Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 76 of 79
Found at i:25417526 original size:6 final size:6
Alignment explanation
Indices: 25417517--25417565 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
25417507 GAAGGCGAGT
* * *
25417517 GTGAGG GTGAGG GTGAGG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG
1 GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG
25417565 G
1 G
25417566 AGGAGATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.57, T:0.16
Consensus pattern (6 bp):
GTGAAG
Found at i:25417575 original size:18 final size:18
Alignment explanation
Indices: 25417536--25417576 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
25417526 AGGGTGAGGG
* *
25417536 TGAAGGTGAAGGTGAAGG
1 TGAAGGTGAAGGAGAAGA
*
25417554 TGAAGGTGAAGGAGGAGA
1 TGAAGGTGAAGGAGAAGA
25417572 TGAAG
1 TGAAG
25417577 AGGAAGAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.15
Consensus pattern (18 bp):
TGAAGGTGAAGGAGAAGA
Found at i:25430223 original size:4 final size:4
Alignment explanation
Indices: 25430214--25430279 Score: 88
Period size: 4 Copynumber: 17.8 Consensus size: 4
25430204 CCCCATTCGT
*
25430214 TTTC TTTC -TTC -TTC -TTC -TTC -TTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
25430257 TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
25430280 TTTATTTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 15 0.25
4 44 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:25435670 original size:23 final size:23
Alignment explanation
Indices: 25435643--25435686 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25435633 AAAATTAAAT
* *
25435643 TATAATTTTTATAATAATAAAAA
1 TATAAATTTTAAAATAATAAAAA
*
25435666 TATAAATTTTAAAATATTAAA
1 TATAAATTTTAAAATAATAAA
25435687 TTAAAATATT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAAATTTTAAAATAATAAAAA
Found at i:25435678 original size:15 final size:15
Alignment explanation
Indices: 25435662--25435697 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
25435652 TATAATAATA
25435662 AAAATA-TAAATTTT
1 AAAATATTAAATTTT
25435676 AAAATATTAAA--TT
1 AAAATATTAAATTTT
25435689 AAAATATTA
1 AAAATATTA
25435698 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 6 0.29
15 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATTAAATTTT
Found at i:25442875 original size:12 final size:11
Alignment explanation
Indices: 25442858--25442900 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 11
25442848 ATTTTGATGC
25442858 TTAATTTTTTAT
1 TTAATTTTTT-T
25442870 TTAATTTTTTGT
1 TTAATTTTTT-T
25442882 TTAATTTTTCTT
1 TTAATTTTT-TT
25442894 TTAATTT
1 TTAATTT
25442901 GATATCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 28 0.97
13 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
TTAATTTTTTT
Found at i:25444849 original size:294 final size:294
Alignment explanation
Indices: 25444320--25444908 Score: 1110
Period size: 294 Copynumber: 2.0 Consensus size: 294
25444310 CATTGCTGTT
* * *
25444320 TTTAGTATATTTTTAGTCATAGTAGAAATTTGAGAAAGTTAAGACTTCGGGGCCCCCCCCCCCTT
1 TTTAGTATATTTTTAGGCAAAGTAGAAATTTGAGAAAGTTAAGACTTCGGGCCCCCCCCCCCCTT
25444385 TTTTAGTCCATCCTCCCCAATCCCATGTTAAGAGCTTTGATGAAGATTCCTTGCTAAATGTTAGA
66 TTTTAGTCCATCCTCCCCAATCCCATGTTAAGAGCTTTGATGAAGATTCCTTGCTAAATGTTAGA
25444450 TCCCCATGCCAAATCCACATTTAACGACCATTACAAAAATTGCTCGTAATAATATAAGTATACAA
131 TCCCCATGCCAAATCCACATTTAACGACCATTACAAAAATTGCTCGTAATAATATAAGTATACAA
25444515 CAAAAGAAAGCTTGTCCTAAAACGTTTGGTGCCATGTCTTTAGCTGCTGGGGCTTTGGATGTAGG
196 CAAAAGAAAGCTTGTCCTAAAACGTTTGGTGCCATGTCTTTAGCTGCTGGGGCTTTGGATGTAGG
25444580 CTTCTCTCATTTCTATCCGAATGGATACTTAGAG
261 CTTCTCTCATTTCTATCCGAATGGATACTTAGAG
*
25444614 TTTAGTAGT-TTTTTAGGCAAAGTTGAAATTTGAGAAAGTTAAG-CTTCGGGTCCCCCCCCCCCC
1 TTTAGTA-TATTTTTAGGCAAAGTAGAAATTTGAGAAAGTTAAGACTTCGGG-CCCCCCCCCCCC
25444677 TTTTTTAGTCCATCCTCCCCAATCCCATGTTAAGAGCTTTGATGAAGATTCCTTGCTAAATGTTA
64 TTTTTTAGTCCATCCTCCCCAATCCCATGTTAAGAGCTTTGATGAAGATTCCTTGCTAAATGTTA
25444742 GATCCCCATGCCAAATCCACATTTAACGACCATTACAAAAATTGCTCGTAATAATATAAGTATAC
129 GATCCCCATGCCAAATCCACATTTAACGACCATTACAAAAATTGCTCGTAATAATATAAGTATAC
25444807 AACAAAAGAAAGCTTGTCCTAAAACGTTTGGTGCCATGTCTTTAGCTGCTGGGGCTTTGGATGTA
194 AACAAAAGAAAGCTTGTCCTAAAACGTTTGGTGCCATGTCTTTAGCTGCTGGGGCTTTGGATGTA
25444872 GGCTTCTCTCATTTCTATCCGAATGGATACTTAGAG
259 GGCTTCTCTCATTTCTATCCGAATGGATACTTAGAG
25444908 T
1 T
25444909 AACCTGGTAA
Statistics
Matches: 289, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
293 7 0.02
294 281 0.97
295 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (294 bp):
TTTAGTATATTTTTAGGCAAAGTAGAAATTTGAGAAAGTTAAGACTTCGGGCCCCCCCCCCCCTT
TTTTAGTCCATCCTCCCCAATCCCATGTTAAGAGCTTTGATGAAGATTCCTTGCTAAATGTTAGA
TCCCCATGCCAAATCCACATTTAACGACCATTACAAAAATTGCTCGTAATAATATAAGTATACAA
CAAAAGAAAGCTTGTCCTAAAACGTTTGGTGCCATGTCTTTAGCTGCTGGGGCTTTGGATGTAGG
CTTCTCTCATTTCTATCCGAATGGATACTTAGAG
Found at i:25452095 original size:5 final size:5
Alignment explanation
Indices: 25452087--25452112 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25452077 TGAAATATTA
25452087 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
25452113 TTAGGGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:25456041 original size:3 final size:3
Alignment explanation
Indices: 25456033--25456059 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25456023 GCCTTTAAGG
25456033 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
25456060 TTCTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25456458 original size:3 final size:3
Alignment explanation
Indices: 25456450--25456509 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
25456440 ATGCTTTTAC
25456450 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25456497 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
25456510 CTATACAGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25460804 original size:17 final size:16
Alignment explanation
Indices: 25460782--25460834 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
25460772 TCAAACAATT
25460782 TTATTTAAATCACTAAA
1 TTATTTAAA-CACTAAA
25460799 TTATTTAAA-A--AAA
1 TTATTTAAACACTAAA
25460812 TTTATTTAAGACACTAAA
1 -TTATTTAA-ACACTAAA
25460830 TTATT
1 TTATT
25460835 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.10
14 8 0.26
15 2 0.06
16 1 0.03
17 14 0.45
18 3 0.10
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (16 bp):
TTATTTAAACACTAAA
Found at i:25464027 original size:5 final size:5
Alignment explanation
Indices: 25464017--25464045 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25464007 TTCATACATA
25464017 TGTTT TGTTT TGTTT TGTTT TGTTT TGTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTT
25464046 ATGGTGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TGTTT
Found at i:25482659 original size:26 final size:28
Alignment explanation
Indices: 25482620--25482671 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
25482610 CAATATAGGC
*
25482620 TTTTACAATATTATCATAA-TTTTTTCA
1 TTTTACAATATTATAATAACTTTTTTCA
*
25482647 TTTTATAA-ATTATAATAACTTTTTT
1 TTTTACAATATTATAATAACTTTTTT
25482672 TTTACTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTACAATATTATAATAACTTTTTTCA
Found at i:25487090 original size:33 final size:33
Alignment explanation
Indices: 25487048--25487112 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
25487038 CATGCTAAAA
* *
25487048 TTTGTGTATAAGTTTATATTTTAGTCGAGTTAT
1 TTTGGGTATAAATTTATATTTTAGTCGAGTTAT
*
25487081 TTTGGGTATAAATTTATATTTTTGTCGAGTTA
1 TTTGGGTATAAATTTATATTTTAGTCGAGTTA
25487113 CAAAATAGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (33 bp):
TTTGGGTATAAATTTATATTTTAGTCGAGTTAT
Found at i:25500442 original size:25 final size:25
Alignment explanation
Indices: 25500413--25500475 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
25500403 CTAATTTCTC
* *
25500413 CTTTCTTTCTT-TCCCTTTTTCTTTT
1 CTTTCTTT-TTCTCCCTGTTTCGTTT
25500438 CTTTCTTTTTCTCCCTGTTTCGTTT
1 CTTTCTTTTTCTCCCTGTTTCGTTT
*
25500463 CTATTCTATTTCT
1 CT-TTCTTTTTCT
25500476 TTTATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 22 0.67
26 9 0.27
ACGTcount: A:0.03, C:0.27, G:0.03, T:0.67
Consensus pattern (25 bp):
CTTTCTTTTTCTCCCTGTTTCGTTT
Found at i:25502077 original size:29 final size:30
Alignment explanation
Indices: 25502034--25502096 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
25502024 TTCAAGACTC
* *
25502034 AAATTTCATAATTCAAAAAA-A-AAGTACT
1 AAATTTAATAATTCAAAAAATATAAGAACT
25502062 AAATTTAATCAATTCAAAAAATATAAGAACT
1 AAATTTAAT-AATTCAAAAAATATAAGAACT
25502093 AAAT
1 AAAT
25502097 CCGCAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 1 0.03
31 10 0.33
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATTTAATAATTCAAAAAATATAAGAACT
Found at i:25502551 original size:21 final size:21
Alignment explanation
Indices: 25502527--25502580 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
25502517 CGAATATAAT
25502527 AAATATATATTTTTATTTTTA
1 AAATATATATTTTTATTTTTA
*
25502548 AAATACT-TTTTTTTATTTTTA
1 AAATA-TATATTTTTATTTTTA
25502569 AAATA-A-ATTTTT
1 AAATATATATTTTT
25502581 GGTGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
21 23 0.79
22 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
AAATATATATTTTTATTTTTA
Found at i:25503993 original size:156 final size:155
Alignment explanation
Indices: 25503679--25503975 Score: 452
Period size: 156 Copynumber: 1.9 Consensus size: 155
25503669 GAATGTGCCA
* * *
25503679 GCGAACCAAACCTCTACCCGCTCCCGATTTCAGCTTTGCATCCTTCTCCGACTCGACGGTGTCAG
1 GCGAACCAAACCTCTACCCGATCCCGATTTCAACTTTGCATCCTTCTCCGACTCGACGGCGTCAG
* *
25503744 ATCTCCGGACGGCTTGAATCAGTAATCTCCGCCAAACTTATAACCTATTTCTTTCCTCTCTGCAT
66 ATCTCCGGACGACTTGAATCAGTAATCTCCGCC-AACTGATAACCTATTTCTTTCCTCTCTGCAT
***
25503809 GCGATTGTTTCACCCTCCCCCCCCCG
130 GCGATTGTTTCACCCTCCCCAAACCG
* * * *
25503835 GCGACCCAACCCTCTAGCCGATCCCGATTTCAACTTTGCATCTTTCTCCGACTCGACGGCGTCAG
1 GCGAACCAAACCTCTACCCGATCCCGATTTCAACTTTGCATCCTTCTCCGACTCGACGGCGTCAG
*
25503900 ATCTCCGGACGACTTGAATCAGTAATCTCCGCC-TCTGAGTAACCTATTTCTTTCCTCTCTGCAT
66 ATCTCCGGACGACTTGAATCAGTAATCTCCGCCAACTGA-TAACCTATTTCTTTCCTCTCTGCAT
25503964 GCGATTGTTTCA
130 GCGATTGTTTCA
25503976 GTTCTTGGTA
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
154 3 0.02
155 37 0.28
156 90 0.69
ACGTcount: A:0.19, C:0.36, G:0.16, T:0.29
Consensus pattern (155 bp):
GCGAACCAAACCTCTACCCGATCCCGATTTCAACTTTGCATCCTTCTCCGACTCGACGGCGTCAG
ATCTCCGGACGACTTGAATCAGTAATCTCCGCCAACTGATAACCTATTTCTTTCCTCTCTGCATG
CGATTGTTTCACCCTCCCCAAACCG
Found at i:25504883 original size:21 final size:22
Alignment explanation
Indices: 25504848--25504902 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
25504838 TTTCCCCCCA
* *
25504848 TTGCATGTGTCTATACAA-TTGT
1 TTGCA-GTGGCTATACAATTTAT
*
25504870 TTGCAGTGGCTATATAATTTAT
1 TTGCAGTGGCTATACAATTTAT
25504892 TTGCAGTGGCT
1 TTGCAGTGGCT
25504903 CCATCTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (22 bp):
TTGCAGTGGCTATACAATTTAT
Found at i:25505136 original size:52 final size:52
Alignment explanation
Indices: 25505073--25505219 Score: 216
Period size: 52 Copynumber: 2.9 Consensus size: 52
25505063 TGCATAGTCC
*
25505073 TGGTGCTGTTAATTTGGTACTGTTAATTTTGAATGCTTTGAAATGTTTGAAA
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
*
25505125 TGGTGTTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
* *
25505177 TGGTGCTGTT-A----CTACT-TCAACTTTGAATGCTTTGAAATGTTTG
1 TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTG
25505220 CTCACTGATA
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
46 26 0.29
47 4 0.04
51 1 0.01
52 59 0.66
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (52 bp):
TGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAA
Found at i:25506316 original size:187 final size:187
Alignment explanation
Indices: 25506001--25510586 Score: 9127
Period size: 187 Copynumber: 24.5 Consensus size: 187
25505991 ATGAGTACTA
* *
25506001 TATAATTTAAAAAGGGCATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATAGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25506066 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25506131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
*
25506188 TATAATTTAGAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25506253 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25506318 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
*
25506375 TATAATTTAGAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25506440 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25506505 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
*
25506562 TATAATTTAGAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25506627 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25506692 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25506749 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25506814 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25506879 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25506936 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507001 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25507066 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25507123 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507188 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25507253 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25507310 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507375 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25507440 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25507497 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507562 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25507627 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25507684 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507749 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25507814 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25507871 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25507936 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508001 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508058 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25508123 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508188 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508245 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25508310 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508375 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508432 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25508497 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508562 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508619 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25508684 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508749 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508806 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25508871 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25508936 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25508993 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509058 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25509123 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25509180 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509245 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25509310 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25509367 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509432 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25509497 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25509554 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509619 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25509684 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25509741 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509806 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25509871 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25509928 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25509993 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25510058 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25510115 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25510180 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25510245 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25510302 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25510367 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
25510432 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
131 TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
25510489 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
1 TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
25510554 GAATGTTGTTATAAAAAGGAGCAATATATAATT
66 GAATGTTGTTATAAAAAGGAGCAATATATAATT
25510587 AATATATTTA
Statistics
Matches: 4395, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 4395 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.41
Consensus pattern (187 bp):
TATAATTTAAAAAGGACATCAAACTTTAGTACCAATTCTTGTATTAAAAAGGAAATTCATGGACA
GAATGTTGTTATAAAAAGGAGCAATATATAATTTGGTACTTGTGTTTTTTCTTTTTTTAATCTAT
TATTTGTATTTGATAAATATTTTGATACTTAAAGATAATGGTGTACCAATTCTTCGT
Found at i:25520602 original size:57 final size:58
Alignment explanation
Indices: 25520525--25520647 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 58
25520515 AAAACTCGAA
* *
25520525 TTTTTTTACTGTACTAGGTGCCGGCCGTTGACAGGCCAGCACCTAAAATTTTTTTTTCC
1 TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACC-AAAAATTTTTTTTCC
*
25520584 TTTTTTT-C-GTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
1 TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
25520640 TTCTTTTT
1 TT-TTTTT
25520648 TGTATATCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 16 0.27
57 36 0.60
58 1 0.02
59 7 0.12
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (58 bp):
TTTTTTTACTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTCC
Found at i:25523917 original size:26 final size:26
Alignment explanation
Indices: 25523887--25523944 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
25523877 TGTTATTTAT
* *
25523887 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAACTATAGAGTAAGA
25523913 ATTATTTGATAAACTATAGAGTAAGA
1 ATTATTTGATAAACTATAGAGTAAGA
25523939 ATTATT
1 ATTATT
25523945 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAACTATAGAGTAAGA
Found at i:25524335 original size:12 final size:12
Alignment explanation
Indices: 25524318--25524342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25524308 CAGGATAGTG
25524318 AAAATTATGAAC
1 AAAATTATGAAC
25524330 AAAATTATGAAC
1 AAAATTATGAAC
25524342 A
1 A
25524343 GTTTCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATTATGAAC
Found at i:25526760 original size:19 final size:21
Alignment explanation
Indices: 25526724--25526763 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
25526714 AAATCATACT
25526724 ATTTGTTTTACGATTATATAA
1 ATTTGTTTTACGATTATATAA
*
25526745 ATTT-TTTTACTA-TATATAA
1 ATTTGTTTTACGATTATATAA
25526764 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTGTTTTACGATTATATAA
Found at i:25527036 original size:42 final size:41
Alignment explanation
Indices: 25526967--25527096 Score: 158
Period size: 41 Copynumber: 3.1 Consensus size: 41
25526957 AATATTTTTT
* *
25526967 GCGGCGC-TTCAACAAAATCGCCGCTAAAACCCCTAACATTA
1 GCGGCGCTTTCAACAAAAACGCCGCTAAAA-CCTTAACATTA
* *
25527008 GCGGCGCTTCTCAA-AAAAACGCCGCTAAAAATCTTAACTTTA
1 GCGGCGCTT-TCAACAAAAACGCCGCT-AAAACCTTAACATTA
*
25527050 GCGGCGCTTT-AACGAAAACGCCGCTAAATACCTTAACATTA
1 GCGGCGCTTTCAACAAAAACGCCGCTAAA-ACCTTAACATTA
25527091 GCGGCG
1 GCGGCG
25527097 GTTGATTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
40 5 0.06
41 35 0.45
42 29 0.38
43 8 0.10
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTCAACAAAAACGCCGCTAAAACCTTAACATTA
Found at i:25527108 original size:83 final size:82
Alignment explanation
Indices: 25526967--25527119 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 82
25526957 AATATTTTTT
* *
25526967 GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAAACGCCG
1 GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCAAAAAAA-GCCA
25527032 CTAAAAATCTTAACTTTA
65 CTAAAAATCTTAACTTTA
* * * *
25527050 GCGGCGCTTTAACGAAAA-CGCCGCTAAATA-CCTTAACATTAGCGGCGGTTGAT-TAAAAAAGC
1 GCGGCGCTTCAAC-AAAATCGCCGCTAAA-ACCCCTAACATTAGCGGCGCTT-ATCAAAAAAAGC
25527112 CACTAAAA
63 CACTAAAA
25527120 CCCCCGACCA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
82 9 0.15
83 46 0.75
84 6 0.10
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (82 bp):
GCGGCGCTTCAACAAAATCGCCGCTAAAACCCCTAACATTAGCGGCGCTTATCAAAAAAAGCCAC
TAAAAATCTTAACTTTA
Found at i:25527298 original size:39 final size:40
Alignment explanation
Indices: 25527252--25527328 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
25527242 GTTTTTTGCA
*
25527252 GAAACGCTGCT-AA-TGCATATTTTTAGCGGCGTTTTCTTT
1 GAAACGCTGCTAAAGTGCAT-TTTTTAGCGGCATTTTCTTT
*
25527291 GAAACGCTGCTAAAGTTCATTTTTTAGCGGCATTTTCT
1 GAAACGCTGCTAAAGTGCATTTTTTAGCGGCATTTTCT
25527329 CACAAGCGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 11 0.32
40 19 0.56
41 4 0.12
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (40 bp):
GAAACGCTGCTAAAGTGCATTTTTTAGCGGCATTTTCTTT
Found at i:25531032 original size:13 final size:11
Alignment explanation
Indices: 25530996--25531026 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25530986 CCGCCCGTAT
25530996 TAATTTTTATA
1 TAATTTTTATA
*
25531007 TTATTTTTATA
1 TAATTTTTATA
25531018 TAATTTTTA
1 TAATTTTTA
25531027 AATATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:25531179 original size:30 final size:30
Alignment explanation
Indices: 25531145--25531207 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
25531135 ACTTAACAAC
*
25531145 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
25531175 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
25531205 CAA
1 CAA
25531208 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:25533886 original size:6 final size:6
Alignment explanation
Indices: 25533875--25533900 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25533865 GCTTGGTTGA
25533875 GATGTT GATGTT GATGTT GATGTT GA
1 GATGTT GATGTT GATGTT GATGTT GA
25533901 CCTTGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (6 bp):
GATGTT
Found at i:25534510 original size:13 final size:13
Alignment explanation
Indices: 25534492--25534556 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
25534482 AATTCTTCAT
25534492 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
25534505 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
25534518 TGCTGTGGAAAA-
1 TGCTTTTGAAAAG
* *
25534530 TGCTTTTGAGAAT
1 TGCTTTTGAAAAG
*
25534543 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
25534556 T
1 T
25534557 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 9 0.21
13 31 0.74
14 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:25535665 original size:22 final size:22
Alignment explanation
Indices: 25535631--25535693 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
25535621 GTAGAAAACG
* * *
25535631 GAATTTAATTATATTTTTTTAT
1 GAATTAAAATATAATTTTTTAT
*
25535653 GAATTAAAATATAAGTTTATTAT
1 GAATTAAAATATAA-TTTTTTAT
* *
25535676 GTATTAATATATAATTTT
1 GAATTAAAATATAATTTT
25535694 ATCTTTCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (22 bp):
GAATTAAAATATAATTTTTTAT
Found at i:25535681 original size:23 final size:23
Alignment explanation
Indices: 25535649--25535695 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
25535639 TTATATTTTT
25535649 TTATGAATTAAAATATAAGTTTA
1 TTATGAATTAAAATATAAGTTTA
* * *
25535672 TTATGTATTAATATATAATTTTA
1 TTATGAATTAAAATATAAGTTTA
25535695 T
1 T
25535696 CTTTCTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
TTATGAATTAAAATATAAGTTTA
Found at i:25535859 original size:83 final size:82
Alignment explanation
Indices: 25535751--25535977 Score: 255
Period size: 83 Copynumber: 2.7 Consensus size: 82
25535741 GGCTAAATGC
* * * *
25535751 AATTTTACTAT-TATTAATTTATAATTTCTTTATTCATAAGAGGACTGAATTG-AATTTTTTATA
1 AATTTCACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTCAATTGAAATTTTTCAT-
* *
25535814 TTTTAGAGAGTTAAA-GTA
65 TTTGAG-GAGTTAAAGGGA
*
25535832 TAATTTCACTATATATTAATTTATAATTTCTTTATTTATAAGAGGATTCAATTGAAAATTTTTCA
1 -AATTTCACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTCAATTG-AAATTTTTCA
*
25535897 TTTTGAGGGGTTAAAGGGA
64 TTTTGAGGAGTTAAAGGGA
* * * * *
25535916 AATTTCACTATATATT-ACTTATTAGTTTCTCTATTTATAAGATGACTTAATTGAAAATTTTT
1 AATTTCACTATATATTAATTTA-TAATTTCTTTATTTATAAGAGGACTCAATTG-AAATTTTT
25535978 TTTAGGGAGG
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
82 14 0.11
83 96 0.76
84 7 0.06
85 9 0.07
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (82 bp):
AATTTCACTATATATTAATTTATAATTTCTTTATTTATAAGAGGACTCAATTGAAATTTTTCATT
TTGAGGAGTTAAAGGGA
Found at i:25543640 original size:27 final size:28
Alignment explanation
Indices: 25543602--25543655 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
25543592 TAGGATCGGG
*
25543602 GTTTGAGGTTTAAAGTTCAA-GTTCAGA
1 GTTTAAGGTTTAAAGTTCAAGGTTCAGA
*
25543629 GTTTAAGGTTTAAGGTTCAAGGTTCAG
1 GTTTAAGGTTTAAAGTTCAAGGTTCAG
25543656 GATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (28 bp):
GTTTAAGGTTTAAAGTTCAAGGTTCAGA
Found at i:25545452 original size:8 final size:8
Alignment explanation
Indices: 25545435--25545465 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
25545425 TTTTCATTGC
*
25545435 ATTTTGTT
1 ATTTTATT
25545443 ATTTTATT
1 ATTTTATT
25545451 ATTTTATT
1 ATTTTATT
25545459 ATTTTAT
1 ATTTTAT
25545466 AGACATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
ATTTTATT
Found at i:25556085 original size:2 final size:2
Alignment explanation
Indices: 25556078--25556107 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25556068 GCAAAACATC
25556078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25556108 CCTCCAATCT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25561007 original size:11 final size:12
Alignment explanation
Indices: 25560976--25561006 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25560966 ACAATTTATC
25560976 TTATTTTTGTAA
1 TTATTTTTGTAA
25560988 TTATTTTTGTAA
1 TTATTTTTGTAA
25561000 TTATTTT
1 TTATTTT
25561007 GATTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATTTTTGTAA
Found at i:25569975 original size:19 final size:18
Alignment explanation
Indices: 25569953--25570023 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
25569943 CTTTAGAAAT
25569953 TTTTTTAAATTTTTCATAA
1 TTTTTTAAATTTTT-ATAA
* *
25569972 TTTTTTAAA-ATATATAA
1 TTTTTTAAATTTTTATAA
* *
25569989 ATTTTGAAATTTTTTATAAA
1 TTTTTTAAA-TTTTTAT-AA
*
25570009 TATTTTAAATTTTTA
1 TTTTTTAAATTTTTA
25570024 AAAAAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 11 0.28
18 2 0.05
19 19 0.47
20 8 0.20
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTTTAAATTTTTATAA
Found at i:25569990 original size:28 final size:29
Alignment explanation
Indices: 25569958--25570022 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
25569948 GAAATTTTTT
25569958 TAAATTTTTCATAATTTTTTA-AAATA-TA
1 TAAATTTTTCA-AATTTTTTATAAATATTA
* *
25569986 TAAA-TTTTGAAATTTTTTATAAATATTT
1 TAAATTTTTCAAATTTTTTATAAATATTA
25570014 TAAATTTTT
1 TAAATTTTT
25570023 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 9 0.28
27 10 0.31
28 9 0.28
29 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TAAATTTTTCAAATTTTTTATAAATATTA
Found at i:25572972 original size:24 final size:25
Alignment explanation
Indices: 25572945--25573003 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
25572935 TATTGTTTTT
25572945 TATTTTAAAAAATAATG-AG-TAATA
1 TATTTTAAAAAAT-ATGTAGTTAATA
*
25572969 TATTTTATAAAATATGTAGTTTAATA
1 TATTTTAAAAAATATGTAG-TTAATA
25572995 TATTTTAAA
1 TATTTTAAA
25573004 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 14 0.47
26 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
TATTTTAAAAAATATGTAGTTAATA
Found at i:25575116 original size:172 final size:164
Alignment explanation
Indices: 25574797--25575119 Score: 373
Period size: 172 Copynumber: 1.9 Consensus size: 164
25574787 GACCACTTTC
* *
25574797 TTTTGGAAGTCAAAACACATCATCACTGAAACCAAGCATTTGTTACAACTGCAACACCTATGGTC
1 TTTTGGAAGTCAAAACACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACACCTATGGTC
*
25574862 CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGACAATAATAATCAAT
66 CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAAT
** *
25574927 GAGTGTATCTTAAAGTGCATTGTTAGAACTTTTA
131 GAACGTATCTCAAAGTGCATTGTTAGAACTTTTA
**
25574961 TTTTGGAAGTCACAACACAACAACATCACTGAAACCTGGCATTTGTTACAAATGCAA-ATCC-AC
1 TTTTGGAAGTCA-AA-AC-ACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACA-CCTA-
* * * ** * *
25575024 TGGTCCCTTATCATTTTTTTTTTGGCCAAATCCTTAGTGAATTCTTAGAGCTTTGACGA-GAAAA
61 TGGTCCC---T--TTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGA-AATGAAAA
**
25575088 TAATAATCGGTGAACGTATCTCAAAGTGCATT
120 TAATAATCAATGAACGTATCTCAAAGTGCATT
25575120 ATTTCTTGAC
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
164 12 0.09
165 2 0.02
166 4 0.03
167 43 0.33
170 1 0.01
172 68 0.52
173 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (164 bp):
TTTTGGAAGTCAAAACACAACATCACTGAAACCAAGCATTTGTTACAAATGCAACACCTATGGTC
CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAAT
GAACGTATCTCAAAGTGCATTGTTAGAACTTTTA
Found at i:25577965 original size:15 final size:16
Alignment explanation
Indices: 25577938--25577968 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
25577928 TCGATCTAGT
25577938 CAATCTAAATTTGATC
1 CAATCTAAATTTGATC
25577954 CAATCT-AATTTGATC
1 CAATCTAAATTTGATC
25577969 ATAAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
CAATCTAAATTTGATC
Found at i:25585746 original size:4 final size:4
Alignment explanation
Indices: 25585737--25585764 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25585727 CCATCAAATA
25585737 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
25585765 ATTCCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:25591206 original size:30 final size:29
Alignment explanation
Indices: 25591140--25591250 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 29
25591130 GATTAAATCA
* * * *
25591140 AAATTAAAGGTTCAAGTATACATTTGAACC
1 AAATTAAA-GTTCATGTATACAATTGCACT
* * *
25591170 ACAATTAGAGTTTCATGTGTATAATTGCACT
1 A-AATTAAAG-TTCATGTATACAATTGCACT
25591201 AAATTAAAGTTCATGTATACAATTGCACATT
1 AAATTAAAGTTCATGTATACAATTGCAC--T
**
25591232 AAATCGAAGTTCATGTATA
1 AAATTAAAGTTCATGTATA
25591251 ATTTTGAGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 17 0.26
30 9 0.14
31 39 0.60
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATACAATTGCACT
Found at i:25602860 original size:20 final size:20
Alignment explanation
Indices: 25602832--25602881 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
25602822 TGCCTACGGA
*
25602832 ACACTCCAAAAGCATAAGTC
1 ACACCCCAAAAGCATAAGTC
25602852 ACACCCCAAAAGCATAAGTC
1 ACACCCCAAAAGCATAAGTC
25602872 ACACCCCAAA
1 ACACCCCAAA
25602882 CAAGGTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.36, G:0.08, T:0.10
Consensus pattern (20 bp):
ACACCCCAAAAGCATAAGTC
Found at i:25603305 original size:2 final size:2
Alignment explanation
Indices: 25603298--25603323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25603288 ATAATAATAA
25603298 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
25603324 TCAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25606094 original size:4 final size:4
Alignment explanation
Indices: 25606085--25606116 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25606075 AAGAATATTA
25606085 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
25606117 TAGAGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:25608008 original size:4 final size:4
Alignment explanation
Indices: 25607999--25608025 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25607989 ACACACGTGC
25607999 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
25608026 ACGACGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:25619467 original size:21 final size:21
Alignment explanation
Indices: 25619434--25619615 Score: 96
Period size: 21 Copynumber: 8.7 Consensus size: 21
25619424 ACTGTACCCA
* *
25619434 GGAGAAGTGGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGAT
* *
25619455 GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * *
25619476 GGAGATGTAGGGCTATAGGAG
1 GGAGAAGTAGGGCTATATGAT
* * * * * *
25619497 GGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTATATGAT
* * * *
25619518 GGAGATGTCGGACTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* * * *
25619539 GGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
* *
25619560 GGAGAAGTGGGGCTGTATGCA-
1 GGAGAAGTAGGGCTATATG-AT
* * **
25619581 GGTGAAGTTGGGCTATATGCC
1 GGAGAAGTAGGGCTATATGAT
*
25619602 GGTGAAGTAGGGCT
1 GGAGAAGTAGGGCT
25619616 GTAGCTTGGT
Statistics
Matches: 127, Mismatches: 32, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
21 126 0.99
22 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.25
Consensus pattern (21 bp):
GGAGAAGTAGGGCTATATGAT
Found at i:25619480 original size:42 final size:42
Alignment explanation
Indices: 25619434--25619599 Score: 147
Period size: 42 Copynumber: 4.0 Consensus size: 42
25619424 ACTGTACCCA
* *
25619434 GGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
* * * * * *
25619476 GGAGATGTAGGGCTATA-GGAGGGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTGGGGCTATATGCAGGG-GAAGTTGGGCTGTATGAT
* * * * * *
25619518 GGAGATGTCGGACTGTATG-ATGGCGATGTTGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCA-GGGGAAGTTGGGCTGTATGAT
* * *
25619560 GGAGAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATG
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATG
25619600 CCGGTGAAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
41 4 0.04
42 91 0.92
43 4 0.04
ACGTcount: A:0.23, C:0.07, G:0.45, T:0.25
Consensus pattern (42 bp):
GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
Found at i:25619609 original size:42 final size:42
Alignment explanation
Indices: 25619434--25619639 Score: 114
Period size: 42 Copynumber: 4.9 Consensus size: 42
25619424 ACTGTACCCA
* * * * * *
25619434 GGAGAAGTGGGGCTATATGCT-GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* * * * * * *
25619476 GGAGATGTAGGGCTATAG-GAGGGTGAGGTTGGGCTGTAAGAA
1 GGAGAAGTAGGGCTGTAGCTA-GGTGAAGTTGGGCTATATGAC
* * * * * * * *
25619518 GGAGATGTCGGACTGTATGAT-GGCGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* *
25619560 GGAGAAGTGGGGCTGTATGC-AGGTGAAGTTGGGCTATATGCC
1 GGAGAAGTAGGGCTGTA-GCTAGGTGAAGTTGGGCTATATGAC
* * *
25619602 GGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATA
1 GGAGAAGTAGGGCTGTAGCTAGGTGAAGTTGGGCTATA
25619640 GCTGGGAGAT
Statistics
Matches: 129, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.02
42 125 0.97
43 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.43, T:0.26
Consensus pattern (42 bp):
GGAGAAGTAGGGCTGTAGCTAGGTGAAGTTGGGCTATATGAC
Found at i:25619669 original size:63 final size:63
Alignment explanation
Indices: 25619602--25619732 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 63
25619592 GCTATATGCC
* * * * *
25619602 GGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGATGT-GGGACTATAACTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGG-CTATAACTT
* * * * *
25619665 GGTGAAGTAGGACTGTAACTTGGAGACGTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACTT
25619728 GGTGA
1 GGTGA
25619733 GGTTGGAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 54 0.95
64 3 0.05
ACGTcount: A:0.24, C:0.10, G:0.40, T:0.27
Consensus pattern (63 bp):
GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTAGGGCTATAACTT
Found at i:25619729 original size:42 final size:42
Alignment explanation
Indices: 25619608--25619729 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
25619598 TGCCGGTGAA
* * *
25619608 GTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGAT
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * * *
25619650 GT-GGGACTATAACTTGGTGAAGTAGGACTGTAACTTGGAGAC
1 GTAGGG-CTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * *
25619692 GTAGGGCTGTAGCTTGGAGAGGTAGGGCTATAGCTTGG
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGG
25619730 TGAGGTTGGA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 3 0.05
42 58 0.91
43 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (42 bp):
GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
Found at i:25619735 original size:21 final size:21
Alignment explanation
Indices: 25619581--25619732 Score: 119
Period size: 21 Copynumber: 7.2 Consensus size: 21
25619571 GCTGTATGCA
* *
25619581 GGTGAAGTTGGGCTATATGC-C
1 GGTGAAGTAGGGCTATA-GCTT
*
25619602 GGTGAAGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
25619623 GGTGAAGTTGGACTATAGCTG
1 GGTGAAGTAGGGCTATAGCTT
* * *
25619644 GGAGATGT-GGGACTATAACTT
1 GGTGAAGTAGGG-CTATAGCTT
* * *
25619665 GGTGAAGTAGGACTGTAACTT
1 GGTGAAGTAGGGCTATAGCTT
* * *
25619686 GGAGACGTAGGGCTGTAGCTT
1 GGTGAAGTAGGGCTATAGCTT
* *
25619707 GGAGAGGTAGGGCTATAGCTT
1 GGTGAAGTAGGGCTATAGCTT
25619728 GGTGA
1 GGTGA
25619733 GGTTGGAGAA
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
20 4 0.04
21 99 0.94
22 2 0.02
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (21 bp):
GGTGAAGTAGGGCTATAGCTT
Found at i:25619825 original size:42 final size:43
Alignment explanation
Indices: 25619779--25619918 Score: 169
Period size: 42 Copynumber: 3.3 Consensus size: 43
25619769 TGGACTTGTT
* * ** * * *
25619779 GGGCTGTAACCTGGTGAACTAGGACTGTAAG-TAGGTGATGTG
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
25619821 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGTA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
*
25619863 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGAA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
* *
25619905 GGACTGTAGCCAGG
1 GGGCTGTAACCAGG
25619919 AGATGATGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 2 0.02
42 85 0.98
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.19
Consensus pattern (43 bp):
GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
Found at i:25619848 original size:21 final size:21
Alignment explanation
Indices: 25619824--25619921 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
25619814 TGATGTGGGG
* *
25619824 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
25619845 CTGTAGCCAGGAGATGTAGGG
1 CTGTAGCCAGGAGAGGTAGGA
* *
25619866 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
25619887 CTGTAGCCAGGAGATGAAGGA
1 CTGTAGCCAGGAGAGGTAGGA
25619908 CTGTAGCCAGGAGA
1 CTGTAGCCAGGAGA
25619922 TGATGGGCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.39, T:0.15
Consensus pattern (21 bp):
CTGTAGCCAGGAGAGGTAGGA
Found at i:25619922 original size:21 final size:21
Alignment explanation
Indices: 25619841--25619945 Score: 120
Period size: 21 Copynumber: 5.0 Consensus size: 21
25619831 CAGGCGAGGT
*
25619841 AGGACTGTAGCCAGGAGATGT
1 AGGACTGTAGCCAGGAGATGA
* * * * *
25619862 AGGGCTGTAACCAGGCGAGGT
1 AGGACTGTAGCCAGGAGATGA
25619883 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
25619904 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
* * * *
25619925 TGGGCTGTAACCAGGGGATGA
1 AGGACTGTAGCCAGGAGATGA
25619946 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.16
Consensus pattern (21 bp):
AGGACTGTAGCCAGGAGATGA
Found at i:25619933 original size:42 final size:42
Alignment explanation
Indices: 25619824--25619945 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
25619814 TGATGTGGGG
* * * *
25619824 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGTAGGG
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* *
25619866 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGAAGGA
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* * * *
25619908 CTGTAGCCAGGAGATGAT-GGGCTGTAACCAGGGGATGA
1 CTGTAACCAGGAGA-GATAGGACTGTAGCCAGGAGATGA
25619946 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.39, T:0.16
Consensus pattern (42 bp):
CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
Found at i:25628934 original size:29 final size:29
Alignment explanation
Indices: 25628891--25628974 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
25628881 TTTAGAAATC
*
25628891 TAAATAATTTAAGGACTAAATTTTAAAAAA
1 TAAA-AATATAAGGACTAAATTTTAAAAAA
** * *
25628921 TAAAAATATAAGGAAAAAATTTCAAATAA
1 TAAAAATATAAGGACTAAATTTTAAAAAA
** *
25628950 -AAAAATATAAAAACTAAATTCTAAA
1 TAAAAATATAAGGACTAAATTTTAAA
25628975 TTTTTGAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
28 19 0.44
29 20 0.47
30 4 0.09
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (29 bp):
TAAAAATATAAGGACTAAATTTTAAAAAA
Found at i:25628968 original size:28 final size:30
Alignment explanation
Indices: 25628905--25628969 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
25628895 TAATTTAAGG
*
25628905 ACTAAATTTTAAAAAATAAAAATATAAGGAA
1 ACTAAATTTCAAAAAATAAAAATATAA-GAA
*
25628936 A--AAATTTCAAATAA-AAAAATATAA-AA
1 ACTAAATTTCAAAAAATAAAAATATAAGAA
25628962 ACTAAATT
1 ACTAAATT
25628970 CTAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 3 0.10
28 15 0.50
29 11 0.37
31 1 0.03
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (30 bp):
ACTAAATTTCAAAAAATAAAAATATAAGAA
Found at i:25631025 original size:1 final size:1
Alignment explanation
Indices: 25631019--25631050 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
25631009 CGGTAGAGGC
25631019 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
25631051 TTGTGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:25639637 original size:31 final size:31
Alignment explanation
Indices: 25639600--25639668 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
25639590 TGGACCCCAA
25639600 AAAGTTTA-AGTACCAACTTAAGAAAAAGTGT
1 AAAGTTTAGA-TACCAACTTAAGAAAAAGTGT
* *
25639631 AAAGTTTAGATACCAAGTTAGGAAAAAGTGT
1 AAAGTTTAGATACCAACTTAAGAAAAAGTGT
*
25639662 CAAGTTT
1 AAAGTTT
25639669 GGGTATCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (31 bp):
AAAGTTTAGATACCAACTTAAGAAAAAGTGT
Found at i:25640520 original size:18 final size:18
Alignment explanation
Indices: 25640481--25640523 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
25640471 GAATAGATTT
*
25640481 TTAATTAAATAATTTTAT
1 TTAATTAAATAATTTTAA
25640499 TTAATTAAA-AATTTTAAA
1 TTAATTAAATAATTTT-AA
25640517 TTAATTA
1 TTAATTA
25640524 TACCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAATAATTTTAA
Found at i:25644031 original size:2 final size:2
Alignment explanation
Indices: 25644024--25644057 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25644014 AGGCAACAAC
25644024 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
25644058 TATATAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:25644437 original size:4 final size:4
Alignment explanation
Indices: 25644428--25644457 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
25644418 TTTGAATTCA
25644428 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
25644458 AAAAGCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:25645078 original size:5 final size:5
Alignment explanation
Indices: 25645070--25645110 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
25645060 GACATCAATT
* *
25645070 AAAAC AAAAAC CAGAC AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
25645111 TCATTTCTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.76, C:0.22, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:25651319 original size:14 final size:13
Alignment explanation
Indices: 25651273--25651335 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
25651263 ACAATAATTA
25651273 TAAAA-ATAAAATT
1 TAAAATATAAAA-T
25651286 TAAAAGTATACCAAAT
1 TAAAA-TATA--AAAT
25651302 TAAAATATAAAGAT
1 TAAAATATAAA-AT
* *
25651316 TAAATTATAAATT
1 TAAAATATAAAAT
25651329 TAAAATA
1 TAAAATA
25651336 GTATAGGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 14 0.33
14 12 0.29
15 7 0.17
16 6 0.14
17 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (13 bp):
TAAAATATAAAAT
Found at i:25653017 original size:28 final size:26
Alignment explanation
Indices: 25652976--25653028 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
25652966 TTTAAAATAC
* *
25652976 TTTTAAAATATTTTTATTTTTATTAT
1 TTTTAAAATATTTTAATGTTTATTAT
25653002 TTTTAAAATAATTTTTAATGTTTATTA
1 TTTTAAAAT-A-TTTTAATGTTTATTA
25653029 AAAAATGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 1 0.04
28 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAAATATTTTAATGTTTATTAT
Found at i:25653029 original size:22 final size:21
Alignment explanation
Indices: 25652991--25653031 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25652981 AAATATTTTT
*
25652991 ATTTTTATTATTTTTAAAATA
1 ATTTTTAATATTTTTAAAATA
*
25653012 ATTTTTAATGTTTATTAAAA
1 ATTTTTAATATTT-TTAAAA
25653032 AATGGGTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTTAATATTTTTAAAATA
Found at i:25656360 original size:26 final size:26
Alignment explanation
Indices: 25656328--25656381 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
25656318 TAACCAAAAT
** *
25656328 ATTATAACTTTTTTTTATTTATCAAA
1 ATTATAAAGTTTTTTTATTTACCAAA
25656354 ATTATAAAGTTTTTTTATTTACCAAA
1 ATTATAAAGTTTTTTTATTTACCAAA
25656380 AT
1 AT
25656382 ATACAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTATAAAGTTTTTTTATTTACCAAA
Found at i:25656411 original size:16 final size:15
Alignment explanation
Indices: 25656392--25656421 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
25656382 ATACAAAAAA
25656392 AAAAACAAAAACCTGC
1 AAAAA-AAAAACCTGC
25656408 AAAAAAAAAACCTG
1 AAAAAAAAAACCTG
25656422 TGATTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAACCTGC
Found at i:25656625 original size:18 final size:18
Alignment explanation
Indices: 25656604--25656638 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25656594 AGTAATAACT
*
25656604 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
25656622 CTATTCTCATTTAATAA
1 CTATTCTAATTTAATAA
25656639 NNNNNNNNNN
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:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:25657575 original size:17 final size:17
Alignment explanation
Indices: 25657553--25657586 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25657543 GGTGCCGCCA
*
25657553 CAGGTTTTTTTTTTTTG
1 CAGGTTTTTGTTTTTTG
25657570 CAGGTTTTTGTTTTTTG
1 CAGGTTTTTGTTTTTTG
25657587 TTTTTGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.68
Consensus pattern (17 bp):
CAGGTTTTTGTTTTTTG
Found at i:25657618 original size:28 final size:28
Alignment explanation
Indices: 25657595--25657656 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
25657585 TGTTTTTGGT
*
25657595 ATATTTTGGTAAATAAAAAATTTTTATA
1 ATATTTTGATAAATAAAAAATTTTTATA
25657623 ATATTTTGATAAATAAAAAA--TTTATA
1 ATATTTTGATAAATAAAAAATTTTTATA
25657649 ATATTTTG
1 ATATTTTG
25657657 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 14 0.42
28 19 0.58
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAATTTTTATA
Found at i:25659596 original size:20 final size:20
Alignment explanation
Indices: 25659573--25659612 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
25659563 AATAAACACC
25659573 AAAAATATAATTTAAAAATAA
1 AAAAAT-TAATTTAAAAATAA
*
25659594 AAAAATTATTTTAAAAATA
1 AAAAATTAATTTAAAAATA
25659613 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTAATTTAAAAATAA
Found at i:25661705 original size:16 final size:16
Alignment explanation
Indices: 25661684--25661722 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
25661674 ATTTTTGTTA
25661684 TAAGAATATTGATTAT
1 TAAGAATATTGATTAT
25661700 TAAGAATATTGATTAT
1 TAAGAATATTGATTAT
25661716 TAAGAAT
1 TAAGAAT
25661723 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (16 bp):
TAAGAATATTGATTAT
Found at i:25661869 original size:18 final size:17
Alignment explanation
Indices: 25661841--25661875 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25661831 ATTATTAAGA
*
25661841 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
25661858 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
25661876 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:25667531 original size:18 final size:20
Alignment explanation
Indices: 25667508--25667569 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
25667498 NNNNNAAAAA
25667508 TATAAAT-TTTT-AAATTTT
1 TATAAATATTTTGAAATTTT
25667526 TATAAATATTTTGAAA--TT
1 TATAAATATTTTGAAATTTT
*
25667544 TAAAAATCATTTTG-AATTTT
1 TATAAAT-ATTTTGAAATTTT
25667564 T-TAAAT
1 TATAAAT
25667570 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 17 0.46
19 14 0.38
20 6 0.16
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATAAATATTTTGAAATTTT
Found at i:25667569 original size:19 final size:18
Alignment explanation
Indices: 25667510--25667569 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
25667500 NNNAAAAATA
*
25667510 TAAAT-TTTTAAATTTTT
1 TAAATATTTTGAATTTTT
* *
25667527 ATAAATATTTTGAAATTTA
1 -TAAATATTTTGAATTTTT
*
25667546 AAAATCATTTTGAATTTTT
1 TAAAT-ATTTTGAATTTTT
25667565 TAAAT
1 TAAAT
25667570 TTATTTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (18 bp):
TAAATATTTTGAATTTTT
Found at i:25669454 original size:11 final size:11
Alignment explanation
Indices: 25669438--25669476 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
25669428 AAAATATAAG
25669438 TTTTTATGAAT
1 TTTTTATGAAT
25669449 TTTTTAT-AAT
1 TTTTTATGAAT
25669459 TTTTT-TGAAT
1 TTTTTATGAAT
25669469 ATTTTTAT
1 -TTTTTAT
25669477 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.04
10 11 0.44
11 12 0.48
12 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (11 bp):
TTTTTATGAAT
Found at i:25669459 original size:10 final size:10
Alignment explanation
Indices: 25669432--25669482 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
25669422 ATTTTAAAAA
*
25669432 TATAAGTTTT
1 TATAATTTTT
25669442 TATGAATTTTT
1 TAT-AATTTTT
25669453 TATAATTTTT
1 TATAATTTTT
25669463 T-TGAATATTTT
1 TAT-AAT-TTTT
25669474 TAT-ATTTTT
1 TATAATTTTT
25669483 AAATTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 5 0.14
10 16 0.44
11 14 0.39
12 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (10 bp):
TATAATTTTT
Found at i:25669467 original size:20 final size:21
Alignment explanation
Indices: 25669432--25669483 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
25669422 ATTTTAAAAA
25669432 TATAAGTTTTTATGAAT-TTTT
1 TATAA-TTTTTATGAATATTTT
*
25669453 TATAATTTTTTTGAATATTTT
1 TATAATTTTTATGAATATTTT
25669474 TAT-ATTTTTA
1 TATAATTTTTA
25669484 AATTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TATAATTTTTATGAATATTTT
Found at i:25674010 original size:249 final size:246
Alignment explanation
Indices: 25673601--25674253 Score: 898
Period size: 250 Copynumber: 2.7 Consensus size: 246
25673591 CCTTTTAATT
*
25673601 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTTC
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
25673666 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACG-------TAT-CAATTTTTATAATTTT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATTTATACAATTTTTA-AATTTT
* *
25673723 TTT--TAAATA-TATGTTTAATTTCAATCAAGTAAGCACTTTACATAATTTTTTTAGAACATTTA
130 TTTAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACATTTA
* *
25673785 GCTTAACATTCTCTTCTACTTAATCTCGCGACGCTTTTGTAACAG-TTCTTC
195 GCTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
* * * ** * *
25673836 AATTTTGCCTGCTCAACTAATAAAACTTTAGCATTGATTTTTTGTTGGTTCACTTTACTTACACC
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
*
25673901 ACCCATTGAAGCGCTCAATGTGAAATTGAGCAATTACGAATTATTATATACTAATTTTTACAATT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATT-TATAC-AATTTTTA-AATT
* *
25673966 TTTTTCAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACCGATTTTTTTTAGAACAT
128 TTTTT-AATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACAT
* * * *
25674031 TTGGCTTAACATTCTCTTCTACTTAATCTTGTGACACTTTTGTCACAGCTTCATC
192 TTAGCTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
* * *
25674086 AATTTTGCCTGCCCAATTTATAAAAATTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCT
1 AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
* * * * *
25674151 ACCCCTTGAAGCACTCGATGTGAAATCGAACAATTACGAATTATTTTGATACCAATTTTTATATT
66 ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTA-TTT-ATA-CAATTTTTAAATT
25674216 TTTTTGAATATATATTATGTTTAATTTCAATCAAGTAA
128 TTTTT-AATATATATTATGTTTAATTTCAATCAAGTAA
25674254 ACTTTATGAC
Statistics
Matches: 363, Mismatches: 37, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
235 94 0.26
243 3 0.01
244 1 0.00
245 17 0.05
248 5 0.01
249 90 0.25
250 139 0.38
251 13 0.04
252 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (246 bp):
AATTTTGCCTGCCCAACTTATAAAACTTTGGCATTGATTTTCGGTTGGTCCACTTTACTTACTCC
ACCCATTGAAGCGCTCGATGTGAAATTGAGCAATTACGAATTATTTATACAATTTTTAAATTTTT
TTAATATATATTATGTTTAATTTCAATCAAGTAAGCACTTTACAGAATTTTTTTAGAACATTTAG
CTTAACATTCTCTTCTACTTAATCTCGCGACACTTTTGTAACAGCTTCATC
Found at i:25683955 original size:17 final size:16
Alignment explanation
Indices: 25683933--25683964 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
25683923 TCAATGTCAT
25683933 AAAAAAAGCAAAAAAAG
1 AAAAAAAG-AAAAAAAG
25683950 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
25683965 CTATACCATG
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:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Found at i:25683964 original size:8 final size:8
Alignment explanation
Indices: 25683933--25683964 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
25683923 TCAATGTCAT
25683933 AAAAAAAG
1 AAAAAAAG
25683941 CAAAAAAAG
1 -AAAAAAAG
25683950 AAAAAAAG
1 AAAAAAAG
25683958 AAAAAAA
1 AAAAAAA
25683965 CTATACCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:25684159 original size:29 final size:29
Alignment explanation
Indices: 25684125--25684217 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
25684115 GAATAGTTAA
25684125 TGACCATTTTGTAACTTTTCATAGTTGGG
1 TGACCATTTTGTAACTTTTCATAGTTGGG
***** *
25684154 TGACCAAAAAAATAA-TTTTACTAATAGTTAGG
1 TGACC-ATTTTGTAACTTTT-C--ATAGTTGGG
* *
25684186 TGATCATTTTGTAACTTTTCATAATTGGG
1 TGACCATTTTGTAACTTTTCATAGTTGGG
25684215 TGA
1 TGA
25684218 TTAAAAAAGA
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
29 19 0.42
30 5 0.11
31 5 0.11
32 16 0.36
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (29 bp):
TGACCATTTTGTAACTTTTCATAGTTGGG
Found at i:25685615 original size:16 final size:17
Alignment explanation
Indices: 25685586--25685625 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
25685576 CGTTTGGTTT
25685586 GCTGTAATCGAATA-AA
1 GCTGTAATCGAATAGAA
25685602 GCTGTAAT-GAAATAGAA
1 GCTGTAATCG-AATAGAA
25685619 -CTGTAAT
1 GCTGTAAT
25685626 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.86
17 2 0.09
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (17 bp):
GCTGTAATCGAATAGAA
Found at i:25688878 original size:15 final size:15
Alignment explanation
Indices: 25688855--25688885 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25688845 TGAAAATGAC
25688855 CTAAAATTTGCAAAT
1 CTAAAATTTGCAAAT
*
25688870 CTAACATTTGCAAAT
1 CTAAAATTTGCAAAT
25688885 C
1 C
25688886 AGCTGTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
CTAAAATTTGCAAAT
Found at i:25690391 original size:24 final size:25
Alignment explanation
Indices: 25690355--25690415 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
25690345 ATAAAAAATA
25690355 ACCAAAATATTAT-CTTTTTTATTT
1 ACCAAAATATTATACTTTTTTATTT
* *
25690379 ACCAAAATGTTATAAATTTTTTTATTT
1 ACCAAAATATTAT--ACTTTTTTATTT
25690406 ACCAAAATAT
1 ACCAAAATAT
25690416 ACAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.39
27 19 0.61
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (25 bp):
ACCAAAATATTATACTTTTTTATTT
Found at i:25690819 original size:20 final size:20
Alignment explanation
Indices: 25690785--25690822 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25690775 ATTTTATTAT
*
25690785 TAAAGTAAATATATTTTACC
1 TAAAGTAAAGATATTTTACC
*
25690805 TAAAGTAAAGCTATTTTA
1 TAAAGTAAAGATATTTTA
25690823 AAAAGTATAA
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:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAAGTAAAGATATTTTACC
Found at i:25691951 original size:19 final size:19
Alignment explanation
Indices: 25691927--25691989 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
25691917 AAGCAATAGT
25691927 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
*** ** * *
25691946 TTATTACTTTTTAATAAAC
1 TTATTAAAGTAAAATAGAG
25691965 TTATTAAAGTAAAATAGAG
1 TTATTAAAGTAAAATAGAG
25691984 TTATTA
1 TTATTA
25691990 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (19 bp):
TTATTAAAGTAAAATAGAG
Found at i:25692525 original size:27 final size:27
Alignment explanation
Indices: 25692463--25692525 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
25692453 TTTTAGTCCT
25692463 GTGCCGCCAATCTCTTTGACACCTTTG
1 GTGCCGCCAATCTCTTTGACACCTTTG
* **
25692490 GT-CAGGCCAATCTCTTTGGTACCTTTG
1 GTGC-CGCCAATCTCTTTGACACCTTTG
25692517 GTGCCGCCA
1 GTGCCGCCA
25692526 CAGTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.14, C:0.32, G:0.22, T:0.32
Consensus pattern (27 bp):
GTGCCGCCAATCTCTTTGACACCTTTG
Found at i:25692595 original size:27 final size:27
Alignment explanation
Indices: 25692541--25692604 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
25692531 TTTTTTTTGT
****
25692541 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAGGGATA
25692568 ATATTTTGGTAAATAAAAAAAGGGATA
1 ATATTTTGGTAAATAAAAAAAGGGATA
*
25692595 ACATTTTGGT
1 ATATTTTGGT
25692605 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGGGATA
Found at i:25693653 original size:22 final size:22
Alignment explanation
Indices: 25693625--25693668 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25693615 TACTCCCCCT
25693625 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
25693647 CATGAGAACATCACATAATATA
1 CATGAGAACATCACATAATATA
25693669 TCATATTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (22 bp):
CATGAGAACATCACATAATATA
Found at i:25695619 original size:27 final size:27
Alignment explanation
Indices: 25695558--25695619 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
25695548 TTTAGTCCTA
*
25695558 TGCCGCCAATCTCTTTGCCACCTTTGG
1 TGCCGCCAATCACTTTGCCACCTTTGG
*
25695585 T-CAGGCCAATCACTTTGCCACCTTTGG
1 TGC-CGCCAATCACTTTGCCACCTTTGG
25695612 TGCCGCCA
1 TGCCGCCA
25695620 CAGGTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.29
Consensus pattern (27 bp):
TGCCGCCAATCACTTTGCCACCTTTGG
Found at i:25695642 original size:17 final size:18
Alignment explanation
Indices: 25695620--25695653 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25695610 GGTGCCGCCA
25695620 CAGGTTTTT-TTTTTTTG
1 CAGGTTTTTGTTTTTTTG
25695637 CAGGTTTTTGTTTTTTT
1 CAGGTTTTTGTTTTTTT
25695654 TGGTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (18 bp):
CAGGTTTTTGTTTTTTTG
Found at i:25695678 original size:27 final size:28
Alignment explanation
Indices: 25695648--25695702 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
25695638 AGGTTTTTGT
*
25695648 TTTTTTTGGT-ATATTTTGATAAATAAA
1 TTTTTTTGATAATATTTTGATAAATAAA
* *
25695675 TTTTTTTTATAATATTTTGGTAAATAAA
1 TTTTTTTGATAATATTTTGATAAATAAA
25695703 AAAAAGGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (28 bp):
TTTTTTTGATAATATTTTGATAAATAAA
Found at i:25696463 original size:57 final size:56
Alignment explanation
Indices: 25696356--25696465 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
25696346 ACCAAATCGA
* **
25696356 ACAAAAAAAAAAGGTACCAAATTAGGGGAAAAAATGTCAAGTTTGGATACCAACTTGG
1 ACAAAAAAAAAAGGTACCAAATTA--GGAAAAAATATCAAGTTCAGATACCAACTTGG
*
25696414 ACAAAAAAAAATTAGGTACCAAATTA-GAAAAAATATCAAGTTCATATACCAA
1 ACAAAAAAAAA--AGGTACCAAATTAGGAAAAAATATCAAGTTCAGATACCAA
25696466 ATGTTATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 22 0.48
58 11 0.24
60 13 0.28
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.20
Consensus pattern (56 bp):
ACAAAAAAAAAAGGTACCAAATTAGGAAAAAATATCAAGTTCAGATACCAACTTGG
Found at i:25699433 original size:15 final size:15
Alignment explanation
Indices: 25699408--25699445 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
25699398 CTAAACTTAT
*
25699408 TTATATAAATTAGTAA
1 TTATTTAAATTA-TAA
25699424 TT-TTTAAATTATAA
1 TTATTTAAATTATAA
25699438 TTATTTAA
1 TTATTTAA
25699446 TATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 13 0.65
16 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATTTAAATTATAA
Found at i:25699942 original size:31 final size:31
Alignment explanation
Indices: 25699906--25699984 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
25699896 AAAAAACAAA
* *
25699906 CAAACTCATGTACCAAACTGAATATTGATG-
1 CAAACTCATGTACCAAACTGAATATTAAAGT
* * *
25699936 CTAAACTCAAGTACCGATCTGAATATTAAAGT
1 C-AAACTCATGTACCAAACTGAATATTAAAGT
25699968 CAAACTCATGTACCAAA
1 CAAACTCATGTACCAAA
25699985 TCGAGAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (31 bp):
CAAACTCATGTACCAAACTGAATATTAAAGT
Found at i:25705058 original size:32 final size:32
Alignment explanation
Indices: 25705004--25705069 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
25704994 CTTGCTTGAA
*
25705004 GACGAAATACGGTTCTTTTCGTGACTTGTTGC
1 GACGAAATACGCTTCTTTTCGTGACTTGTTGC
*
25705036 GACGAAATATGCTT-TTTCTCGTGACTTGTTGC
1 GACGAAATACGCTTCTTT-TCGTGACTTGTTGC
25705068 GA
1 GA
25705070 AATGAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (32 bp):
GACGAAATACGCTTCTTTTCGTGACTTGTTGC
Found at i:25715806 original size:2 final size:2
Alignment explanation
Indices: 25715789--25715824 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
25715779 TCTCTACTGA
* *
25715789 AT AT GT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25715825 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25723406 original size:28 final size:28
Alignment explanation
Indices: 25723374--25723430 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25723364 CAAGAAAAGA
25723374 TAAATTCAAACTCTAGTAACGATATTAT
1 TAAATTCAAACTCTAGTAACGATATTAT
25723402 TAAATTCAAACTCTAGTAACGATATTAT
1 TAAATTCAAACTCTAGTAACGATATTAT
25723430 T
1 T
25723431 GAGAAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAATTCAAACTCTAGTAACGATATTAT
Found at i:25729773 original size:72 final size:72
Alignment explanation
Indices: 25729687--25729830 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
25729677 AACTGCTCCG
*
25729687 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGGCTCAAGCTCAAGTAG
1 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
25729752 GAATGCA
66 GAATGCA
* *
25729759 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAATCAAGCTCAGCCTCAAGCTCAAGTAG
1 AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
25729824 GAATGCA
66 GAATGCA
25729831 TATGAAACAC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (72 bp):
AGCCTTATCAAGCTCAAGCATGAATACATACAAGCTTAACCAAACTCAGCCTCAAGCTCAAGTAG
GAATGCA
Found at i:25730690 original size:192 final size:193
Alignment explanation
Indices: 25730363--25730750 Score: 724
Period size: 192 Copynumber: 2.0 Consensus size: 193
25730353 AAACATCAAT
25730363 CTTCATGCAGGGGCTTCTTGCTTATTGCTTTTTGTTAGGCAAGGCATCATCAAAGAATCAATCTT
1 CTTCATGCAGGGGCTTCTTGCTTATTGCTTTTTGTTAGGCAAGGCATCATCAAAGAATCAATCTT
25730428 TTTCATCTTAATGAAAATCACAAATTAGGCTTTTGCTTGTCAAGTGAAACAAGACCTTTAAACCA
66 TTTCATCTTAATGAAAATCACAAATTAGGCTTTTGCTTGTCAAGTGAAACAAGACCTTTAAACCA
**
25730493 AGAGAGAACAAAGCAAAAAAAAAAAAAAAGAACAAGATAATTATACCAGGG-CACAAACCTTA
131 AGAGAGAACAAAAAAAAAAAAAAAAAAAAGAACAAGATAATTATACCAGGGCCACAAACCTTA
25730555 CTTCATGCAGGGGCTTCTTGCTTATTGCTTTTTGTTAGGCAAGGCATCATCAAAGAATCAATCTT
1 CTTCATGCAGGGGCTTCTTGCTTATTGCTTTTTGTTAGGCAAGGCATCATCAAAGAATCAATCTT
25730620 TTTCATCTTAATGAAAATCACAAATTAGGCTTTTGCTTGTCAAGTGAAACAAGACCTTTAAACCA
66 TTTCATCTTAATGAAAATCACAAATTAGGCTTTTGCTTGTCAAGTGAAACAAGACCTTTAAACCA
* * *
25730685 AGAGAGAACAAAAAAAAAAAAAAAAAAAAGAACATGATAATTATACCAGGGCCACAAGCTTTA
131 AGAGAGAACAAAAAAAAAAAAAAAAAAAAGAACAAGATAATTATACCAGGGCCACAAACCTTA
25730748 CTT
1 CTT
25730751 TACTTATGCA
Statistics
Matches: 190, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
192 178 0.94
193 12 0.06
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (193 bp):
CTTCATGCAGGGGCTTCTTGCTTATTGCTTTTTGTTAGGCAAGGCATCATCAAAGAATCAATCTT
TTTCATCTTAATGAAAATCACAAATTAGGCTTTTGCTTGTCAAGTGAAACAAGACCTTTAAACCA
AGAGAGAACAAAAAAAAAAAAAAAAAAAAGAACAAGATAATTATACCAGGGCCACAAACCTTA
Found at i:25733063 original size:3 final size:3
Alignment explanation
Indices: 25733055--25733089 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
25733045 CGTTCTTTAC
25733055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A
25733090 CATAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:25735279 original size:30 final size:31
Alignment explanation
Indices: 25735219--25735283 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 31
25735209 ACTTAACAAC
25735219 CAAATGCCTCTAAAATAATAAAAAAAAATTAA
1 CAAATGCCTCTAAAATAAT-AAAAAAAATTAA
* *
25735251 CAAATGCCTTTAAAATAAT-AACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAAATTAA
25735281 CAA
1 CAA
25735284 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.42
32 18 0.58
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAAAAAAAATTAA
Found at i:25741182 original size:27 final size:27
Alignment explanation
Indices: 25741152--25741213 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
25741142 CCTATCAGGT
*
25741152 AGGCGTCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
* *
25741179 AGGCACCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
25741206 AGGCGCCA
1 AGGCGCCA
25741214 TTACTAGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.32, T:0.16
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:25743864 original size:40 final size:42
Alignment explanation
Indices: 25743787--25743864 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 42
25743777 GAACCAATTT
* * *
25743787 AAATTATATATTTAAATAGTTTATTTGAATTTAAAATTCAAC
1 AAATTAAATATTTAAATAGATTATTTGAAATTAAAATTCAAC
25743829 AAATTAAAT-TTTAAATA-ATTA-TTGAAATTAGAAATT
1 AAATTAAATATTTAAATAGATTATTTGAAATTA-AAATT
25743865 TATTTTCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 8 0.25
40 8 0.25
41 8 0.25
42 8 0.25
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (42 bp):
AAATTAAATATTTAAATAGATTATTTGAAATTAAAATTCAAC
Found at i:25744884 original size:24 final size:24
Alignment explanation
Indices: 25744856--25744908 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
25744846 TTAGTAGGTC
* * *
25744856 AAATAAACTGTGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
25744880 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
25744904 AAATA
1 AAATA
25744909 TTCTAGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:25745549 original size:13 final size:13
Alignment explanation
Indices: 25745522--25745563 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
25745512 CAGAACTCAA
25745522 GTTTA-AGTTCAAG
1 GTTTAGAGTTC-AG
25745535 GTTTAGA-TTCGAG
1 GTTTAGAGTTC-AG
25745548 GTTTAGAGTTCAG
1 GTTTAGAGTTCAG
25745561 GTT
1 GTT
25745564 CGGGTTCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (13 bp):
GTTTAGAGTTCAG
Found at i:25750761 original size:9 final size:9
Alignment explanation
Indices: 25750747--25750822 Score: 125
Period size: 9 Copynumber: 8.4 Consensus size: 9
25750737 TTTGGTTAAA
25750747 AATTAACCG
1 AATTAACCG
*
25750756 AATTAACCA
1 AATTAACCG
25750765 AATTAACCG
1 AATTAACCG
25750774 AATTAACCG
1 AATTAACCG
25750783 AATTAACCG
1 AATTAACCG
25750792 AATTAACCG
1 AATTAACCG
*
25750801 AATTACCCG
1 AATTAACCG
*
25750810 AATTAACCT
1 AATTAACCG
25750819 AATT
1 AATT
25750823 GAATCATACA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:25752391 original size:19 final size:20
Alignment explanation
Indices: 25752357--25752398 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
25752347 AATTTTTAAT
25752357 TTTATTGTATATTATAATAA
1 TTTATTGTATATTATAATAA
* *
25752377 TTTATTTTA-ATTATAATTA
1 TTTATTGTATATTATAATAA
25752396 TTT
1 TTT
25752399 GAATGTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATTGTATATTATAATAA
Found at i:25755385 original size:329 final size:329
Alignment explanation
Indices: 25754787--25755438 Score: 1286
Period size: 329 Copynumber: 2.0 Consensus size: 329
25754777 GAAAGCGGAC
*
25754787 TTTAACAGAAGCAGAATTCCTTTAATCACTTAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
1 TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
25754852 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
66 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
25754917 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
131 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
25754982 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
196 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
25755047 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
261 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
25755112 TTTT
326 TTTT
*
25755116 TTTAACAGAAGCAGAATTCCTTTGATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
1 TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
25755181 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
66 GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
25755246 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
131 AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
25755311 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
196 ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
25755376 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAA
261 ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAA
25755439 TTTATTATAT
Statistics
Matches: 321, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
329 321 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (329 bp):
TTTAACAGAAGCAGAATTCCTTTAATCACATAAGTTTTCTATTTAATCTTTAATCTTCTTTTGAA
GTTTTTTTTTTCTTTATACAATCAGCCTCTCTATAATAGCCACCCCTATAGTAGTATTTTGTTAT
AACAGTCAGGTTTCTAGTAGAATCGATTTTTTATGTTTTATTTTAACCCTTTATAACAACTTTTT
ACTTATAAAAGCAACAGCCATAGTTATAAAGAACATTCTTTAATAAATTAGTTCTCTATAATAGC
ATATTGTTTAAAATTTTAAGTAAAATTATAGCTATTTTATATAAATAAGCCTATTAATTATAAGT
TTTT
Found at i:25758638 original size:39 final size:39
Alignment explanation
Indices: 25758579--25758657 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
25758569 TTCTTATATT
25758579 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
1 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
* *
25758618 AAAATTCGAATCTAGTAGTCTTGAGTTTTAAGGTGTTCA
1 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
25758657 A
1 A
25758658 GAAAATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (39 bp):
AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTCA
Found at i:25760692 original size:24 final size:22
Alignment explanation
Indices: 25760647--25760693 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
25760637 TGTTGAAATA
**
25760647 ATATTTAATTTACTTATTTATT
1 ATATTTAATTTACTTAAATATT
25760669 ATATTATATATTTACTTAAATATT
1 ATATT-TA-ATTTACTTAAATATT
25760693 A
1 A
25760694 AGTAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 14 0.67
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTAATTTACTTAAATATT
Found at i:25760720 original size:99 final size:100
Alignment explanation
Indices: 25760549--25760765 Score: 393
Period size: 99 Copynumber: 2.2 Consensus size: 100
25760539 TTTCTTTCTT
25760549 TATTTAATTTACTTATTTATTATATTATATATTTACTTAAATATTAAGTAATATTATCTTTACAC
1 TATTTAATTTACTTATTTATTATATTATATATTTACTTAAATATTAAGTAATATTATCTTTACAC
25760614 ATGTAATCACTATTACCATCCAC-TGTTGAAATAA
66 ATGTAATCACTATTACCATCCACTTGTTGAAATAA
25760648 TATTTAATTTACTTATTTATTATATTATATATTTACTTAAATATTAAGTAATATTATCTTTACAC
1 TATTTAATTTACTTATTTATTATATTATATATTTACTTAAATATTAAGTAATATTATCTTTACAC
25760713 ATGTAATCACTATTACCATCCACTTGTTGAAATAA
66 ATGTAATCACTATTACCATCCACTTGTTGAAATAA
** *
25760748 GGTTTAA-TTGCTTATTTA
1 TATTTAATTTACTTATTTA
25760766 GTCCCTTTAC
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
99 98 0.86
100 16 0.14
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (100 bp):
TATTTAATTTACTTATTTATTATATTATATATTTACTTAAATATTAAGTAATATTATCTTTACAC
ATGTAATCACTATTACCATCCACTTGTTGAAATAA
Found at i:25763605 original size:4 final size:4
Alignment explanation
Indices: 25763596--25763626 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
25763586 TTAAAACTTC
25763596 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
25763627 CCTGCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Done.