Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 88 of 136
Found at i:29182277 original size:27 final size:27
Alignment explanation
Indices: 29182240--29182298 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
29182230 AATATATAAT
29182240 AAATATATTTTTTATTTTTTAATTTTA
1 AAATATATTTTTTATTTTTTAATTTTA
* *
29182267 AAATATTTTTTTTATTTTTTATTTTTA
1 AAATATATTTTTTATTTTTTAATTTTA
29182294 AAATA
1 AAATA
29182299 AAATTTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
AAATATATTTTTTATTTTTTAATTTTA
Found at i:29182305 original size:26 final size:27
Alignment explanation
Indices: 29182240--29182305 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
29182230 AATATATAAT
**
29182240 AAATATATTTTTTATTTTTTAATTTTA
1 AAATATAAATTTTATTTTTTAATTTTA
*** *
29182267 AAATATTTTTTTTATTTTTTATTTTTA
1 AAATATAAATTTTATTTTTTAATTTTA
29182294 AAATA-AAATTTT
1 AAATATAAATTTT
29182306 GGTGTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
AAATATAAATTTTATTTTTTAATTTTA
Found at i:29182305 original size:27 final size:27
Alignment explanation
Indices: 29182248--29182305 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
29182238 ATAAATATAT
***
29182248 TTTTTATTTTTTAATTTTAAAATATTT
1 TTTTTATTTTTTAATTTTAAAATAAAA
*
29182275 TTTTTATTTTTTATTTTTAAAATAAAA
1 TTTTTATTTTTTAATTTTAAAATAAAA
29182302 TTTT
1 TTTT
29182306 GGTGTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTTTAATTTTAAAATAAAA
Found at i:29183082 original size:72 final size:73
Alignment explanation
Indices: 29182964--29183103 Score: 255
Period size: 72 Copynumber: 1.9 Consensus size: 73
29182954 TTATGAGGTA
*
29182964 ATGAAAGTTAATAAAAAAAATTGATTAAGGTGGACAAATTTTATTACGATGGGTGGCAGTGGTTA
1 ATGAAAGTTAATAAAAAAAATTGATTAAGGTGGACAAATTTTATTACGATGGGTGACAGTGGTTA
29183029 CAATGGTG
66 CAATGGTG
*
29183037 ATGAAAGTTAAT-AAAAAATTTGATTAAGGTGGACAAATTTTATTACGATGGGTGACAGTGGTTA
1 ATGAAAGTTAATAAAAAAAATTGATTAAGGTGGACAAATTTTATTACGATGGGTGACAGTGGTTA
29183101 CAA
66 CAA
29183104 AGACCCAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 53 0.82
73 12 0.18
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (73 bp):
ATGAAAGTTAATAAAAAAAATTGATTAAGGTGGACAAATTTTATTACGATGGGTGACAGTGGTTA
CAATGGTG
Found at i:29187967 original size:13 final size:13
Alignment explanation
Indices: 29187949--29187988 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
29187939 AGTTCTTTAT
29187949 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
29187962 TACTTTTTAGAAG
1 TACTTTTGAAAAG
*
29187975 TATTTTTGAAAAG
1 TACTTTTGAAAAG
29187988 T
1 T
29187989 TTGATTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:29189433 original size:19 final size:21
Alignment explanation
Indices: 29189387--29189436 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29189377 GGGCTTGAAT
*
29189387 AATATTATTTTATA-AATTATA
1 AATA-TATTTTAAATAATTATA
*
29189408 AATATATTTTAAATAATTAAA
1 AATATATTTTAAATAATTATA
29189429 AATATATT
1 AATATATT
29189437 AAATTAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATATTTTAAATAATTATA
Found at i:29189438 original size:19 final size:21
Alignment explanation
Indices: 29189401--29189440 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29189391 TTATTTTATA
*
29189401 AATTATAAATATATTTTAAAT
1 AATTATAAATATATATTAAAT
29189422 AATTA-AAA-ATATATTAAAT
1 AATTATAAATATATATTAAAT
29189441 TAAATCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATAAATATATATTAAAT
Found at i:29197614 original size:17 final size:18
Alignment explanation
Indices: 29197592--29197629 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
29197582 AATTTATATG
*
29197592 TATATG-AAGAATATTAT
1 TATATGAAAAAATATTAT
29197609 TATATGTAAAAAATATTAT
1 TATATG-AAAAAATATTAT
29197628 TA
1 TA
29197630 CGTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
TATATGAAAAAATATTAT
Found at i:29199642 original size:133 final size:133
Alignment explanation
Indices: 29199385--29199645 Score: 316
Period size: 133 Copynumber: 2.0 Consensus size: 133
29199375 ATCACACTAA
* *
29199385 TGGTCTTTTATGCATCTAGACATCCACAATATGCAAAATGCATGTATTACAACACTTCCTTTTGG
1 TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACACTTCCCTTTGG
* * * * * * *
29199450 ATGACTATTTACTATGAATGTATTTCATTAAAACTTTGTGATAAAAAACCCGATGAGATAAAAGC
66 ATGACTATTTACTATAAATGTACTTCACTAAAACCTTGTCATAAAAAACCCAATAAGATAAAAGC
29199515 TAT
131 TAT
* * *
29199518 TGGTCTTTTATGTATCTAGCCATCTACAACATGCAAAATGCATGTATTACAACACTTTCCCTTT-
1 TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACAC-TTCCCTTTG
**
29199582 GATGACTATTCT-CTATAAACATGT-CTT-ACTAAAACCTTGTCA-AGAAAAATTCAATAAGATA
65 GATGACTATT-TACTAT-AA-ATGTACTTCACTAAAACCTTGTCATA-AAAAACCCAATAAGATA
29199643 AAA
126 AAA
29199646 ACTTAGTAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
132 1 0.01
133 93 0.85
134 11 0.10
135 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (133 bp):
TGGTCTTTTATGCATCTAGACATCCACAACATGCAAAATGCATGTATTACAACACTTCCCTTTGG
ATGACTATTTACTATAAATGTACTTCACTAAAACCTTGTCATAAAAAACCCAATAAGATAAAAGC
TAT
Found at i:29199764 original size:26 final size:24
Alignment explanation
Indices: 29199714--29199764 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
29199704 ACAGAAAATG
*
29199714 ATAAAATATTTTTTATTAGATCAA
1 ATAAAATATTTTTTATTAGACCAA
*
29199738 ATAAAATTATTTTTTGATTGGACCAA
1 ATAAAA-TATTTTTT-ATTAGACCAA
29199764 A
1 A
29199765 GATTACACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 8 0.35
26 9 0.39
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (24 bp):
ATAAAATATTTTTTATTAGACCAA
Found at i:29213485 original size:18 final size:18
Alignment explanation
Indices: 29213464--29213499 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29213454 GAGAATTTAT
29213464 TCTACAGTGAGAAGGTGA
1 TCTACAGTGAGAAGGTGA
29213482 TCTACAGTGAGAAGGTGA
1 TCTACAGTGAGAAGGTGA
29213500 GAATGCCAGA
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:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (18 bp):
TCTACAGTGAGAAGGTGA
Found at i:29216947 original size:19 final size:19
Alignment explanation
Indices: 29216910--29216948 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29216900 ATAGAAAACC
* *
29216910 ATAATAATAATTAATAATT
1 ATAATAATAATAAAAAATT
*
29216929 ATAATTATAATAAAAAATT
1 ATAATAATAATAAAAAATT
29216948 A
1 A
29216949 ATAACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATAATAAAAAATT
Found at i:29225028 original size:19 final size:17
Alignment explanation
Indices: 29224988--29225021 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29224978 TAAAAACTTG
*
29224988 TAAAAGTTATAATAATA
1 TAAAAGTTATAAGAATA
29225005 TAAAAGTTATATAGAAT
1 TAAAAGTTATA-AGAAT
29225022 TTTAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAAAGTTATAAGAATA
Found at i:29229804 original size:25 final size:25
Alignment explanation
Indices: 29229767--29229817 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
29229757 ATAATTGTAG
29229767 TTTTTTTAACCAATGATT-TAAATATTA
1 TTTTTTT-ACCAA-G-TTCTAAATATTA
29229794 TTTTTTT-CCAAGTTCTAAATATTA
1 TTTTTTTACCAAGTTCTAAATATTA
29229818 AATAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 10 0.43
25 4 0.17
27 7 0.30
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTTTTACCAAGTTCTAAATATTA
Found at i:29241864 original size:80 final size:80
Alignment explanation
Indices: 29241731--29241893 Score: 256
Period size: 80 Copynumber: 2.0 Consensus size: 80
29241721 ATAAAATATG
* * * *
29241731 TTGGTGTGATCAGGGTGAGATGCTTGAACATATTCTTTTATATTGTCCGAATGTTAAGCCACTTT
1 TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
29241796 GG-GCTTCTATACATA
66 GGCG-TTCTATACATA
* *
29241811 TTGGTATGATCAGGCTGAGATGCTTGACCATATTCTTTTATATTGTCAGAATGTTGAGCCACTTC
1 TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
29241876 GGCGTTCTATACATA
66 GGCGTTCTATACATA
29241891 TTG
1 TTG
29241894 ATGCTCTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 75 0.99
81 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (80 bp):
TTGGTATGATCAGGCTGAGATGCTTGAACATATTCTTTTATATTGTCAGAATGTTAAGCCACTTC
GGCGTTCTATACATA
Found at i:29242114 original size:29 final size:30
Alignment explanation
Indices: 29242057--29242113 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29242047 ATAAATACAT
29242057 AAATATAAATAAATATTTATATATAAAATA
1 AAATATAAATAAATATTTATATATAAAATA
*
29242087 AAATA-AAATAAATAATTTATATTTAAA
1 AAATATAAATAAAT-ATTTATATATAAA
29242114 TTATCAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATATAAATAAATATTTATATATAAAATA
Found at i:29262150 original size:6 final size:6
Alignment explanation
Indices: 29262139--29262168 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29262129 TGAGTAACAT
29262139 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
1 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
29262169 GAAAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
AGGCAA
Found at i:29269654 original size:101 final size:101
Alignment explanation
Indices: 29269474--29269682 Score: 265
Period size: 101 Copynumber: 2.1 Consensus size: 101
29269464 GGATAAGAGT
* * * * * *
29269474 ATGGTTGAACCATGACAATGTTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAA
1 ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
* ** *
29269539 ACCACAACTAGGTTATGGCACTTTGAATGTAAGATC
66 ACCACAACTAGGTTATGACACTACGAATGTAAGACC
* * * *
29269575 ATGGTTGAACCATGACAGTATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTGATGATAAG
1 ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
* *
29269640 ACCATAACTGGGTTATGACACTACGAATGTAAGACC
66 ACCACAACTAGGTTATGACACTACGAATGTAAGACC
*
29269676 ATCGTTG
1 ATGGTTG
29269683 GGCCATGGCA
Statistics
Matches: 91, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 91 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (101 bp):
ATGGTTGAACCATGACAATATTTATAAGTAAGACAATAGCTAGGCTATGACATTCTAATGAAAAA
ACCACAACTAGGTTATGACACTACGAATGTAAGACC
Found at i:29276408 original size:158 final size:159
Alignment explanation
Indices: 29276129--29276445 Score: 627
Period size: 158 Copynumber: 2.0 Consensus size: 159
29276119 TTTTATAAAA
29276129 AAAGAAAAAGTAAAGGAGCTAAATCCTTAAATTTTCATGTTTAATGATGCATTTTTATCAATAAT
1 AAAGAAAAAGTAAAGGAGCTAAATCCTTAAATTTTCATGTTTAATGATGCATTTTTATCAATAAT
29276194 TTTGGATTTATTTGAATGTTAAATTTTTATTTTTGAGTTTATTAATAAATAATTTATATAATTGA
66 TTTGGATTTATTTGAATGTTAAATTTTTATTTTTGAGTTTATTAATAAATAATTTATATAATTGA
29276259 TGAATATTTTATATTTG-AATTTATTTAG
131 TGAATATTTTATATTTGAAATTTATTTAG
29276287 AAAGAAAAAGTAAAGGAGCTAAATCCTTAAATTTTCATGTTTAATGATGCATTTTTATCAATAAT
1 AAAGAAAAAGTAAAGGAGCTAAATCCTTAAATTTTCATGTTTAATGATGCATTTTTATCAATAAT
29276352 TTTGGATTTATTTGAATGTTAAATTTTTATTTTTGAGTTTATTAATAAATAATTTATATAATTGA
66 TTTGGATTTATTTGAATGTTAAATTTTTATTTTTGAGTTTATTAATAAATAATTTATATAATTGA
29276417 TGAATATTTTATATTTGAAATTTATTTAG
131 TGAATATTTTATATTTGAAATTTATTTAG
29276446 TTTCAGTTAT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 147 0.93
159 11 0.07
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (159 bp):
AAAGAAAAAGTAAAGGAGCTAAATCCTTAAATTTTCATGTTTAATGATGCATTTTTATCAATAAT
TTTGGATTTATTTGAATGTTAAATTTTTATTTTTGAGTTTATTAATAAATAATTTATATAATTGA
TGAATATTTTATATTTGAAATTTATTTAG
Found at i:29277690 original size:49 final size:48
Alignment explanation
Indices: 29277558--29277710 Score: 161
Period size: 49 Copynumber: 3.1 Consensus size: 48
29277548 GCACGAACTA
* * ***
29277558 TTTTCTTTCTCAGTATTTTCTTTGTTTGAAAACCCCAAATTCATTTCTCC
1 TTTTCTTTCTCAGTCTTTTCTTTG-TTGAAAACCCCAAAATCCCGTC-CC
*
29277608 -TTTCTTTC-CTAGAC-TTTCTTTGCTTG-AAACCCCAAAATCCCGTCCC
1 TTTTCTTTCTC-AGTCTTTTCTTTG-TTGAAAACCCCAAAATCCCGTCCC
*
29277654 TTTTCTTTCTCAGTCTTTTCGTTGTTGGAAAACCCCAAAATCCCGTCCC
1 TTTTCTTTCTCAGTCTTTTCTTTGTT-GAAAACCCCAAAATCCCGTCCC
29277703 TTGTTCTT
1 TT-TTCTT
29277711 CTATTTTAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
46 2 0.02
47 27 0.31
48 21 0.24
49 32 0.37
50 5 0.06
ACGTcount: A:0.18, C:0.29, G:0.09, T:0.44
Consensus pattern (48 bp):
TTTTCTTTCTCAGTCTTTTCTTTGTTGAAAACCCCAAAATCCCGTCCC
Found at i:29279696 original size:43 final size:43
Alignment explanation
Indices: 29279633--29279782 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 43
29279623 ATCACTTGAT
* ** * * *
29279633 TTTGTGGGGAAAGCATCGCTAAATGTTATGTTCTTTAGCGGCT
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
*
29279676 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTATTTAGCGGCG
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
* * * * * * * * *
29279719 TTTGTAAGAAAAGTGTCACCAGAGGTCATGCTCTTTAGCGGCG
1 TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
29279762 TTTGT-GGGAAAAGCGCCGCTA
1 TTTGTAGGG-AAAGCGCCGCTA
29279783 TAGAACCGCT
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 1 0.01
43 82 0.99
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TTTGTAGGGAAAGCGCCGCTAAAAGTCATGTTCTTTAGCGGCG
Found at i:29281884 original size:19 final size:18
Alignment explanation
Indices: 29281840--29281884 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
29281830 ATTACTCCTG
29281840 CTTAGCTTTTCCTTATCA
1 CTTAGCTTTTCCTTATCA
29281858 CTTGAGCTTCTTCCTTATCA
1 CTT-AGCTT-TTCCTTATCA
*
29281878 GTTAGCT
1 CTTAGCT
29281885 AAACATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.47
Consensus pattern (18 bp):
CTTAGCTTTTCCTTATCA
Found at i:29283943 original size:21 final size:21
Alignment explanation
Indices: 29283880--29284028 Score: 97
Period size: 21 Copynumber: 7.1 Consensus size: 21
29283870 TAGAAGGCTG
* *
29283880 AACAGAAGCTCATTAGAGTTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
29283901 AACAAAACCT-ATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* *
29283921 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
29283942 AACGGAAACCCATAA-AGGTTA
1 AACAGAAGCTCATAAGA-GCTA
*
29283963 AACAGAAGTTCA-ATAGAGCTA
1 AACAGAAGCTCATA-AGAGCTA
* * *
29283984 AACAGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
*
29284005 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
29284026 AAC
1 AAC
29284029 GGAAAGTAAA
Statistics
Matches: 94, Mismatches: 29, Indels: 10
0.71 0.22 0.08
Matches are distributed among these distances:
20 17 0.18
21 75 0.80
22 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:29283968 original size:42 final size:42
Alignment explanation
Indices: 29283880--29284033 Score: 152
Period size: 42 Copynumber: 3.7 Consensus size: 42
29283870 TAGAAGGCTG
* * * * * * *
29283880 AACAGAAGCTCATTAGAGTTAAAC-AAAACCTATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
*
29283921 AACAGAAGCTCGTAAGAGCTGAACGGAAACCCATAAAGGTTA
1 AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
* * * * *
29283963 AACAGAAGTTC-AATAGAGCTAAACAGAAACTCAT-ATGAGTTA
1 AACAGAAGCTCGTA-AGAGCTAAACGGAAACCCATAAAG-GTTA
29284005 AACAGAAGCTCGTAAGAGCTAAACGGAAA
1 AACAGAAGCTCGTAAGAGCTAAACGGAAA
29284034 GTAAACACAA
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 23 0.25
42 68 0.74
43 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACGGAAACCCATAAAGGTTA
Found at i:29284023 original size:84 final size:83
Alignment explanation
Indices: 29283880--29284033 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 83
29283870 TAGAAGGCTG
* * * * *
29283880 AACAGAAGCTCATTAGAGTTAAACAAAACCTATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAAC
1 AACAGAAGCTCAATAGAGCTAAACAAAACCTATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
29283945 GGAAACCCATAAAGGTTA
66 GGAAACCCATAAAGGTTA
* *
29283963 AACAGAAGTTCAATAGAGCTAAACAGAAA-CTCATATGAGTTAAACAGAAGCTCGTAAGAGCTAA
1 AACAGAAGCTCAATAGAGCTAAACA-AAACCT-ATAAGAGTTAAACAGAAGCTCGTAAGAGCTAA
29284027 ACGGAAA
64 ACGGAAA
29284034 GTAAACACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 24 0.39
84 38 0.61
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (83 bp):
AACAGAAGCTCAATAGAGCTAAACAAAACCTATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
GGAAACCCATAAAGGTTA
Found at i:29289757 original size:9 final size:8
Alignment explanation
Indices: 29289736--29289767 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
29289726 ATAATTTTAG
29289736 TTTAAAAT
1 TTTAAAAT
29289744 TTTAAAATT
1 TTTAAAA-T
29289753 TTTAAAAT
1 TTTAAAAT
29289761 TTTAAAA
1 TTTAAAA
29289768 AGTTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:29296954 original size:17 final size:19
Alignment explanation
Indices: 29296934--29296977 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
29296924 ATTTTACTTT
*
29296934 AAAATTTTAAAATA-TT-A
1 AAAATTTTAAAAAATTTAA
29296951 AAAATTTTAAAAAATTTAA
1 AAAATTTTAAAAAATTTAA
29296970 AAAATTTT
1 AAAATTTT
29296978 CCATTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTTAAAAAATTTAA
Found at i:29296960 original size:9 final size:9
Alignment explanation
Indices: 29296934--29296977 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
29296924 ATTTTACTTT
29296934 AAAATTTT-
1 AAAATTTTA
*
29296942 AAAATATTA
1 AAAATTTTA
29296951 AAAATTTTAA
1 AAAATTTT-A
*
29296961 AAAATTTAA
1 AAAATTTTA
29296970 AAAATTTT
1 AAAATTTT
29296978 CCATTTTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:29300567 original size:49 final size:49
Alignment explanation
Indices: 29300514--29300719 Score: 394
Period size: 49 Copynumber: 4.2 Consensus size: 49
29300504 GACATGAATG
* *
29300514 ATATTTTTAAATGAATTGGTTGAATCTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
29300563 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
29300612 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
29300661 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
1 ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
29300710 ATATTTTTAA
1 ATATTTTTAA
29300720 TGTTATTGTT
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 155 1.00
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (49 bp):
ATATTTTTAAATGAACTGGTTGAATTTAGAGCATGTTTTGATTGTGTTC
Found at i:29306647 original size:58 final size:58
Alignment explanation
Indices: 29306579--29306688 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
29306569 CCGATGGTAG
29306579 TGATTTGACACGATTTTTATCACGT-AAGTCCAAGCTGAGTAGACTTGGTTGAAAGCTA
1 TGATTTGACACGATTTTTATCACGTAAAGTCCAA-CTGAGTAGACTTGGTTGAAAGCTA
* * * *
29306637 TGATTTGACACGATTTTTATTATGTAAATTCCAATTGAGTAGACTTGGTTGA
1 TGATTTGACACGATTTTTATCACGTAAAGTCCAACTGAGTAGACTTGGTTGA
29306689 TGTGATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 40 0.85
59 7 0.15
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (58 bp):
TGATTTGACACGATTTTTATCACGTAAAGTCCAACTGAGTAGACTTGGTTGAAAGCTA
Found at i:29306874 original size:49 final size:48
Alignment explanation
Indices: 29306811--29306937 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 48
29306801 CAATACCTTC
* * * ** *
29306811 TTACTTTCCGTAAGCCTCCATCCATGCGTTTTGGAGTAGGGCCACTTTA
1 TTACTTTCCATAAGCCTCC-TCCATGCATCTCAGAATAGGGCCACTTTA
*
29306860 TTACTTTCTATAAGCCT-CTCCCATGCATCTCAGAATAGGGCCACTTTA
1 TTACTTTCCATAAGCCTCCT-CCATGCATCTCAGAATAGGGCCACTTTA
29306908 TTACTTTCCATAAGCCTCCCTCCATGCATC
1 TTACTTTCCATAAGCCT-CCTCCATGCATC
29306938 GAGGAATAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 1 0.01
48 40 0.60
49 24 0.36
50 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (48 bp):
TTACTTTCCATAAGCCTCCTCCATGCATCTCAGAATAGGGCCACTTTA
Found at i:29307061 original size:49 final size:48
Alignment explanation
Indices: 29306954--29307172 Score: 154
Period size: 49 Copynumber: 4.5 Consensus size: 48
29306944 TAGGGTTATC
* * * * * * * **
29306954 TTATTACCTTCCGTAAGTCTCCCCTTATACGTTTGGGAGTAAGGTCAAG
1 TTATTACTTTTCGTAAGCCTCCCC-CATACGTCTGGGAGCAAGCTCACT
* *
29307003 TTATCACTTTTCATAAGCCTCCCCCTATACGTCTGGGAGCAAGCTCACT
1 TTATTACTTTTCGTAAGCCTCCCCC-ATACGTCTGGGAGCAAGCTCACT
* * * * ** * * *
29307052 TTATTACTTTTTGTAAGCTTCACCCCATGCGTCTAGGAATAGGGTTA-T
1 TTATTACTTTTCGTAAGCCTC-CCCCATACGTCTGGGAGCAAGCTCACT
** *
29307100 ATTATTACTTTTCGTAAGCCTTCCCCCATGTGTTTGGGAGCAGAGC-CACT
1 -TTATTACTTTTCGTAAGCC-TCCCCCATACGTCTGGGAGCA-AGCTCACT
*
29307150 TTATTACCTTTCGTAAGCCTCCC
1 TTATTACTTTTCGTAAGCCTCCC
29307173 TCATGTGATT
Statistics
Matches: 131, Mismatches: 33, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
48 5 0.04
49 118 0.90
50 8 0.06
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (48 bp):
TTATTACTTTTCGTAAGCCTCCCCCATACGTCTGGGAGCAAGCTCACT
Found at i:29307168 original size:147 final size:147
Alignment explanation
Indices: 29306901--29307172 Score: 316
Period size: 147 Copynumber: 1.9 Consensus size: 147
29306891 AGAATAGGGC
*
29306901 CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATCTTATTACCTTCC
1 CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTCC
* * * * *
29306966 GTAAGTCTCCCCTTATACGTTTGGGAGTAAGGTCAAGTTATCACTTTTCATAAGCCTCCCCCTAT
66 GTAAGCCTCCCCTCATACGTTTGGGAGCAAGGCCAAGTTATCACCTTTCATAAGCCTCCCCCTAT
29307031 ACGTCTGGGAGCAAGCT
131 ACGTCTGGGAGCAAGCT
*** * * * * *
29307048 CACTTTATTACTTTTTGTAAGCTTCACC-CCATGCGTCTAGGAATAGGGTTATATTATTACTTTT
1 CACTTTATTACTTTCCATAAGCCTC-CCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTC
** ** * *
29307112 CGTAAGCCTTCCCC-CATGTGTTTGGGAGC-AGAGCCACTTTATTACCTTTCGTAAGCCTCCC
65 CGTAAGCC-TCCCCTCATACGTTTGGGAGCAAG-GCCAAGTTATCACCTTTCATAAGCCTCCC
29307173 TCATGTGATT
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
146 2 0.02
147 93 0.91
148 7 0.07
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (147 bp):
CACTTTATTACTTTCCATAAGCCTCCCTCCATGCATCGAGGAATAGGGTTATATTATTACCTTCC
GTAAGCCTCCCCTCATACGTTTGGGAGCAAGGCCAAGTTATCACCTTTCATAAGCCTCCCCCTAT
ACGTCTGGGAGCAAGCT
Found at i:29307204 original size:48 final size:48
Alignment explanation
Indices: 29307103--29307226 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 48
29307093 GGGTTATATT
* * * *
29307103 ATTACTTTTCGTAAGCCTTCCCCCATGTGTTTGGGAGCAGAGCCACTTT
1 ATTACCTTTCGTAAGCC-TCCCTCATGTGATTGGGAGCAGAGCCACTTA
* **
29307152 ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGGGTTACTTA
1 ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGAGCCACTTA
*
29307200 ATTA-CTTGCCGTAAGCCTCTCCT-ATGT
1 ATTACCTT-TCGTAAGCCTC-CCTCATGT
29307227 ATCTGGAAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
47 3 0.05
48 43 0.66
49 19 0.29
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (48 bp):
ATTACCTTTCGTAAGCCTCCCTCATGTGATTGGGAGCAGAGCCACTTA
Found at i:29309120 original size:42 final size:42
Alignment explanation
Indices: 29309061--29309171 Score: 161
Period size: 42 Copynumber: 2.6 Consensus size: 42
29309051 GTTTACTTTA
* * *
29309061 TGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTT
1 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
29309103 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
1 TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
* *
29309145 TATTTAGCTCTCA-TGAGCTTCTGTTCA
1 TGTTCAGCTCT-ATTGAGCTTCTGTTCA
29309172 GCCTTTAGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TGTTCAGCTCTATTGAGCTTCTGTTCAACCCTTATGGGTTTC
Found at i:29309129 original size:21 final size:20
Alignment explanation
Indices: 29309061--29309186 Score: 67
Period size: 21 Copynumber: 6.1 Consensus size: 20
29309051 GTTTACTTTA
29309061 TGTTCAGCTCTTTTGAGCTTC
1 TGTTCAGCTC-TTTGAGCTTC
* * * * * *
29309082 TGTTTAACCCTTATGGGTTTT
1 TGTTCAGCTCTT-TGAGCTTC
29309103 TGTTCAGCTCTATTGAGCTTC
1 TGTTCAGCTCT-TTGAGCTTC
* * * *
29309124 TGTTCAACCCTTATGGGTTTC
1 TGTTCAGCTCTT-TGAGCTTC
* * *
29309145 TATTTAGCTCTCATGAGCTTC
1 TGTTCAGCTCT-TTGAGCTTC
29309166 TGTTCAGC-CTTT-AGGCTTC
1 TGTTCAGCTCTTTGA-GCTTC
29309185 TG
1 TG
29309187 AAAATGATGT
Statistics
Matches: 74, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
18 1 0.01
19 8 0.11
20 5 0.07
21 59 0.80
22 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
TGTTCAGCTCTTTGAGCTTC
Found at i:29312001 original size:21 final size:21
Alignment explanation
Indices: 29311975--29312128 Score: 107
Period size: 21 Copynumber: 7.3 Consensus size: 21
29311965 CATGTTTACT
*
29311975 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
29311996 TTCTGTTTAAC-CTTTATGGGT
1 TTCTGTTTAGCTC-TTATGAGC
29312017 TTAC-GTTTAGCTC-TATCGAGC
1 TT-CTGTTTAGCTCTTAT-GAGC
* * * *
29312038 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
* **
29312059 TTCTGTTCAGCTCTTACAAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
29312080 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
*
29312101 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
29312122 TTCTGTT
1 TTCTGTT
29312129 CAGCCTTCGG
Statistics
Matches: 97, Mismatches: 30, Indels: 12
0.70 0.22 0.09
Matches are distributed among these distances:
20 5 0.05
21 87 0.90
22 5 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:29312129 original size:42 final size:42
Alignment explanation
Indices: 29311974--29312130 Score: 210
Period size: 42 Copynumber: 3.7 Consensus size: 42
29311964 TCATGTTTAC
* * *
29311974 TTTCTGTTTAGCTCTTTTGAGCTTCTGTTTAACCTTTATGGG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
*
29312016 TTTAC-GTTTAGCTC-TATCGAGCTTCTGTTTAACCCTTATGGG
1 TTT-CTGTTTAGCTCTTAT-GAGCTTCTGTTCAACCCTTATGGG
* **
29312058 TTTCTGTTCAGCTCTTACAAGCTTCTGTTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
*
29312100 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTCA
29312131 GCCTTCGGGC
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 3 0.03
42 95 0.94
43 3 0.03
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:29322592 original size:29 final size:30
Alignment explanation
Indices: 29322533--29322592 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
29322523 CATTATTTTT
** *
29322533 AAAAAATTATTTTATTCTCTCGATTATTTA
1 AAAAAATTAAATTATTCTCTCGATTAATTA
29322563 AAAAAATTAAATTATTC-CTC-ATTTAATTA
1 AAAAAATTAAATTATTCTCTCGA-TTAATTA
29322592 A
1 A
29322593 TATATATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 10 0.38
30 15 0.58
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAAAATTAAATTATTCTCTCGATTAATTA
Found at i:29324695 original size:26 final size:24
Alignment explanation
Indices: 29324639--29324687 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29324629 ATGATTTTTG
*
29324639 AAGATAATTTATTCAAAATACTTC
1 AAGATAATTTATTCAAAAGACTTC
29324663 AAGATAATTTATTCGAAAAAGACTT
1 AAGATAATTTATTC--AAAAGACTT
29324688 GTAGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
26 8 0.36
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (24 bp):
AAGATAATTTATTCAAAAGACTTC
Found at i:29325542 original size:11 final size:10
Alignment explanation
Indices: 29325526--29325568 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
29325516 CGTATTTACA
29325526 TTTTATGTTAT
1 TTTTA-GTTAT
* *
29325537 TTTTATTTGT
1 TTTTAGTTAT
29325547 TTTTAGTTAAT
1 TTTTAGTT-AT
29325558 TTTTAGTTAT
1 TTTTAGTTAT
29325568 T
1 T
29325569 CTGAGTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (10 bp):
TTTTAGTTAT
Found at i:29327885 original size:21 final size:21
Alignment explanation
Indices: 29327842--29327925 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
29327832 AATACACCAG
29327842 CAGAAGCTCG-AA-AGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
* *
29327861 CAGAAGCTCGTAAGAGCTAAA
1 CAGAAGCTCGTAAGAGTTGAA
* *
29327882 CAGAAACTCATAAGAGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
* * *
29327903 CAGAAACTCATAAAAGTTGAA
1 CAGAAGCTCGTAAGAGTTGAA
29327924 CA
1 CA
29327926 AAAAGTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.18
20 2 0.04
21 44 0.79
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CAGAAGCTCGTAAGAGTTGAA
Found at i:29328795 original size:17 final size:17
Alignment explanation
Indices: 29328758--29328796 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29328748 TTATTTATTC
*
29328758 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
29328775 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
29328792 TATTG
1 TATTG
29328797 AGTTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:29328962 original size:21 final size:21
Alignment explanation
Indices: 29328935--29329044 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
29328925 GTGTTTTACT
*
29328935 TTCTGTTCAGCTCTTCTGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
29328956 TTTTGTTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
29328977 TTCTGTTTAGCTATTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
*
29328998 TTCTGTTCAACT-TT-TGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
29329017 TTCTATTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
29329038 TTCTGTT
1 TTCTGTT
29329045 GGTGTATTCA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
19 14 0.20
20 4 0.06
21 53 0.75
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:29328982 original size:42 final size:40
Alignment explanation
Indices: 29328934--29329044 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 40
29328924 TGTGTTTTAC
* *
29328934 TTTCTGTTCAGCTCTTCTGAGCTTTTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACT-TT-TGAG
* *
29328976 TTTCTGTTTAGCTATTATGAGCTTCTGTTCAACTTTTGAG
1 TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACTTTTGAG
* *
29329016 CTTCTATTTAGCTCTTAC-GAGCTTCTGTT
1 TTTCTGTTTAGCTCTT-CTGAGCTTCTGTT
29329045 GGTGTATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 28 0.47
41 2 0.03
42 30 0.50
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (40 bp):
TTTCTGTTTAGCTCTTCTGAGCTTCTGTTCAACTTTTGAG
Found at i:29329038 original size:40 final size:42
Alignment explanation
Indices: 29328943--29329044 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 42
29328933 CTTTCTGTTC
* * *
29328943 AGCTCTT-CTGAGCTTTTGTTCAACTCTTATGAGTTTCTGTTT
1 AGCTCTTAC-GAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
* *
29328985 AGCTATTATGAGCTTCTGTTCAACT-TT-TGAGCTTCTATTT
1 AGCTCTTACGAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
29329025 AGCTCTTACGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
29329045 GGTGTATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 29 0.56
41 2 0.04
42 21 0.40
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTGTTCAACTCTTATGAGCTTCTATTT
Found at i:29332136 original size:68 final size:68
Alignment explanation
Indices: 29332027--29332166 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
29332017 ATGTGATGGG
*
29332027 CACAGGCCCTAGACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
1 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
29332092 TTA
66 TTA
*
29332095 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTGGGGA
1 CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
29332160 TTA
66 TTA
29332163 CACA
1 CACA
29332167 CTGAGTTTGC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (68 bp):
CACAGGCCCTAAACTGTATCTAACTAAATTATGTTGATTATCTGTATGCATGTTTTCTGTAGGGA
TTA
Found at i:29343350 original size:5 final size:5
Alignment explanation
Indices: 29343342--29343411 Score: 90
Period size: 5 Copynumber: 14.2 Consensus size: 5
29343332 TATTTAATTT
* *
29343342 ATATA ATATA AAACA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
29343391 ATAATA AAATA ATAT- ATATA A
1 AT-ATA ATATA ATATA ATATA A
29343412 AACATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 6 0.11
5 49 0.88
6 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:29350522 original size:46 final size:46
Alignment explanation
Indices: 29350452--29350545 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
29350442 GTGATATGAA
* * * *
29350452 CAAAATATGTTTAACTTGATATATTAGAAAGTGTAAGAATAGTGGG
1 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
* *
29350498 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGATTAGTTGG
1 CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
29350544 CA
1 CA
29350546 CACTATTGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (46 bp):
CAAAATATGTTTAACTCGAGATATTACAAAATGTAAGAATAGTGGG
Found at i:29359421 original size:3 final size:3
Alignment explanation
Indices: 29359413--29359442 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29359403 TATAATGTTA
29359413 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29359443 CAAACCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29366185 original size:37 final size:36
Alignment explanation
Indices: 29366139--29366210 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
29366129 GTTCGGAGTC
* * *
29366139 TGTCATTTTTTGCCTGGGACAATTTCTTTCTGGCTG
1 TGTCATTTTTTGCCTGAGACAATGTCTCTCTGGCTG
*
29366175 TGTCATTTTTTTTCCTGAGACAATGTCTCTCTGGCT
1 TGTCA-TTTTTTGCCTGAGACAATGTCTCTCTGGCT
29366211 CAGTGCAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (36 bp):
TGTCATTTTTTGCCTGAGACAATGTCTCTCTGGCTG
Found at i:29370385 original size:20 final size:21
Alignment explanation
Indices: 29370359--29370403 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
29370349 CCAAATTAAA
29370359 AAAAAAAGATAGTTGAGTGA-C
1 AAAAAAA-ATAGTTGAGTGATC
*
29370380 AAAAAAAATAGTTGGGTGATC
1 AAAAAAAATAGTTGAGTGATC
29370401 AAA
1 AAA
29370404 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAAAAAATAGTTGAGTGATC
Found at i:29372190 original size:6 final size:6
Alignment explanation
Indices: 29372157--29372188 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
29372147 CTACGATGAC
*
29372157 GACGAT GACGAT GACGAT GACGAT GATGAT GA
1 GACGAT GACGAT GACGAT GACGAT GACGAT GA
29372189 TGTTGAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.19
Consensus pattern (6 bp):
GACGAT
Found at i:29375064 original size:34 final size:34
Alignment explanation
Indices: 29375026--29375094 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
29375016 TTATCCTAAT
*
29375026 TTCCAAGAGTAAGTGTTTTTATTCAACCCTAAGA
1 TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
*
29375060 TTCCAAGAGTAAGTGTTTTTACTCAACCCTGAGA
1 TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
29375094 T
1 T
29375095 ACTTTGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (34 bp):
TTCCAAGAGTAAGTGTTTTTACTCAACCCTAAGA
Found at i:29375154 original size:21 final size:19
Alignment explanation
Indices: 29375111--29375164 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
29375101 CAAATAAAGC
29375111 TTATATGTGATGTGATATG
1 TTATATGTGATGTGATATG
29375130 -TATATGATG-TGTTGATATG
1 TTATATG-TGATG-TGATATG
*
29375149 ATTATATGTTATGTGA
1 -TTATATGTGATGTGA
29375165 GAATGTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 4 0.14
21 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (19 bp):
TTATATGTGATGTGATATG
Found at i:29376191 original size:10 final size:10
Alignment explanation
Indices: 29376178--29376202 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29376168 TGTTAATGTA
29376178 TGATTTAGTG
1 TGATTTAGTG
29376188 TGATTTAGTG
1 TGATTTAGTG
29376198 TGATT
1 TGATT
29376203 GAGCATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (10 bp):
TGATTTAGTG
Found at i:29381629 original size:20 final size:21
Alignment explanation
Indices: 29381572--29381629 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
29381562 AAACAACAAT
29381572 AAAATAGCACCAAAAACAACTCC
1 AAAATAGCA-CAAAAACAAC-CC
* * *
29381595 AAAACATCACCAAAACAA-CC
1 AAAATAGCACAAAAACAACCC
29381615 AAAATAGCACAAAAA
1 AAAATAGCACAAAAA
29381630 ATAACCTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (21 bp):
AAAATAGCACAAAAACAACCC
Found at i:29385939 original size:3 final size:3
Alignment explanation
Indices: 29385931--29385982 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
29385921 ATAAATTTCA
*
29385931 TAT TAT TAT TGT TAT TAT TAT TAAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
29385976 TAT TAT T
1 TAT TAT T
29385983 GCTTTTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:29385943 original size:33 final size:33
Alignment explanation
Indices: 29385910--29385982 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
29385900 GTTAGTTTGT
*
29385910 TTATT-TTCTTAATAAATT-TCATATTATTATTG
1 TTATTATTATTAAT-AATTATCATATTATTATTG
* * *
29385942 TTATTATTATTAATTATTATTATATTATTATTA
1 TTATTATTATTAATAATTATCATATTATTATTG
29385975 TTATTATT
1 TTATTATT
29385983 GCTTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (33 bp):
TTATTATTATTAATAATTATCATATTATTATTG
Found at i:29385996 original size:30 final size:31
Alignment explanation
Indices: 29385930--29385996 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
29385920 AATAAATTTC
*
29385930 ATAT-TATTATTGTTATTATTATTAATTATT
1 ATATATATTATTATTATTATTATTAATTATT
**
29385960 AT-TATATTATTATTATTATTATTGCTT-TT
1 ATATATATTATTATTATTATTATTAATTATT
29385989 ATATATAT
1 ATATATAT
29385997 AGGAGTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (31 bp):
ATATATATTATTATTATTATTATTAATTATT
Found at i:29386384 original size:18 final size:18
Alignment explanation
Indices: 29386353--29386390 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
29386343 TATATGTCCA
29386353 TAATTTTCTTTTAATGTTT
1 TAATTTTCTTTTAAT-TTT
29386372 TAATTTT-TTTTAATTTT
1 TAATTTTCTTTTAATTTT
29386389 TA
1 TA
29386391 CTTGTTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TAATTTTCTTTTAATTTT
Found at i:29386703 original size:109 final size:109
Alignment explanation
Indices: 29386507--29387040 Score: 815
Period size: 109 Copynumber: 4.9 Consensus size: 109
29386497 AAGGAAAATT
*
29386507 TTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
29386572 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * ** *
29386616 TTTCAAAATAAGGCAATGTTTGGCGTTTGGGAATTCGAGGTAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
29386681 CGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTTTGAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * *
29386725 TTTCAAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCACTAATGTGCTGGGTT
1 TTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
* *
29386790 TTGATTTCT-TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
65 TCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* *
29386834 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTAGAGAAAACGTGCCCTAATATGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
29386899 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * * *
29386943 TTTCAAAATAAGGAAATGTTTCGCGTTTGGAAATTCGAG-GAACGTGCCTTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
29387007 CGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
29387041 CTTGAATTTT
Statistics
Matches: 388, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
106 30 0.08
108 87 0.22
109 212 0.55
110 59 0.15
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
Found at i:29387452 original size:24 final size:24
Alignment explanation
Indices: 29387423--29387486 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
29387413 CACGTTCAAC
*
29387423 AACATAGGTTCGTATACTTCATAT
1 AACATAGGTTCGCATACTTCATAT
*
29387447 AGCATAGGTTCGCATACTTCATAT
1 AACATAGGTTCGCATACTTCATAT
*
29387471 AACATAGGTTTGCATA
1 AACATAGGTTCGCATA
29387487 ACAACATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (24 bp):
AACATAGGTTCGCATACTTCATAT
Found at i:29389803 original size:10 final size:9
Alignment explanation
Indices: 29389784--29389873 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 9
29389774 AGAATTTACA
29389784 TTTTATAAAT
1 TTTTA-AAAT
29389794 TTTTACAAAT
1 TTTTA-AAAT
*
29389804 TTTT-AATT
1 TTTTAAAAT
29389812 TTTTAACAATT
1 TTTTAA-AA-T
29389823 TTTTAAAACT
1 TTTTAAAA-T
*
29389833 TTTTAAATAAA
1 TTTT-AA-AAT
*
29389844 ATTTAAAAT
1 TTTTAAAAT
29389853 TTATTAACTAAT
1 TT-TTAA--AAT
29389865 TTTTAAAAT
1 TTTTAAAAT
29389874 GCTTTTTCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
8 7 0.11
9 7 0.11
10 27 0.42
11 16 0.25
12 7 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:29389816 original size:18 final size:19
Alignment explanation
Indices: 29389783--29389871 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
29389773 CAGAATTTAC
29389783 ATTTTATAAATTTTT-ACAA
1 ATTTT-TAAATTTTTAACAA
*
29389802 ATTTTTAATTTTTTAACAA
1 ATTTTTAAATTTTTAACAA
* *
29389821 TTTTTTAAAACTTTTTAAATAA
1 ATTTTT-AAA-TTTTT-AACAA
* * *
29389843 AATTTAAAATTTATTAACTA
1 ATTTTTAAATTT-TTAACAA
29389863 ATTTTTAAA
1 ATTTTTAAA
29389872 ATGCTTTTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.15
19 14 0.26
20 15 0.28
21 10 0.19
22 7 0.13
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTTAAATTTTTAACAA
Found at i:29390038 original size:39 final size:39
Alignment explanation
Indices: 29389984--29390059 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
29389974 ATCAACTTGA
* * *
29389984 TCAATGTGCTATGTCATTGATGAACCTGCCATGTCATGG
1 TCAATGTGCTATGTCATCGATCAACCTACCATGTCATGG
*
29390023 TCAATGTG-TCATGTCATCGGTCAACCTACCATGTCAT
1 TCAATGTGCT-ATGTCATCGATCAACCTACCATGTCAT
29390060 CAATCACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (39 bp):
TCAATGTGCTATGTCATCGATCAACCTACCATGTCATGG
Found at i:29393655 original size:6 final size:6
Alignment explanation
Indices: 29393644--29393668 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29393634 CGCCACAGGT
29393644 AGACTG AGACTG AGACTG AGACTG A
1 AGACTG AGACTG AGACTG AGACTG A
29393669 TGACAGCAAT
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AGACTG
Found at i:29399758 original size:26 final size:25
Alignment explanation
Indices: 29399737--29399804 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
29399727 CTTAATATTT
*
29399737 AAGTAAATATATATAATATAATAATA
1 AAGTAAATATA-ATAAAATAATAATA
29399763 AAGTAAATATAATAAAATAAATAAGTA
1 AAGTAAATATAATAAAAT-AATAA-TA
29399790 AA-TGAAATA-AATAAA
1 AAGT-AAATATAATAAA
29399805 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 6 0.16
26 23 0.61
27 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
AAGTAAATATAATAAAATAATAATA
Found at i:29399775 original size:22 final size:22
Alignment explanation
Indices: 29399736--29399804 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
29399726 ACTTAATATT
*
29399736 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAAAAT-A-AA
29399761 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
29399784 TAAGTAAATGA-AAT-AAATAAA
1 TAAGTAAAT-ATAATAAAATAAA
29399805 GAAAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 7 0.17
22 11 0.27
23 4 0.10
24 1 0.02
25 7 0.17
26 11 0.27
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:29399797 original size:5 final size:4
Alignment explanation
Indices: 29399740--29399804 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
29399730 AATATTTAAG
* *
29399740 TAAA TATA TATAA TATAA T-AA TAAA GTAAA TATAA TAAAA TAAA TAAG
1 TAAA TAAA TA-AA TA-AA TAAA TAAA -TAAA TA-AA T-AAA TAAA TAAA
29399788 TAAA TGAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA
29399805 GAAAATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 26 0.51
5 21 0.41
6 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:29399817 original size:12 final size:13
Alignment explanation
Indices: 29399759--29399819 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
29399749 ATAATATAAT
*
29399759 AATAAAGTAAATA
1 AATAAAGAAAATA
29399772 TAATAAA-ATAAATA
1 -AATAAAGA-AAATA
*
29399786 AGTAAATG-AAATA
1 AATAAA-GAAAATA
29399799 AATAAAGAAAATA
1 AATAAAGAAAATA
29399812 AA-AAAGAA
1 AATAAAGAA
29399820 TAGAAAGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 7 0.17
13 22 0.55
14 11 0.28
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AATAAAGAAAATA
Found at i:29400851 original size:37 final size:38
Alignment explanation
Indices: 29400787--29400863 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 38
29400777 GTCAATTTAC
* * *
29400787 TACTTCGGATTAGTTCGATGAGGCACTGTGTGCCAATT
1 TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
* *
29400825 TACTTCGGTTTAG-CCGATGAGACACTGGGTGTCAATT
1 TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
29400862 TA
1 TA
29400864 TTATTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (38 bp):
TACTTCGGATTAGTCCGATGAGACACTGGGTGCCAATT
Found at i:29404773 original size:24 final size:24
Alignment explanation
Indices: 29404741--29404905 Score: 122
Period size: 24 Copynumber: 6.8 Consensus size: 24
29404731 AGCCATGTAA
29404741 CGGGAAGCTCATAAGAGCCATAAT
1 CGGGAAGCTCATAAGAGCCATAAT
**
29404765 CGGGAAGCTCATGCGAGCCA-ACAT
1 CGGGAAGCTCATAAGAGCCATA-AT
29404789 CGGGAAGCTC-TAGAGAGCCATTAAT
1 CGGGAAGCTCATA-AGAGCCA-TAAT
*** * *
29404814 CGGGAAGCTCCGGAGAACCAATTAT
1 CGGGAAGCTCATAAGAGCC-ATAAT
* * * *
29404839 CGAGAAGCTCATACGAGCCGTAAA
1 CGGGAAGCTCATAAGAGCCATAAT
*
29404863 CGAGAAGCTCA-AGAGAGCCATTAAT
1 CGGGAAGCTCATA-AGAGCCA-TAAT
*
29404888 C-GGAATGCTCATGAGAGC
1 CGGGAA-GCTCATAAGAGC
29404906 TAAATAACGG
Statistics
Matches: 109, Mismatches: 22, Indels: 19
0.73 0.15 0.13
Matches are distributed among these distances:
23 3 0.03
24 57 0.52
25 47 0.43
26 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCATAAT
Found at i:29404784 original size:49 final size:49
Alignment explanation
Indices: 29404712--29404823 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
29404702 TAAGTGCACG
* * **
29404712 TAATCGGGAAGCTCTTTCAAGCCATGTAACGGGAAGCTCATA-AGAGCCA-
1 TAATCGGGAAGCTCATGCAAGCCA-ACAACGGGAAGCTC-TAGAGAGCCAT
* *
29404761 TAATCGGGAAGCTCATGCGAGCCAACATCGGGAAGCTCTAGAGAGCCAT
1 TAATCGGGAAGCTCATGCAAGCCAACAACGGGAAGCTCTAGAGAGCCAT
29404810 TAATCGGGAAGCTC
1 TAATCGGGAAGCTC
29404824 CGGAGAACCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.04
48 18 0.33
49 35 0.64
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (49 bp):
TAATCGGGAAGCTCATGCAAGCCAACAACGGGAAGCTCTAGAGAGCCAT
Found at i:29404829 original size:25 final size:25
Alignment explanation
Indices: 29404712--29404905 Score: 147
Period size: 25 Copynumber: 7.9 Consensus size: 25
29404702 TAAGTGCACG
* *
29404712 TAATCGGGAAGCTCTTTCA-AGCCAT
1 TAATCGGGAAGCTC-ATGAGAGCCAT
*
29404737 GTAA-CGGGAAGCTCATAAGAGCCA-
1 -TAATCGGGAAGCTCATGAGAGCCAT
*
29404761 TAATCGGGAAGCTCATGCGAGCCA-
1 TAATCGGGAAGCTCATGAGAGCCAT
29404785 -ACATCGGGAAGCTC-TAGAGAGCCAT
1 TA-ATCGGGAAGCTCAT-GAGAGCCAT
** *
29404810 TAATCGGGAAGCTCCGGAGAACCAAT
1 TAATCGGGAAGCTCATGAGAGCC-AT
* *
29404836 T-ATCGAGAAGCTCAT-ACGAGCC-G
1 TAATCGGGAAGCTCATGA-GAGCCAT
* * *
29404859 TAAACGAGAAGCTCAAGAGAGCCAT
1 TAATCGGGAAGCTCATGAGAGCCAT
29404884 TAATC-GGAATGCTCATGAGAGC
1 TAATCGGGAA-GCTCATGAGAGC
29404906 TAAATAACGG
Statistics
Matches: 137, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
23 6 0.04
24 60 0.44
25 64 0.47
26 7 0.05
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (25 bp):
TAATCGGGAAGCTCATGAGAGCCAT
Found at i:29406860 original size:19 final size:18
Alignment explanation
Indices: 29406832--29406868 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29406822 TTATTTGATC
29406832 TTTAAACCAACTCATATAA
1 TTTAAACCAACTCA-ATAA
*
29406851 TTTAATCCAACTCAATAA
1 TTTAAACCAACTCAATAA
29406869 ACAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAACCAACTCAATAA
Found at i:29406920 original size:23 final size:23
Alignment explanation
Indices: 29406878--29406921 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29406868 AACAATTTTC
*
29406878 TATTTATTAAAATATTATTTATT
1 TATTTATTAAAATATAATTTATT
29406901 TATTTATTTAAAATA-AATTTA
1 TATTTA-TTAAAATATAATTTA
29406922 ATTAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTATTAAAATATAATTTATT
Found at i:29407720 original size:14 final size:14
Alignment explanation
Indices: 29407701--29407738 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
29407691 TATAAATTTT
29407701 TTTATTAATTTATA
1 TTTATTAATTTATA
*
29407715 TTTATTAA-ATATA
1 TTTATTAATTTATA
*
29407728 TTTTTTAATTT
1 TTTATTAATTT
29407739 TTCTAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATTAATTTATA
Found at i:29409814 original size:12 final size:12
Alignment explanation
Indices: 29409797--29409823 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29409787 AGGCGTTGCT
29409797 GAAGATGAAGAG
1 GAAGATGAAGAG
29409809 GAAGATGAAGAG
1 GAAGATGAAGAG
29409821 GAA
1 GAA
29409824 AAGATGGACA
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:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (12 bp):
GAAGATGAAGAG
Found at i:29410413 original size:2 final size:2
Alignment explanation
Indices: 29410401--29410430 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29410391 TTCATAAAGA
29410401 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29410431 AAAGTCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29412027 original size:8 final size:8
Alignment explanation
Indices: 29412014--29412056 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
29412004 TCTTGGTATT
29412014 TATATCTA
1 TATATCTA
29412022 TATATCTA
1 TATATCTA
29412030 TATATCTA
1 TATATCTA
*
29412038 TATATATA
1 TATATCTA
* *
29412046 TCTGTCTA
1 TATATCTA
29412054 TAT
1 TAT
29412057 TAGTTCTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (8 bp):
TATATCTA
Found at i:29421891 original size:11 final size:11
Alignment explanation
Indices: 29421877--29421926 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
29421867 AGATAAATAT
29421877 TATTTTATTAA
1 TATTTTATTAA
*
29421888 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
29421901 TATTTTATTAT
1 TATTTTATTAA
29421912 TATTTTATTTAA
1 TATTTTA-TTAA
29421924 TAT
1 TAT
29421927 ATATCGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 13 0.41
12 12 0.38
13 7 0.22
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:29421930 original size:27 final size:26
Alignment explanation
Indices: 29421846--29421930 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
29421836 TATTTTGATG
* *
29421846 ATATTTTATAATTATTTAATTAGATAA
1 ATATTTTATTATTATTTATTTA-ATAA
* *
29421873 ATATTATT-TTATTA-ATATTTTAATGAG
1 ATATT-TTATTATTATTTA-TTTAAT-AA
*
29421900 ATATTTTATTATTATTTTATTTAATAT
1 ATATTTTATTATTA-TTTATTTAATAA
29421927 ATAT
1 ATAT
29421931 CGAAAGAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
26 6 0.13
27 30 0.65
28 8 0.17
29 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
ATATTTTATTATTATTTATTTAATAA
Found at i:29432097 original size:7 final size:7
Alignment explanation
Indices: 29432085--29432116 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
29432075 GCCTTTGTTC
29432085 TTCAATT
1 TTCAATT
29432092 TTCAATT
1 TTCAATT
29432099 TTCAATT
1 TTCAATT
29432106 TTCAATT
1 TTCAATT
29432113 TTCA
1 TTCA
29432117 TATACTATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCAATT
Found at i:29440780 original size:17 final size:17
Alignment explanation
Indices: 29440758--29440795 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
29440748 TCACACACCC
29440758 AACAATAGATCAGAAAG
1 AACAATAGATCAGAAAG
29440775 AACAATAGATCAGAAAG
1 AACAATAGATCAGAAAG
29440792 AACA
1 AACA
29440796 GGAGAAAACC
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:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (17 bp):
AACAATAGATCAGAAAG
Found at i:29448071 original size:18 final size:18
Alignment explanation
Indices: 29448048--29448085 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29448038 AATGAATAAA
29448048 TATCCATAAAGAGAACTG
1 TATCCATAAAGAGAACTG
29448066 TATCCATAAAGAGAACTG
1 TATCCATAAAGAGAACTG
29448084 TA
1 TA
29448086 ATTTTAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TATCCATAAAGAGAACTG
Found at i:29451619 original size:22 final size:22
Alignment explanation
Indices: 29451594--29451635 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29451584 ATCTATATCT
*
29451594 TTTTAATTTTTA-ATTTTAAATA
1 TTTT-ATTTTTAGATATTAAATA
29451616 TTTTATTTTTAGATATTAAA
1 TTTTATTTTTAGATATTAAA
29451636 GACACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATTTTTAGATATTAAATA
Found at i:29454444 original size:32 final size:33
Alignment explanation
Indices: 29454386--29454447 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
29454376 ACTGTAATTG
* *
29454386 TAAAAAGTTATAATTTTTTTAAACAATTTTGAT
1 TAAAAAGTTATAATATTTTAAAACAATTTTGAT
*
29454419 TAAAAA-TTTTAATATTTTAAAACAATTTT
1 TAAAAAGTTATAATATTTTAAAACAATTTT
29454448 ACAACTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TAAAAAGTTATAATATTTTAAAACAATTTTGAT
Found at i:29463644 original size:42 final size:42
Alignment explanation
Indices: 29463575--29463725 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
29463565 AGGCTATACA
* * * * *
29463575 GAAGCACATAAGTGCTAAGCGGAAACCCATAAGGGTTGAATG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * * **
29463617 GAAGCTCATAGGAGCTGAACGAAAACCCAGAAGGGTTAAACA
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * *
29463659 GAAGCTTAAAAGAGCTAAACGAAAACCCATTAGGGTTAAATG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
* * * *
29463701 AAAACTCATATGAGTTAAACAGAAA
1 GAAGCTCATAAGAGCTAAAC-GAAA
29463726 CTCGAAAGAG
Statistics
Matches: 84, Mismatches: 24, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
42 80 0.95
43 4 0.05
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAATG
Found at i:29469177 original size:20 final size:17
Alignment explanation
Indices: 29469152--29469197 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
29469142 ATCAATTATT
29469152 TTTTAAAAATTTTAATATA
1 TTTTAAAAATTTT-ATA-A
*
29469171 GTTTTAATAATTTTATAA
1 -TTTTAAAAATTTTATAA
29469189 TTTTAAAAA
1 TTTTAAAAA
29469198 ATTAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 3 0.12
20 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTTAAAAATTTTATAA
Found at i:29474852 original size:992 final size:984
Alignment explanation
Indices: 29472142--29474857 Score: 3497
Period size: 992 Copynumber: 2.8 Consensus size: 984
29472132 GACTAGAATC
29472142 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
* * *
29472207 GTTTTTACTTTGCCA--T--CAA-ACCAC--TGACAAAAGAATTTTAACATTAAACTAAACATCG
66 GTTTCTACTTTGCCATCTAACAAGACCACATTGACAAAAGAATTTTAATATTAAAAT-AA-A-C-
* * * * *
29472265 ATCAAAGGTTAAGCGACTTAGACTTGAGCAATAAATTCTTTCATTATCTAAATTTTTTTCAATAC
127 ATCAAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATAC
* * *
29472330 AATTGTTGAATAATTCTATTAGTAAAATATAATTTAAATATTATACATTATATTTTGAAAGTTCT
192 AATCGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCT
* * * * **
29472395 AAAACAATATTTGTAAGCAAATTGAGTAATGCCAACTATTTTCGACACTGATGATTAACAATAAA
257 AAAACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAA
* * * * *
29472460 GAACACAAC---ATGTTTGCGTAGTTTAGTTTCCATACATTAGCAAGGCCGTAGCTGTGAGATAA
322 GAACACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAA
* * * * * *
29472522 TCTATTATCTTAGTATTTTG-TACAACAAATAGTTACAAACACAAGCTTTCACAAAGATAGGATC
387 TCCATCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACACAA-CTTTCACAAAAATAGGATC
* * * * * *
29472586 ACACTTTTGTACTTAAGATCTAGACAAGTTCCATTTAAATTTCCTCCCCGCATATATAGGAT-AA
451 TCACTTTTGTACCTAAGATCTAGACAAGTTCC-TCTAAATTTCCTCCCTGAAAATATAGGATAAA
* * * *
29472650 AACC---CAACACAATTGATTTTATACTCAGTGCAATCTAACTAAACATTCCTCACTAAACAGAA
515 AACCAAGTAACACACTTGATTTTACACTCAGTG-AATCTAAATAAACATTCCTCACTAAACAGAA
*
29472712 ATAAGTGCTCTCAAATTAG---------TA-T-AGTCTTCTCAATTTATAATGAAATTAGAC--T
579 ATAAGTGCTCTCAAATTAGTACATAACCTATTAAGTCTTCTCAATTTATAATGAAATAAGACTGT
* * *
29472764 ----TGCTAGATCAGTGACAATCAATCTTCCAACTAAAACAATAAGATAATCAGCTCTAAGAATA
644 AACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAATA
* *
29472825 ATGGATTCGGATTCTTTTTAGTTTAAAATTTTTATTTACTTTTACTTACAAAAACCCTTTAAAAA
709 ATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTAC---T--TT---AAAA--CTTTAAAAA
* *
29472890 GATAATTTTAATATTTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATCACAAT
764 GATAATTTTAATAATTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAAT
* *
29472955 TAGTTAGTGCAATACATAAATAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGA
829 TAATTAGTGCAATACATAAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGA
*
29473020 ATCAACCAAAGCAATTTAATGCACAAAGAGACATATTAATAATCAAAATATATATAGATATGGAA
894 ATCAACCAAAGCAATTTAATGCACAAAGAGACATATTAATAATCAAAATATATACAGATATGGAA
*
29473085 TGCACGTATTTTGATTTAAATAAAAA
959 GGCACGTATTTTGATTTAAATAAAAA
* * * * *
29473111 AAACTATGTATTAAAAACCTACAAATGATATTTATGCATGGTTGGAGTCGACTTGGA-ATAACAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTT-GATATCACAA
*
29473175 AGTTTCTACTTTGCCATCAAACCAAGACCACATTGACAAAAGAATTTTAATATTAAAA-AAACAT
65 AGTTTCTACTTTGCCATCTAA-CAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACAT
* * * * *
29473239 CAAAAGTTAAGTGACTTAGAAATAAGCAAGAAATTATTTTATTATCTAAATTTGA-TTCAATACA
129 CAAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTT-ATTTCAATACA
* * *
29473303 ATCATTGAATAATTCTACTACTAAAATATAATTTAAATTTTATATATTATATTTTGAAAGTTCTA
193 ATCGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTA
* * * * * *
29473368 GAACGATACTTGCAAGCAAATTAAATAGTGCCAACTATTTTCGGCACTCATGAAGAACAATAAAT
258 AAACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAG
* * * *
29473433 AACACAACAATATGTTTGTGCATTTTAGTTTGCATACATCAACGAGGCCTTAGCAGTGAGATAAT
323 AACACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAAT
* *
29473498 TCATCATCTTAGCACTTTG-TACAATAAGTAGTTACAAACACAAACTTTCACAAAAATAGGATCT
388 CCATCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACAC-AACTTTCACAAAAATAGGATCT
* * * * *
29473562 CACTTTTGTACCTAAGAT-TAAGACAAGTCCCCTCTAAATTTCATCACTAAAAATATAAGATAAA
452 CACTTTTGTACCTAAGATCT-AGACAAGT-TCCTCTAAATTTCCTCCCTGAAAATATAGGATAAA
* * * *
29473626 AACCAAGTAACACACTAGATTTTACACTAAGTGCAGA-CTAAATAAACATTCCTTAATAAACAGA
515 AACCAAGTAACACACTTGATTTTACACTCAGTG-A-ATCTAAATAAACATTCCTCACTAAACAGA
* * * * *
29473690 AATAAGTGTTCTCAAATCAGTACATAACCTATACAAATCTTCTCAATTTATAATGAAACAAGACT
578 AATAAGTGCTCTCAAATTAGTACATAACCTAT-TAAGTCTTCTCAATTTATAATGAAATAAGACT
* * **
29473755 CGCTAACATACTAGATCAATGACAATTAATCTTCCAACTAAAACAACAAGATAATCAGCTAAAAC
642 -G-TAACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAAC
* * * *
29473820 AATAATGGATTTGGATTCTTTTTAATTTTAAATCTTTATTTACTTT-AAA--TTATGAAA-ATCA
705 AATAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTTAAAACTTTA-AAAAGATAA
* * *
29473881 TTTTAATAATTTTTGAAGTTACAATTATAATTAATATATCTATGTAACAATAATAACAATTAATT
769 TTTTAATAATTTTTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAATTAATT
* * ** * * * *
29473946 AGTGCAATACATAAACAAAATCACGATTACAATCGATATGTCCGTACAATTATGACTAGAATTAA
834 AGTGCAATACATAAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGAATCAA
* * * **
29474011 CCAATGGAATTTAATGCACAAACG-GACAT-TT-ATAATCGACGTATATACAGATATGGAAGGCA
899 CCAAAGCAATTTAATGCACAAA-GAGACATATTAATAATCAAAATATATACAGATATGGAAGGCA
*
29474073 CGTGTTTTGATTTAAATAAATAAAAA
963 CGTATTTTGA-TT---TAAATAAAAA
* * *
29474099 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCAACCTGTTATCACAAA
1 AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
*
29474164 GTTTCTATTTTGCCATCTAACGAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATC
66 GTTTCTACTTTGCCATCTAAC-AAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATC
* *
29474229 AAAGGTTAAGCCACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCACTACAAT
130 AAAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATACAAT
* * *
29474294 CGTTGAATAATTCTACTAGTAAAATTTAATTTAAATATTATATATTATATTTTAAAAATTCTAAA
195 CGTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTAAA
* *
29474359 ACGATACTTGCAAGCAAATTGAGTAGTGTCAACTATTTTCGACAATGATGAAGAACAATAAAGAA
260 ACGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAGAA
29474424 CACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCC
325 CACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCC
*
29474489 ATCATCTTAGCACTTTGTATAACAACAAGTAGTTACAAACACTAACTCTCACAAAAATAGGATCT
390 ATCATCTTAGCACTTTGT-T-ACAACAAGTAGTTACAAACAC-AACTTTCACAAAAATAGGATCT
* *
29474554 CACTTTTATACCTGAGATCTAGACAAGTTCTCTCTAAATTTCCTCCCTGAAAATATAGGATAAAA
452 CACTTTTGTACCTAAGATCTAGACAAGTTC-CTCTAAATTTCCTCCCTGAAAATATAGGATAAAA
* * * *
29474619 ACCAAGTAACACACTTGATTCTACACTCAGTGAACTCTAAATAAACTTTCCTCGCTAAGCAGAAA
516 ACCAAGTAACACACTTGATTTTACACTCAGTGAA-TCTAAATAAACATTCCTCACTAAACAGAAA
* *
29474684 TAAATGCTCTCAAATTAGTACATAACCTATGTAAGTATTCTCAATTTATAATGAAATAAGACTTG
580 TAAGTGCTCTCAAATTAGTACATAACCTAT-TAAGTCTTCTCAATTTATAATGAAATAAGAC-TG
* *
29474749 TTAACATGCTAAATTAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAA
643 -TAACATGCTAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAA
29474814 TAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTT
707 TAATGGATTCGGATTCTTTTTAATTTTAAATTTTTATTTACTTT
29474858 TAATCTGAAC
Statistics
Matches: 1503, Mismatches: 185, Indels: 95
0.84 0.10 0.05
Matches are distributed among these distances:
969 71 0.05
970 2 0.00
972 176 0.12
973 1 0.00
974 5 0.00
975 150 0.10
976 10 0.01
977 23 0.02
979 65 0.04
980 1 0.00
984 35 0.02
985 4 0.00
986 146 0.10
987 6 0.00
988 121 0.08
989 256 0.17
990 4 0.00
991 29 0.02
992 303 0.20
993 2 0.00
994 2 0.00
995 1 0.00
996 1 0.00
999 89 0.06
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (984 bp):
AAACTACGTATTGAAAACCCACAAATGATATTTATGCATGGTGGGAGTCGACTTGATATCACAAA
GTTTCTACTTTGCCATCTAACAAGACCACATTGACAAAAGAATTTTAATATTAAAATAAACATCA
AAGGTTAAGCGACTTAGACATAAGCAAGAAATTCTTTAATTATCTAAATTTATTTCAATACAATC
GTTGAATAATTCTACTAGTAAAATATAATTTAAATATTATATATTATATTTTGAAAGTTCTAAAA
CGATACTTGCAAGCAAATTGAGTAGTGCCAACTATTTTCGACACTGATGAAGAACAATAAAGAAC
ACAACAATATGTTTGCGTAGTTTAGTTTCCATACATCAACGAGGCCTTAGCAGTGAGATAATCCA
TCATCTTAGCACTTTGTTACAACAAGTAGTTACAAACACAACTTTCACAAAAATAGGATCTCACT
TTTGTACCTAAGATCTAGACAAGTTCCTCTAAATTTCCTCCCTGAAAATATAGGATAAAAACCAA
GTAACACACTTGATTTTACACTCAGTGAATCTAAATAAACATTCCTCACTAAACAGAAATAAGTG
CTCTCAAATTAGTACATAACCTATTAAGTCTTCTCAATTTATAATGAAATAAGACTGTAACATGC
TAGATCAATGACAATCAATCTTCCAACTAAAACAACAAGATAATCAGCTCTAACAATAATGGATT
CGGATTCTTTTTAATTTTAAATTTTTATTTACTTTAAAACTTTAAAAAGATAATTTTAATAATTT
TTGAAGATACAATTATAATTAATATACCTATATAACAATAATAACAATTAATTAGTGCAATACAT
AAACAAAATCACAAGTACAATCGATACATCCATACAACTACGACTAGAATCAACCAAAGCAATTT
AATGCACAAAGAGACATATTAATAATCAAAATATATACAGATATGGAAGGCACGTATTTTGATTT
AAATAAAAA
Found at i:29489374 original size:2 final size:2
Alignment explanation
Indices: 29489367--29489394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29489357 CATTGGTTTC
29489367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29489395 TAAAAAAGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29494973 original size:139 final size:139
Alignment explanation
Indices: 29494723--29495003 Score: 544
Period size: 139 Copynumber: 2.0 Consensus size: 139
29494713 TCCGTTTAAC
* *
29494723 TAAAGCCCATGATTATTAGAGACAGAAGTATGGTAAATTTTGATGCTTCATGTCGTACAAAAGAC
1 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
29494788 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
66 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
29494853 GCTTCAAAG
131 GCTTCAAAG
29494862 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
1 TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
29494927 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
66 GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
29494992 GCTTCAAAG
131 GCTTCAAAG
29495001 TAA
1 TAA
29495004 TTTATAAGAA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (139 bp):
TAAAGACCATGATTATTAGAGACAGAAGTATGGTAAATTTGGATGCTTCATGTCGTACAAAAGAC
GAGTAAGAAAGATAGCCCATTATAATAATGTCTGATATGATAGCATATGTTCTTTGTAAACCTAA
GCTTCAAAG
Found at i:29498436 original size:136 final size:136
Alignment explanation
Indices: 29498255--29498525 Score: 542
Period size: 136 Copynumber: 2.0 Consensus size: 136
29498245 ATTTTTTGGG
29498255 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
1 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
29498320 AAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
66 AAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
29498385 AAAACT
131 AAAACT
29498391 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
1 CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
29498456 AAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
66 AAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
29498521 AAAAC
131 AAAAC
29498526 CCCACACAAA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (136 bp):
CGTTTGTGAAATCAAACCTAGCTCGCTTCATTACAATCGCGGAATAATTATAAATTACAGAAAAA
AAATCAATAGAAAGTCGGGATGAAAGATTTTTTTCGCTTAAAATCATGTCGAGGCAGAGAATCAA
AAAACT
Found at i:29514983 original size:21 final size:21
Alignment explanation
Indices: 29514954--29514993 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29514944 ACATATACAA
29514954 AAACAACTT-AAAAACACTAGT
1 AAACAACTTGAAAAA-ACTAGT
*
29514975 AAACCACTTGAAAAAACTA
1 AAACAACTTGAAAAAACTA
29514994 AAACACCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.17
Consensus pattern (21 bp):
AAACAACTTGAAAAAACTAGT
Found at i:29515840 original size:11 final size:11
Alignment explanation
Indices: 29515818--29515868 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
29515808 AACAAATCCT
29515818 CTCTCAAATTTC
1 CTCTC-AATTTC
*
29515830 CTCTTAATTTC
1 CTCTCAATTTC
29515841 CTCTCAATTTC
1 CTCTCAATTTC
29515852 CTCTCAATTT-
1 CTCTCAATTTC
29515862 CTCTCAA
1 CTCTCAA
29515869 ATTTATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 7 0.19
11 26 0.70
12 4 0.11
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29515871 original size:22 final size:22
Alignment explanation
Indices: 29515817--29515872 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
29515807 AAACAAATCC
*
29515817 TCTCTCAAATTTCCTCTTAATT
1 TCTCTCAAATTTCCTCTCAATT
29515839 TCCTCTC-AATTTCCTCTCAATT
1 T-CTCTCAAATTTCCTCTCAATT
29515861 TCTCTCAAATTT
1 TCTCTCAAATTT
29515873 ATATTTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.16
22 21 0.68
23 5 0.16
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:29516852 original size:7 final size:8
Alignment explanation
Indices: 29516836--29516861 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29516826 TTGAAAGATG
29516836 AAGTGAAA
1 AAGTGAAA
29516844 AAGTGAAA
1 AAGTGAAA
29516852 AAGTGAAA
1 AAGTGAAA
29516860 AA
1 AA
29516862 AAAATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (8 bp):
AAGTGAAA
Found at i:29517490 original size:18 final size:18
Alignment explanation
Indices: 29517467--29517509 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
29517457 TTTTTATTTT
29517467 TTTTAAAATATTTTTTAA
1 TTTTAAAATATTTTTTAA
** * *
29517485 TTTTAATTTTTTTTTTAC
1 TTTTAAAATATTTTTTAA
29517503 TTTTAAA
1 TTTTAAA
29517510 GGGTAATGAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:29520915 original size:18 final size:18
Alignment explanation
Indices: 29520879--29520914 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29520869 ATTAAAGGAG
*
29520879 GGAAGAAGAAAGGTAAAA
1 GGAAGAAGAAAGATAAAA
29520897 GGAAGAAGAAAAGATAAA
1 GGAAGAAG-AAAGATAAA
29520915 GTACTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
GGAAGAAGAAAGATAAAA
Found at i:29534398 original size:9 final size:9
Alignment explanation
Indices: 29534386--29534411 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29534376 GTTGTTGTTG
29534386 TTATTATTC
1 TTATTATTC
29534395 TTATTATTC
1 TTATTATTC
29534404 TTATTATT
1 TTATTATT
29534412 ATACGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTATTC
Found at i:29539370 original size:11 final size:11
Alignment explanation
Indices: 29539343--29539384 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
29539333 ATTTTAAAAA
29539343 TAAAAA-ATTT
1 TAAAAATATTT
29539353 TAAAAAAGTATTT
1 T-AAAAA-TATTT
29539366 TAAAAATATTT
1 TAAAAATATTT
29539377 TAAAAATA
1 TAAAAATA
29539385 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.03
11 18 0.62
12 5 0.17
13 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:29540888 original size:21 final size:21
Alignment explanation
Indices: 29540864--29540903 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29540854 TACTGGGAAA
29540864 TGACCAAAATAAAAATAATTG
1 TGACCAAAATAAAAATAATTG
*
29540885 TGACCAAAATAGAAATAAT
1 TGACCAAAATAAAAATAAT
29540904 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
TGACCAAAATAAAAATAATTG
Found at i:29543529 original size:2 final size:2
Alignment explanation
Indices: 29543524--29543553 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29543514 ATATATATAT
29543524 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29543554 GAGGGACGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29546960 original size:20 final size:21
Alignment explanation
Indices: 29546920--29546963 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29546910 CTTCAAGCAC
29546920 TTATAATTAAATATAATATAA
1 TTATAATTAAATATAATATAA
* *
29546941 TTATATTTAAATA-CATATAA
1 TTATAATTAAATATAATATAA
29546961 TTA
1 TTA
29546964 AAATCTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATAATTAAATATAATATAA
Found at i:29548640 original size:6 final size:6
Alignment explanation
Indices: 29548629--29548659 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29548619 TTCCACTATC
29548629 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
29548660 GGTAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:29555689 original size:36 final size:36
Alignment explanation
Indices: 29555642--29555718 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
29555632 AATATGTAAA
29555642 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
1 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
29555678 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
1 AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
29555714 AATTT
1 AATTT
29555719 GCAACGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (36 bp):
AATTTTATTAATTCAAATAGTTGGAAACATTACAAG
Found at i:29568076 original size:2 final size:2
Alignment explanation
Indices: 29568071--29568099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29568061 ATATATAAAT
29568071 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29568100 AGTTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29572976 original size:19 final size:21
Alignment explanation
Indices: 29572952--29572998 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29572942 ATAATTTGTT
* *
29572952 TTTCAAT-CATA-AAATTTGG
1 TTTCAATCCATAGAAAGTTGA
29572971 TTTCAATCCATAGAAAGTTGA
1 TTTCAATCCATAGAAAGTTGA
29572992 TTTCAAT
1 TTTCAAT
29572999 AAATTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTCAATCCATAGAAAGTTGA
Found at i:29576476 original size:23 final size:24
Alignment explanation
Indices: 29576447--29576491 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
29576437 AAACTGAACA
29576447 AAAATAAAATAAAAAT-AGAAAAC
1 AAAATAAAATAAAAATGAGAAAAC
* *
29576470 AAAATAAACTGAAAATGAGAAA
1 AAAATAAAATAAAAATGAGAAA
29576492 TAAACATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAATAAAATAAAAATGAGAAAAC
Found at i:29577715 original size:14 final size:14
Alignment explanation
Indices: 29577696--29577722 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29577686 AAGCACATAG
29577696 AGTGTACAAAACTA
1 AGTGTACAAAACTA
29577710 AGTGTACAAAACT
1 AGTGTACAAAACT
29577723 GTAATCCGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (14 bp):
AGTGTACAAAACTA
Found at i:29577823 original size:25 final size:24
Alignment explanation
Indices: 29577795--29577856 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
29577785 CATATAACAA
* * *
29577795 GAAGCTCATGTGAGTCGTATATCGG
1 GAAGCTCATGAGAATCATA-ATCGG
*
29577820 GAAGCTCATAAGAATCATAATCGG
1 GAAGCTCATGAGAATCATAATCGG
29577844 GAAGCTCATGAGA
1 GAAGCTCATGAGA
29577857 GAACCTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.53
25 15 0.47
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (24 bp):
GAAGCTCATGAGAATCATAATCGG
Found at i:29583091 original size:81 final size:81
Alignment explanation
Indices: 29582916--29583095 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
29582906 AAAGGTTGTT
** * *
29582916 AAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATCCCCCTGAAGGGTAAAATTACCGAA
1 AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGAAAGGTAAAATTACCGAA
29582981 ATACCTTCAAAGAGTA
66 ATACCTTCAAAGAGTA
* * * * *
29582997 AAATTACCGAAATACCTTCGATGGGTAAAATTACTGAAATACCCCT-ATAAGGTAAAATTACTGA
1 AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGA-AAGGTAAAATTACCGA
*
29583061 AATACCTT-AATAGGGTA
65 AATACCTTCAA-AGAGTA
*
29583078 GAATGACCAAAATACCCT
1 AAATGACCAAAATACCCT
29583096 TATTAGTGTA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 3 0.04
81 82 0.96
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (81 bp):
AAATGACCAAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTGAAAGGTAAAATTACCGAA
ATACCTTCAAAGAGTA
Found at i:29583149 original size:27 final size:26
Alignment explanation
Indices: 29582916--29583231 Score: 179
Period size: 27 Copynumber: 11.7 Consensus size: 26
29582906 AAAGGTTGTT
*
29582916 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * * *
29582943 AAATTACTGAAATCCCCCTGAAGGGTA
1 AAATGACCGAAAT-ACCCTCAAGGGTA
* * *
29582970 AAATTACCGAAATACCTTCAAAGAGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * *
29582997 AAATTACCGAAATACCTTCGATGGGTA
1 AAATGACCGAAATACCCTC-AAGGGTA
* * *
29583024 AAATTACTGAAATACCC-CTATAAGGTA
1 AAATGACCGAAATACCCTC-A-AGGGTA
* * * *
29583051 AAATTACTGAAATACCTTAATAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
* * * *
29583078 GAATGACCAAAATACCCTTATTAGTGTA
1 AAATGACCGAAATACCCTCA--AGGGTA
* *
29583106 AAATAACCAAAATACCCTCACAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
*
29583133 AAATGACCGAAATACCCCCACAGGGTA
1 AAATGACCGAAATACCCTCA-AGGGTA
* * * *
29583160 AAA-GAACCGTAATACCCCCATAAGGTT
1 AAATG-ACCGAAATACCCTCA-AGGGTA
** *
29583187 AAATGGTCGAAATACTCCTGTAA-GGTA
1 AAATGACCGAAATAC-CCT-CAAGGGTA
*
29583214 AAATGACCGTAATACCCT
1 AAATGACCGAAATACCCT
29583232 TGGAGGGTAA
Statistics
Matches: 233, Mismatches: 47, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
26 9 0.04
27 192 0.82
28 31 0.13
29 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (26 bp):
AAATGACCGAAATACCCTCAAGGGTA
Found at i:29583294 original size:24 final size:24
Alignment explanation
Indices: 29583263--29583359 Score: 126
Period size: 24 Copynumber: 4.0 Consensus size: 24
29583253 TCCCCTCGAG
* *
29583263 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
29583287 TGTAAATGACTGATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
29583311 TTTAAATGACTGATTTGTCTGTGAA
1 TGTAAATGACTGATTTGTCTGTG-A
*
29583336 TGGT--ATGACTGATTTGTCTATGA
1 T-GTAAATGACTGATTTGTCTGTGA
29583359 T
1 T
29583360 TTGTATGATT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 2 0.03
26 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:29583365 original size:24 final size:24
Alignment explanation
Indices: 29583268--29583373 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
29583258 TCGAGTGTAA
* * * **
29583268 ATGATTGATTTGTCCGTGATGTAA
1 ATGACTGATTTGTCTGTGATTTGT
**
29583292 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTGATTTGTCTGTGATTTGT
* *
29583316 ATGACTGATTTGTCTGTGAATGGT
1 ATGACTGATTTGTCTGTGATTTGT
*
29583340 ATGACTGATTTGTCTATGATTTGT
1 ATGACTGATTTGTCTGTGATTTGT
*
29583364 ATGATTGATT
1 ATGACTGATT
29583374 CTGAGTATGG
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTTGT
Found at i:29583373 original size:48 final size:47
Alignment explanation
Indices: 29583265--29583373 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
29583255 CCCTCGAGTG
*
29583265 TAAATGATTGATTTGTCCGTGATGTAAATGACTGATTTGTCTGTGATT
1 TAAATGATTGATTTGTCCGTGATGT-AATGACTGATTTGTCTATGATT
* *
29583313 TAAATGACTGATTTGTCTGTGAATGGT-ATGACTGATTTGTCTATGATT
1 TAAATGATTGATTTGTCCGTG-AT-GTAATGACTGATTTGTCTATGATT
**
29583361 TGTATGATTGATT
1 TAAATGATTGATT
29583374 CTGAGTATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 49 0.92
49 2 0.04
50 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (47 bp):
TAAATGATTGATTTGTCCGTGATGTAATGACTGATTTGTCTATGATT
Found at i:29583606 original size:32 final size:32
Alignment explanation
Indices: 29583516--29583613 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
29583506 TTTGCTACGA
*
29583516 TGCTACTGATGGCTTTGTGTCGATCATATTA-
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* * * * * *
29583547 TCGTTATTGATGGCTGTGTACTGATCATATCAC
1 T-GCTACTGATGGCTTTGTGCCGATCATATTAC
*
29583580 TGCTACTGATGGCTTTGTGCCAATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
29583612 TG
1 TG
29583614 TATTTATGGC
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.96
33 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:29590967 original size:17 final size:17
Alignment explanation
Indices: 29590926--29590978 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
29590916 ATAGAAAGTC
* *
29590926 AAAGATATGGGTATTAG
1 AAAGATATGGGTATCAA
* *
29590943 AAATATATAGGTATCAA
1 AAAGATATGGGTATCAA
29590960 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
29590977 AA
1 AA
29590979 TCTGAGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (17 bp):
AAAGATATGGGTATCAA
Found at i:29593678 original size:15 final size:15
Alignment explanation
Indices: 29593640--29593668 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29593630 GAAATTTGAG
29593640 AACAAAT-AATAAAT
1 AACAAATAAATAAAT
29593654 AACAAATAAATAAAT
1 AACAAATAAATAAAT
29593669 GAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (15 bp):
AACAAATAAATAAAT
Done.