 GATCGTATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATAAAATTCATATTATA
Found at i:471540 original size:20 final size:22
Alignment explanation
Indices: 471497--471540 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
471487 TTAATTTTAA
*
471497 TTTTTCTTATTTTTAATTCTTTT
1 TTTTTCTTATTTTT-ATTCCTTT
471520 TTTTTCTT-TTTTT-TTCCTTT
1 TTTTTCTTATTTTTATTCCTTT
471540 T
1 T
471541 AATTCCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCTTATTTTTATTCCTTT
Found at i:473063 original size:2 final size:2
Alignment explanation
Indices: 473056--473086 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
473046 TTTTAACTTG
473056 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
473087 ACCGTAGGTC
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:475518 original size:20 final size:18
Alignment explanation
Indices: 475484--475541 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
475474 ACTATTTACC
475484 TTTTAAT-TTTAAAATTACT
1 TTTTAATATTT-AAATTA-T
475503 TATTTAATATTTAAATTAT
1 T-TTTAATATTTAAATTAT
*
475522 TTTT-TTATTTAAATTGAT
1 TTTTAATATTTAAATT-AT
475540 TT
1 TT
475542 ATTTGGTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 10 0.29
18 7 0.20
19 3 0.09
20 12 0.34
21 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTAATATTTAAATTAT
Found at i:476043 original size:18 final size:19
Alignment explanation
Indices: 475999--476043 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
475989 GAATTGGATA
475999 AAAACTTATTTTATTATTT
1 AAAACTTATTTTATTATTT
476018 AAAA-TTATTTT-TGT-TTT
1 AAAACTTATTTTAT-TATTT
476035 AAAACTTAT
1 AAAACTTAT
476044 AACTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
AAAACTTATTTTATTATTT
Found at i:476700 original size:13 final size:14
Alignment explanation
Indices: 476674--476712 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
476664 TCTCAAAATT
476674 TTTTAAAAATATGA
1 TTTTAAAAATATGA
476688 TTTTAAAAA-ATGA
1 TTTTAAAAATATGA
476701 TTATTAAAAATA
1 TT-TTAAAAATA
476713 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 16 0.70
15 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATATGA
Found at i:477223 original size:18 final size:20
Alignment explanation
Indices: 477180--477224 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
477170 TTGAACCATT
*
477180 AATAAAAATTATTCTCATAA
1 AATAAAAATTATTCTAATAA
477200 AATAAAAATTA-T-TAATAA
1 AATAAAAATTATTCTAATAA
*
477218 AGTAAAA
1 AATAAAA
477225 TCTCAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAATTATTCTAATAA
Found at i:477360 original size:20 final size:20
Alignment explanation
Indices: 477331--477372 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
477321 ATATAAATAA
*
477331 TAATTTAAA-TAAAATAAAAT
1 TAATTAAAATTAAAA-AAAAT
477351 TAATTAAAATTAAAAAAAAT
1 TAATTAAAATTAAAAAAAAT
477371 TA
1 TA
477373 CCAACCGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATTAAAATTAAAAAAAAT
Found at i:480966 original size:14 final size:14
Alignment explanation
Indices: 480947--481001 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
480937 ATATTTAATT
480947 TATTTTAATATTTA
1 TATTTTAATATTTA
* *
480961 TATTTTTTAAAAATTA
1 TA--TTTTAATATTTA
480977 TATGTTT-ATATTTA
1 TAT-TTTAATATTTA
480991 TATTTTAATAT
1 TATTTTAATAT
481002 GTGTTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.09
14 15 0.45
15 3 0.09
16 12 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTTTAATATTTA
Found at i:480970 original size:16 final size:16
Alignment explanation
Indices: 480949--480996 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
480939 ATTTAATTTA
480949 TTTTAATATTTATATT
1 TTTTAATATTTATATT
* *
480965 TTTTAAAAATTATA-T
1 TTTTAATATTTATATT
*
480980 GTTT-ATATTTATATT
1 TTTTAATATTTATATT
480995 TT
1 TT
480997 AATATGTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTAATATTTATATT
Found at i:481568 original size:2 final size:2
Alignment explanation
Indices: 481561--481592 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
481551 TGAAATTTTC
481561 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
481593 GAAACAAATG
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):
TA
Found at i:484702 original size:11 final size:11
Alignment explanation
Indices: 484686--484710 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
484676 ACATTACTTT
484686 TTTTTTATATA
1 TTTTTTATATA
484697 TTTTTTATATA
1 TTTTTTATATA
484708 TTT
1 TTT
484711 ATTTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTATATA
Found at i:484702 original size:13 final size:12
Alignment explanation
Indices: 484683--484721 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
484673 GATACATTAC
484683 TTTTTTTTTATA
1 TTTTTTTTTATA
*
484695 TATTTTTTATATA
1 T-TTTTTTTTATA
484708 TTTATTTTTTATA
1 TTT-TTTTTTATA
484721 T
1 T
484722 GTTTATCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTATA
Found at i:484713 original size:15 final size:15
Alignment explanation
Indices: 484695--484727 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
484685 TTTTTTTATA
484695 TATTTTTTATATATT
1 TATTTTTTATATATT
*
484710 TATTTTTTATATGTT
1 TATTTTTTATATATT
484725 TAT
1 TAT
484728 CGAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TATTTTTTATATATT
Found at i:485532 original size:38 final size:38
Alignment explanation
Indices: 485490--485570 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
485480 AATATGATAA
*
485490 ATAAAATATAAGATATTTAAATAAAATTAATTTAATGT
1 ATAAAATATAAGATATTTAAATAAAATTAATATAATGT
* * * * *
485528 ATAAATTTTAATATGTTTAAATAAGATTAATATAATGT
1 ATAAAATATAAGATATTTAAATAAAATTAATATAATGT
485566 ATAAA
1 ATAAA
485571 TTTTAATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (38 bp):
ATAAAATATAAGATATTTAAATAAAATTAATATAATGT
Found at i:485571 original size:38 final size:38
Alignment explanation
Indices: 485505--485577 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
485495 ATATAAGATA
*
485505 TTTAAATAAAATTAATTTAATGTATAAATTTTAATATG
1 TTTAAATAAAATTAATATAATGTATAAATTTTAATATG
*
485543 TTTAAATAAGATTAATATAATGTATAAATTTTAAT
1 TTTAAATAAAATTAATATAATGTATAAATTTTAAT
485578 GAACATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTAAATAAAATTAATATAATGTATAAATTTTAATATG
Found at i:485576 original size:19 final size:19
Alignment explanation
Indices: 485516--485577 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
485506 TTAAATAAAA
*
485516 TTAATTTAATGTATAAATT
1 TTAATATAATGTATAAATT
* * * **
485535 TTAATAT-GTTTAAATAAGA
1 TTAATATAATGTATA-AATT
485554 TTAATATAATGTATAAATT
1 TTAATATAATGTATAAATT
485573 TTAAT
1 TTAAT
485578 GAACATAATA
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (19 bp):
TTAATATAATGTATAAATT
Found at i:489315 original size:24 final size:23
Alignment explanation
Indices: 489247--489311 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 23
489237 AATTATTGTT
* * *
489247 TAATTAAAAAAATTATTTAAAAT
1 TAATTATAAATATTATTTAAAAA
*
489270 TAATTATAAATATTAATATAAAAA
1 TAATTATAAATATT-ATTTAAAAA
* *
489294 TAATTTTTAATATTATTT
1 TAATTATAAATATTATTT
489312 TAAATAGTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTATAAATATTATTTAAAAA
Found at i:489316 original size:36 final size:36
Alignment explanation
Indices: 489246--489317 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
489236 AAATTATTGT
489246 TTAATTAAAAAAATTATTTAAAATTAATTATAAATA
1 TTAATTAAAAAAATTATTTAAAATTAATTATAAATA
* *
489282 TTAATATAAAAATAATT-TTTAATATT-ATTTTAAATA
1 TTAAT-TAAAAA-AATTATTTAAAATTAATTATAAATA
489318 GTAAAATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 14 0.44
37 14 0.44
38 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
TTAATTAAAAAAATTATTTAAAATTAATTATAAATA
Found at i:489470 original size:14 final size:14
Alignment explanation
Indices: 489451--489484 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
489441 AAAAATAAAA
489451 AAAATTTAAATATT
1 AAAATTTAAATATT
*
489465 AAAATTTAAATTTT
1 AAAATTTAAATATT
489479 AAAATT
1 AAAATT
489485 ATTGACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:490104 original size:14 final size:14
Alignment explanation
Indices: 490085--490112 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
490075 ACTAAATCTT
490085 GTTTTTTTTTTAAA
1 GTTTTTTTTTTAAA
490099 GTTTTTTTTTTAAA
1 GTTTTTTTTTTAAA
490113 TTTAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
GTTTTTTTTTTAAA
Found at i:492256 original size:33 final size:32
Alignment explanation
Indices: 492203--492302 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 32
492193 AAGGCGGAGG
*
492203 AAAGAGAAGGAAAAGAAGAGGAGAAGGAAAGAA
1 AAAGAGAAGGAAAAGAAGAGGA-AAAGAAAGAA
492236 AAAGAG-AGAGAAGAAG-AGAGGAAAAGAAAG-A
1 AAAGAGAAG-GAA-AAGAAGAGGAAAAGAAAGAA
* *
492267 AGAGA-AAAGAGAAAGAA-AGG-AAAGAAAAGAA
1 AAAGAGAAGGA-AAAGAAGAGGAAAAG-AAAGAA
492298 AAAGA
1 AAAGA
492303 AGGAGAAATC
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
29 4 0.07
30 12 0.21
31 13 0.23
32 9 0.16
33 15 0.27
34 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (32 bp):
AAAGAGAAGGAAAAGAAGAGGAAAAGAAAGAA
Found at i:492281 original size:20 final size:20
Alignment explanation
Indices: 492231--492303 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
492221 AGGAGAAGGA
*
492231 AAGA-AAAAGAGAGAG-AAG
1 AAGAGAAAAGAGAAAGAAAG
*
492249 AAGAG--AGGA-AAAGAAAG
1 AAGAGAAAAGAGAAAGAAAG
492266 AAGAGAAAAGAGAAAGAAAGG
1 AAGAGAAAAGAGAAAGAAA-G
*
492287 AA-AGAAAAGAAAAAGAA
1 AAGAGAAAAGAGAAAGAA
492304 GGAGAAATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.07
17 11 0.24
18 4 0.09
19 3 0.07
20 21 0.47
21 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
AAGAGAAAAGAGAAAGAAAG
Found at i:492839 original size:246 final size:245
Alignment explanation
Indices: 492394--492858 Score: 643
Period size: 246 Copynumber: 1.9 Consensus size: 245
492384 GGTAAATTTC
* * * *
492394 ATTTATTTTCACCATCTATTTACTTTTTTTTTTTTTGGTAAATTGCTGGAAATGAGACAACTTTA
1 ATTTATTTTCACCATCTATTTACTTTTTTATTTTTTGGTAAATTGCTGAAAATGAGACAAATTCA
492459 CATAAGCGAAAAAGGAAGTGAAAATTGTAGCTTAATTTTGAGTAGGAAATGTCTTTATTGCAATG
66 CATAAGCGAAAAAGGAAGTGAAAATTGTAGCTTAATTTTGAGTAGGAAATGTCTTTATTGCAATG
* * * * * *
492524 TTGGATGCAGTTCTTGTAGAATGTCATATTTCAGTTGCCAAGGTTGTCTTTTTACGTTAGAAGAA
131 CTGGAT-CAGTTCTTGCAGAATCTCATATTTCAGTTGCCAAGGTTATCCTTTTACGTTACAAGAA
*
492589 TGCTGATTCCAAGGTTTTATTATGGTTAGATTGAATTTTTTTTTATTTTTT
195 TGCTGATTCCAAGGTTCTATTATGGTTAGATTGAATTTTTTTTTATTTTTT
*
492640 ATTTATTTTCATCC-TCTATTTACTTTTTTATTTTTTGAG-AAATTGTTGAAAATGAGACAAATT
1 ATTTATTTTCA-CCATCTATTTACTTTTTTATTTTTTG-GTAAATTGCTGAAAATGAGACAAATT
** * * * *
492703 CACATGTGTGAAAATGGAAGTGAAAATTGTAGCTTGATTTTGAGCT-GGAAATGTTTTTATTGCA
64 CACATAAGCGAAAAAGGAAGTGAAAATTGTAGCTTAATTTTGAG-TAGGAAATGTCTTTATTGCA
* *
492767 ATGCTGGAT-ATGTTTCTTGCAGAATCTTATATTTCAGTTGCCAAGGTTATCCTTTTATGTTAC-
128 ATGCTGGATCA-G-TTCTTGCAGAATCTCATATTTCAGTTGCCAAGGTTATCCTTTTACGTTACA
*
492830 AGAAATGCTGGTTCCAAGGTTCTATTATG
191 AG-AATGCTGATTCCAAGGTTCTATTATG
492859 ATTGAGACTT
Statistics
Matches: 192, Mismatches: 21, Indels: 12
0.85 0.09 0.05
Matches are distributed among these distances:
244 1 0.01
245 3 0.02
246 184 0.96
247 4 0.02
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (245 bp):
ATTTATTTTCACCATCTATTTACTTTTTTATTTTTTGGTAAATTGCTGAAAATGAGACAAATTCA
CATAAGCGAAAAAGGAAGTGAAAATTGTAGCTTAATTTTGAGTAGGAAATGTCTTTATTGCAATG
CTGGATCAGTTCTTGCAGAATCTCATATTTCAGTTGCCAAGGTTATCCTTTTACGTTACAAGAAT
GCTGATTCCAAGGTTCTATTATGGTTAGATTGAATTTTTTTTTATTTTTT
Found at i:496325 original size:24 final size:24
Alignment explanation
Indices: 496275--496354 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
496265 AAAATTAATT
* ** *
496275 TTATTATTTAAAATAATATAAAAAA
1 TTATT-TTTAAATTAATATTTATAA
496300 TTATTTTTAAATTAATATTTATAA
1 TTATTTTTAAATTAATATTTATAA
** * * *
496324 TTAAATTTAAATAAAATATTTTTTA
1 TTATTTTTAAAT-TAATATTTATAA
496349 TTATTT
1 TTATTT
496355 AATATCATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
24 25 0.58
25 18 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTTTTAAATTAATATTTATAA
Found at i:496338 original size:42 final size:41
Alignment explanation
Indices: 496266--496347 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
496256 TTAAATTTAA
*
496266 AAATTAATTTTATTATTTAAAATAATATAAAAAATTATTTTT
1 AAATTAATTTTATTAATTAAAATAATATAAAAAATT-TTTTT
* *
496308 AAATTAATATTTA-TAATTAAATTTAA-ATAAAATATTTTTT
1 AAATTAAT-TTTATTAATTAAA-ATAATATAAAAAATTTTTT
496348 ATTATTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 4 0.11
42 24 0.69
43 7 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (41 bp):
AAATTAATTTTATTAATTAAAATAATATAAAAAATTTTTTT
Found at i:496449 original size:13 final size:13
Alignment explanation
Indices: 496431--496456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
496421 GAAAGCTAAA
496431 CTTATTAAATTGT
1 CTTATTAAATTGT
496444 CTTATTAAATTGT
1 CTTATTAAATTGT
496457 ACAAAGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTATTAAATTGT
Found at i:496753 original size:2 final size:2
Alignment explanation
Indices: 496746--496775 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
496736 CTCCAAAAGC
496746 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
496776 GCAAATTCTC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:502308 original size:14 final size:14
Alignment explanation
Indices: 502289--502319 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
502279 AGAACAATAT
*
502289 AACCAACGCATGAG
1 AACCAACACATGAG
502303 AACCAACACATGAG
1 AACCAACACATGAG
502317 AAC
1 AAC
502320 TTGGTATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.29, G:0.16, T:0.06
Consensus pattern (14 bp):
AACCAACACATGAG
Found at i:502608 original size:86 final size:87
Alignment explanation
Indices: 502463--502641 Score: 308
Period size: 86 Copynumber: 2.1 Consensus size: 87
502453 GGAGAAACTA
*
502463 ACAGTTTATCCATGCAGACAACATCTGCAAGCAAACATATTAAGCTCTAATCATTCATGATAAGG
1 ACAGTTTATCCATGCAGACAACATCTGCAAGCAAACATATTAAGCTCTAATCATTCATGATAAGA
*
502528 AATTTTTCTTTGTTGCTGC-TG
66 AATTTTGCTTTGTTGCTGCTTG
* *
502549 ACAGTTTATCCATGCAGATACCATCTGCAAGCAAACATATTAAGCTCTAATCATTCATGATAAGA
1 ACAGTTTATCCATGCAGACAACATCTGCAAGCAAACATATTAAGCTCTAATCATTCATGATAAGA
502614 AATTTTGCTTTGTTGCTGCTTG
66 AATTTTGCTTTGTTGCTGCTTG
502636 -CAGTTT
1 ACAGTTT
502642 TCTAAAATTA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 86 0.98
87 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (87 bp):
ACAGTTTATCCATGCAGACAACATCTGCAAGCAAACATATTAAGCTCTAATCATTCATGATAAGA
AATTTTGCTTTGTTGCTGCTTG
Found at i:503238 original size:2 final size:2
Alignment explanation
Indices: 503233--503274 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
503223 TTAAAATAAA
* *
503233 AT AT AT TT AT AT CAT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
503275 ATCTAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:507506 original size:33 final size:33
Alignment explanation
Indices: 507465--507530 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
507455 GGTCAGGAAT
507465 TGGCATCGGGTACGGGCTAGGAGATGGGAGTGG
1 TGGCATCGGGTACGGGCTAGGAGATGGGAGTGG
* *
507498 TGGCATCGGGTATGGGTTAGGAGATGGGAGTGG
1 TGGCATCGGGTACGGGCTAGGAGATGGGAGTGG
507531 GTTAGGAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.18, C:0.09, G:0.52, T:0.21
Consensus pattern (33 bp):
TGGCATCGGGTACGGGCTAGGAGATGGGAGTGG
Found at i:507567 original size:42 final size:42
Alignment explanation
Indices: 507498--507604 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
507488 ATGGGAGTGG
* * * * *
507498 TGGCATCGGGTATGGGTTAGGAGATGGGAGTGGGTTAGGAAC
1 TGGCATTGGATATGGATTAGGAGATGGGAGTGGATCAGGAAC
* *
507540 TGGTATTGGATATGGTTTAGGAGATGGGAGTGGATCAGGAAC
1 TGGCATTGGATATGGATTAGGAGATGGGAGTGGATCAGGAAC
*
507582 TGGCATTGGGTATGGATTAGGAG
1 TGGCATTGGATATGGATTAGGAG
507605 GCGGTAATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.23, C:0.06, G:0.44, T:0.27
Consensus pattern (42 bp):
TGGCATTGGATATGGATTAGGAGATGGGAGTGGATCAGGAAC
Found at i:507693 original size:63 final size:63
Alignment explanation
Indices: 507620--507926 Score: 347
Period size: 63 Copynumber: 5.0 Consensus size: 63
507610 AATGGCTATT
* * * * * ** * * * *
507620 GGCCTGGGTCTGGTTTTGGATATGGACTTGGAATTGGATCAGGACCCGGTGGATTTGAGTTAG
1 GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
* * * * * * *
507683 GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGATCAGG---A---GGATTTGGGCTTG
1 GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
* * *
507740 GGCCTGGATCTGGGGTTGGAGAAGGAATTGGAATTGGAGGAGGACAAGGCGGATATGGGATAG
1 GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
*
507803 GGCCTGGGTCTGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
1 GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
* * *
507866 GGCCTGGGTCTGGGGTTGGAGAAGGAATTGGGATTGGAGGAGGACAAGGCGGATATGGGAT
1 GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGAT
507927 TGGAGAAGGA
Statistics
Matches: 216, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
57 46 0.21
60 1 0.00
63 169 0.78
ACGTcount: A:0.23, C:0.09, G:0.44, T:0.24
Consensus pattern (63 bp):
GGCCTGGGTCTGGGTTTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAG
Found at i:507731 original size:57 final size:58
Alignment explanation
Indices: 507620--507777 Score: 176
Period size: 57 Copynumber: 2.7 Consensus size: 58
507610 AATGGCTATT
* *
507620 GGCCTGGGTCTGGTTTTGGATATGGACTTGGAATTGGATCAGGACCCGGTGGATTTGAG-TTAG
1 GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGATCAGGA--C---GGATTTGAGCTT-G
*
507683 GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGATCAGGA-GGATTTGGGCTTG
1 GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGATCAGGACGGATTTGAGCTTG
* ** * *
507740 GGCCTGGATCTGGGGTTGGAGAAGGAATTGGAATTGGA
1 GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGA
507778 GGAGGACAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
57 42 0.49
58 2 0.02
63 42 0.49
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.30
Consensus pattern (58 bp):
GGCCTGGGTCTGGATTTGGATATGGAATTGGAATTGGATCAGGACGGATTTGAGCTTG
Found at i:507943 original size:108 final size:108
Alignment explanation
Indices: 507813--508033 Score: 284
Period size: 108 Copynumber: 2.0 Consensus size: 108
507803 GGCCTGGGTC
* * * *
507813 TGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAGGGCCTGGG-TCT
1 TGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCAGACATGGAACAGGGCCTGGGAT-T
* * * * *
507877 GGGGTTGGAGAAGGAATTGGGATTGGA-GGAGGACAAGGCGGATA
65 GGGATCGGAAAAGGAATTGGAATTGGATCG-GGACAAGGCGGATA
* * *
507921 TGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACCAGGTAGACATGGAACAGGGCCTGGGATTG
1 TGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCAGACATGGAACAGGGCCTGGGATTG
* *
507986 GGATCGGAAAAGGAATTGGAATTGGATCGGGACCAGGTGGATA
66 GGATCGGAAAAGGAATTGGAATTGGATCGGGACAAGGCGGATA
508029 TGGGA
1 TGGGA
508034 CAGGGCCTGG
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
108 95 0.98
109 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.44, T:0.19
Consensus pattern (108 bp):
TGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCAGACATGGAACAGGGCCTGGGATTG
GGATCGGAAAAGGAATTGGAATTGGATCGGGACAAGGCGGATA
Found at i:507951 original size:171 final size:171
Alignment explanation
Indices: 507745--508094 Score: 461
Period size: 171 Copynumber: 2.0 Consensus size: 171
507735 GCTTGGGCCT
* * * * * *
507745 GGATCTGGGGTTGGAGAAGGAATTGGAATTGGAGGAGGACAAGGCGGATATGGGATAGGGCCTGG
1 GGATATGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACAAGGCAGACATGGAACAGGGCCTGG
* * *
507810 G-TCTGGGATTGGAGAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGATAGGGCCTGGG
66 GAT-TGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGACAGGGCCTGGG
* * * * *
507874 -TCTGGGGTTGGAGAAGGAATTGGGATTGGAGGAGGACAAGGC
130 AT-TGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGC
* *
507916 GGATATGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACCAGGTAGACATGGAACAGGGCCTGG
1 GGATATGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACAAGGCAGACATGGAACAGGGCCTGG
* * * *
507981 GATTGGGATCGGAAAAGGAATTGGAATTGGATCGGGACCAGGTGGATATGGGACAGGGCCTGGGA
66 GATTGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGACAGGGCCTGGGA
* * *
508046 TTGGGATCGGAAAAGGAATTGGAATTGGATCAGGACCAGGT
131 TTGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGC
508087 GGATATGG
1 GGATATGG
508095 TACTGGGCCT
Statistics
Matches: 154, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
171 152 0.99
172 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.44, T:0.19
Consensus pattern (171 bp):
GGATATGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACAAGGCAGACATGGAACAGGGCCTGG
GATTGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGCGGATATGGGACAGGGCCTGGGA
TTGGGATCGGAAAAGGAATTGGAATTGGAGCAGGACAAGGC
Found at i:507988 original size:63 final size:63
Alignment explanation
Indices: 507916--508410 Score: 559
Period size: 63 Copynumber: 7.7 Consensus size: 63
507906 AGGACAAGGC
* ** * *
507916 GGATATGGGATTGGAGAAGGAATTGGAATTGGAGGAGGACCAGGTAGACATGGAACAGGGCCTG
1 GGAT-TGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
* * *
507980 GGATTGGGATCGGAAAAGGAATTGGAATTGGATCGGGACCAGGTGGATATGGGACAGGGCCTG
1 GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
* * *
508043 GGATTGGGATCGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGTACTGGGCCTG
1 GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
* * * * * * *
508106 AGACTGGGATCGGAAAGGGAATTGGAATTGGAACAGGACCAGGAGGACT-TGGGACAGGGCCTG
1 GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGA-TATGGAACAGGGCCTG
* * *
508169 GGATTGGGGTTGGAAAAGGAGTTGGAATTGGATCAGGACCAGGTGGATATGTG-ACAGGGCCTT
1 GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATG-GAACAGGGCCTG
* * * * * **
508232 GG-TCTGGGGTTGGAAAAGGAATTGGAATCGGATTAGGACCGGGTGGGTATGTTACAGGGCCTG
1 GGAT-TGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
* * * *
508295 GGTTTGGGATTGGAAAAGGCATTGGAATTGGATCAGGTCCAGGTGGATATGAAACAGGGCCT-
1 GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
508357 GGATCT-GGAGTTGGAGAAGGAATAGGAATTGGAATTGGATCAGGACCAGGTGGA
1 GGAT-TGGGA-TT-G-G-A--AA-AGGAATTGGAATTGGATCAGGACCAGGTGGA
508411 CATAATTCTG
Statistics
Matches: 371, Mismatches: 46, Indels: 23
0.84 0.10 0.05
Matches are distributed among these distances:
62 8 0.02
63 322 0.87
64 8 0.02
65 1 0.00
66 1 0.00
68 2 0.01
69 29 0.08
ACGTcount: A:0.28, C:0.11, G:0.41, T:0.21
Consensus pattern (63 bp):
GGATTGGGATTGGAAAAGGAATTGGAATTGGATCAGGACCAGGTGGATATGGAACAGGGCCTG
Found at i:518180 original size:32 final size:30
Alignment explanation
Indices: 518127--518244 Score: 83
Period size: 32 Copynumber: 4.1 Consensus size: 30
518117 TATTTAAAAA
* *
518127 ATATTTATATATATATATATATAATATATT
1 ATATTTATATTTATATTTATATAATATATT
* *
518157 ATAATTTAATATTTATATTTATATTATTTATT
1 AT-ATTT-ATATTTATATTTATATAATATATT
* *
518189 AT-TTT-T-TATATA-TTATATTATA-ATT
1 ATATTTATATTTATATTTATATAATATATT
*
518214 ATATTT-T-TTTAT-TATA-ATAATAATATT
1 ATATTTATATTTATATTTATATAAT-ATATT
518241 ATAT
1 ATAT
518245 CAATATTGCG
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
25 9 0.12
26 20 0.27
27 12 0.16
28 1 0.01
30 5 0.07
31 4 0.05
32 22 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATTTATATTTATATTTATATAATATATT
Found at i:518181 original size:6 final size:6
Alignment explanation
Indices: 518127--518219 Score: 57
Period size: 6 Copynumber: 15.0 Consensus size: 6
518117 TATTTAAAAA
* * *
518127 ATATTT ATATAT ATATAT ATA-TA ATATATT ATAATTT AATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATAT-TT AT-ATTT -ATATTT ATATTT
* * *
518177 ATA-TT ATTTATT ATTTTTT ATATATT ATA-TT ATAATT ATATTT
1 ATATTT ATAT-TT A-TATTT ATAT-TT ATATTT ATATTT ATATTT
518220 TTTTATTATA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
5 12 0.17
6 32 0.45
7 20 0.28
8 7 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:518188 original size:19 final size:20
Alignment explanation
Indices: 518127--518218 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 20
518117 TATTTAAAAA
*
518127 ATATTTATA-TATA-TATAT
1 ATATTTATATTATATTATTT
*
518145 ATATAATATATTATA--ATTT
1 ATAT-TTATATTATATTATTT
518164 AATATTTATATTTATATTATTT
1 -ATATTTATA-TTATATTATTT
*
518186 ATTATTT-TTTATATATTATATT
1 A-TATTTATAT-TATATTAT-TT
*
518208 ATAATTATATT
1 ATATTTATATT
518219 TTTTTATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.07
19 11 0.19
20 14 0.24
21 15 0.26
22 14 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTATATTATATTATTT
Found at i:518200 original size:27 final size:26
Alignment explanation
Indices: 518144--518244 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 26
518134 TATATATATA
* * *
518144 TATATAATATATTATAATT-TAATATT
1 TATATATTATATTAT-ATTATATTTTT
518170 TATAT-TTATATTAT-TTATTATTTTT
1 TATATATTATATTATATTA-TATTTTT
518195 TATATATTATATTATAATTATATTTTT
1 TATATATTATATTAT-ATTATATTTTT
* *
518222 T-TATTATAATAATAATATTATAT
1 TATA-TATTAT-ATTATATTATAT
518245 CAATATTGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.03
25 18 0.29
26 16 0.25
27 20 0.32
28 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATATTATATTATATTATATTTTT
Found at i:518208 original size:26 final size:26
Alignment explanation
Indices: 518144--518229 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 26
518134 TATATATATA
* *
518144 TATATAATATATTATAATT-TAATATT
1 TATATATTATATTATAATTAT-ATTTT
*
518170 TATAT-TTATATTATTTATTAT-TTTT
1 TATATATTATATTA-TAATTATATTTT
518195 TATATATTATATTATAATTATATTTT
1 TATATATTATATTATAATTATATTTT
518221 T-T-TATTATA
1 TATATATTATA
518230 ATAATAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
24 7 0.13
25 22 0.42
26 22 0.42
27 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATATTATATTATAATTATATTTT
Found at i:518490 original size:13 final size:13
Alignment explanation
Indices: 518472--518539 Score: 56
Period size: 13 Copynumber: 5.6 Consensus size: 13
518462 AACTTACATT
518472 TTATATAAAAATA
1 TTATATAAAAATA
*
518485 TTATATAAAAGTA
1 TTATATAAAAATA
518498 --ATAT--AAATA
1 TTATATAAAAATA
*
518507 TAATATAAAAATA
1 TTATATAAAAATA
* * *
518520 -AAAATAAAAAAA
1 TTATATAAAAATA
518532 TTATATAA
1 TTATATAA
518540 TATAAATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 4 0.09
11 8 0.18
12 10 0.23
13 22 0.50
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (13 bp):
TTATATAAAAATA
Found at i:518553 original size:13 final size:14
Alignment explanation
Indices: 518529--518605 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 14
518519 AAAAATAAAA
518529 AAATTATATAATAT
1 AAATTATATAATAT
518543 AAATTAT-TAATATATT
1 AAATTATAT-A-ATA-T
518559 AAATTTATATAAATAT
1 AAA-TTATAT-AATAT
* *
518575 ATAATAATTTAATAT
1 A-AATTATATAATAT
518590 -AATTATA-ATATAT
1 AAATTATATA-ATAT
518603 AAA
1 AAA
518606 AATAATACGA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
12 1 0.02
13 10 0.20
14 10 0.20
15 8 0.16
16 10 0.20
17 9 0.18
18 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTATATAATAT
Found at i:518587 original size:34 final size:34
Alignment explanation
Indices: 518532--518609 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 34
518522 AATAAAAAAA
*
518532 TTATAT-AATATAAATTATTAATAT-ATTA-AAT
1 TTATATAAATATAAATAATTAATATAATTATAAT
518563 TTATATAAATATATAATAATTTAATATAATTATAAT
1 TTATATAAATATA-AATAA-TTAATATAATTATAAT
* *
518599 ATATAAAAATA
1 TTATATAAATA
518610 ATACGAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.15
32 6 0.15
33 4 0.10
34 7 0.18
35 4 0.10
36 12 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
TTATATAAATATAAATAATTAATATAATTATAAT
Found at i:518589 original size:21 final size:19
Alignment explanation
Indices: 518541--518599 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
518531 ATTATATAAT
* *
518541 ATAAATTAT-TAATATATT
1 ATAATTTATATAATATATA
518559 A-AATTTATATAAATATATA
1 ATAATTTATAT-AATATATA
518578 ATAATTTAATATAAT-TATA
1 ATAATTT-ATATAATATATA
518597 ATA
1 ATA
518600 TATAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 6 0.17
18 2 0.06
19 15 0.43
20 8 0.23
21 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATTTATATAATATATA
Found at i:519765 original size:20 final size:20
Alignment explanation
Indices: 519742--519781 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
519732 AATTATATTT
*
519742 ATAATACATAAATTAAAATA
1 ATAATACATAAAATAAAATA
**
519762 ATAATTTATAAAATAAAATA
1 ATAATACATAAAATAAAATA
519782 TTTTCATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATACATAAAATAAAATA
Found at i:521595 original size:19 final size:20
Alignment explanation
Indices: 521571--521614 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
521561 GAAACCACCT
521571 ATTTAT-AAAAT-AAAAAAA
1 ATTTATCAAAATCAAAAAAA
*
521589 CATTTATCAAAATCAAATAAA
1 -ATTTATCAAAATCAAAAAAA
521610 ATTTA
1 ATTTA
521615 ATAGTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTTATCAAAATCAAAAAAA
Found at i:523224 original size:14 final size:14
Alignment explanation
Indices: 523190--523227 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
523180 TATGATATGA
523190 ATATATAT-TTAAT
1 ATATATATATTAAT
*
523203 ATAAATATATTAAT
1 ATATATATATTAAT
*
523217 ATTTATATATT
1 ATATATATATT
523228 TTATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATATATTAAT
Found at i:523530 original size:13 final size:13
Alignment explanation
Indices: 523512--523536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
523502 ATTAACTTTT
523512 CTATTATATAATG
1 CTATTATATAATG
523525 CTATTATATAAT
1 CTATTATATAAT
523537 ATTGAAATTA
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTATTATATAATG
Found at i:526931 original size:27 final size:27
Alignment explanation
Indices: 526900--526959 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
526890 GAGCTAGTAC
526900 CTCCAAGTCCAGCCTCATCATCAGAGG
1 CTCCAAGTCCAGCCTCATCATCAGAGG
526927 CTCCAAGTCCAGCCTCATCATCAGAGG
1 CTCCAAGTCCAGCCTCATCATCAGAGG
526954 CTCCAA
1 CTCCAA
526960 CTTCGGCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.18
Consensus pattern (27 bp):
CTCCAAGTCCAGCCTCATCATCAGAGG
Found at i:532196 original size:12 final size:12
Alignment explanation
Indices: 532174--532211 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
532164 TTATTTTTTA
532174 AATATTTATATTT
1 AATA-TTATATTT
532187 AATATTATATTT
1 AATATTATATTT
*
532199 GATA-TATATTT
1 AATATTATATTT
532210 AA
1 AA
532212 ATTGAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 11 0.48
13 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
AATATTATATTT
Found at i:532449 original size:23 final size:22
Alignment explanation
Indices: 532402--532463 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
532392 TAATTATATG
532402 AAATAA-A-TATTATATAATAA
1 AAATAATATTATTATATAATAA
* *
532422 TAATAATATTATTATATTATTAA
1 AAATAATATTATTATA-TAATAA
532445 AAATAATATTA--ATATAATA
1 AAATAATATTATTATATAATA
532464 TGTATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 9 0.26
21 4 0.11
22 7 0.20
23 15 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATATTATTATATAATAA
Found at i:535813 original size:17 final size:18
Alignment explanation
Indices: 535791--535829 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
535781 ACAACTATGC
*
535791 ATTATGATTCATTTT-TA
1 ATTATGATTAATTTTATA
535808 ATTATGATTAATTTTATA
1 ATTATGATTAATTTTATA
535826 ATTA
1 ATTA
535830 ATATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTATGATTAATTTTATA
Found at i:535906 original size:27 final size:25
Alignment explanation
Indices: 535874--535951 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 25
535864 TTATAATTAT
535874 AATTAAAATATTTTATATTTATATA
1 AATTAAAATATTTTATATTTATATA
* * *
535899 AATTTTAACATA-TTAATAATTTAATTTA
1 AA--TTAAAATATTTTAT-ATTT-ATATA
535927 AATTAAAATATTTATATATTTATAT
1 AATTAAAATATTT-TATATTTATAT
535952 TATATATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
25 2 0.05
26 14 0.34
27 17 0.41
28 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
AATTAAAATATTTTATATTTATATA
Found at i:536471 original size:10 final size:10
Alignment explanation
Indices: 536456--536688 Score: 80
Period size: 10 Copynumber: 25.1 Consensus size: 10
536446 AAAACATCAT
536456 ATATAATATA
1 ATATAATATA
536466 ATATAATATA
1 ATATAATATA
536476 ATATAATATA
1 ATATAATATA
*
536486 A-ATAAAATA
1 ATATAATATA
536495 A-A-AATAT-
1 ATATAATATA
536502 ATA-AATAT-
1 ATATAATATA
*
536510 ATA-AATATTT
1 ATATAATA-TA
*
536520 ATATGA-ATA
1 ATATAATATA
536529 AT-TAATAT-
1 ATATAATATA
* * *
536537 ATAAAAAATT
1 ATATAATATA
*
536547 ATATAATATT
1 ATATAATATA
*
536557 TTA-AATAT-
1 ATATAATATA
* *
536565 ATTTATATAAA
1 ATATA-ATATA
*
536576 ATATAATATG
1 ATATAATATA
* *
536586 ATAAAAAATA
1 ATATAATATA
*
536596 ATA-AA-AAA
1 ATATAATATA
* *
536604 ATAAAAT-TT
1 ATATAATATA
*
536613 ATATAA-ATT
1 ATATAATATA
536622 AT-TAATAT-
1 ATATAATATA
* *
536630 ATTTAA-ATTT
1 ATATAATA-TA
536640 ATATAA-AT-
1 ATATAATATA
536648 ATATAATATA
1 ATATAATATA
*
536658 TTA-AATATA
1 ATATAATATA
536667 ATTATAATATTA
1 A-TATAATA-TA
536679 A-ATAATATA
1 ATATAATATA
536688 A
1 A
536689 ATTATAAATA
Statistics
Matches: 175, Mismatches: 26, Indels: 45
0.71 0.11 0.18
Matches are distributed among these distances:
7 1 0.01
8 39 0.22
9 56 0.32
10 67 0.38
11 9 0.05
12 3 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (10 bp):
ATATAATATA
Found at i:536476 original size:15 final size:15
Alignment explanation
Indices: 536456--536688 Score: 80
Period size: 15 Copynumber: 16.7 Consensus size: 15
536446 AAAACATCAT
536456 ATATAATATAATATA
1 ATATAATATAATATA
536471 ATATAATATAATATA
1 ATATAATATAATATA
*
536486 A-ATAAAATAA-A-A
1 ATATAATATAATATA
536498 ATAT-ATA-AATAT-
1 ATATAATATAATATA
* *
536510 ATA-AATATTTATATG
1 ATATAATA-TAATATA
536525 A-ATAAT-TAATAT-
1 ATATAATATAATATA
* * *
536537 ATAAAAAATTATATA
1 ATATAATATAATATA
**
536552 ATATTTTA-AATAT-
1 ATATAATATAATATA
* *
536565 ATTTATATAAAATATA
1 ATATA-ATATAATATA
* * *
536581 ATATGATAAAAAATA
1 ATATAATATAATATA
* *
536596 ATA-AA-AAAATAAA
1 ATATAATATAATATA
* *
536609 AT-TTATATAA-ATT
1 ATATAATATAATATA
*
536622 AT-TAATAT-ATTTA
1 ATATAATATAATATA
*
536635 A-ATTTATATAA-AT-
1 ATA-TAATATAATATA
*
536648 ATATAATATATTA-A
1 ATATAATATAATATA
536662 ATATAATTATAATATTA
1 ATATAA-TATAATA-TA
536679 A-ATAATATAA
1 ATATAATATAA
536689 ATTATAAATA
Statistics
Matches: 159, Mismatches: 33, Indels: 52
0.65 0.14 0.21
Matches are distributed among these distances:
11 2 0.01
12 13 0.08
13 40 0.25
14 42 0.26
15 53 0.33
16 7 0.04
17 2 0.01
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (15 bp):
ATATAATATAATATA
Found at i:536484 original size:27 final size:27
Alignment explanation
Indices: 536454--536688 Score: 76
Period size: 27 Copynumber: 9.0 Consensus size: 27
536444 AAAAAACATC
536454 ATATATAATATAATATAATATAATATA
1 ATATATAATATAATATAATATAATATA
* *
536481 ATATA-AATAAAATA-AAAAT-ATATAA
1 ATATATAATATAATATAATATAATAT-A
* *
536506 ATATATAAATATTTATATGA-ATAAT-TA
1 ATATAT-AATA-TAATATAATATAATATA
* *
536533 ATATATAA-A-AA-ATTATATAATATT
1 ATATATAATATAATATAATATAATATA
* * * * *
536557 TTAAATATATTTATATAAAATATAATATG
1 ATATATA-ATATA-ATATAATATAATATA
* * * * * *
536586 ATAAAAAATAATAAAAAAATAAAAT-TT
1 ATATATAAT-ATAATATAATATAATATA
*
536613 ATATA-AATTATTAATAT-ATTTAA-AT-
1 ATATATAA-TA-TAATATAATATAATATA
*
536638 TTATATAA-AT-ATATAATAT-AT-TA
1 ATATATAATATAATATAATATAATATA
536661 A-ATATAATTATAATATTAA-ATAATATA
1 ATATATAA-TATAATA-TAATATAATATA
536688 A
1 A
536689 ATTATAAATA
Statistics
Matches: 153, Mismatches: 28, Indels: 54
0.65 0.12 0.23
Matches are distributed among these distances:
22 15 0.10
23 10 0.07
24 13 0.08
25 21 0.14
26 25 0.16
27 30 0.20
28 19 0.12
29 20 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
ATATATAATATAATATAATATAATATA
Found at i:536691 original size:70 final size:70
Alignment explanation
Indices: 536542--536709 Score: 178
Period size: 71 Copynumber: 2.3 Consensus size: 70
536532 AATATATAAA
536542 AAATTATATAATATTTTAAATATATTTATATAAAATATAATATGATAAAAAATAATAAAAAAATA
1 AAATTATA-AATATTTT--A-A-ATTTATATAAAATATAATATGATAAAAAATAATAAAAAAATA
*
536607 AAATTTATAT
61 AAATTAATAT
* * * * * * *
536617 AAATTATTAATATATTTAAATTTATATAAATATATAATAT-ATTAAATATAATTATAATATTAAA
1 AAATTATAAATAT-TTTAAATTTATATAAA-ATATAATATGATAAAAAATAATAAAAAAATAAAA
536681 -TAATAT
64 TTAATAT
*
536687 AAATTATAAATATTTTTAATTTA
1 AAATTATAAATATTTTAAATTTA
536710 ATATTTTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
69 9 0.11
70 17 0.21
71 29 0.36
72 10 0.12
73 1 0.01
74 5 0.06
75 10 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (70 bp):
AAATTATAAATATTTTAAATTTATATAAAATATAATATGATAAAAAATAATAAAAAAATAAAATT
AATAT
Found at i:536706 original size:22 final size:22
Alignment explanation
Indices: 536613--536706 Score: 59
Period size: 22 Copynumber: 4.1 Consensus size: 22
536603 AATAAAATTT
*
536613 ATATAAATTATTAATATATTTAAATTT
1 ATATAAATTA-TAA-ATATTT---TTA
* *
536640 ATATAAA-TATATAATATATTAA
1 ATATAAATTATA-AATATTTTTA
**
536662 ATAT-AATTAT-AATATTAAATA
1 ATATAAATTATAAATATT-TTTA
536683 ATATAAATTATAAATATTTTTA
1 ATATAAATTATAAATATTTTTA
536705 AT
1 AT
536707 TTAATATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
20 5 0.09
21 7 0.13
22 18 0.34
23 6 0.11
25 7 0.13
26 3 0.06
27 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAAATTATAAATATTTTTA
Found at i:536870 original size:22 final size:23
Alignment explanation
Indices: 536845--536888 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
536835 ATTAAATAAT
536845 TTAATTTATAATA-TTTATTTTG
1 TTAATTTATAATATTTTATTTTG
*
536867 TTAATTTATATTATTTTATTTT
1 TTAATTTATAATATTTTATTTT
536889 AAATTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTAATTTATAATATTTTATTTTG
Found at i:537006 original size:19 final size:20
Alignment explanation
Indices: 536984--537023 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
536974 TAAATTAAAT
536984 AAAT-ATAAATAAAAAATTA
1 AAATAATAAATAAAAAATTA
**
537003 AAATAATCGATAAAAAATTA
1 AAATAATAAATAAAAAATTA
537023 A
1 A
537024 TTAATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
AAATAATAAATAAAAAATTA
Found at i:539172 original size:7 final size:7
Alignment explanation
Indices: 539162--539189 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
539152 GATGTAGTAT
539162 GTTGGCA
1 GTTGGCA
539169 GTTGGCA
1 GTTGGCA
539176 GTTGGCA
1 GTTGGCA
539183 GTTGGCA
1 GTTGGCA
539190 TGCCATGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.29
Consensus pattern (7 bp):
GTTGGCA
Found at i:546253 original size:13 final size:13
Alignment explanation
Indices: 546224--546256 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
546214 CTTCTTTTTC
*
546224 TTTAATA-TTATA
1 TTTAATATTTACA
546236 TTTAATATTTACA
1 TTTAATATTTACA
546249 TTTAATAT
1 TTTAATAT
546257 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAATATTTACA
Found at i:546315 original size:28 final size:26
Alignment explanation
Indices: 546255--546315 Score: 61
Period size: 29 Copynumber: 2.2 Consensus size: 26
546245 TACATTTAAT
* *
546255 ATATTTTTAAATATAAATATAAATAT
1 ATATTTTTAAACATAAATATAAATAA
546281 ATAATTTTTAAAAACATAAA-ATAAATAAA
1 AT-ATTTTT--AAACATAAATATAAAT-AA
546310 ATATTT
1 ATATTT
546316 ATACGTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 2 0.07
27 6 0.21
28 10 0.34
29 11 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATTTTTAAACATAAATATAAATAA
Found at i:546924 original size:22 final size:21
Alignment explanation
Indices: 546893--546933 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
546883 TGAATTTTAA
546893 AATTTAATTAATTTAAATTTG
1 AATTTAATTAATTTAAATTTG
*
546914 AATTTGAATTATTTTAAATT
1 AATTT-AATTAATTTAAATT
546934 ATTTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
AATTTAATTAATTTAAATTTG
Found at i:547490 original size:19 final size:20
Alignment explanation
Indices: 547452--547490 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
547442 ACAATAAAAC
*
547452 TTATTAAAAAATATATTTAA
1 TTATTAAAAAATATAATTAA
*
547472 TTATTAAAAATTA-AATTAA
1 TTATTAAAAAATATAATTAA
547491 AAAGCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTAAAAAATATAATTAA
Found at i:548153 original size:2 final size:2
Alignment explanation
Indices: 548146--548171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
548136 TTAAATTTAA
548146 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
548172 TTTAAGAATG
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:548888 original size:19 final size:19
Alignment explanation
Indices: 548866--548902 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
548856 TTAAAATTAT
548866 AATTTAAAAATAATAAAAA
1 AATTTAAAAATAATAAAAA
* *
548885 AATTTATAAATATTAAAA
1 AATTTAAAAATAATAAAA
548903 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTTAAAAATAATAAAAA
Found at i:551229 original size:17 final size:17
Alignment explanation
Indices: 551204--551338 Score: 63
Period size: 16 Copynumber: 8.2 Consensus size: 17
551194 TAATATAAAA
551204 ATAAT-TAAAATATAAT
1 ATAATATAAAATATAAT
*
551220 ATAATATAAATATTTAA-
1 ATAATATAAA-ATATAAT
* * * *
551237 ATATTTTAAATTTTAA-
1 ATAATATAAAATATAAT
* *
551253 ATAATATTAATTATTAAT
1 ATAATATAAAATA-TAAT
*
551271 AT-ATA-AAAAT-TTAT
1 ATAATATAAAATATAAT
**
551285 ATAAATATAAAATATTTT
1 AT-AATATAAAATATAAT
* *
551303 A-AAT-TTAATTATAAT
1 ATAATATAAAATATAAT
551318 ATAATA-AAATATATAAT
1 ATAATATAAA-ATATAAT
551335 ATAA
1 ATAA
551339 ACATAAAAAT
Statistics
Matches: 90, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
14 5 0.06
15 8 0.09
16 33 0.37
17 33 0.37
18 11 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATATAAAATATAAT
Done.