Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 127 of 318
Found at i:39463544 original size:20 final size:20
Alignment explanation
Indices: 39463503--39463546 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39463493 CAGAAAATAA
* *
39463503 TTTTCAAAAAATAATTTATT
1 TTTTAAAAAAATAATATATT
39463523 TTTTAAAAAAATTAATAT-TT
1 TTTTAAAAAAA-TAATATATT
39463543 TTTT
1 TTTT
39463547 GATGTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAAAAATAATATATT
Found at i:39464076 original size:13 final size:14
Alignment explanation
Indices: 39464041--39464086 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
39464031 TAATATGTAA
*
39464041 AAAATATTA-TTTA
1 AAAATATTATTTTT
39464054 AAAATATTATTTTT
1 AAAATATTATTTTT
*
39464068 AAAAT-TTATTATT
1 AAAATATTATTTTT
39464081 AAAATA
1 AAAATA
39464087 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTATTTTT
Found at i:39464077 original size:16 final size:16
Alignment explanation
Indices: 39464045--39464084 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
39464035 ATGTAAAAAA
39464045 TATTATTTAAAAATAT
1 TATTATTTAAAAATAT
39464061 TATT-TTT-AAAAT-T
1 TATTATTTAAAAATAT
39464074 TATTA-TTAAAA
1 TATTATTTAAAA
39464085 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTTAAAAATAT
Found at i:39464133 original size:22 final size:22
Alignment explanation
Indices: 39464089--39464148 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
39464079 TTAAAATAAA
*
39464089 ATTAAAATATTAAA-TA-ATTT
1 ATTAAAATAATAAATTATATTT
39464109 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
39464131 ATTATATTAATAATTTAT
1 ATTAAAATAATAAATTAT
39464149 TATATGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.38
21 2 0.06
22 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:39464887 original size:18 final size:18
Alignment explanation
Indices: 39464864--39464898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39464854 CTAACCAGTT
*
39464864 TAATCAATTTGATCGATA
1 TAATCAATTTGACCGATA
*
39464882 TAATCAGTTTGACCGAT
1 TAATCAATTTGACCGAT
39464899 TTACCTGACT
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:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
TAATCAATTTGACCGATA
Found at i:39467122 original size:66 final size:66
Alignment explanation
Indices: 39467011--39467148 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 66
39467001 CTAACTCCCA
** ** * * * * *
39467011 TAATTCCCTATTAGGTCAATTAGAGTTCTCTAATTCCTTGCTAGGTCGAGAACACATTATTACCT
1 TAATTCCCTATTAGGTCAAGAAGAGTTCTCTAACACCTTACTAGGTCAAGAAAAAACTATTACCT
39467076 C
66 C
* * * *
39467077 TAATTTCCTATTAGGTCAAGAATAGTTCTCTAACACCTTATTAGGTCAAGAAAAAACTGTTACCT
1 TAATTCCCTATTAGGTCAAGAAGAGTTCTCTAACACCTTACTAGGTCAAGAAAAAACTATTACCT
39467142 C
66 C
39467143 TAATTC
1 TAATTC
39467149 TTTGTTGGGT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (66 bp):
TAATTCCCTATTAGGTCAAGAAGAGTTCTCTAACACCTTACTAGGTCAAGAAAAAACTATTACCT
C
Found at i:39471778 original size:21 final size:20
Alignment explanation
Indices: 39471734--39471778 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39471724 TTAAATATGA
39471734 ATTTAAAATTTCTAATATAT
1 ATTTAAAATTTCTAATATAT
* *
39471754 ATTTAAAATTTTTGATATAAT
1 ATTTAAAATTTCTAATAT-AT
39471775 ATTT
1 ATTT
39471779 TTAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAAAATTTCTAATATAT
Found at i:39475520 original size:23 final size:22
Alignment explanation
Indices: 39475491--39475542 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
39475481 AGCGCCTAAA
*
39475491 ACGACACACGAGGTGTCTG-AT
1 ACGACACACGAGGTGCCTGAAT
39475512 ACGACACACGAGGTGCCTGAAAT
1 ACGACACACGAGGTGCCTG-AAT
39475535 ACGACACA
1 ACGACACA
39475543 TAAAGTGCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 18 0.64
23 10 0.36
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (22 bp):
ACGACACACGAGGTGCCTGAAT
Found at i:39475550 original size:23 final size:23
Alignment explanation
Indices: 39475468--39475554 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 23
39475458 CCTGATCAGT
* *
39475468 ATACGACACATAAAGCGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
39475490 A-ACGACACACGAGGTGTCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
39475510 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
39475533 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
39475555 TCAGTAAAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 31 0.60
22 1 0.02
23 19 0.37
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:39476112 original size:51 final size:51
Alignment explanation
Indices: 39476045--39476164 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 51
39476035 TCCCAAACTT
* * *
39476045 ACTTCATACTTT-ATCCGGAATTATTACTTTGTTGTTCCGGCCTCAACAAGA
1 ACTTCATA-TTTCATCCGGAATTATTACTTTATTGCTCCAGCCTCAACAAGA
* * * **
39476096 ACTTCATATTTCATCCGGATTTTTTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCCAGCCTCAACAAGA
*
39476147 GCTTCATA-TTCATCCGGA
1 ACTTCATATTTCATCCGGA
39476165 TAACTTAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 13 0.22
51 46 0.78
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (51 bp):
ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCCAGCCTCAACAAGA
Found at i:39477394 original size:19 final size:20
Alignment explanation
Indices: 39477363--39477401 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39477353 TACAATTTGG
39477363 GCTATGTTCACACGATCTGA
1 GCTATGTTCACACGATCTGA
*
39477383 GCTATG-TCACACGGTCTGA
1 GCTATGTTCACACGATCTGA
39477402 CCACACAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (20 bp):
GCTATGTTCACACGATCTGA
Found at i:39477446 original size:17 final size:18
Alignment explanation
Indices: 39477424--39477460 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39477414 GTGACCCCTA
39477424 TTTT-CCAAAA-TTTCATG
1 TTTTCCCAAAACTTTC-TG
39477441 TTTTCCCAAAACTTTCTG
1 TTTTCCCAAAACTTTCTG
39477459 TT
1 TT
39477461 CTACTTCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTTCCCAAAACTTTCTG
Found at i:39478776 original size:22 final size:22
Alignment explanation
Indices: 39478750--39478792 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39478740 TATATCTTTA
39478750 AATAAAAATAAAAAAATTAAAG
1 AATAAAAATAAAAAAATTAAAG
* **
39478772 AATAAAGATAAATCAATTAAA
1 AATAAAAATAAAAAAATTAAA
39478793 TAATTTTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (22 bp):
AATAAAAATAAAAAAATTAAAG
Found at i:39479620 original size:30 final size:30
Alignment explanation
Indices: 39479559--39479627 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
39479549 AAAACAGAAT
* *
39479559 AGAGCAGAACAAAACCAAATGGTATAGAGC
1 AGAGCAGAACAAAACAAAATGGTACAGAGC
* *
39479589 AGAGCAGAACAGAACAAAATGG-AGCATAGC
1 AGAGCAGAACAAAACAAAATGGTA-CAGAGC
*
39479619 AGAACAGAA
1 AGAGCAGAA
39479628 AGAGCAGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.52, C:0.16, G:0.25, T:0.07
Consensus pattern (30 bp):
AGAGCAGAACAAAACAAAATGGTACAGAGC
Found at i:39479635 original size:14 final size:15
Alignment explanation
Indices: 39479616--39479648 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39479606 AATGGAGCAT
39479616 AGCAGAACAGAA-AG
1 AGCAGAACAGAATAG
39479630 AGCAGAACAGAATAG
1 AGCAGAACAGAATAG
39479645 AGCA
1 AGCA
39479649 ATATGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.55, C:0.15, G:0.27, T:0.03
Consensus pattern (15 bp):
AGCAGAACAGAATAG
Found at i:39487530 original size:27 final size:27
Alignment explanation
Indices: 39487499--39487557 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
39487489 AAAAACATTA
39487499 TTCTAAAATAAAATAAAAGAAGTCTAG
1 TTCTAAAATAAAATAAAAGAAGTCTAG
39487526 TTCTAAAATAAAATAAAAGAAGTCTAG
1 TTCTAAAATAAAATAAAAGAAGTCTAG
39487553 TTCTA
1 TTCTA
39487558 TATAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (27 bp):
TTCTAAAATAAAATAAAAGAAGTCTAG
Found at i:39487994 original size:35 final size:34
Alignment explanation
Indices: 39487925--39488000 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
39487915 AAGAGGTCAT
* * *
39487925 TAAATT-GTTGTACCATATTGATGTGATGTGTCTC
1 TAAATTAG-TGTACCATATTGATGTCATATCTCTC
* *
39487959 TTAATTAGTGTACTATATTTGATGTCATATCTCTC
1 TAAATTAGTGTACCATA-TTGATGTCATATCTCTC
39487994 TAAATTA
1 TAAATTA
39488001 TTGCTAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (34 bp):
TAAATTAGTGTACCATATTGATGTCATATCTCTC
Found at i:39488663 original size:14 final size:14
Alignment explanation
Indices: 39488630--39488663 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39488620 TATAATATCC
*
39488630 AAATAATAACAATA
1 AAATAGTAACAATA
39488644 AAATAGTAACAATA
1 AAATAGTAACAATA
*
39488658 TAATAG
1 AAATAG
39488664 CGAAATAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:39489906 original size:18 final size:19
Alignment explanation
Indices: 39489883--39489922 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
39489873 GCTTACACAA
39489883 AAACCAAAA-AAACAAAA-T
1 AAACCAAAATAAA-AAAACT
39489901 AAACCAAAATAAAAAAACT
1 AAACCAAAATAAAAAAACT
39489920 AAA
1 AAA
39489923 ATTAAAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.78, C:0.15, G:0.00, T:0.07
Consensus pattern (19 bp):
AAACCAAAATAAAAAAACT
Found at i:39491407 original size:21 final size:20
Alignment explanation
Indices: 39491373--39491411 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39491363 TTTATTCATA
39491373 TATATATGTATATTGTTTTG
1 TATATATGTATATTGTTTTG
*
39491393 TATATCATTTATATTGTTT
1 TATAT-ATGTATATTGTTT
39491412 CGTTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (20 bp):
TATATATGTATATTGTTTTG
Found at i:39493551 original size:31 final size:31
Alignment explanation
Indices: 39493513--39493776 Score: 368
Period size: 31 Copynumber: 8.5 Consensus size: 31
39493503 AAATGACAAC
39493513 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
39493544 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
39493575 TGAAAAGTGGTAACTTCTA-CTACCTAATCAG
1 TGAAAAGTGGTAGCTTC-AGCTACCTGATCAG
*
39493606 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
39493637 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
39493668 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* * *
39493699 TGAAAAGTGGTAGCTCCGGCTACCTGATAAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* ** *
39493730 TGAAAAATGGTAGCACCAGTTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
39493761 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
39493777 TGGCTACAAG
Statistics
Matches: 208, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
31 207 1.00
32 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:39493883 original size:47 final size:48
Alignment explanation
Indices: 39493814--39493939 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 48
39493804 CAAGTGATTT
* *
39493814 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
39493861 CTGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* ** *
39493909 C-GTGTAAGACCATAGATGGGCTATGGCATCA
1 CTGTATAAGACCATATCTGGGATATGGCATCA
39493940 TTATGTAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 65 0.96
48 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (48 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
Found at i:39498317 original size:13 final size:14
Alignment explanation
Indices: 39498301--39498333 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39498291 GTATTTTTCC
39498301 TTATTTATT-TTAT
1 TTATTTATTATTAT
39498314 TTATTTATTATTAT
1 TTATTTATTATTAT
*
39498328 TAATTT
1 TTATTT
39498334 TAAAAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:39498401 original size:22 final size:21
Alignment explanation
Indices: 39498362--39498422 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
39498352 ATTTGATATG
39498362 TTTTATAATATATATTTTTTAAA
1 TTTTA-AATATAT-TTTTTTAAA
*
39498385 TTTTAAATAT-TATTTTTAAA
1 TTTTAAATATATTTTTTTAAA
*
39498405 TATTAAATATATTTTTTT
1 TTTTAAATATATTTTTTT
39498423 TAATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.50
21 7 0.21
22 5 0.15
23 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAATATATTTTTTTAAA
Found at i:39498403 original size:13 final size:13
Alignment explanation
Indices: 39498385--39498409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39498375 ATTTTTTAAA
39498385 TTTTAAATATTAT
1 TTTTAAATATTAT
39498398 TTTTAAATATTA
1 TTTTAAATATTA
39498410 AATATATTTT
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:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:39498423 original size:22 final size:21
Alignment explanation
Indices: 39498363--39498425 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
39498353 TTTGATATGT
*
39498363 TTTATAATATATATTTTTTAAA
1 TTTA-AATATATTTTTTTTAAA
* *
39498385 TTTTAA-ATATTATTTTTAAA
1 TTTAAATATATTTTTTTTAAA
39498405 TATTAAATATATTTTTTTTAA
1 T-TTAAATATATTTTTTTTAA
39498426 TAATATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.38
21 6 0.18
22 15 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAAATATATTTTTTTTAAA
Found at i:39498647 original size:20 final size:19
Alignment explanation
Indices: 39498600--39498648 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
39498590 TAGAAAAAAT
39498600 AAAAAAAA--TATTTGTTA
1 AAAAAAAATTTATTTGTTA
* *
39498617 AAAATATATTTATTTGTTA
1 AAAAAAAATTTATTTGTTA
39498636 AAAAAAGAATTTA
1 AAAAAA-AATTTA
39498649 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
AAAAAAAATTTATTTGTTA
Found at i:39498705 original size:20 final size:20
Alignment explanation
Indices: 39498648--39498705 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
39498638 AAAAGAATTT
39498648 AATTAAAATATATATATT-AA
1 AATTAAAA-ATATATATTAAA
* * *
39498668 AAGTAAAAATTTAAATTAAA
1 AATTAAAAATATATATTAAA
39498688 AATTAAAAATATATATTA
1 AATTAAAAATATATATTA
39498706 TAACTTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTAAAAATATATATTAAA
Found at i:39498764 original size:14 final size:15
Alignment explanation
Indices: 39498747--39498779 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39498737 TATATTTTAA
39498747 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
39498761 ATAATTTAAAATATT
1 ATAATTTAAAATATT
39498776 ATAA
1 ATAA
39498780 AATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:39498767 original size:24 final size:24
Alignment explanation
Indices: 39498726--39498795 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 24
39498716 AGGTCATGTC
*
39498726 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATAATATATTTAAAAT-A
*
39498751 TTTAAAAATTATA-ATTTAAAATA
1 TTTAAAAATAATATATTTAAAATA
*
39498774 -TT-ATAA-AATATATTTAAAATA
1 TTTAAAAATAATATATTTAAAATA
39498795 T
1 T
39498796 ACATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.08
21 13 0.33
22 2 0.05
23 1 0.03
24 8 0.21
25 12 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTAAAAATAATATATTTAAAATA
Found at i:39498793 original size:34 final size:35
Alignment explanation
Indices: 39498745--39498821 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 35
39498735 AATATATTTT
39498745 AAATAATTTAAAAATTATA-ATTTAAAAT-ATTATA
1 AAATAATTTAAAAA-TATACATTTAAAATAATTATA
39498779 AAATATATTT-AAAATATACATTTAAAATAATTATA
1 AAATA-ATTTAAAAATATACATTTAAAATAATTATA
39498814 AAACTAAT
1 AAA-TAAT
39498822 AATAAATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
33 4 0.10
34 18 0.46
35 15 0.38
36 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (35 bp):
AAATAATTTAAAAATATACATTTAAAATAATTATA
Found at i:39498803 original size:13 final size:11
Alignment explanation
Indices: 39498735--39498816 Score: 71
Period size: 11 Copynumber: 7.2 Consensus size: 11
39498725 CTTTAAAAAT
*
39498735 AATATATTTTA
1 AATATATTTAA
39498746 AATA-ATTTAAA
1 AATATATTT-AA
39498757 AATTATAATTTAA
1 AA-TAT-ATTTAA
*
39498770 AATAT-TATAA
1 AATATATTTAA
39498780 AATATATTTAA
1 AATATATTTAA
39498791 AATATACATTTAA
1 AATAT--ATTTAA
39498804 AATA-ATTATAA
1 AATATATT-TAA
39498815 AA
1 AA
39498817 CTAATAATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
10 16 0.27
11 21 0.35
12 5 0.08
13 14 0.23
14 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATATTTAA
Found at i:39498886 original size:20 final size:20
Alignment explanation
Indices: 39498863--39498926 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
39498853 TTTAAATGTT
*
39498863 TTTATATTATTAAAAAT-ATA
1 TTTATATT-TAAAAAATAATA
39498883 TTTAATATTTAAAAAATAATA
1 TTT-ATATTTAAAAAATAATA
*
39498904 TTTAAAATTTAGAAAAATAATA
1 TTT-ATATTTA-AAAAATAATA
39498926 T
1 T
39498927 CAAAAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.26
21 18 0.46
22 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTATATTTAAAAAATAATA
Found at i:39498898 original size:21 final size:20
Alignment explanation
Indices: 39498874--39498959 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
39498864 TTATATTATT
*
39498874 AAAAATATATTTAATATTTA
1 AAAAATATATTTAAAATTTA
39498894 AAAAATAATATTTAAAATTTA
1 AAAAAT-ATATTTAAAATTTA
*
39498915 GAAAAATA-A--T---A-TCA
1 -AAAAATATATTTAAAATTTA
39498929 AAAATATATATTTAAAATTTA
1 AAAA-ATATATTTAAAATTTA
39498950 AAAAATATAT
1 AAAAATATAT
39498960 ATTATAAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
13 4 0.08
14 5 0.09
15 2 0.04
17 1 0.02
18 1 0.02
20 14 0.26
21 20 0.38
22 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAATATATTTAAAATTTA
Found at i:39498922 original size:22 final size:21
Alignment explanation
Indices: 39498874--39498926 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
39498864 TTATATTATT
*
39498874 AAAAAT-ATATTTAATATTTA
1 AAAAATAATATTTAAAATTTA
39498894 AAAAATAATATTTAAAATTTA
1 AAAAATAATATTTAAAATTTA
39498915 GAAAAATAATAT
1 -AAAAATAATAT
39498927 CAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 11 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAATATTTAAAATTTA
Found at i:39498932 original size:22 final size:21
Alignment explanation
Indices: 39498889--39498933 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
39498879 TATATTTAAT
**
39498889 ATTTAAAAAATAATATTTAAA
1 ATTTAAAAAATAATATCAAAA
39498910 ATTTAGAAAAATAATATCAAAA
1 ATTTA-AAAAATAATATCAAAA
39498932 AT
1 AT
39498934 ATATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTTAAAAAATAATATCAAAA
Found at i:39498954 original size:34 final size:35
Alignment explanation
Indices: 39498894--39498961 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
39498884 TTAATATTTA
39498894 AAAAATAATATTTAAAATTTAGAAAAATA-ATATC
1 AAAAATAATATTTAAAATTTAGAAAAATATATATC
39498928 AAAAATATATATTTAAAATTTA-AAAAATATATAT
1 AAAAATA-ATATTTAAAATTTAGAAAAATATATAT
39498962 TATAAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAAATAATATTTAAAATTTAGAAAAATATATATC
Found at i:39500215 original size:3 final size:3
Alignment explanation
Indices: 39500201--39500254 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
39500191 GACAATAAAG
*
39500201 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
39500245 AAT AAT AAT A
1 AAT AAT AAT A
39500255 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39500478 original size:3 final size:3
Alignment explanation
Indices: 39500470--39500523 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
39500460 TTTAAATATG
* * * *
39500470 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA ATA ATA AT- ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39500517 ATA ATA A
1 ATA ATA A
39500524 AAGTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39500924 original size:17 final size:17
Alignment explanation
Indices: 39500865--39500926 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
39500855 AAAATAATAT
39500865 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
39500885 TAAAAATGTATTCGTAT
1 TAAAAATATATACATAA
*
39500902 TTAAAATATATACATAA
1 TAAAAATATATACATAA
39500919 TAAAAATA
1 TAAAAATA
39500927 CAATATTTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
17 21 0.66
19 6 0.19
20 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:39501095 original size:22 final size:22
Alignment explanation
Indices: 39501053--39501095 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39501043 GTACATAACA
*
39501053 TAAATATCATACATATAATATC
1 TAAATATCATACATACAATATC
39501075 TAAATAT-ATACATACATATAT
1 TAAATATCATACATACA-ATAT
39501096 ATGTAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATCATACATACAATATC
Found at i:39501977 original size:18 final size:20
Alignment explanation
Indices: 39501946--39501998 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
39501936 AAGCAAATTC
*
39501946 GAAAATAA-AATAA-A-AAG
1 GAAAATAATAATAATAGAAA
39501963 GAAAATAATAATAAATAGAAA
1 GAAAATAATAAT-AATAGAAA
39501984 GAAAATAATAATAAT
1 GAAAATAATAATAAT
39501999 GTAATATCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 2 0.06
20 4 0.13
21 14 0.45
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (20 bp):
GAAAATAATAATAATAGAAA
Found at i:39501989 original size:21 final size:22
Alignment explanation
Indices: 39501953--39501997 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
39501943 TTCGAAAATA
39501953 AAATAAAAAGGAAAATAATAAT
1 AAATAAAAAGGAAAATAATAAT
*
39501975 AAATAGAAA-GAAAATAATAAT
1 AAATAAAAAGGAAAATAATAAT
39501996 AA
1 AA
39501998 TGTAATATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (22 bp):
AAATAAAAAGGAAAATAATAAT
Found at i:39502974 original size:14 final size:14
Alignment explanation
Indices: 39502952--39502986 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39502942 ACTATTAGCA
*
39502952 AGTTATTAAGAAGT
1 AGTTATTAAAAAGT
*
39502966 AGTTGTTAAAAAGT
1 AGTTATTAAAAAGT
39502980 AGTTATT
1 AGTTATT
39502987 CCATAAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AGTTATTAAAAAGT
Found at i:39515265 original size:16 final size:17
Alignment explanation
Indices: 39515235--39515266 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39515225 GTTATCAGAT
39515235 AATTAAATATTTAAAAA
1 AATTAAATATTTAAAAA
39515252 AATTAAAT-TTTAAAA
1 AATTAAATATTTAAAA
39515267 TCTAAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATATTTAAAAA
Found at i:39519622 original size:4 final size:4
Alignment explanation
Indices: 39519613--39519641 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39519603 AGCAAACGTG
39519613 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
39519642 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:39523672 original size:5 final size:5
Alignment explanation
Indices: 39523662--39523686 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39523652 ATTATTATTT
39523662 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
39523687 GAAAAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:39523933 original size:17 final size:18
Alignment explanation
Indices: 39523911--39523944 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39523901 TATAAAAAAA
39523911 CTTTT-AAATTTTTTTAT
1 CTTTTAAAATTTTTTTAT
39523928 CTTTTAAAATTTTTTTA
1 CTTTTAAAATTTTTTTA
39523945 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTAAAATTTTTTTAT
Found at i:39536907 original size:25 final size:26
Alignment explanation
Indices: 39536869--39536926 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
39536859 TGCATAATTG
*
39536869 TTTG-TTTTTATTTAACAGGTTCGT-
1 TTTGTTTTTTATTTAACAGGCTCGTC
*
39536893 TTTGTTTTTTGTTTAACAGGCTCGTCC
1 TTTGTTTTTTATTTAACAGGCTCGT-C
39536920 TTTGTTT
1 TTTGTTT
39536927 AAAGATAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 18 0.62
27 7 0.24
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (26 bp):
TTTGTTTTTTATTTAACAGGCTCGTC
Found at i:39540250 original size:14 final size:14
Alignment explanation
Indices: 39540233--39540262 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39540223 AAAACTGAGC
39540233 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
39540247 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
39540261 AA
1 AA
39540263 AAAATGCAGG
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:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AAGGAAAAATGGAA
Found at i:39554922 original size:39 final size:39
Alignment explanation
Indices: 39554749--39554927 Score: 277
Period size: 39 Copynumber: 4.6 Consensus size: 39
39554739 GCTCTGATGA
39554749 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
39554788 GCTTCAGTTAGCCTCCGCGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* * *
39554827 GCTTCAGTTAGCCTCCGGGTTTCCTTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
39554866 GCTTCAATTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
39554905 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
39554928 AGATCATGAT
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 127 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:39567830 original size:25 final size:26
Alignment explanation
Indices: 39567802--39567861 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
39567792 TTATAATATT
*
39567802 AATTTAACATTAAAATT-AAATAAAA
1 AATTTAACAATAAAATTCAAATAAAA
* *
39567827 AA-TTAATAATAAAATTCAATTAAAA
1 AATTTAACAATAAAATTCAAATAAAA
*
39567852 CATTTAACAA
1 AATTTAACAA
39567862 CCGGCCACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 12 0.43
25 10 0.36
26 6 0.21
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.32
Consensus pattern (26 bp):
AATTTAACAATAAAATTCAAATAAAA
Found at i:39573356 original size:15 final size:16
Alignment explanation
Indices: 39573330--39573360 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39573320 TCTAATATTG
39573330 TATTACATAAAATATC
1 TATTACATAAAATATC
39573346 TATTA-ATAAAATATC
1 TATTACATAAAATATC
39573361 GGAACTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
TATTACATAAAATATC
Found at i:39581279 original size:21 final size:22
Alignment explanation
Indices: 39581229--39581284 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
39581219 AATTTATGTA
**
39581229 ATTATATTTGTTTATATGATTT
1 ATTATATTACTTTATATGATTT
* *
39581251 -TTAAATTACTTTATAT-TTTT
1 ATTATATTACTTTATATGATTT
39581271 ATTATATTAGCTTT
1 ATTATATTA-CTTT
39581285 TAATGGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTATATTACTTTATATGATTT
Found at i:39583614 original size:31 final size:30
Alignment explanation
Indices: 39583567--39583624 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
39583557 GAAATATGAG
* *
39583567 TTTAAAATTATTATTTAAGTTT-TTTTATA
1 TTTAAAATAATTATTTAAATTTATTTTATA
39583596 TTTATAAATAATTAATTTAAATTTATTTT
1 TTTA-AAATAATT-ATTTAAATTTATTTT
39583625 TGGCTAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 7 0.29
31 9 0.38
32 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTAAAATAATTATTTAAATTTATTTTATA
Found at i:39583680 original size:25 final size:22
Alignment explanation
Indices: 39583656--39583701 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39583646 AAAAAATTTA
*
39583656 AAATTATATATTTATATTATTTTT
1 AAATTA-ATATTTA-ATGATTTTT
*
39583680 AATTTAATATTTAATGATTTTT
1 AAATTAATATTTAATGATTTTT
39583702 TATTCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATTAATATTTAATGATTTTT
Found at i:39583818 original size:22 final size:22
Alignment explanation
Indices: 39583793--39583834 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39583783 TATTTTTATG
* *
39583793 TTTATAAATTACATAATATATT
1 TTTAAAAATAACATAATATATT
39583815 TTTAAAAATAACATAATATA
1 TTTAAAAATAACATAATATA
39583835 AAACCTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAAATAACATAATATATT
Found at i:39587655 original size:18 final size:18
Alignment explanation
Indices: 39587628--39587666 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
39587618 TACAGGCTGC
39587628 AATCACTTATATAAATGG
1 AATCACTTATATAAATGG
*
39587646 AATCAGTTATATAAATGG
1 AATCACTTATATAAATGG
39587664 AAT
1 AAT
39587667 TGATCGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (18 bp):
AATCACTTATATAAATGG
Found at i:39588780 original size:3 final size:3
Alignment explanation
Indices: 39588772--39588806 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39588762 AAGAATATAG
39588772 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39588807 GACACAGGGG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39589200 original size:19 final size:19
Alignment explanation
Indices: 39589176--39589212 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39589166 TATTAAAAAT
39589176 ATAAAAGC-TAAAACTTTAA
1 ATAAAAGCTTAAAA-TTTAA
39589195 ATAAAAGCTTAAAATTTA
1 ATAAAAGCTTAAAATTTA
39589213 GAAATTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAAAAGCTTAAAATTTAA
Found at i:39590570 original size:34 final size:34
Alignment explanation
Indices: 39590519--39590596 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
39590509 ATTTTCATCA
* * *
39590519 TAAT-AATTTTCTTTCAAAGTTGATCCATAATGT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
39590552 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
39590586 TAATGAATCTT
1 TAATGAATCTT
39590597 TTACATGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 4 0.10
34 37 0.90
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (34 bp):
TAATGAATCTTCTTTCAAAATTGATCCATAATAT
Found at i:39595680 original size:47 final size:47
Alignment explanation
Indices: 39595523--39595655 Score: 230
Period size: 47 Copynumber: 2.8 Consensus size: 47
39595513 CTGGGATAAG
* * *
39595523 CACATAGTGCTTCATCGGAGCAAATCCGGAACTTTAACATTATAGTA
1 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
*
39595570 CACAAAGTACTTCATCAGAACAAATCCGGAACTTTAACATTATAGTA
1 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
39595617 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACA
1 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACA
39595656 GTAGTCGACA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 81 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (47 bp):
CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
Found at i:39596181 original size:14 final size:14
Alignment explanation
Indices: 39596158--39596201 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
39596148 TCATAAATCT
39596158 ATATTCAATATAATA
1 ATATT-AATATAATA
39596173 ATATTAATA-ATATA
1 ATATTAATATA-ATA
*
39596187 ATATTATTATAATA
1 ATATTAATATAATA
39596201 A
1 A
39596202 AATAACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 19 0.73
15 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAATATAATA
Found at i:39597136 original size:22 final size:22
Alignment explanation
Indices: 39597110--39597152 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39597100 TAAACAAGTG
39597110 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39597132 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
39597153 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39610871 original size:22 final size:22
Alignment explanation
Indices: 39610843--39610885 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39610833 AGGGGGAGTG
39610843 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39610865 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
39610886 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39611395 original size:20 final size:21
Alignment explanation
Indices: 39611364--39611411 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
39611354 TAATAAAAGA
*
39611364 AATAAT-AAAATAACAAGAAT
1 AATAATAAAAATAACAACAAT
*
39611384 AA-AATAAAAATAACGACAAT
1 AATAATAAAAATAACAACAAT
39611404 AATAATAA
1 AATAATAA
39611412 CTGAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 5 0.21
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (21 bp):
AATAATAAAAATAACAACAAT
Found at i:39617270 original size:17 final size:17
Alignment explanation
Indices: 39617248--39617285 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39617238 AAAAGGAGAA
39617248 AAAAAAACTATATGTAC
1 AAAAAAACTATATGTAC
39617265 AAAAAAACTATATGTAC
1 AAAAAAACTATATGTAC
39617282 AAAA
1 AAAA
39617286 TACATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAAACTATATGTAC
Found at i:39619255 original size:40 final size:40
Alignment explanation
Indices: 39619191--39619269 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
39619181 ACAGACCATG
* *
39619191 TGGGGATGAAATCGACTCACCCAGCCCTACACACCAAGTA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
* *
39619231 TGGGGATAAAATTGACCCATCCAGCCCTACACACCAAGT
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
39619270 GGTACTGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.32, G:0.19, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
Found at i:39626404 original size:38 final size:38
Alignment explanation
Indices: 39626362--39626452 Score: 92
Period size: 40 Copynumber: 2.3 Consensus size: 38
39626352 GTCCAACCCA
* *
39626362 ACACACCATGTGGGGATAAAAACGACCCACCCAGCCCT
1 ACACACCATGTGGGAATAAAAACAACCCACCCAGCCCT
* * * * *
39626400 ACACACCAAGTGTGAGAATAAAATCAACCCATCTAGTCCT
1 ACACACC-A-TGTGGGAATAAAAACAACCCACCCAGCCCT
*
39626440 ACACACCAAGTGG
1 ACACACCATGTGG
39626453 TACTGTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
38 10 0.24
39 2 0.05
40 30 0.71
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.14
Consensus pattern (38 bp):
ACACACCATGTGGGAATAAAAACAACCCACCCAGCCCT
Found at i:39627852 original size:35 final size:36
Alignment explanation
Indices: 39627752--39627880 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 36
39627742 GGAAAAGTGT
* **
39627752 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
39627787 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATC----CCATACTGAGTTAA
* *
39627827 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGAA
1 GAAATGTAGGTATGGTATTATCCCATACTGAGTT-AA
*
39627863 -AAATATAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
39627881 TCAATGAGGA
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
35 48 0.59
36 2 0.02
39 2 0.02
40 29 0.36
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (36 bp):
GAAATGTAGGTATGGTATTATCCCATACTGAGTTAA
Found at i:39629062 original size:30 final size:30
Alignment explanation
Indices: 39629026--39629094 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
39629016 ACACCTACAC
*
39629026 GCTCGTGTCG-TTCA-CTCGTGTGACCCACAA
1 GCTCGTG-CGATTCACCT-GTGTAACCCACAA
39629056 GCTCGTGCGATTCACCTGTGTAACCCACAA
1 GCTCGTGCGATTCACCTGTGTAACCCACAA
*
39629086 GCCCGTGCG
1 GCTCGTGCG
39629095 GTTTACACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 31 0.89
31 2 0.06
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (30 bp):
GCTCGTGCGATTCACCTGTGTAACCCACAA
Found at i:39630110 original size:40 final size:40
Alignment explanation
Indices: 39630055--39630130 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
39630045 GGCCATGTAG
*
39630055 GGATAAAATCGACCCACCCAGCCTTACACACCAAGTATGA
1 GGATAAAATCGACCCACCCAGCCCTACACACCAAGTATGA
* *
39630095 GGATAAAATCGACCCATCTAGCCCTACACACCAAGT
1 GGATAAAATCGACCCACCCAGCCCTACACACCAAGT
39630131 GGTACAGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.37, C:0.33, G:0.14, T:0.16
Consensus pattern (40 bp):
GGATAAAATCGACCCACCCAGCCCTACACACCAAGTATGA
Found at i:39634369 original size:47 final size:47
Alignment explanation
Indices: 39634243--39634372 Score: 161
Period size: 47 Copynumber: 2.8 Consensus size: 47
39634233 ACAATCGATA
* * * *
39634243 AATACCTATACCATGGCTTGTAGTCAAATCAAAGTAACTTATCCCGG
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
* * * * * *
39634290 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
*
39634337 AATACTTATACCATGACCTGTAGTCAAATCAAGGTA
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTA
39634373 TCATTCGTAC
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (47 bp):
AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
Found at i:39635094 original size:19 final size:19
Alignment explanation
Indices: 39635055--39635092 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39635045 ACATGAATTC
39635055 ATCAATGAAAACTTTCAAA
1 ATCAATGAAAACTTTCAAA
*
39635074 ATCAAT-AATACTTTCAAA
1 ATCAATGAAAACTTTCAAA
39635092 A
1 A
39635093 ATTGAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (19 bp):
ATCAATGAAAACTTTCAAA
Found at i:39637786 original size:29 final size:29
Alignment explanation
Indices: 39637753--39637821 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
39637743 TGTGTGTACC
*
39637753 ATGTGAAAAGGGATATCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
39637782 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
39637811 ATATGAAAAGG
1 ATGTGAAAAGG
39637822 AAATGTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.25
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCGA
Found at i:39640864 original size:11 final size:11
Alignment explanation
Indices: 39640848--39640875 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39640838 TTGTTTTATA
39640848 TTCTTTCAACT
1 TTCTTTCAACT
39640859 TTCTTTCAACT
1 TTCTTTCAACT
39640870 TTCTTT
1 TTCTTT
39640876 ATTTTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCTTTCAACT
Found at i:39641800 original size:30 final size:30
Alignment explanation
Indices: 39641766--39641824 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
39641756 AAGGAGAAGC
*
39641766 AAAAGAGAATGAAAAAAAAAGAAAAAAAAG
1 AAAAGAGAAAGAAAAAAAAAGAAAAAAAAG
** * *
39641796 AAAAGTTAAAGAACATAAAAGAAAAAAAA
1 AAAAGAGAAAGAAAAAAAAAGAAAAAAAA
39641825 TTAAATTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.07
Consensus pattern (30 bp):
AAAAGAGAAAGAAAAAAAAAGAAAAAAAAG
Found at i:39643254 original size:3 final size:3
Alignment explanation
Indices: 39643246--39643281 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39643236 ACTAAATTTG
39643246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39643282 TGGTAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39649503 original size:31 final size:31
Alignment explanation
Indices: 39649465--39649525 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
39649455 AAATGAAGAG
39649465 AGTGGGTGTAACATCCCAAAAATTATGTTAT
1 AGTGGGTGTAACATCCCAAAAATTATGTTAT
39649496 AGTGGGTGTAACATCCCAAAAATTATGTTA
1 AGTGGGTGTAACATCCCAAAAATTATGTTA
39649526 GAAGAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTGGGTGTAACATCCCAAAAATTATGTTAT
Found at i:39651331 original size:7 final size:7
Alignment explanation
Indices: 39651319--39651347 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39651309 GGTTACTCGA
39651319 CGACTTT
1 CGACTTT
39651326 CGACTTT
1 CGACTTT
39651333 CGACTTT
1 CGACTTT
39651340 CGACTTT
1 CGACTTT
39651347 C
1 C
39651348 CCCGATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (7 bp):
CGACTTT
Found at i:39653073 original size:12 final size:12
Alignment explanation
Indices: 39653053--39653091 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
39653043 CACACGGGCA
*
39653053 TGTGCTAGGCCG
1 TGTGATAGGCCG
*
39653065 TGTGATAGGCTG
1 TGTGATAGGCCG
39653077 TGTGATAGGCCG
1 TGTGATAGGCCG
39653089 TGT
1 TGT
39653092 AACCCATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.41, T:0.31
Consensus pattern (12 bp):
TGTGATAGGCCG
Found at i:39660723 original size:13 final size:13
Alignment explanation
Indices: 39660705--39660730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39660695 CTGTGCATTC
39660705 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39660718 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39660731 AACAAATCCC
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:39662521 original size:30 final size:30
Alignment explanation
Indices: 39662487--39662545 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
39662477 CAGTTAATCG
39662487 AACGAATTCGGTTAATCGGTCGGTTAACCA
1 AACGAATTCGGTTAATCGGTCGGTTAACCA
39662517 AACGAATTCGGTTAATCGGTCGGTTAACC
1 AACGAATTCGGTTAATCGGTCGGTTAACC
39662546 GAATTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (30 bp):
AACGAATTCGGTTAATCGGTCGGTTAACCA
Found at i:39662765 original size:18 final size:18
Alignment explanation
Indices: 39662742--39662779 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39662732 AATATAGATT
39662742 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
* *
39662760 AACCCAATTTCCCAACCC
1 AACCCAAGTACCCAACCC
39662778 AA
1 AA
39662780 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.47, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:39662773 original size:13 final size:13
Alignment explanation
Indices: 39662757--39662781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39662747 AAGTACCCAA
39662757 CCCAACCCAATTT
1 CCCAACCCAATTT
39662770 CCCAACCCAATT
1 CCCAACCCAATT
39662782 ATAAAAATTA
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:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (13 bp):
CCCAACCCAATTT
Found at i:39662844 original size:5 final size:6
Alignment explanation
Indices: 39662808--39662851 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
39662798 AATTAATAAG
*
39662808 TAAAAA TAAAAA TCTAAAAC TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA --TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
39662852 ACATATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:39662852 original size:20 final size:20
Alignment explanation
Indices: 39662808--39662845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39662798 AATTAATAAG
**
39662808 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
39662828 TAAAAATAAAAATAAAAA
1 TAAAAATAAAAATAAAAA
39662846 TAAAAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:39662885 original size:9 final size:9
Alignment explanation
Indices: 39662871--39662929 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
39662861 TTTATACAAA
39662871 TAATTCGGT
1 TAATTCGGT
39662880 TAATTCGGT
1 TAATTCGGT
* *
39662889 TAATTTGGG
1 TAATTCGGT
39662898 TAATTCAGG-
1 TAATTC-GGT
**
39662907 TAATTCAAT
1 TAATTCGGT
*
39662916 TAATTCTGT
1 TAATTCGGT
39662925 TAATT
1 TAATT
39662930 TTATACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 39 0.95
10 2 0.05
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:39665622 original size:61 final size:61
Alignment explanation
Indices: 39665504--39665632 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
39665494 GTAGGAAATC
* * * * *
39665504 AACACGGCCTGGACTTCCCTACACTGGTATACCACAAGCCCGTATAGTGTTAGCAGACTCT
1 AACACGGCCTGGACTTCCCTACACGGGTAGACCACAAGCCCGTATACTATTAACAGACTCT
* * * *
39665565 AACACGGCCTGGACTTCCTTACACGGGTAGACCACACGGCCGTGT-CTATTCAACAGACTCT
1 AACACGGCCTGGACTTCCCTACACGGGTAGACCACAAGCCCGTATACTATT-AACAGACTCT
39665626 AACACGG
1 AACACGG
39665633 TTTGAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 3 0.05
61 55 0.95
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (61 bp):
AACACGGCCTGGACTTCCCTACACGGGTAGACCACAAGCCCGTATACTATTAACAGACTCT
Found at i:39666498 original size:13 final size:13
Alignment explanation
Indices: 39666480--39666505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39666470 CTGTGCATTC
39666480 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39666493 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39666506 AACAAATCCC
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:39667359 original size:40 final size:40
Alignment explanation
Indices: 39667286--39667362 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
39667276 ATGGTACCAT
** * *
39667286 TTGGTGTGTAGGGTTGGATGGGTTGATTTTATCCCCATAC
1 TTGGTGTGTAGGACTGGATGGGTCGATTCTATCCCCATAC
* *
39667326 TTGGTGTGTAGGACTGGGTTGGTCGATTCTATCCCCA
1 TTGGTGTGTAGGACTGGATGGGTCGATTCTATCCCCA
39667363 CATGATGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (40 bp):
TTGGTGTGTAGGACTGGATGGGTCGATTCTATCCCCATAC
Found at i:39667417 original size:22 final size:23
Alignment explanation
Indices: 39667374--39667418 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
39667364 ATGATGTGTT
* *
39667374 GGGTTGGACGGAGATGGTATGCA
1 GGGTTGGACGGAGATAGCATGCA
*
39667397 GGGTTGGA-TGAGATAGCATGCA
1 GGGTTGGACGGAGATAGCATGCA
39667419 TCCATGCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.24, C:0.09, G:0.44, T:0.22
Consensus pattern (23 bp):
GGGTTGGACGGAGATAGCATGCA
Found at i:39670360 original size:40 final size:39
Alignment explanation
Indices: 39670310--39670408 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
39670300 TTACGGTACC
* * *
39670310 ATTGGATGTGTAGGGTTGGATAGGTTGATTTTATCCCTAT
1 ATTGG-TGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
* * *
39670350 ACTTGGTGTGTAAGGCTGGGTAGGTCGATTCTATCCCCAT
1 A-TTGGTGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
*
39670390 A-TGGTGTGTTGGGTTGGAT
1 ATTGGTGTGTAGGGTTGGAT
39670409 GAATATAGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
38 14 0.29
40 30 0.62
41 4 0.08
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.38
Consensus pattern (39 bp):
ATTGGTGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
Found at i:39672303 original size:20 final size:20
Alignment explanation
Indices: 39672278--39672340 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
39672268 TAGATTTTAG
39672278 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
39672298 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
39672318 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
39672338 ATG
1 ATG
39672341 GGATGAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGCCAACTTGGATTTCTAA
Found at i:39672374 original size:13 final size:14
Alignment explanation
Indices: 39672356--39672412 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
39672346 AAAATAGATT
39672356 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
39672369 TTTAATTAATTAAAA
1 TTTAATTAA-TAAAA
39672384 TTT--TTAAACCTAAAA
1 TTTAATT-AA--TAAAA
39672399 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
39672412 T
1 T
39672413 ATGTTCATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 16 0.43
14 2 0.05
15 15 0.41
16 2 0.05
17 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAATTAATAAAA
Found at i:39674074 original size:21 final size:20
Alignment explanation
Indices: 39674041--39674084 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
39674031 AAAATTAATT
* *
39674041 AAAAATTCTAAAAGTAAAAA
1 AAAAATTATAAAAGCAAAAA
39674061 AAAAATTATCAAAAGCATAAAA
1 AAAAATTAT-AAAAGCA-AAAA
39674083 AA
1 AA
39674085 GTTATAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAATTATAAAAGCAAAAA
Found at i:39676247 original size:8 final size:8
Alignment explanation
Indices: 39676236--39676268 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
39676226 TTTAAAATGC
39676236 AAAAA-AA
1 AAAAAGAA
39676243 AAAAAGAA
1 AAAAAGAA
39676251 AAAAAGAA
1 AAAAAGAA
39676259 AAAAGAGAA
1 AAAA-AGAA
39676268 A
1 A
39676269 GTAATAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 5 0.21
8 14 0.58
9 5 0.21
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:39677398 original size:18 final size:18
Alignment explanation
Indices: 39677367--39677401 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39677357 ATAACTCAAT
**
39677367 TATTTTATTTTATTTTTA
1 TATTTTATAATATTTTTA
39677385 TATTTTATAATATTTTT
1 TATTTTATAATATTTTT
39677402 TTTATCTATA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTATAATATTTTTA
Found at i:39680232 original size:23 final size:23
Alignment explanation
Indices: 39680205--39680248 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
39680195 TACAAAAAAT
*
39680205 TTTAAAACAAGTAAATATAAAGG
1 TTTAAAACAAGTAAAAATAAAGG
* *
39680228 TTTAAAATAGGTAAAAATAAA
1 TTTAAAACAAGTAAAAATAAA
39680249 TAATATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.27
Consensus pattern (23 bp):
TTTAAAACAAGTAAAAATAAAGG
Found at i:39681596 original size:44 final size:43
Alignment explanation
Indices: 39681504--39681594 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
39681494 CAACTTTCCG
*
39681504 AAAATTTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
1 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
39681547 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
1 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
39681590 AAAAA
1 AAAAA
39681595 ATAAAATACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.22, C:0.29, G:0.04, T:0.45
Consensus pattern (43 bp):
AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
Found at i:39681681 original size:4 final size:5
Alignment explanation
Indices: 39681653--39681698 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
39681643 CTAATTTAAT
*
39681653 AATAA AATAA AATAA AATAA AAT-A AATAAA AACAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AA-TAA AATAA AATAA
39681699 TATCTTCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 25 0.69
6 7 0.19
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:39683997 original size:30 final size:29
Alignment explanation
Indices: 39683945--39684001 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
39683935 CCACATCTTC
*
39683945 ACTCAATCGATTACTATCTTTAAATTAAAA
1 ACTCAATCGATTACAATCTTT-AATTAAAA
*
39683975 ACTCAATCGATTGCAAAT-TTTAATTAA
1 ACTCAATCGATTAC-AATCTTTAATTAA
39684002 GAGTTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 16 0.67
31 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (29 bp):
ACTCAATCGATTACAATCTTTAATTAAAA
Found at i:39684921 original size:43 final size:43
Alignment explanation
Indices: 39684872--39684960 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
39684862 TTACCCAAAA
39684872 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
1 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
39684915 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
1 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
39684958 TAC
1 TAC
39684961 TTTTATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (43 bp):
TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
Found at i:39692876 original size:22 final size:22
Alignment explanation
Indices: 39692851--39692904 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
39692841 ATCCTAGTCT
*
39692851 CGTCGTGACGACCATCGCTTGA
1 CGTCGTGACGACCATCACTTGA
* * * *
39692873 CGTCGCGATGATCATCATTTGA
1 CGTCGTGACGACCATCACTTGA
*
39692895 CATCGTGACG
1 CGTCGTGACG
39692905 TGGACTTTGT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CGTCGTGACGACCATCACTTGA
Found at i:39693308 original size:22 final size:24
Alignment explanation
Indices: 39693283--39693326 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
39693273 GGCACGTTAT
39693283 TTTTTGTTC-TGT-TTCTTCTTGG
1 TTTTTGTTCTTGTGTTCTTCTTGG
39693305 TTTTTGTTCTTGTGTTCTTCTT
1 TTTTTGTTCTTGTGTTCTTCTT
39693327 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTGTTCTTGTGTTCTTCTTGG
Found at i:39697714 original size:20 final size:19
Alignment explanation
Indices: 39697689--39697738 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
39697679 GATATACATT
*
39697689 ATTAATTCATTAATCATTTA
1 ATTAATTAATTAATC-TTTA
39697709 ATTAATCTAATTAATCTTTA
1 ATTAAT-TAATTAATCTTTA
39697729 ATTAATTAAT
1 ATTAATTAAT
39697739 CTTAATCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAATTAATTAATCTTTA
Found at i:39697736 original size:15 final size:16
Alignment explanation
Indices: 39697710--39697746 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
39697700 AATCATTTAA
39697710 TTAATCTAATTAATCT
1 TTAATCTAATTAATCT
39697726 TTAAT-TAATTAATC-
1 TTAATCTAATTAATCT
39697740 TTAATCT
1 TTAATCT
39697747 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATCTAATTAATCT
Found at i:39698151 original size:20 final size:20
Alignment explanation
Indices: 39698089--39698152 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39698079 ATGAGCATTT
*
39698089 TTAAATT-ATGTTTAATATATA
1 TTAAATTAATCTTTAAT-TA-A
* *
39698110 TT-AATTAATTCATTAA-TCA
1 TTAAATTAA-TCTTTAATTAA
39698129 TTAAATTAATCTTTAATTAA
1 TTAAATTAATCTTTAATTAA
39698149 TTAA
1 TTAA
39698153 CCTTAATCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
19 9 0.26
20 17 0.50
21 3 0.09
22 5 0.15
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAATTAATCTTTAATTAA
Found at i:39698508 original size:16 final size:15
Alignment explanation
Indices: 39698487--39698531 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
39698477 ATTAAATTTT
39698487 ATTAATTGAGATTAAG
1 ATTAATT-AGATTAAG
39698503 ATTAATTA-ATTAAAG
1 ATTAATTAGATT-AAG
*
39698518 ATTTATTAGATTAA
1 ATTAATTAGATTAA
39698532 TTAAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 13 0.50
16 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (15 bp):
ATTAATTAGATTAAG
Found at i:39698530 original size:20 final size:19
Alignment explanation
Indices: 39698503--39698557 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
39698493 TGAGATTAAG
*
39698503 ATTAATTAATTAAAGATTT
1 ATTAATTAATTAAAGATTA
39698522 ATTAGATTAATTAAATGATTA
1 ATTA-ATTAATTAAA-GATTA
*
39698543 ATGAATTAATTAAAG
1 ATTAATTAATTAAAG
39698558 TATATACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 20 0.62
21 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
ATTAATTAATTAAAGATTA
Found at i:39702651 original size:71 final size:71
Alignment explanation
Indices: 39702569--39702714 Score: 238
Period size: 71 Copynumber: 2.1 Consensus size: 71
39702559 CCATCAGAGT
* * **
39702569 ATCGATAAAAGTGCAGGGGATGTTGAACTTTGGCTACTGGCTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
39702634 CAAGGA
66 CAAGGA
*
39702640 ATCGATAAAAGTACAGGAGATGTTGAACTTTTGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
*
39702705 CAAGGT
66 CAAGGA
39702711 ATCG
1 ATCG
39702715 GTAGCACTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (71 bp):
ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
CAAGGA
Found at i:39704914 original size:22 final size:20
Alignment explanation
Indices: 39704889--39704951 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
39704879 TCCAAACAAT
39704889 AACAACAAAATAGTGAAATGAC
1 AACAACAAAATAGTGAAA--AC
* *
39704911 AACAA-ACAAT-GAGAAAAC
1 AACAACAAAATAGTGAAAAC
*
39704929 AACAGCAAAATAGTGGAAAAC
1 AACAACAAAATAGT-GAAAAC
39704950 AA
1 AA
39704952 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 6 0.18
21 12 0.36
22 5 0.15
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (20 bp):
AACAACAAAATAGTGAAAAC
Found at i:39705394 original size:24 final size:24
Alignment explanation
Indices: 39705366--39705422 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
39705356 ATATATTTAA
*
39705366 ATAATATTTAAATTTGTTAATATT
1 ATAATATTTAAATTAGTTAATATT
39705390 ATAATATTTAAATTAGTTAATATT
1 ATAATATTTAAATTAGTTAATATT
*
39705414 ATTATATTT
1 ATAATATTT
39705423 TAGTAAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATAATATTTAAATTAGTTAATATT
Found at i:39710947 original size:16 final size:16
Alignment explanation
Indices: 39710898--39710950 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
39710888 AAAAATTATG
*
39710898 TTTTCCATCATTCTAA
1 TTTTCCATCCTTCTAA
*
39710914 TTTTCTATCCCTT-TAA
1 TTTTCCAT-CCTTCTAA
*
39710930 TTTTCCATCCTTCCAA
1 TTTTCCATCCTTCTAA
39710946 TTTTC
1 TTTTC
39710951 TTTCCACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.13
16 24 0.77
17 3 0.10
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:39712620 original size:17 final size:17
Alignment explanation
Indices: 39712598--39712634 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39712588 GCACATGGCC
39712598 GTGTGG-ACACAGCCCAT
1 GTGTGGCACAC-GCCCAT
39712615 GTGTGGCACACGCCCAT
1 GTGTGGCACACGCCCAT
39712632 GTG
1 GTG
39712635 GCCATTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (17 bp):
GTGTGGCACACGCCCAT
Found at i:39714865 original size:43 final size:39
Alignment explanation
Indices: 39714788--39714890 Score: 102
Period size: 43 Copynumber: 2.5 Consensus size: 39
39714778 TTTTATATTC
*
39714788 TTTAGAATTTTTTTAATAAATTATATTTTTTTAAAATATCAAT
1 TTTAGAATTTTTTT-AT-AATTATATTTTATTAAAA-AT-AAT
*
39714831 TTTAGAATTTTTTTATAATTAT-TTTGAATATTAAAAATTAT
1 TTTAGAATTTTTTTATAATTATATTT---TATTAAAAATAAT
*
39714872 TTT-GAATTTTTTTGTAATT
1 TTTAGAATTTTTTTATAATT
39714891 TTTGTTGAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
40 18 0.33
41 11 0.20
42 4 0.07
43 21 0.39
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (39 bp):
TTTAGAATTTTTTTATAATTATATTTTATTAAAAATAAT
Found at i:39718459 original size:39 final size:39
Alignment explanation
Indices: 39718415--39718492 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39718405 ATTTATTTGT
39718415 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
1 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
39718454 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
1 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
39718493 GAAGGTTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (39 bp):
TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
Found at i:39723835 original size:20 final size:20
Alignment explanation
Indices: 39723796--39723835 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39723786 ATTTATTTTC
* *
39723796 ATTTATTTTTAATTATCTTT
1 ATTTATTTGTAATTACCTTT
*
39723816 ATTTATTTGTATTTACCTTT
1 ATTTATTTGTAATTACCTTT
39723836 TAGAATTTAA
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:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTATTTGTAATTACCTTT
Found at i:39727535 original size:22 final size:20
Alignment explanation
Indices: 39727510--39727552 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
39727500 AAACACAATA
39727510 ACAAGTCAATATTCTAATATTC
1 ACAA-TCAA-ATTCTAATATTC
* *
39727532 ACAATCAAATTTTATTATTC
1 ACAATCAAATTCTAATATTC
39727552 A
1 A
39727553 TTCCTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
ACAATCAAATTCTAATATTC
Found at i:39728633 original size:18 final size:18
Alignment explanation
Indices: 39728607--39728644 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39728597 ATTTTTATAC
*
39728607 ATATTTTTTAATCTTATT
1 ATATATTTTAATCTTATT
*
39728625 ATATATTTTAATTTTATT
1 ATATATTTTAATCTTATT
39728643 AT
1 AT
39728645 GCACGCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATATTTTAATCTTATT
Done.