Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 3 of 325
Found at i:568707 original size:21 final size:20
Alignment explanation
Indices: 568668--568712 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
568658 TAATATTAAA
568668 ATTTTTTTCATTTAAAAAAAT
1 ATTTTTTTCATTT-AAAAAAT
* **
568689 ATTTTTTTTATTTTTAAAAT
1 ATTTTTTTCATTTAAAAAAT
568709 ATTT
1 ATTT
568713 ATATTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTTCATTTAAAAAAT
Found at i:569451 original size:21 final size:22
Alignment explanation
Indices: 569414--569471 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
569404 TTACCCGTAT
*
569414 ATAAATATAA-ATATTTTAAA-A
1 ATAAAAATAATAT-TTTTAAACA
569435 ATAAAAATAATATTTTTTAAACA
1 ATAAAAATAATA-TTTTTAAACA
569458 A-AAAAATTAATATT
1 ATAAAAA-TAATATT
569472 AAAAAAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATAATATTTTTAAACA
Found at i:569460 original size:20 final size:20
Alignment explanation
Indices: 569423--569461 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
569413 TATAAATATA
*
569423 AATATTTTAAAAATAAAAAT
1 AATATTTTAAAAACAAAAAT
**
569443 AATATTTTTTAAACAAAAA
1 AATATTTTAAAAACAAAAA
569462 AATTAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATTTTAAAAACAAAAAT
Found at i:569463 original size:23 final size:22
Alignment explanation
Indices: 569427--569471 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
569417 AATATAAATA
*
569427 TTTTAAAAATAAAAATAATATT
1 TTTTAAAAAAAAAAATAATATT
*
569449 TTTTAAACAAAAAAATTAATATT
1 TTTTAAA-AAAAAAAATAATATT
569472 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAAAAAAAAATAATATT
Found at i:571325 original size:17 final size:18
Alignment explanation
Indices: 571305--571339 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
571295 TTCTTTAGTA
*
571305 TTTTTGTTA-TTTTATTT
1 TTTTTGGTATTTTTATTT
571322 TTTTTGGTATTTTTATTT
1 TTTTTGGTATTTTTATTT
571340 AACAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTTGGTATTTTTATTT
Found at i:571524 original size:17 final size:17
Alignment explanation
Indices: 571502--571535 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
571492 TATCTATTGG
571502 ATTAAATTAAAAGTAAA
1 ATTAAATTAAAAGTAAA
*
571519 ATTAAATTAACAGTAAA
1 ATTAAATTAAAAGTAAA
571536 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAAATTAAAAGTAAA
Found at i:572097 original size:11 final size:11
Alignment explanation
Indices: 572081--572112 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
572071 ACGGTAGAGT
572081 AAAAAGAAAAA
1 AAAAAGAAAAA
*
572092 AAAAAGAAAAG
1 AAAAAGAAAAA
572103 AAAAAGAAAA
1 AAAAAGAAAA
572113 CCCACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:572807 original size:45 final size:45
Alignment explanation
Indices: 572720--572842 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
572710 GTTTGTACAT
* * * * *
572720 AGTTTCAGCCTC-AACATTATTTAAAATGGGTTTTTGTTTATAAGA
1 AGTTTCAGCTTCAAACATTCTTGAAAAT-AGTTTATGTTTATAAGA
*
572765 AG-TTCTAGCTTCAAATATTCTTGAAAATAGTTTATGTTTATAAGA
1 AGTTTC-AGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
*
572810 AGTTTCAGCTTCAAACATTCTTGTAAATA-TTTA
1 AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTA
572843 ATGAAGCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
44 7 0.10
45 45 0.67
46 15 0.22
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (45 bp):
AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
Found at i:588467 original size:32 final size:32
Alignment explanation
Indices: 588427--588495 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
588417 ATGTGAAGGT
588427 AGGT-TATAGGGTTTTTCTTTTATATAATAGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
*
588458 AGGTATATAGGGTTTTTCTTTTATATAATTGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
588490 AGGTAT
1 AGGTAT
588496 TGTTAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (32 bp):
AGGTATATAGGGTTTTTCTTTTATATAATAGG
Found at i:603318 original size:14 final size:16
Alignment explanation
Indices: 603288--603340 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
603278 TTATGTATAT
603288 AATT-ATATTAAATTAA
1 AATTCATATT-AATTAA
603304 AATTCATA-T-ATT-A
1 AATTCATATTAATTAA
*
603317 AATTACATATTAATCAA
1 AATT-CATATTAATTAA
603334 AATTCAT
1 AATTCAT
603341 GTATAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 1 0.03
16 10 0.32
17 8 0.26
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTCATATTAATTAA
Found at i:603355 original size:29 final size:29
Alignment explanation
Indices: 603280--603356 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
603270 AATCACTTTT
*
603280 ATGTATATAATT-ATATTAAATTAAAATTC
1 ATGTATA-AATTAATATTAAATCAAAATTC
*
603309 ATATATTAAATTACATATT-AATCAAAATTC
1 ATGTA-TAAATTA-ATATTAAATCAAAATTC
603339 ATGTATAAATTTAATATT
1 ATGTATAAA-TTAATATT
603357 GATCTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 17 0.41
30 19 0.46
31 5 0.12
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
ATGTATAAATTAATATTAAATCAAAATTC
Found at i:603520 original size:27 final size:25
Alignment explanation
Indices: 603490--603552 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
603480 CTCTTGAAAT
603490 AAACATAAAAAAAAAAGTTAAGTATCA
1 AAACATAAAAAAAAAA-TTAA-TATCA
* *
603517 AAACACAATAAAAAAAATTAATGTCA
1 AAACATAA-AAAAAAAATTAATATCA
*
603543 AAATATAAAA
1 AAACATAAAA
603553 GCATAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 10 0.32
27 11 0.35
28 8 0.26
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.19
Consensus pattern (25 bp):
AAACATAAAAAAAAAATTAATATCA
Found at i:603942 original size:18 final size:18
Alignment explanation
Indices: 603919--604018 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 18
603909 GTTAATGATC
*
603919 AAATTTAGCTAAAAAAT-T
1 AAATTTAAC-AAAAAATAT
603937 AAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
*
603955 AAATATTAA-AAATTAAATTT
1 AAAT-TTAACAAA--AAATAT
603975 AACATTATACCACAAAAAAT-T
1 AA-ATT-TA--ACAAAAAATAT
*
603996 TAATTTAACAAAAAATAT
1 AAATTTAACAAAAAATAT
604014 AAATT
1 AAATT
604019 AAAAATTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
17 16 0.24
18 21 0.31
19 6 0.09
20 11 0.16
21 6 0.09
22 4 0.06
23 1 0.01
24 3 0.04
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (18 bp):
AAATTTAACAAAAAATAT
Found at i:603970 original size:32 final size:31
Alignment explanation
Indices: 603930--604031 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 31
603920 AATTTAGCTA
603930 AAAAATTAAATTTAACAAAAAATATAAATATT
1 AAAAATTAAATTTAACAAAAAATATAAA-ATT
* ** **
603962 AAAAATTAAATTTAAC----ATTATACCACA
1 AAAAATTAAATTTAACAAAAAATATAAAATT
*
603989 AAAAATTTAATTTAACAAAAAATAT-AAATT
1 AAAAATTAAATTTAACAAAAAATATAAAATT
604019 AAAAATTAAATTT
1 AAAAATTAAATTT
604032 TGCAATAACT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
27 16 0.30
28 5 0.09
30 13 0.24
31 4 0.07
32 16 0.30
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAATTAAATTTAACAAAAAATATAAAATT
Found at i:605630 original size:51 final size:51
Alignment explanation
Indices: 605559--605770 Score: 325
Period size: 51 Copynumber: 4.2 Consensus size: 51
605549 CTGATCACAT
605559 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * * * *
605610 TTATCACTTTTCATTGATCAGGTAAGTGTAGCTAAAGCTACCACTTGTCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
605661 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * *
605712 TTATCACTTGTCATTGATCAGATAAGTATAGCTAAAGCTACCATTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
605763 TTGTCACT
1 TTATCACT
605771 GATCAGAAGT
Statistics
Matches: 144, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 144 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:605682 original size:102 final size:102
Alignment explanation
Indices: 605556--605754 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
605546 ACACTGATCA
*
605556 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTTT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
* *
605621 CATTGATCAGGTAAGTGTAGCTAAAGCTACCACTTGT
66 CATTGATCAGATAAGTATAGCTAAAGCTACCACTTGT
605658 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
605723 CATTGATCAGATAAGTATAGCTAAAGCTACCA
66 CATTGATCAGATAAGTATAGCTAAAGCTACCA
605755 TTTATCACTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT
CATTGATCAGATAAGTATAGCTAAAGCTACCACTTGT
Found at i:605911 original size:20 final size:22
Alignment explanation
Indices: 605878--605925 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
605868 ATCATACATT
605878 ATATAATTCATAAAATT-AA-C
1 ATATAATTCATAAAATTCAACC
*
605898 ATATAA-TCATTAAACTTCAACC
1 ATATAATTCA-TAAAATTCAACC
605920 ATATAA
1 ATATAA
605926 ACTTACCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 2 0.08
22 7 0.29
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAATTCATAAAATTCAACC
Found at i:613167 original size:27 final size:28
Alignment explanation
Indices: 613106--613159 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
613096 ATTTTTTTTA
*
613106 AATATAAATATTATATTAGGCCAAAAAAT
1 AATAAAAATATTATATTAGG-CAAAAAAT
613135 AATAAAAATAATT-TATTAGG-AAAAA
1 AATAAAAAT-ATTATATTAGGCAAAAA
613160 GTATTAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
29 15 0.65
30 3 0.13
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAAAAATATTATATTAGGCAAAAAAT
Found at i:618320 original size:18 final size:19
Alignment explanation
Indices: 618283--618320 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
618273 ATAAAATCAA
* *
618283 ATAATAAATATGTAATTTT
1 ATAATAAAAATATAATTTT
618302 ATAATAAAAATAT-ATTTT
1 ATAATAAAAATATAATTTT
618320 A
1 A
618321 CATATATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAATAAAAATATAATTTT
Found at i:623199 original size:28 final size:28
Alignment explanation
Indices: 623167--623221 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
623157 AATTAAATGC
*
623167 TAGCGTATTATTTACATGACAATTCATA
1 TAGCGTATTATCTACATGACAATTCATA
*
623195 TAGCGTATTATCTATATGACAATTCAT
1 TAGCGTATTATCTACATGACAATTCAT
623222 GTGTATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (28 bp):
TAGCGTATTATCTACATGACAATTCATA
Found at i:623542 original size:35 final size:34
Alignment explanation
Indices: 623496--623565 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
623486 TTGCTGATAA
623496 GCCACTTAAATAAATCTAAATCCCAATATCTATTT
1 GCCACTTAAATAAATCTAAATCCCAATATCT-TTT
*
623531 GCCACTTAAATAAATTTAAATCCCAATATCTTTT
1 GCCACTTAAATAAATCTAAATCCCAATATCTTTT
623565 G
1 G
623566 AAAAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (34 bp):
GCCACTTAAATAAATCTAAATCCCAATATCTTTT
Found at i:633633 original size:26 final size:26
Alignment explanation
Indices: 633594--633647 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
633584 AAGGGGGTTT
633594 AATTTTTTTCTTTA-TCATTTTTATAA
1 AATTTTTTTCTTTACT-ATTTTTATAA
633620 AATTTTATTT-TTTACTATTTTTATAA
1 AATTTT-TTTCTTTACTATTTTTATAA
633646 AA
1 AA
633648 AAAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
AATTTTTTTCTTTACTATTTTTATAA
Found at i:633714 original size:46 final size:45
Alignment explanation
Indices: 633610--633715 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 45
633600 TTTCTTTATC
* *
633610 ATTTTTATAAAATTTTATTTTTTACTATTTTTATAAAAAAAATTA
1 ATTTTTCTAAAATTTTAATTTTTACTATTTTTATAAAAAAAATTA
* **
633655 A-TTTTCAATAAATTTTAGATTTTTA-TATTTTTATTAAAATTTAA-TA
1 ATTTTTCTA-AAATTTTA-ATTTTTACTATTTTTA-TAAAA-AAAATTA
633701 ATTTTTCTAAAATTT
1 ATTTTTCTAAAATTT
633716 ATTATTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
44 5 0.10
45 17 0.34
46 20 0.40
47 8 0.16
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.57
Consensus pattern (45 bp):
ATTTTTCTAAAATTTTAATTTTTACTATTTTTATAAAAAAAATTA
Found at i:637785 original size:7 final size:7
Alignment explanation
Indices: 637773--637806 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
637763 TGTATATACT
637773 CATATCA
1 CATATCA
637780 CATATCA
1 CATATCA
637787 CATATCA
1 CATATCA
*
637794 CATATCC
1 CATATCA
637801 CATATC
1 CATATC
637807 GCTTGAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (7 bp):
CATATCA
Found at i:639146 original size:20 final size:20
Alignment explanation
Indices: 639121--639164 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
639111 ATATTATTAA
*
639121 ATTATT-TTGAAATAATAAAT
1 ATTATTATTCAAAT-ATAAAT
*
639141 ATTATTATTCAAATTTAAAT
1 ATTATTATTCAAATATAAAT
639161 ATTA
1 ATTA
639165 AAAAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATTATTCAAATATAAAT
Found at i:639827 original size:19 final size:18
Alignment explanation
Indices: 639783--639827 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
639773 TTTGAAGAAA
639783 GTGAATTTAAAATTCAAC
1 GTGAATTTAAAATTCAAC
*
639801 GTGAATTTAAAATTCGAC
1 GTGAATTTAAAATTCAAC
639819 GTAGAATTT
1 GT-GAATTT
639828 GTGTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
GTGAATTTAAAATTCAAC
Found at i:653162 original size:83 final size:85
Alignment explanation
Indices: 653036--653205 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 85
653026 AAAGAGCATG
* *
653036 AGTTGGTTAGAAGTGAGGGGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCTACTTAT
1 AGTTGGTTAGAAGTGA-GAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTAT
653101 CGCACTTATCGCACAAAGACT
65 CGCACTTATCGCACAAAGACT
653122 AGTTGGTTAGAAGTGA-AGGG-GGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
1 AGTTGGTTAGAAGTGAGAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
653185 GCACTTATCGCACAAAGACT
66 GCACTTATCGCACAAAGACT
653205 A
1 A
653206 AAAATAAGTG
Statistics
Matches: 82, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
83 63 0.77
84 3 0.04
86 16 0.20
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (85 bp):
AGTTGGTTAGAAGTGAGAGGGAGGGGGGAACTTAATGGTTTTTACAGCTTTTTTCCCCACTTATC
GCACTTATCGCACAAAGACT
Found at i:653364 original size:16 final size:16
Alignment explanation
Indices: 653343--653375 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
653333 CATGTAATGG
653343 CTTATAAAGTTTTGAT
1 CTTATAAAGTTTTGAT
653359 CTTATAAAGTTTTGAT
1 CTTATAAAGTTTTGAT
653375 C
1 C
653376 ATTAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (16 bp):
CTTATAAAGTTTTGAT
Found at i:664496 original size:3 final size:3
Alignment explanation
Indices: 664488--664519 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
664478 AGTAAATTAA
664488 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
664520 ACTATTGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:681924 original size:29 final size:28
Alignment explanation
Indices: 681885--681969 Score: 134
Period size: 29 Copynumber: 3.0 Consensus size: 28
681875 CACTTTGTGC
681885 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
681914 TATTCTGGTGTGTTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTT-GGAGGATTATAT
* *
681943 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
681970 CTGGTGTGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
28 11 0.21
29 39 0.74
30 3 0.06
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.47
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:682221 original size:21 final size:21
Alignment explanation
Indices: 682173--682259 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
682163 GGCTATACTG
*
682173 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
682194 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
**
682217 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
682238 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
682258 AT
1 AT
682260 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.19
21 27 0.47
23 19 0.33
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:683499 original size:46 final size:48
Alignment explanation
Indices: 683341--683527 Score: 172
Period size: 46 Copynumber: 3.9 Consensus size: 48
683331 TGGTTGGACC
683341 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * *
683387 ATGGCATCAGAGATATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
*
683440 ATGGCATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
683486 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
683528 TTTTACTATG
Statistics
Matches: 116, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
45 1 0.01
46 33 0.28
47 9 0.08
48 18 0.16
49 13 0.11
50 1 0.01
51 7 0.06
52 6 0.05
53 27 0.23
54 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:699402 original size:13 final size:14
Alignment explanation
Indices: 699354--699401 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
699344 TATAACTAAA
*
699354 AAAATAACATTGTAAT
1 AAAATAA-ATT-TAAC
699370 AAACATAAATTTAAC
1 AAA-ATAAATTTAAC
*
699385 AAAATAATTTTAAC
1 AAAATAAATTTAAC
699399 AAA
1 AAA
699402 TGAACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 6 0.21
17 4 0.14
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAATAAATTTAAC
Found at i:699486 original size:29 final size:31
Alignment explanation
Indices: 699432--699500 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
699422 TGAGAAATAG
699432 AGGGACTAAATTCCTAGAAAT-AAA-AGTAT
1 AGGGACTAAATTCCTAGAAATAAAAGAGTAT
*
699461 AGGGACTAAATT-CTA-AATTTACAAAGAGTAT
1 AGGGACTAAATTCCTAGAA-ATA-AAAGAGTAT
699492 AGGGACTAA
1 AGGGACTAA
699501 TGTCATGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 12 0.34
30 3 0.09
31 14 0.40
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AGGGACTAAATTCCTAGAAATAAAAGAGTAT
Found at i:710265 original size:6 final size:6
Alignment explanation
Indices: 710254--710292 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
710244 GAAGGAGTAA
*
710254 TATATC TATATC TATATC TATATC --TATC TATATA TATAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATAT
710293 ATAATGAGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.13
6 26 0.87
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:710283 original size:10 final size:11
Alignment explanation
Indices: 710255--710295 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
710245 AAGGAGTAAT
710255 ATATCTATATC
1 ATATCTATATC
710266 TATATCTATATC
1 -ATATCTATATC
710278 -TATCTATAT-
1 ATATCTATATC
*
710287 ATATATATA
1 ATATCTATA
710296 ATGAGCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 16 0.59
12 11 0.41
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATCTATATC
Found at i:710283 original size:16 final size:16
Alignment explanation
Indices: 710262--710292 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
710252 AATATATCTA
*
710262 TATCTATATCTATATC
1 TATCTATATATATATC
710278 TATCTATATATATAT
1 TATCTATATATATAT
710293 ATAATGAGCT
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:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATATATATATC
Found at i:712414 original size:21 final size:21
Alignment explanation
Indices: 712390--712440 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
712380 GACACCGTCC
712390 GTGACGGCGATAACTCACCTT
1 GTGACGGCGATAACTCACCTT
* **
712411 GTGACGTCGATGTCTCACCTT
1 GTGACGGCGATAACTCACCTT
**
712432 CCGACGGCG
1 GTGACGGCG
712441 GAGAATCCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (21 bp):
GTGACGGCGATAACTCACCTT
Found at i:713228 original size:15 final size:16
Alignment explanation
Indices: 713208--713237 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
713198 GTTTTAGAGA
713208 AATGGAAA-ATAATTG
1 AATGGAAATATAATTG
713223 AATGGAAATATAATT
1 AATGGAAATATAATT
713238 ATAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
AATGGAAATATAATTG
Found at i:719964 original size:22 final size:21
Alignment explanation
Indices: 719934--719977 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
719924 AAACAATGTT
719934 AAATTTATTAATAT-TGATTTA
1 AAATTTATTAATATAT-ATTTA
*
719955 AAATATTATTTATATATATTTA
1 AAAT-TTATTAATATATATTTA
719977 A
1 A
719978 CTATTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 15 0.75
23 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAATTTATTAATATATATTTA
Found at i:720507 original size:24 final size:24
Alignment explanation
Indices: 720457--720508 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
720447 TTCGTAGGTC
* *
720457 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
* *
720481 AAATATATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATACT
720505 AAAT
1 AAAT
720509 GTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:723825 original size:23 final size:23
Alignment explanation
Indices: 723797--723842 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
723787 TTATTTTGAG
723797 GTTTTCATGGTAGTAATAAAAAT
1 GTTTTCATGGTAGTAATAAAAAT
723820 GTTTTCATGGTAGTAATAAAAAT
1 GTTTTCATGGTAGTAATAAAAAT
723843 CATTCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (23 bp):
GTTTTCATGGTAGTAATAAAAAT
Found at i:723848 original size:22 final size:23
Alignment explanation
Indices: 723800--723848 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
723790 TTTTGAGGTT
**
723800 TTCATGGTAGTAATAAAAATGTT
1 TTCATGGTAGTAATAAAAATGCA
723823 TTCATGGTAGTAATAAAAAT-CA
1 TTCATGGTAGTAATAAAAATGCA
723845 TTCA
1 TTCA
723849 CACACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (23 bp):
TTCATGGTAGTAATAAAAATGCA
Found at i:730060 original size:18 final size:20
Alignment explanation
Indices: 730037--730073 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
730027 AGTCCCCCAA
730037 AAAATAAAA-C-CATAAAAT
1 AAAATAAAATCTCATAAAAT
730055 AAAATAAAATCTCATAAAA
1 AAAATAAAATCTCATAAAA
730074 ACCTCCCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAATCTCATAAAAT
Found at i:733922 original size:13 final size:13
Alignment explanation
Indices: 733904--733929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
733894 AAATAATGAA
733904 ATAACTAAATAAT
1 ATAACTAAATAAT
733917 ATAACTAAATAAT
1 ATAACTAAATAAT
733930 GACAGATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAACTAAATAAT
Found at i:738501 original size:21 final size:22
Alignment explanation
Indices: 738472--738522 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
738462 GATATGTTAA
*
738472 AAATATTTTAATTAT-TATTTG
1 AAATTTTTTAATTATATATTTG
738493 AAATTTTTTAATTATAATATTTG
1 AAATTTTTTAATTAT-ATATTTG
738516 -AATTTTT
1 AAATTTTT
738523 ACTCAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.52
22 7 0.26
23 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (22 bp):
AAATTTTTTAATTATATATTTG
Found at i:741039 original size:18 final size:19
Alignment explanation
Indices: 740986--741028 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
740976 GATGAATCAT
*
740986 ATAGAAAGAG--ATAGAAA
1 ATAGAAAGAGAAAAAGAAA
741003 ATAGAAAGAGAAAAAGAAA
1 ATAGAAAGAGAAAAAGAAA
741022 A-AGAAAG
1 ATAGAAAG
741029 GGGAAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (19 bp):
ATAGAAAGAGAAAAAGAAA
Found at i:741461 original size:3 final size:3
Alignment explanation
Indices: 741453--741479 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
741443 AAGGAAGAGG
741453 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
741480 TGAGAGCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:749129 original size:31 final size:33
Alignment explanation
Indices: 749069--749130 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
749059 TTGTATTTTA
* *
749069 CTTTATTTATTCAAAAAAAATAAGTAAATTAAT
1 CTTTATATATTCAAAAAAAAGAAGTAAATTAAT
*
749102 CTTTATATATT-AAATAAAAGAA-TAAATTA
1 CTTTATATATTCAAAAAAAAGAAGTAAATTA
749131 GTTTATTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.27
32 9 0.35
33 10 0.38
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (33 bp):
CTTTATATATTCAAAAAAAAGAAGTAAATTAAT
Found at i:750323 original size:12 final size:12
Alignment explanation
Indices: 750306--750330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
750296 ACATTATAGA
750306 TTTTATATAAAT
1 TTTTATATAAAT
750318 TTTTATATAAAT
1 TTTTATATAAAT
750330 T
1 T
750331 ATATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTATATAAAT
Found at i:757975 original size:31 final size:30
Alignment explanation
Indices: 757940--758017 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
757930 TTAAAAGTCA
757940 AAAAGTACAAAGACTAAAATTGAAT-AAATAG
1 AAAAGTACAAAGACTAAAATTG-ATCAAAT-G
* * * *
757971 AAAAGTGCAAGGACTCAAATTGATCAAATT
1 AAAAGTACAAAGACTAAAATTGATCAAATG
758001 AAAA-TACAAAGACTAAA
1 AAAAGTACAAAGACTAAA
758018 TTTACAACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 10 0.26
30 6 0.15
31 23 0.59
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (30 bp):
AAAAGTACAAAGACTAAAATTGATCAAATG
Found at i:760665 original size:17 final size:17
Alignment explanation
Indices: 760643--760691 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
760633 TTATCATTCC
760643 TCAATTTTATAATTTAA
1 TCAATTTTATAATTTAA
*
760660 TCAATTTAAT-ATTTAA
1 TCAATTTTATAATTTAA
760676 TAACAA-TTTATAATTT
1 T--CAATTTTATAATTT
760692 TATTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
17 13 0.48
18 7 0.26
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TCAATTTTATAATTTAA
Found at i:760691 original size:18 final size:16
Alignment explanation
Indices: 760643--760691 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
760633 TTATCATTCC
760643 TCAATTTTATAATTTAA
1 TCAA-TTTATAATTTAA
760660 TCAATTTA-ATATTTAA
1 TCAATTTATA-ATTTAA
760676 TAACAATTTATAATTT
1 T--CAATTTATAATTT
760692 TATTATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 11 0.39
17 4 0.14
18 11 0.39
19 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TCAATTTATAATTTAA
Found at i:777494 original size:13 final size:15
Alignment explanation
Indices: 777467--777500 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
777457 GTATGATTAT
777467 ATTTATTTTTCGTGA
1 ATTTATTTTTCGTGA
777482 ATTT-TTTTT-GTGA
1 ATTTATTTTTCGTGA
777495 ATTTAT
1 ATTTAT
777501 AACTCTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 6 0.33
15 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.65
Consensus pattern (15 bp):
ATTTATTTTTCGTGA
Found at i:793038 original size:6 final size:6
Alignment explanation
Indices: 793027--793051 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
793017 AATGAAGGAG
793027 CCATAC CCATAC CCATAC CCATAC C
1 CCATAC CCATAC CCATAC CCATAC C
793052 AGATCCTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATAC
Found at i:795423 original size:63 final size:63
Alignment explanation
Indices: 795324--795447 Score: 248
Period size: 63 Copynumber: 2.0 Consensus size: 63
795314 ACCGCCTAAA
795324 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAAGT
1 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAAGT
795387 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAA
1 GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAA
795448 TTGAAGCGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (63 bp):
GTATTGGTCTGGAGAGGAGCTTTGATCAAATATGAACTTATTGAGTTAGGAAAATAAACAAGT
Found at i:801206 original size:70 final size:67
Alignment explanation
Indices: 801080--801212 Score: 149
Period size: 70 Copynumber: 1.9 Consensus size: 67
801070 ATAGACAATA
* * * * * * *
801080 TAATGGTTTTGCCTTTTAATTTAATAAATAAATATTTATCAGAATGACGTAATTTTGCCTTTTAA
1 TAATGATTTTGACTTTTAATTTAAAAAATAAACATTTATCAAAACGACGTAATTTTGCATTTTAA
801145 GT
66 GT
* **
801147 TAATGATTTTGACTTTTAACTTTAGAAAATATAAACATTTATCAAAACGATGTGGTTTTGCATTT
1 TAATGATTTTGACTTTTAA-TTTA-AAAA-ATAAACATTTATCAAAACGACGTAATTTTGCATTT
801212 T
63 T
801213 CTTATTCGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
67 17 0.32
68 4 0.08
69 3 0.06
70 29 0.55
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAATTTAAAAAATAAACATTTATCAAAACGACGTAATTTTGCATTTTAA
GT
Found at i:804908 original size:19 final size:20
Alignment explanation
Indices: 804868--804909 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
804858 TTGGTTCATG
804868 TTTTCAATCTCATATCTCAA
1 TTTTCAATCTCATATCTCAA
804888 TTTTCAATTCTCA-AT-TCAA
1 TTTTCAA-TCTCATATCTCAA
804907 TTT
1 TTT
804910 CTCATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAATCTCATATCTCAA
Found at i:805433 original size:18 final size:19
Alignment explanation
Indices: 805407--805445 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
805397 TTTCAATTCA
805407 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
805426 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
805444 AT
1 AT
805446 ATATCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:806773 original size:5 final size:5
Alignment explanation
Indices: 806763--806819 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
806753 TTACTTATTT
* *
806763 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
806811 ATAT- ATATA
1 ATATA ATATA
806820 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:806779 original size:12 final size:12
Alignment explanation
Indices: 806762--806817 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
806752 TTTACTTATT
806762 TATATAATATAA
1 TATATAATATAA
806774 TATATAATATAATA
1 TATATAATAT-A-A
806788 TACTATAATATAA
1 TA-TATAATATAA
*
806801 TA-ATAATTTAA
1 TATATAATATAA
806812 TATATA
1 TATATA
806818 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:806832 original size:26 final size:26
Alignment explanation
Indices: 806764--806819 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
806754 TACTTATTTA
*
806764 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
806791 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
806816 TATA
1 TATA
806820 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:811345 original size:13 final size:14
Alignment explanation
Indices: 811329--811364 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
811319 CAATCTCATA
811329 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
811342 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
811355 TCTC-ATTTCA
1 TCTCAATTTCA
811365 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:811354 original size:18 final size:19
Alignment explanation
Indices: 811316--811356 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
811306 TGGTTCATGT
811316 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
811335 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
811353 TTTC
1 TTTC
811357 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:811878 original size:18 final size:19
Alignment explanation
Indices: 811852--811890 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
811842 TTTCAATTCA
811852 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
811871 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
811889 AT
1 AT
811891 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:813216 original size:5 final size:5
Alignment explanation
Indices: 813206--813262 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
813196 TTACTTATTT
* *
813206 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
813254 ATAT- ATATA
1 ATATA ATATA
813263 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:813222 original size:12 final size:12
Alignment explanation
Indices: 813205--813260 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
813195 TTTACTTATT
813205 TATATAATATAA
1 TATATAATATAA
813217 TATATAATATAATA
1 TATATAATAT-A-A
813231 TACTATAATATAA
1 TA-TATAATATAA
*
813244 TA-ATAATTTAA
1 TATATAATATAA
813255 TATATA
1 TATATA
813261 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:813275 original size:26 final size:26
Alignment explanation
Indices: 813207--813262 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
813197 TACTTATTTA
*
813207 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
813234 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
813259 TATA
1 TATA
813263 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:814267 original size:3 final size:3
Alignment explanation
Indices: 814261--814287 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
814251 TTTTAATTTG
814261 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
814288 GTGATTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:824228 original size:34 final size:35
Alignment explanation
Indices: 824162--824235 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 35
824152 TGTTTTTCTT
824162 TGAATGGTTCTTGTTGTTGCAGTGCGTTAGGAAGCCATCC
1 TGAATGGTTCTTGTTGTTGCA----G-TAGGAAGCCATCC
824202 TGAATGGTTCTTGTTGTTGCA-TAGGAAGCCATCC
1 TGAATGGTTCTTGTTGTTGCAGTAGGAAGCCATCC
824236 CTTCAAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
34 13 0.38
40 21 0.62
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (35 bp):
TGAATGGTTCTTGTTGTTGCAGTAGGAAGCCATCC
Found at i:832678 original size:16 final size:17
Alignment explanation
Indices: 832648--832681 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
832638 GGAAGTTGGA
832648 GGAGAGGGGAAGGGATG
1 GGAGAGGGGAAGGGATG
*
832665 GGAG-GGGGAGGGGATG
1 GGAGAGGGGAAGGGATG
832681 G
1 G
832682 CTTTTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.06
Consensus pattern (17 bp):
GGAGAGGGGAAGGGATG
Found at i:836280 original size:24 final size:24
Alignment explanation
Indices: 836248--836304 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
836238 ATTGAATCCA
*
836248 AAAAAAGAAGGGGAGATGATATTT
1 AAAAAAGAAGGGAAGATGATATTT
836272 AAAAAAGAAGGGAAGATGATATTT
1 AAAAAAGAAGGGAAGATGATATTT
836296 AAAAAAGAA
1 AAAAAAGAA
836305 AGAAAAGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.18
Consensus pattern (24 bp):
AAAAAAGAAGGGAAGATGATATTT
Found at i:839269 original size:29 final size:28
Alignment explanation
Indices: 839230--839313 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
839220 CACTTTGTGC
839230 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
839259 TATTCTGGTGTGTTTGGGAGGACTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* * *
839287 GATACTGGTGTGTTTTGGAGAATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
839314 CTGGTGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 30 0.62
29 18 0.38
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:839313 original size:28 final size:28
Alignment explanation
Indices: 839234--839327 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
839224 TTGTGCTATT
* *
839234 CTGGTGTGTTTTGGATGGATTATATTATT
1 CTGGTGTGTTTTGGA-GGATTATATGATA
* *
839263 CTGGTGTGTTTGGGAGGACTATATGATA
1 CTGGTGTGTTTTGGAGGATTATATGATA
839291 CTGGTGTGTTTTGGA-GA--AT-T-ATA
1 CTGGTGTGTTTTGGAGGATTATATGATA
839314 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
839328 TTGGACATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
23 17 0.28
24 1 0.02
25 2 0.03
27 2 0.03
28 24 0.40
29 14 0.23
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (28 bp):
CTGGTGTGTTTTGGAGGATTATATGATA
Found at i:839590 original size:21 final size:21
Alignment explanation
Indices: 839530--839590 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
839520 AGGCACTTTA
*
839530 TGTGTCGTATTTCAGGCACCTTG
1 TGTGTCG--TTTCAGGCACCTCG
*** *
839553 TGTGTCGCAGCATGCACCTCG
1 TGTGTCGTTTCAGGCACCTCG
839574 TGTGTCGTTTCAGGCAC
1 TGTGTCGTTTCAGGCAC
839591 TTATGTGTTG
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 22 0.76
23 7 0.24
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TGTGTCGTTTCAGGCACCTCG
Found at i:839781 original size:23 final size:23
Alignment explanation
Indices: 839737--839781 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
839727 ATCAATTAAA
*
839737 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
839760 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
839782 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:843861 original size:14 final size:14
Alignment explanation
Indices: 843842--843871 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
843832 GACACTTATA
843842 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
843856 ATTGAGGTAAAAGT
1 ATTGAGGTAAAAGT
843870 AT
1 AT
843872 CATGCGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (14 bp):
ATTGAGGTAAAAGT
Found at i:862856 original size:21 final size:19
Alignment explanation
Indices: 862832--862874 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
862822 TTAAGGATTA
*
862832 TTATTTGATAGTATAATTTTT
1 TTATTTGATA-AAT-ATTTTT
*
862853 TTATTTTATAAATATTTTT
1 TTATTTGATAAATATTTTT
862872 TTA
1 TTA
862875 AAAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
TTATTTGATAAATATTTTT
Found at i:862997 original size:25 final size:23
Alignment explanation
Indices: 862935--862998 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
862925 TCTTTCAATT
*
862935 TAATTTATTTAAAT-TTGAAAAA
1 TAATTTTTTTAAATATTGAAAAA
*
862957 T-ATCTTTTTT-ATTATTGATAAAAA
1 TAAT-TTTTTTAAATATTG--AAAAA
862981 TAATTTTTTTAAATATTG
1 TAATTTTTTTAAATATTG
862999 TTTTTGTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
24 12 0.36
25 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TAATTTTTTTAAATATTGAAAAA
Found at i:863049 original size:17 final size:18
Alignment explanation
Indices: 863020--863065 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
863010 TGTTGAGATA
*
863020 AAAT-TTAAAATTA-TAC
1 AAATATTAATATTATTAC
*
863036 AAATATTAATATTATTAT
1 AAATATTAATATTATTAC
*
863054 AAATATAAATAT
1 AAATATTAATAT
863066 ATCGTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.16
17 8 0.32
18 13 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATTAATATTATTAC
Found at i:880444 original size:15 final size:14
Alignment explanation
Indices: 880419--880458 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
880409 TTTTAACTTT
880419 ATTTT-AATAATAA
1 ATTTTAAATAATAA
880432 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
880446 ATTTTAAATAATA
1 ATTTTAAATAATA
880459 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:881451 original size:33 final size:33
Alignment explanation
Indices: 881414--881510 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
881404 GTTTTTTATA
881414 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
* *
881447 ATTATGTTAAAATT-TTTTG-T-GT--TTGTA--
1 ATTATTTTAAAATTAATTTGTTAGTAATT-TAGG
*
881474 ATTATTTTAAAATTAATTTATTAGTAATTTAGG
1 ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
881507 ATTA
1 ATTA
881511 AGTTATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
27 13 0.25
28 5 0.10
29 3 0.06
30 4 0.08
31 3 0.06
32 6 0.12
33 17 0.33
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (33 bp):
ATTATTTTAAAATTAATTTGTTAGTAATTTAGG
Found at i:881490 original size:60 final size:60
Alignment explanation
Indices: 881412--881530 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
881402 CTGTTTTTTA
* * *
881412 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTA-AAATTTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA-TTGTTGTGTTTG
881472 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
881531 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 52 0.95
61 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:883015 original size:5 final size:5
Alignment explanation
Indices: 882989--883046 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
882979 ATGTGTTAAA
* *
882989 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
883038 ATATT ATAT
1 ATATT ATAT
883047 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:883025 original size:10 final size:9
Alignment explanation
Indices: 882990--883047 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
882980 TGTGTTAAAA
882990 TATATATAT
1 TATATATAT
*
882999 TAAAT-TAT
1 TATATATAT
883007 TAT-TATAT
1 TATATATAT
883015 TATAGTATAT
1 TATA-TATAT
883025 TATAT-TA-
1 TATATATAT
883032 TATATTATAT
1 TATA-TATAT
883042 TATATA
1 TATATA
883048 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:883037 original size:12 final size:12
Alignment explanation
Indices: 882992--883047 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
882982 TGTTAAAATA
*
882992 TATATATTAAAT
1 TATATATTATAT
883004 TAT-TATTATATT
1 TATATATTATA-T
883016 ATAGTATATTATAT
1 -TA-TATATTATAT
883030 TATATATTATAT
1 TATATATTATAT
883042 TATATA
1 TATATA
883048 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:884373 original size:18 final size:19
Alignment explanation
Indices: 884350--884388 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
884340 ATATATAGAT
884350 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
884368 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
884387 AT
1 AT
884389 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:888347 original size:29 final size:30
Alignment explanation
Indices: 888284--888357 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
888274 AATAATGCTT
* * * *
888284 ATAGGTCGATTTTGAAATTTATTTAGGTAT
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
888314 TTAGGCCGATTTT-AAAATTATTTAGGGAA
1 ATAGGCCGATTTTGAAAATTATTTAGGGAA
*
888343 ATAGGCTGATTTTGA
1 ATAGGCCGATTTTGA
888358 GGGAAAGCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (30 bp):
ATAGGCCGATTTTGAAAATTATTTAGGGAA
Found at i:889175 original size:23 final size:21
Alignment explanation
Indices: 889116--889181 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
889106 TTCAAATATT
*
889116 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
* * *
889137 TTAATTATTTGAAATATCATTATG
1 TTTA-TATGTGAAATAT-ATTA-A
*
889161 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATATTAA
889182 ATACACGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 14 0.41
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTATATGTGAAATATATTAA
Found at i:889846 original size:5 final size:5
Alignment explanation
Indices: 889836--889872 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
889826 AATTATTTGA
*
889836 AAAAT AAAAT AAAAT AAAAT TAAA- AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
889873 ACTCTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:904197 original size:17 final size:16
Alignment explanation
Indices: 904167--904213 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
904157 AACATGTCAA
* *
904167 TTTGTGTGTATTTTAT
1 TTTGTTTGTTTTTTAT
904183 GTTTGTTTGTTTTTTAT
1 -TTTGTTTGTTTTTTAT
904200 TTT-TTTGATTTTTT
1 TTTGTTTG-TTTTTT
904214 TTAATGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 14 0.52
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.77
Consensus pattern (16 bp):
TTTGTTTGTTTTTTAT
Found at i:904206 original size:15 final size:18
Alignment explanation
Indices: 904177--904213 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
904167 TTTGTGTGTA
904177 TTTTATGTTTGTTTG-TT
1 TTTTATGTTTGTTTGATT
904194 TTTTAT-TTT-TTTGATT
1 TTTTATGTTTGTTTGATT
904210 TTTT
1 TTTT
904214 TTAATGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTATGTTTGTTTGATT
Found at i:910218 original size:18 final size:18
Alignment explanation
Indices: 910192--910226 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
910182 TATCAAAAAA
* *
910192 AAATTTATATTTATATTG
1 AAATGTATATTAATATTG
910210 AAATGTATATTAATATT
1 AAATGTATATTAATATT
910227 TGCATTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AAATGTATATTAATATTG
Found at i:911732 original size:28 final size:29
Alignment explanation
Indices: 911692--911768 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
911682 GAATTAACCG
*
911692 AAAAAGTTCGGTTCGGTTA-TTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
911720 AAAAAATTTGGTTCGGTTATTTTTTTTGA
1 AAAAAATTCGGTTCGGTTATTTTTTTTGA
*
911749 AAACAAATTCAGTTCGGTTA
1 AAA-AAATTCGGTTCGGTTA
911769 ACGGTTAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
29 12 0.28
30 14 0.33
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
AAAAAATTCGGTTCGGTTATTTTTTTTGA
Found at i:911992 original size:19 final size:20
Alignment explanation
Indices: 911964--912007 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
911954 TTAATCCATT
*
911964 TTTAATATTTT-CAAAAAAA
1 TTTAACATTTTACAAAAAAA
911983 TTTAACATTTTAACAAAAAAA
1 TTTAACATTTT-ACAAAAAAA
912004 TTTA
1 TTTA
912008 TTAACTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAACATTTTACAAAAAAA
Found at i:918603 original size:15 final size:15
Alignment explanation
Indices: 918585--918619 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
918575 ATATCGACTC
918585 AAAAAAGAAGAAAAG
1 AAAAAAGAAGAAAAG
*
918600 AAAAAATAAGAAAAG
1 AAAAAAGAAGAAAAG
918615 AAAAA
1 AAAAA
918620 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAGAAAAG
Found at i:924744 original size:12 final size:12
Alignment explanation
Indices: 924729--924755 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
924719 TTTTAATAAA
924729 AAATAAATAATT
1 AAATAAATAATT
924741 AAATAAATAATT
1 AAATAAATAATT
924753 AAA
1 AAA
924756 AATAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAATAATT
Found at i:925236 original size:30 final size:29
Alignment explanation
Indices: 925177--925251 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
925167 TTAAATAAGT
*
925177 AATGATAAAATTATACTTTTTCTCCCTAAA
1 AATGATAAAATTATACTTTATCT-CCTAAA
925207 AATGATAAAATTATACTTTAATCAT-CTAAA
1 AATGATAAAATTATACTTT-ATC-TCCTAAA
* *
925237 AATTATAAAAATATA
1 AATGATAAAATTATA
925252 AGCTATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 37 0.93
31 2 0.05
32 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (29 bp):
AATGATAAAATTATACTTTATCTCCTAAA
Found at i:930213 original size:14 final size:15
Alignment explanation
Indices: 930191--930224 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
930181 CTCCCTCTTG
*
930191 TTTTCTCCCCTTCTC
1 TTTTCTCCCCCTCTC
930206 TTTT-TCCCCCTCTC
1 TTTTCTCCCCCTCTC
930220 TTTTC
1 TTTTC
930225 CATTTTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTCTCCCCCTCTC
Found at i:946416 original size:13 final size:13
Alignment explanation
Indices: 946369--946418 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
946359 TTTGGCAATT
*
946369 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
946382 CTTTTG-AAAGTG
1 CTTTTGAAAAGTG
*
946394 C-TGTGAAAAAGTG
1 CTTTTG-AAAAGTG
946407 CTTTTGAAAAGT
1 CTTTTGAAAAGT
946419 TTAGTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 18 0.58
14 3 0.10
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:959229 original size:27 final size:26
Alignment explanation
Indices: 959159--959237 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
959149 ATACTTTACA
* *
959159 TATTATTTCTTTTAAACTATTATATG
1 TATTATTTATTTTAAATTATTATATG
*
959185 TATTATTTATTTTGAAATTTTTATATG
1 TATTATTTATTTT-AAATTATTATATG
959212 TATCT-TTGTATTTTAAATTATTATAT
1 TAT-TATT-TATTTTAAATTATTATAT
959238 ATATACATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 12 0.26
27 27 0.59
28 7 0.15
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (26 bp):
TATTATTTATTTTAAATTATTATATG
Found at i:959671 original size:27 final size:26
Alignment explanation
Indices: 959629--959699 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 26
959619 TACTTTGTGA
959629 ATTATTTATCTT-AATTT-ATTTAACAT
1 ATTATTTAT-TTAAATTTGATTT-ACAT
* *
959655 ATTATTTATTTAAAATTTGCTTTATAT
1 ATTATTTATTT-AAATTTGATTTACAT
959682 ATTATTTTATTTCAAATT
1 ATTA-TTTATTT-AAATT
959700 GTTTTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 9 0.24
27 12 0.32
28 15 0.39
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTATTTATTTAAATTTGATTTACAT
Found at i:959705 original size:27 final size:28
Alignment explanation
Indices: 959653--959714 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
959643 TTTATTTAAC
959653 ATATTA-TTTATTTAAAATTTGCTTTAT
1 ATATTATTTTATTTAAAATTTGCTTTAT
* *
959680 ATATTATTTTATTTCAAA-TTGTTTTAT
1 ATATTATTTTATTTAAAATTTGCTTTAT
*
959707 ATTTTATT
1 ATATTATT
959715 CATATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
ATATTATTTTATTTAAAATTTGCTTTAT
Found at i:965857 original size:5 final size:5
Alignment explanation
Indices: 965841--965874 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
965831 TTGTGTGTTC
*
965841 TTTAT CTTTAT TTTAT TTTAT TTTAT TCTAT TTT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTT
965875 TCACAGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:968598 original size:50 final size:50
Alignment explanation
Indices: 968474--968722 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
968464 GATAATAACA
* * ** * *
968474 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
968525 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
968575 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
968625 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
968680 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
968723 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:968652 original size:100 final size:104
Alignment explanation
Indices: 968473--968722 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
968463 TGATAATAAC
**
968473 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
968538 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
968575 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
968638 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
968680 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
968723 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:968838 original size:13 final size:13
Alignment explanation
Indices: 968817--968848 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
968807 GCTTGGATCA
*
968817 TCATCAAATAAAT
1 TCATAAAATAAAT
968830 TCATAAAATAAAT
1 TCATAAAATAAAT
968843 TCATAA
1 TCATAA
968849 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:969095 original size:30 final size:30
Alignment explanation
Indices: 969060--969117 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
969050 CCTCGACTCT
*
969060 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
969090 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
969118 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:976156 original size:50 final size:50
Alignment explanation
Indices: 976032--976280 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
976022 GATAATAACA
* * ** * *
976032 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
976083 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
976133 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
976183 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
976238 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
976281 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:976210 original size:100 final size:104
Alignment explanation
Indices: 976031--976280 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
976021 TGATAATAAC
**
976031 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
976096 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
976133 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
976196 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
976238 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
976281 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:976396 original size:13 final size:13
Alignment explanation
Indices: 976375--976406 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
976365 GCTTGGATCA
*
976375 TCATCAAATAAAT
1 TCATAAAATAAAT
976388 TCATAAAATAAAT
1 TCATAAAATAAAT
976401 TCATAA
1 TCATAA
976407 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:976653 original size:30 final size:30
Alignment explanation
Indices: 976618--976675 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
976608 CCTCGACTCT
*
976618 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
976648 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
976676 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:978012 original size:18 final size:18
Alignment explanation
Indices: 977989--978024 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
977979 ACTGTATGTT
977989 AGAATAGATTAGAGGCAA
1 AGAATAGATTAGAGGCAA
978007 AGAATAGATTAGAGGCAA
1 AGAATAGATTAGAGGCAA
978025 CAGATTATAT
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:0.50, C:0.06, G:0.28, T:0.17
Consensus pattern (18 bp):
AGAATAGATTAGAGGCAA
Found at i:980243 original size:72 final size:72
Alignment explanation
Indices: 980126--980273 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
980116 CAATTTCTTC
* *
980126 CAAACTTGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
980191 ATGTTGA
66 ATGTTGA
* *
980198 CAAACTTGACATATTCTCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
1 CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
980263 ATGTTGA
66 ATGTTGA
980270 CAAA
1 CAAA
980274 AAGGAGCAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (72 bp):
CAAACTTGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCA
ATGTTGA
Found at i:982294 original size:18 final size:18
Alignment explanation
Indices: 982267--982381 Score: 176
Period size: 18 Copynumber: 6.4 Consensus size: 18
982257 TATGACTGTT
982267 TACAGTACTATTCACGTA
1 TACAGTACTATTCACGTA
*
982285 TACGGTACTATTCACGTA
1 TACAGTACTATTCACGTA
*
982303 TACAGTACTATTCATGTA
1 TACAGTACTATTCACGTA
*
982321 TACAGTACTATTCATGTA
1 TACAGTACTATTCACGTA
*
982339 TACAGCACTATTCACGTA
1 TACAGTACTATTCACGTA
* *
982357 TACGGTACTGTTCACGTA
1 TACAGTACTATTCACGTA
982375 TACAGTA
1 TACAGTA
982382 GTTGGGATTG
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (18 bp):
TACAGTACTATTCACGTA
Found at i:991172 original size:14 final size:15
Alignment explanation
Indices: 991153--991189 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
991143 CAAAAATTGA
*
991153 AAAATAATAC-TATT
1 AAAATAAAACTTATT
991167 AAAATAAAACTTATT
1 AAAATAAAACTTATT
991182 AAAATAAA
1 AAAATAAA
991190 CACACATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAACTTATT
Found at i:991883 original size:5 final size:5
Alignment explanation
Indices: 991873--991901 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
991863 TATAATTTCA
991873 TATAT TATAT TATAT TATAT TA-AT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
991902 ATTATCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:993348 original size:21 final size:22
Alignment explanation
Indices: 993309--993349 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
993299 TATTCTTTAC
993309 AAAGGTTTTAATATCAATTAGA
1 AAAGGTTTTAATATCAATTAGA
* *
993331 AAAGTTTTTATTAT-AATTA
1 AAAGGTTTTAATATCAATTA
993350 TATTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
AAAGGTTTTAATATCAATTAGA
Found at i:1007834 original size:16 final size:16
Alignment explanation
Indices: 1007813--1007843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1007803 ATAATACTTC
*
1007813 ATATTATGTTATTTAT
1 ATATTATGTAATTTAT
1007829 ATATTATGTAATTTA
1 ATATTATGTAATTTA
1007844 GAACACATTA
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:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATATTATGTAATTTAT
Found at i:1012457 original size:13 final size:13
Alignment explanation
Indices: 1012439--1012468 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1012429 TCACTCTATT
1012439 ATATAACTAAAGA
1 ATATAACTAAAGA
*
1012452 ATATAAGTAAAGA
1 ATATAACTAAAGA
1012465 ATAT
1 ATAT
1012469 TTGTTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (13 bp):
ATATAACTAAAGA
Done.