Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 131 of 208
Found at i:42980061 original size:23 final size:22
Alignment explanation
Indices: 42980031--42980074 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42980021 CCCGTATAAT
*
42980031 GAAATTTATTTATTTATTGTTAG
1 GAAATTTAATTATTTA-TGTTAG
*
42980054 GAAATTTAATTGTTTATGTTA
1 GAAATTTAATTATTTATGTTA
42980075 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
GAAATTTAATTATTTATGTTAG
Found at i:42980254 original size:43 final size:42
Alignment explanation
Indices: 42980206--42980516 Score: 333
Period size: 43 Copynumber: 7.3 Consensus size: 42
42980196 ATGGCACTTT
* * *
42980206 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTT-TGATCTA
* * *
42980249 TAGCGGCGTTCGT-AGGAGAAGCGTCGCTAACGGTCTTGATCTA
1 TAGCGGCGTTTGTGA-GAAAAGCGTCGCTAAAGGT-TTGATCTA
* * *
42980292 TAGTGGCGTTTGTGGGAAAAGCGTCACTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGT-TTGATCTA
* * *
42980335 TAGCGGCATTTGTGGGAAAAGCG-CTGCGAAAGGTTTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGTC-GCTAAAGG-TTTGATCTA
*
42980378 TAGCGGCGTTTGTCGA-AAAAGCGTCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGT-GAGAAAAGCGTCGCTAAAGGT-TTGATCTA
*
42980421 TAGCGGCGTTTGTG-GGAAAGCGTCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGT-TTGATCTA
* * * * *
42980463 TAGTGACGTTTGTGAGAAAAGCGCCGCTAAAGGTCCTGATCTT
1 TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGT-TTGATCTA
42980506 TAGCGGCGTTT
1 TAGCGGCGTTT
42980517 ATTTCTTTTG
Statistics
Matches: 228, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
42 41 0.18
43 183 0.80
44 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTTTGATCTA
Found at i:42980357 original size:86 final size:86
Alignment explanation
Indices: 42980210--42980516 Score: 395
Period size: 86 Copynumber: 3.6 Consensus size: 86
42980200 CACTTTTAGC
* ** * * *
42980210 GGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTATAGCGGCGTTCGTAGGAGAAGCGTCG
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGTCG
*
42980275 CTAACGGTCTTGATCTATAGT
66 CTAAAGGTCTTGATCTATAGT
** * * * *
42980296 GGCGTTTGTGGGAAAAGCGTCACTAAAGGTCTTGATCTATAGCGGCATTTGTGGGAAAAGCG-CT
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGTC-
* * *
42980360 GCGAAAGGTTTTGATCTATAGC
65 GCTAAAGGTCTTGATCTATAGT
*
42980382 GGCGTTTGTCG-AAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG-AAAGCGTC
1 GGCGTTTGT-GAAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGTC
42980445 GCTAAAGGTCTTGATCTATAGT
65 GCTAAAGGTCTTGATCTATAGT
* * *
42980467 GACGTTTGTGAGAAAAGCGCCGCTAAAGGTCCTGATCTTTAGCGGCGTTT
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
42980517 ATTTCTTTTG
Statistics
Matches: 191, Mismatches: 26, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
84 1 0.01
85 70 0.37
86 119 0.62
87 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (86 bp):
GGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGTCG
CTAAAGGTCTTGATCTATAGT
Found at i:42980436 original size:129 final size:128
Alignment explanation
Indices: 42980206--42980516 Score: 433
Period size: 129 Copynumber: 2.4 Consensus size: 128
42980196 ATGGCACTTT
* * * * *
42980206 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTATAGCGGCGTTCGTAGGAGAAGC
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTATGATCTATAGCGGCGTTTGTAGAAAAAGC
* * *
42980271 GTCGCTAACGGTCTTGATCTATAGTGGCGTTTGTGGGAAAAGCGTCACTAAAGGTCTTGATCTA
66 GTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG-AAAGCGTCACTAAAGGTCTTGATCTA
* * * * * *
42980335 TAGCGGCATTTGTGGGAAAAGCGCTGCGAAAGGTTTTGATCTATAGCGGCGTTTGTCGAAAAAGC
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTATGATCTATAGCGGCGTTTGTAGAAAAAGC
*
42980400 GTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAGCGTCGCTAAAGGTCTTGATCTA
66 GTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAGCGTCACTAAAGGTCTTGATCTA
* * ** *
42980463 TAGTGACGTTTGTGAGAAAAGCGCCGCTAAAGGTCCTGATCTTTAGCGGCGTTT
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTATGATCTATAGCGGCGTTT
42980517 ATTTCTTTTG
Statistics
Matches: 158, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
128 70 0.44
129 88 0.56
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (128 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTATGATCTATAGCGGCGTTTGTAGAAAAAGC
GTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAGCGTCACTAAAGGTCTTGATCTA
Found at i:42980611 original size:22 final size:21
Alignment explanation
Indices: 42980565--42980611 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
42980555 TTTAGCGGCG
* * *
42980565 CTAAAAAATGCCGCTAAAGGT
1 CTAAAAAACGCCGCTAAAAGC
42980586 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
42980608 CTAA
1 CTAA
42980612 TTTGGTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:42982503 original size:79 final size:78
Alignment explanation
Indices: 42982314--42982505 Score: 240
Period size: 79 Copynumber: 2.4 Consensus size: 78
42982304 AGTGGCACAC
* * *
42982314 AATCACATTTTGGGATTGATTCCCATCGTTCAACGATTTTATTCCAAAATATTTTTATTTCAAAA
1 AATCA-ATTTCGGGATTGATTCCCACCGTTCAACGATGTTATTCCAAAATATTTTTATTTCAAAA
*
42982379 AATGAGTAAAATAA
65 AACGAGTAAAATAA
** * * * * *
42982393 AATCCGTTTCGGGATTGATTCCCGCTGTTCAACGATGTTATTCCAAATTTTGTTTTATTTCCAAA
1 AATCAATTTCGGGATTGATTCCCACCGTTCAACGATGTTATTCCAAAATAT-TTTTATTTCAAAA
42982458 AACGAGTAAAATAA
65 AACGAGTAAAATAA
* * *
42982472 AATCAATTTCGGGATTGACTCCTACCATTCAACG
1 AATCAATTTCGGGATTGATTCCCACCGTTCAACG
42982506 GATTATTACA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 38 0.40
79 56 0.60
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (78 bp):
AATCAATTTCGGGATTGATTCCCACCGTTCAACGATGTTATTCCAAAATATTTTTATTTCAAAAA
ACGAGTAAAATAA
Found at i:42982572 original size:85 final size:86
Alignment explanation
Indices: 42982464--42982658 Score: 216
Period size: 86 Copynumber: 2.3 Consensus size: 86
42982454 CAAAAACGAG
* * * **
42982464 TAAAATAAAATCAATTTCGGGATTGACTCCTACC-ATTCA-ACGGA-TTATTACATTTTGATTTT
1 TAAAATAAAATCTATTTCGGGATTGACTCCCACCGATTAATAAAGATTTATTACA-TTTGATTTT
42982526 GTTGCCAAAAATGAAAAATTAAA
65 -TTGCCAAAAATGAAAAATTAAA
* * * * * * **
42982549 TTAAATAAAATCTGTTTCAGGATTTATTCCCACCGTTTAATAAAGATTTATTGTATTTGATTTTT
1 TAAAATAAAATCTATTTCGGGATTGACTCCCACCGATTAATAAAGATTTATTACATTTGATTTTT
* *
42982614 TGCCAGAAATGAGAAATTAAA
66 TGCCAAAAATGAAAAATTAAA
42982635 TAAAATAAAATCTATTTCGGGATT
1 TAAAATAAAATCTATTTCGGGATT
42982659 TATTCCTATC
Statistics
Matches: 89, Mismatches: 18, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
85 27 0.30
86 44 0.49
87 12 0.13
88 6 0.07
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (86 bp):
TAAAATAAAATCTATTTCGGGATTGACTCCCACCGATTAATAAAGATTTATTACATTTGATTTTT
TGCCAAAAATGAAAAATTAAA
Found at i:42982757 original size:83 final size:85
Alignment explanation
Indices: 42982517--42982768 Score: 285
Period size: 86 Copynumber: 3.0 Consensus size: 85
42982507 ATTATTACAT
* * *
42982517 TTTGATTTTGTTGCCAAAAATGAAAAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCCAC
1 TTTGATTTT-TTGCC-AAAATGACAAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCAC
*
42982582 CGTTTAATAAAGA-TTTATTGTA
64 CGTTTAA-CAAGATTTTATTGTA
* * * *
42982604 TTTGATTTTTTGCCAGAAATGAGAAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCTATC
1 TTTGATTTTTTGCCA-AAATGACAAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCACC
* *
42982669 GTTTAACAAGATTTTCTTTTA
65 GTTTAACAAGATTTTATTGTA
* * * * * * * *
42982690 TTTTATTTTTTTCC-AAAT-TCAAATTGAATTAAATAAAATTTATTTCGGGATTTGTTCCCGCCA
1 TTTGATTTTTTGCCAAAATGACAAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCACCG
42982753 TTTAACAAGATTTTAT
66 TTTAACAAGATTTTAT
42982769 CGATATTATC
Statistics
Matches: 141, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
83 50 0.35
84 4 0.03
85 5 0.04
86 73 0.52
87 9 0.06
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (85 bp):
TTTGATTTTTTGCCAAAATGACAAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCACCG
TTTAACAAGATTTTATTGTA
Found at i:42982786 original size:83 final size:83
Alignment explanation
Indices: 42982541--42982789 Score: 202
Period size: 83 Copynumber: 3.0 Consensus size: 83
42982531 CAAAAATGAA
* * * * * *
42982541 AAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCCACCGTTTAATAAAGA-TTT-ATTG-T
1 AAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCCACCATTTAA-CAAGATTTTCATCGAT
**
42982603 ATTTGATTT-TTTGCCAGAAATGAG
65 A-TT-ATTTGTTT-CC--AAAT-TC
* * * * ** *
42982627 AAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCTATCGTTTAACAAGATTTTCTTTTATT
1 AAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCCACCATTTAACAAGATTTTCATCGATA
*
42982692 TTATTTTTTTCCAAATTC
66 TTATTTGTTTCCAAATTC
* * * * *
42982710 AAATTGAATTAAATAAAATTTATTTCGGGATTTGTTCCCGCCATTTAACAAGATTTT-ATCGATA
1 AAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCCACCATTTAACAAGATTTTCATCGATA
42982774 TTATCTTGTTTCCAAA
66 TTAT-TTGTTTCCAAA
42982790 CAAATACGTA
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
82 7 0.05
83 59 0.44
84 4 0.03
85 4 0.03
86 52 0.39
87 7 0.05
88 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (83 bp):
AAATTAAATAAAATAAAATCTATTTCGGGATTTATTCCCACCATTTAACAAGATTTTCATCGATA
TTATTTGTTTCCAAATTC
Found at i:42982807 original size:83 final size:81
Alignment explanation
Indices: 42982637--42982848 Score: 196
Period size: 83 Copynumber: 2.6 Consensus size: 81
42982627 AAATTAAATA
* ** * * ** * *
42982637 AAATAAAATCTATTTCGGGATTTATTCCTATCGTTTAACAAGATTTTCTTTTATTTTATTTTTTT
1 AAATAAAATTTATTTCGGGATTTATTCCCGTCATTTAACAAGATTTT-ATCGATATTATTTGTTT
* *
42982702 CCAAATTCAAATTGAATT
65 CCAAA-TCAAATCGAATC
* *
42982720 AAATAAAATTTATTTCGGGATTTGTTCCCGCCATTTAACAAGATTTTATCGATATTATCTTGTTT
1 AAATAAAATTTATTTCGGGATTTATTCCCGTCATTTAACAAGATTTTATCGATATTAT-TTGTTT
42982785 CCAAA-CAAATACGTAATC
65 CCAAATCAAAT-CG-AATC
* * ** *
42982803 AAAT-AATTTTGTTTCGAAATTTATTCCCGTCATTTAA-TAGATTTTA
1 AAATAAAATTTATTTCGGGATTTATTCCCGTCATTTAACAAGATTTTA
42982849 ATTTGATTTA
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
81 13 0.12
82 35 0.33
83 58 0.55
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (81 bp):
AAATAAAATTTATTTCGGGATTTATTCCCGTCATTTAACAAGATTTTATCGATATTATTTGTTTC
CAAATCAAATCGAATC
Found at i:42989136 original size:100 final size:100
Alignment explanation
Indices: 42988962--42989160 Score: 317
Period size: 100 Copynumber: 2.0 Consensus size: 100
42988952 CCAATTTTTT
* * * *
42988962 CTTAATCGTAAATTAACCATAGGAACCACCTAACAATTAAGCCTTATCAAACAAATAGCCCCGAA
1 CTTAATCGTAAATTAACCACAGGAAACACATAACAATTAAGCCTTATCAAACAAATAGCCCCAAA
* * *
42989027 ATTCGCTTCCATGGTTTAATCCTTCTGGAACCTTC
66 AGTCACTTCCATGGTTTAATCCTTCTGCAACCTTC
* *
42989062 CTTAATCGTAAATTAATCACAGGAAACACATGACAATTAAGCCTTATCAAACAAATAGCCCCAAA
1 CTTAATCGTAAATTAACCACAGGAAACACATAACAATTAAGCCTTATCAAACAAATAGCCCCAAA
42989127 AGTCACTTCCATGGTTTAATCCTTCTGCAACCTT
66 AGTCACTTCCATGGTTTAATCCTTCTGCAACCTT
42989161 GCGAACTATA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.28
Consensus pattern (100 bp):
CTTAATCGTAAATTAACCACAGGAAACACATAACAATTAAGCCTTATCAAACAAATAGCCCCAAA
AGTCACTTCCATGGTTTAATCCTTCTGCAACCTTC
Found at i:42996173 original size:28 final size:27
Alignment explanation
Indices: 42996098--42996200 Score: 77
Period size: 26 Copynumber: 3.8 Consensus size: 27
42996088 TTGTCAAAAA
* * * *
42996098 TATAACAAATATATATGTGTATATAAAT
1 TATAA-AATTATATAAGTATATATATAT
* *
42996126 TATAAAATATATGTAA--ATATATGTAT
1 TATAAAAT-TATATAAGTATATATATAT
*
42996152 TATAAAATGTATATAAGTATATGTATAT
1 TATAAAAT-TATATAAGTATATATATAT
* *
42996180 TTTAAGATTATA-AAGTATATA
1 TATAAAATTATATAAGTATATA
42996201 CAAGAAAAGA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
26 29 0.49
27 6 0.10
28 24 0.41
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.42
Consensus pattern (27 bp):
TATAAAATTATATAAGTATATATATAT
Found at i:42996174 original size:26 final size:26
Alignment explanation
Indices: 42996124--42996177 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
42996114 GTGTATATAA
*
42996124 ATTATAAAATATATGTAAATATATGT
1 ATTATAAAATATATATAAATATATGT
* *
42996150 ATTATAAAATGTATATAAGTATATGT
1 ATTATAAAATATATATAAATATATGT
42996176 AT
1 AT
42996178 ATTTTAAGAT
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:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (26 bp):
ATTATAAAATATATATAAATATATGT
Found at i:42998170 original size:44 final size:44
Alignment explanation
Indices: 42998110--42998534 Score: 246
Period size: 44 Copynumber: 9.8 Consensus size: 44
42998100 TCATTGTTTT
*
42998110 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * *
42998154 AATCTGCCCCATTGCAACTTCAGGGGGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * *
42998198 AATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTA-TGGTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTAGCTTC
* * * * * * **
42998242 AATCCGCTTCATTGCAACTTCAGGGAAATATGATTGGTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * * * *
42998286 TATCTGCTCCACCGTAACTTCAGGGAGATAAGACT-G--GATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * * * *
42998327 GATCTGCTCTACTGCAACTTTAGAGAGATAAGATCT-GT-GTTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TAGTAG-CTTC
* * **
42998371 AATC-GACTCCACTGCAAC-TCTAGAGAGATAGGATTGGTTTCTTC
1 AATCTG-CTCCACTGCAACTTC-AGGGAGATAGGATTAGTAGCTTC
** * * * *
42998415 TGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAG-A--TGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
* * * * *
42998456 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-GT-GTTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TAGTAG-CTTC
* * **
42998500 AATCTGCTCTACTACAACTTCAAAGAGATAGGATT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATT
42998535 GGTTTCTTCG
Statistics
Matches: 293, Mismatches: 72, Indels: 33
0.74 0.18 0.08
Matches are distributed among these distances:
41 60 0.20
42 3 0.01
43 8 0.03
44 216 0.74
45 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
Found at i:42998387 original size:129 final size:130
Alignment explanation
Indices: 42998074--42998551 Score: 531
Period size: 129 Copynumber: 3.7 Consensus size: 130
42998064 TTAATCCGAC
* * *
42998074 CTACTGCAACTTCAGAGATATATGATTCAT-TG-TTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 CTACTGCAACTTCAGAGAGATAAGA-TCATGTGTTTTTAATCCGCTCCACTGCAACTTCAGAGAG
* ** * * * * * * * * *
42998137 ATAGGATTAGTAGCTTCAATCTGCCCCATTGCAACTTCAGGGGGATAGGATTAGTAGCTTCAATC
65 ATAGGATTGGTTTCTTCTATCTGCTCCACTGTAACTTCAGGGAGATAAGACT-G--GATGCAATC
42998202 TGCT
127 TGCT
* * * * * * * *
42998206 CCACTGTAACTTCAGGGAGATAAGACTTATG-G-TTTTAATCCGCTTCATTGCAACTTCAGGGAA
1 CTACTGCAACTTCAGAGAGATAAGA-TCATGTGTTTTTAATCCGCTCCACTGCAACTTCAGAGAG
* * *
42998269 ATATGATTGGTTTCTTCTATCTGCTCCACCGTAACTTCAGGGAGATAAGACTGGATGCGATCTGC
65 ATAGGATTGGTTTCTTCTATCTGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGCAATCTGC
42998334 T
130 T
*
42998335 CTACTGCAACTTTAGAGAGATAAGATC-TGTGTTTTTAAT-CGACTCCACTGCAAC-TCTAGAGA
1 CTACTGCAACTTCAGAGAGATAAGATCATGTGTTTTTAATCCG-CTCCACTGCAACTTC-AGAGA
* *
42998397 GATAGGATTGGTTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCAATCTG
64 GATAGGATTGGTTTCTTCTATCTGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGCAATCTG
42998462 CT
129 CT
* * * *
42998464 CTACTGCAACTTCAGAGAGATAAGATC-TGTGTTTTTAATCTGCTCTACTACAACTTCAAAGAGA
1 CTACTGCAACTTCAGAGAGATAAGATCATGTGTTTTTAATCCGCTCCACTGCAACTTCAGAGAGA
*
42998528 TAGGATTGGTTTCTTCGATCTGCT
66 TAGGATTGGTTTCTTCTATCTGCT
42998552 TCGCTGCCAA
Statistics
Matches: 293, Mismatches: 46, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
127 2 0.01
128 6 0.02
129 189 0.65
130 3 0.01
131 1 0.00
132 92 0.31
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (130 bp):
CTACTGCAACTTCAGAGAGATAAGATCATGTGTTTTTAATCCGCTCCACTGCAACTTCAGAGAGA
TAGGATTGGTTTCTTCTATCTGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGCAATCTGCT
Found at i:43003415 original size:26 final size:26
Alignment explanation
Indices: 43003367--43003420 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
43003357 GTGTATATAA
* *
43003367 ATTATAAAATATATGTAAATATATGT
1 ATTATAAAATATATATAAATATACGT
* *
43003393 ATTATAAAATGTATATAAGTATACGT
1 ATTATAAAATATATATAAATATACGT
43003419 AT
1 AT
43003421 ATTTTAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (26 bp):
ATTATAAAATATATATAAATATACGT
Found at i:43013574 original size:16 final size:16
Alignment explanation
Indices: 43013549--43013579 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43013539 AAAGAAAATA
*
43013549 TTTTTCAAAAATTAAT
1 TTTTTAAAAAATTAAT
43013565 TTTTTAAAAAATTAA
1 TTTTTAAAAAATTAA
43013580 ATAAATCCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTAAAAAATTAAT
Found at i:43013832 original size:79 final size:80
Alignment explanation
Indices: 43013652--43013906 Score: 280
Period size: 79 Copynumber: 3.1 Consensus size: 80
43013642 TAAAAGTACG
* * * * *
43013652 TAAAATCCGTTACGGGATTGATTCCCACCGTTCAACGAATTTTATTCCATTATTTTGATTTTATT
1 TAAAATCCATTTCGAGATTAATTCCCACCGTTCAACG-ATTTTATTCCA-AATTTTG-TTTTATT
*
43013717 TCCAAACGGGAAATTAAAG-ATAAA
63 TCCAAA----AAA--CAAGCA-AAA
* *
43013741 TAAAATCTATTTCGAGATTAATTCCCACTGTTCAACGATTTTATTCCAAATTTTGTTTTATTT-C
1 TAAAATCCATTTCGAGATTAATTCCCACCGTTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
*
43013805 AAAAAACGAGCAAAA
66 AAAAAACAAGCAAAA
* * **
43013820 TAAAATCCATTTCGGGATTCATTCCTGCCGTTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
1 TAAAATCCATTTCGAGATTAATTCCCACCGTTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
*
43013885 AAAAAACAAGTAAAA
66 AAAAAACAAGCAAAA
43013900 TAAAATC
1 TAAAATC
43013907 TGTTTTAGGA
Statistics
Matches: 147, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
79 62 0.42
80 22 0.15
81 3 0.02
85 4 0.03
86 8 0.05
87 6 0.04
88 11 0.07
89 31 0.21
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (80 bp):
TAAAATCCATTTCGAGATTAATTCCCACCGTTCAACGATTTTATTCCAAATTTTGTTTTATTTCC
AAAAAACAAGCAAAA
Found at i:43013944 original size:80 final size:79
Alignment explanation
Indices: 43013771--43013941 Score: 236
Period size: 80 Copynumber: 2.1 Consensus size: 79
43013761 ATTCCCACTG
* *
43013771 TTCAACGATTTTATTCCAAATTTTGTTTTATTTCAAAAAACGAGCAAAATAAAATCCATTTCGGG
1 TTCAACGATTTTATTCCAAATTTTGTTTTATTTCAAAAAACAAGCAAAATAAAATCCATTTCAGG
*
43013836 ATTCATTCCTGCCG
66 ATTCATTCCTGCCA
* ** *
43013850 TTCAACGATTTTATTCCAAATTTTGTTTTATTTCCAAAAAACAAGTAAAATAAAATCTGTTTTAG
1 TTCAACGATTTTATTCCAAATTTTGTTTTATTT-CAAAAAACAAGCAAAATAAAATCCATTTCAG
*
43013915 GATTGATT-CTCGCCA
65 GATTCATTCCT-GCCA
43013930 TTCAACGGATTT
1 TTCAAC-GATTT
43013942 ATTACATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 35 0.43
80 41 0.51
81 5 0.06
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (79 bp):
TTCAACGATTTTATTCCAAATTTTGTTTTATTTCAAAAAACAAGCAAAATAAAATCCATTTCAGG
ATTCATTCCTGCCA
Found at i:43014003 original size:85 final size:84
Alignment explanation
Indices: 43013897--43014093 Score: 227
Period size: 84 Copynumber: 2.3 Consensus size: 84
43013887 AAAACAAGTA
* * * * *
43013897 AAATAAAATCTGTTTTAGGATTGATTCTCGCCA-TTCA-ACGGATTTATTACATTTTGATTTTGT
1 AAATAAAATCTGTTTTGGGATTTATTCTCACCATTTAATAAGGATTTATTACA-TTTGATTTTGT
*
43013960 TGCCAAAATGAGAAATAAAATT
65 TGCCAAAA--AAAAATAAAATT
* * * * **
43013982 AAATAGAATCTGTTTCGGGATTTATTCCCACCATTTAATAATGATTTATTTGATTTGATTTTGTT
1 AAATAAAATCTGTTTTGGGATTTATTCTCACCATTTAATAAGGATTTATTACATTTGATTTTGTT
* *
43014047 TCCAAAAAAAAATTAAATT
66 GCCAAAAAAAAATAAAATT
43014066 AAATAAAATCTGTTTTGGGATTTATTCT
1 AAATAAAATCTGTTTTGGGATTTATTCT
43014094 TATAACAACC
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
84 35 0.38
85 27 0.29
86 21 0.23
87 10 0.11
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (84 bp):
AAATAAAATCTGTTTTGGGATTTATTCTCACCATTTAATAAGGATTTATTACATTTGATTTTGTT
GCCAAAAAAAAATAAAATT
Found at i:43015394 original size:24 final size:25
Alignment explanation
Indices: 43015362--43015409 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
43015352 AAATGACATG
*
43015362 TCATTAGAGATTACTGATT-TCAGA
1 TCATGAGAGATTACTGATTCTCAGA
* *
43015386 TCATGAGAGCTTATTGATTCTCAG
1 TCATGAGAGATTACTGATTCTCAG
43015410 CTCGTATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (25 bp):
TCATGAGAGATTACTGATTCTCAGA
Found at i:43015420 original size:25 final size:25
Alignment explanation
Indices: 43015392--43015470 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
43015382 CAGATCATGA
*
43015392 GAGCTTATTGATTCTCAGCTCGTAT
1 GAGCTTATCGATTCTCAGCTCGTAT
*
43015417 GAGCTTATCGATT-TCAGCTTGTGA-
1 GAGCTTATCGATTCTCAGCTCGT-AT
* * *
43015441 GAGCTTACCGATTCTTAGCTCATAT
1 GAGCTTATCGATTCTCAGCTCGTAT
43015466 GAGCT
1 GAGCT
43015471 GACAGATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 21 0.47
25 24 0.53
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (25 bp):
GAGCTTATCGATTCTCAGCTCGTAT
Found at i:43015444 original size:24 final size:25
Alignment explanation
Indices: 43015389--43015461 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
43015379 TTTCAGATCA
*
43015389 TGAGAGCTTATTGATTCTCAGCTCG
1 TGAGAGCTTATCGATTCTCAGCTCG
*
43015414 T-ATGAGCTTATCGATT-TCAGCTTG
1 TGA-GAGCTTATCGATTCTCAGCTCG
* *
43015438 TGAGAGCTTACCGATTCTTAGCTC
1 TGAGAGCTTATCGATTCTCAGCTC
43015462 ATATGAGCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 21 0.52
25 19 0.47
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (25 bp):
TGAGAGCTTATCGATTCTCAGCTCG
Found at i:43015454 original size:49 final size:49
Alignment explanation
Indices: 43015389--43015519 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 49
43015379 TTTCAGATCA
** * * * *
43015389 TGAGAGCTTATTGATTCTCAGCTCGTATGAGCTTATC-GATTT-CAGCTTG
1 TGAGAGCTTACCGATTCT-AGCTCATATGAGCTGA-CAGATTTACAACTCG
43015438 TGAGAGCTTACCGATTCTTAGCTCATATGAGCTGACAGATTTACAACTCG
1 TGAGAGCTTACCGATTC-TAGCTCATATGAGCTGACAGATTTACAACTCG
*
43015488 TGAGAGCATACCGATTCATAGCTCATATGAGC
1 TGAGAGCTTACCGATTC-TAGCTCATATGAGC
43015520 ATACATGTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.48
50 36 0.51
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (49 bp):
TGAGAGCTTACCGATTCTAGCTCATATGAGCTGACAGATTTACAACTCG
Found at i:43015519 original size:25 final size:25
Alignment explanation
Indices: 43015441--43015523 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
43015431 CAGCTTGTGA
* *
43015441 GAGCTTACCGATTCTTAGCTCATAT
1 GAGCATACCGATTCATAGCTCATAT
* * * * *
43015466 GAGC-TGACAGATTTACAACTCGTGA-
1 GAGCAT-ACCGATTCATAGCTCAT-AT
43015491 GAGCATACCGATTCATAGCTCATAT
1 GAGCATACCGATTCATAGCTCATAT
43015516 GAGCATAC
1 GAGCATAC
43015524 ATGTACAAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
24 2 0.05
25 39 0.91
26 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (25 bp):
GAGCATACCGATTCATAGCTCATAT
Found at i:43017298 original size:20 final size:20
Alignment explanation
Indices: 43017273--43017311 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43017263 TACTTTATTC
43017273 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
43017293 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
43017312 AAATAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:43017656 original size:50 final size:50
Alignment explanation
Indices: 43017602--43017708 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
43017592 ACATGAGAGT
* * * * *
43017602 TCTCATATCGGTGCCCATGCCATGTCCCTGACATTGTCTTACGGGGGACC
1 TCTCATATAGGTACCAACGCCATGTCCCAGACATTGTCTTACGGGGGACC
* *
43017652 TCTCATCTAGGTACCAACGCCATGTCCCAGACATTGTCTTACGTGGGACC
1 TCTCATATAGGTACCAACGCCATGTCCCAGACATTGTCTTACGGGGGACC
43017702 TCTCATA
1 TCTCATA
43017709 ACCTCAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.28
Consensus pattern (50 bp):
TCTCATATAGGTACCAACGCCATGTCCCAGACATTGTCTTACGGGGGACC
Found at i:43019029 original size:348 final size:340
Alignment explanation
Indices: 43018393--43019084 Score: 1154
Period size: 348 Copynumber: 2.0 Consensus size: 340
43018383 AATATGAACC
* *
43018393 CTAACATGAATTAGCGGTAGAATAAGCTAAACTGAGCTACGAGGACTCCAAAAACGTAAAAAAAA
1 CTAACATGAATTAACGGTAGAATAAGCTAAACCGAGCTACGAGGACTCCAAAAACGTAAAAAAAA
*
43018458 CATTAAAAAACGGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGATGAAACCCTAGCTATG
66 CATTAAAAAACGGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGAAGAAACCCTAGCTATG
43018523 GAGTCCCTTGAAGTTTCGGCCCTTATGCAAGAAGATGAGCATCTTTTTCCCTTTAATTCTTTTTA
131 GAGTCCCTTGAAGTTTCGGCCCTTATGCAAGAAGATGAGCATCTTTTTCCCTTTAATTCTTTTTA
*
43018588 TTACCAAATGACTAAAATGCCCTTCATTAAAACTTTTGTTATTTTTATCTATGCATGCCCATTTT
196 TTACCAAATGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCATGCCCATTTT
* * *
43018653 TGTCAATAAAAATCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATTATGCACTTCTAT
261 TGTCAATAAAAACCTAATGGTATAATTACCATTTAAGGACCTCTACTTCAATAATGCACTTCTAT
*
43018718 TAAATCCTTTATCAT
326 TAAATCATTTATCAT
*
43018733 CTAACATGAATTAATGGTAGAATAAGCTAAACCGAGCTACGAGGACTCCAAAAACGT-AAAAAAA
1 CTAACATGAATTAACGGTAGAATAAGCTAAACCGAGCTACGAGGACTCCAAAAACGTAAAAAAAA
43018797 CATT-AAAAACGGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGAAGAAACCCTAGCTATG
66 CATTAAAAAACGGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGAAGAAACCCTAGCTATG
*
43018861 GAGTCCCTTGAAGTTTCGGCCCTTATGGAAGAAGATGAGCAAATTTTGCCATCTTTTTCCCTTTA
131 GAGTCCCTTGAAGTTTCGGCCCTTATGCAAGAAGAT--G---A----G-CATCTTTTTCCCTTTA
*
43018926 ATTCTTTTTATTACCAAATGACTAAAATGGCCTTCATTAAAACTTTAGTTATTTTTATCTATGCA
186 ATTCTTTTTATTACCAAATGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCA
* * *
43018991 TGCCCATTTTTGTCCATGAAAACCTAATGGTATAATTACCATTTAAGGAGCTCTACTTCAATAAT
251 TGCCCATTTTTGTCAATAAAAACCTAATGGTATAATTACCATTTAAGGACCTCTACTTCAATAAT
43019056 GCACTTCTATTAAATCATTTATCAT
316 GCACTTCTATTAAATCATTTATCAT
43019081 CTAA
1 CTAA
43019085 AGCTCATATT
Statistics
Matches: 328, Mismatches: 14, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
338 94 0.29
339 11 0.03
340 55 0.17
343 1 0.00
347 1 0.00
348 166 0.51
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (340 bp):
CTAACATGAATTAACGGTAGAATAAGCTAAACCGAGCTACGAGGACTCCAAAAACGTAAAAAAAA
CATTAAAAAACGGGGCTTGGATGCACTTACTATGAGCTTGAGAAAATGAAGAAACCCTAGCTATG
GAGTCCCTTGAAGTTTCGGCCCTTATGCAAGAAGATGAGCATCTTTTTCCCTTTAATTCTTTTTA
TTACCAAATGACTAAAATGCCCTTCATTAAAACTTTAGTTATTTTTATCTATGCATGCCCATTTT
TGTCAATAAAAACCTAATGGTATAATTACCATTTAAGGACCTCTACTTCAATAATGCACTTCTAT
TAAATCATTTATCAT
Found at i:43025288 original size:20 final size:20
Alignment explanation
Indices: 43025263--43025301 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43025253 TACTTTATTC
43025263 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
43025283 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
43025302 AAATAAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:43025633 original size:50 final size:49
Alignment explanation
Indices: 43025513--43025634 Score: 129
Period size: 49 Copynumber: 2.5 Consensus size: 49
43025503 CATGCCAAAA
* *
43025513 CCATGTACCAGACATGGTCTTACATGAGATGTTTCCTGTACTGCAAATG
1 CCATGTCCCAGACATGGTCTTACATGAGATGTTTCATGTACTGCAAATG
* * * ** **
43025562 CCATATCCTAGATATGGTCTTACATGAGA-GTTCTCATAGTGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGAGATGTT-TCAT-GTACTGCAAATG
*
43025612 CCATGTCCCAAACATGGTCTTAC
1 CCATGTCCCAGACATGGTCTTAC
43025635 GAGGGACCTC
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
48 3 0.05
49 28 0.48
50 27 0.47
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGAGATGTTTCATGTACTGCAAATG
Found at i:43029804 original size:15 final size:15
Alignment explanation
Indices: 43029786--43029814 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43029776 GATGTTTTAT
43029786 TTGACCATGTTAAAC
1 TTGACCATGTTAAAC
43029801 TTGACCATGTTAAA
1 TTGACCATGTTAAA
43029815 GAGGGCGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTGACCATGTTAAAC
Found at i:43039184 original size:13 final size:11
Alignment explanation
Indices: 43039158--43039194 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
43039148 TATCATAAAC
43039158 AAAATAAAATA
1 AAAATAAAATA
43039169 AAAATAAAGCATA
1 AAAATAAA--ATA
43039182 AAAATAAAATA
1 AAAATAAAATA
43039193 AA
1 AA
43039195 TAACCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:43044269 original size:30 final size:30
Alignment explanation
Indices: 43044235--43044292 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43044225 CACAGGCTGG
* * * *
43044235 CACACGGGCTTGTGTCCAGCCCGTGTGGCT
1 CACACAGGCGTGTGCCCAACCCGTGTGGCT
43044265 CACACAGGCGTGTGCCCAACCCGTGTGG
1 CACACAGGCGTGTGCCCAACCCGTGTGG
43044293 AAATGCCCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.34, G:0.33, T:0.19
Consensus pattern (30 bp):
CACACAGGCGTGTGCCCAACCCGTGTGGCT
Found at i:43044383 original size:12 final size:12
Alignment explanation
Indices: 43044368--43044401 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
43044358 TAATTTGTAT
43044368 AATTAAGAATAA
1 AATTAAGAATAA
43044380 AATTAAGAATAA
1 AATTAAGAATAA
43044392 AATTAA-AATA
1 AATTAAGAATA
43044402 TGTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (12 bp):
AATTAAGAATAA
Found at i:43051860 original size:17 final size:17
Alignment explanation
Indices: 43051827--43051860 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43051817 AGGTTTCGAT
**
43051827 GCCTCACATTCCTCAAG
1 GCCTCACATTCAGCAAG
43051844 GCCTCACATTCAGCAAG
1 GCCTCACATTCAGCAAG
43051861 AAAACTCTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (17 bp):
GCCTCACATTCAGCAAG
Found at i:43056620 original size:18 final size:18
Alignment explanation
Indices: 43056580--43056614 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43056570 CCAGGTGCGT
*
43056580 ATCCTAGCCCTTATATGC
1 ATCCTAACCCTTATATGC
43056598 ATCCTAACCCTTATATG
1 ATCCTAACCCTTATATG
43056615 TTTCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCCTAACCCTTATATGC
Found at i:43057125 original size:8 final size:9
Alignment explanation
Indices: 43057109--43057138 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43057099 TGAATAAGGC
43057109 AATATTTTT
1 AATATTTTT
43057118 AATATTTTT
1 AATATTTTT
43057127 -ATATTTTT
1 AATATTTTT
43057135 AATA
1 AATA
43057139 AAATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:43060624 original size:19 final size:20
Alignment explanation
Indices: 43060596--43060638 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
43060586 CTGTCACTAC
43060596 AGTT-TTTCAAA-AG-TGTA
1 AGTTGTTTCAAATAGTTGTA
43060613 ATGTTGTTTCAAATAGTTGTA
1 A-GTTGTTTCAAATAGTTGTA
43060634 AGTTG
1 AGTTG
43060639 GATTCGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 7 0.32
20 6 0.27
21 5 0.23
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
AGTTGTTTCAAATAGTTGTA
Found at i:43063482 original size:14 final size:15
Alignment explanation
Indices: 43063452--43063484 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
43063442 GTTGTTATGA
43063452 TAGTTAGTAGTTAGG
1 TAGTTAGTAGTTAGG
*
43063467 TAGTTAG-AGTTTGG
1 TAGTTAGTAGTTAGG
43063481 TAGT
1 TAGT
43063485 GAAGGTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (15 bp):
TAGTTAGTAGTTAGG
Found at i:43064149 original size:13 final size:12
Alignment explanation
Indices: 43064120--43064162 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
43064110 CATTTTTTTT
43064120 ATTTTTTATATA
1 ATTTTTTATATA
*
43064132 A-TTTTAATATA
1 ATTTTTTATATA
43064143 ATTTTTTTATATAA
1 A-TTTTTTATAT-A
43064157 ATTTTT
1 ATTTTT
43064163 CACCTGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 13 0.50
14 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTATATA
Found at i:43064796 original size:25 final size:26
Alignment explanation
Indices: 43064737--43064797 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
43064727 TGAAAACAGA
43064737 GTGAACAAAACAAAACCACGAAAACT
1 GTGAACAAAACAAAACCACGAAAACT
* * *
43064763 GT-AGGCAAAACAAAATCAC-AAAATT
1 GTGA-ACAAAACAAAACCACGAAAACT
43064788 GTGAACAAAA
1 GTGAACAAAA
43064798 TTACGATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.11
Consensus pattern (26 bp):
GTGAACAAAACAAAACCACGAAAACT
Found at i:43066982 original size:2 final size:2
Alignment explanation
Indices: 43066977--43067022 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
43066967 GATATATATA
**
43066977 TG TG TG TG TG TG TG CA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43067019 TG TG
1 TG TG
43067023 CGCGTACGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.02, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:43070247 original size:19 final size:18
Alignment explanation
Indices: 43070219--43070275 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 18
43070209 ATTCAGCAAC
43070219 TAAA-ATGTTCACACACTA
1 TAAACATGTTCACACAC-A
43070237 TAAACATGTTCACACTTAACA
1 TAAACATGTTCACAC---ACA
*
43070258 TTAACATGTTCACACACA
1 TAAACATGTTCACACACA
43070276 ACTAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 7 0.21
19 10 0.29
21 15 0.44
22 2 0.06
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (18 bp):
TAAACATGTTCACACACA
Found at i:43075076 original size:22 final size:23
Alignment explanation
Indices: 43075056--43075178 Score: 119
Period size: 22 Copynumber: 5.3 Consensus size: 23
43075046 AAATACATAA
*
43075056 ACAGA-AACAAGATATATCATAT
1 ACAGATAACAAGATATATCAGAT
*
43075078 ACAG-TTACAAGATATATCAGAT
1 ACAGATAACAAGATATATCAGAT
*
43075100 ACA-ATTACAAGATATATCAGAT
1 ACAGATAACAAGATATATCAGAT
*
43075122 ACAGATAA-ATGATATATCAGAT
1 ACAGATAACAAGATATATCAGAT
*
43075144 ATCAGATATAGATACAGATCATATCAGAT
1 A-CAG--ATA-ACA-AGAT-ATATCAGAT
43075173 ACAGAT
1 ACAGAT
43075179 GAAGATTTCT
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
22 57 0.66
23 6 0.07
25 3 0.03
26 3 0.03
27 1 0.01
28 6 0.07
29 10 0.12
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (23 bp):
ACAGATAACAAGATATATCAGAT
Found at i:43075151 original size:16 final size:15
Alignment explanation
Indices: 43075132--43075178 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
43075122 ACAGATAAAT
43075132 GATATATCAGATATCA
1 GATATATCAGATA-CA
43075148 G--ATAT-AGATACA
1 GATATATCAGATACA
43075160 GATCATATCAGATACA
1 GAT-ATATCAGATACA
43075176 GAT
1 GAT
43075179 GAAGATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 4 0.15
15 4 0.15
16 11 0.41
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (15 bp):
GATATATCAGATACA
Found at i:43075156 original size:29 final size:29
Alignment explanation
Indices: 43075113--43075178 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
43075103 ATTACAAGAT
43075113 ATATCAGATACAGATAAATGAT-ATATCAG
1 ATATCAGATACAGATAAA-GATCATATCAG
* *
43075142 ATATCAGATATAGATACAGATCATATCAG
1 ATATCAGATACAGATAAAGATCATATCAG
43075171 ATA-CAGAT
1 ATATCAGAT
43075179 GAAGATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 26 0.76
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (29 bp):
ATATCAGATACAGATAAAGATCATATCAG
Found at i:43080670 original size:56 final size:56
Alignment explanation
Indices: 43080604--43080710 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
43080594 TTATACATAC
* * **
43080604 ATATGTGTTTTATATTCTATAACT-TTAATATATATATGTACATACATTCTTATAAT
1 ATATGTGTTTTACATTCTATAACTCCT-ATATATATACATACATACATTCTTATAAT
* *
43080660 ATATGTGTTTTACATTTTATAACTCCTATATATATACATACATATATTCTT
1 ATATGTGTTTTACATTCTATAACTCCTATATATATACATACATACATTCTT
43080711 TTTTTTGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 43 0.98
57 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.50
Consensus pattern (56 bp):
ATATGTGTTTTACATTCTATAACTCCTATATATATACATACATACATTCTTATAAT
Found at i:43080810 original size:26 final size:26
Alignment explanation
Indices: 43080741--43080818 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
43080731 ATCTTAAAAT
* *
43080741 ATACGTATACTTATATACATTTTATA
1 ATACATATACTTATATATATTTTATA
* *
43080767 ATACATATATTTACATATATTTTATA
1 ATACATATACTTATATATATTTTATA
** *
43080793 ATTTATATACATATATAT-TTGTTATA
1 ATACATATACTTATATATATT-TTATA
43080819 TTTTTGACAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 2 0.05
26 40 0.95
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.50
Consensus pattern (26 bp):
ATACATATACTTATATATATTTTATA
Found at i:43087926 original size:100 final size:99
Alignment explanation
Indices: 43087748--43087945 Score: 315
Period size: 100 Copynumber: 2.0 Consensus size: 99
43087738 TATAGTTCGC
* * * *
43087748 AAGGTTGCAGAAGGATTAAACCATGGAAGCGACTTTTGGGGTATTTGTTTGATAAGGCTTAATTG
1 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGCTATTTGTTTGATAAGGCTTAATTG
* *
43087813 TCATGTGTTTCCTATGATTAATTTACGATTAAGG
66 TCAGGTGGTTCCTATGATTAATTTACGATTAAGG
43087847 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGACTATTTGTTTGATAAGGCTTAATT
1 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGG-CTATTTGTTTGATAAGGCTTAATT
* *
43087912 GTTAGGTGGTTCCTATGGTTAATTTACGATTAAG
65 GTCAGGTGGTTCCTATGATTAATTTACGATTAAG
43087946 AAAAAATTGG
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
99 37 0.41
100 53 0.59
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (99 bp):
AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGCTATTTGTTTGATAAGGCTTAATTG
TCAGGTGGTTCCTATGATTAATTTACGATTAAGG
Found at i:43093669 original size:100 final size:100
Alignment explanation
Indices: 43093496--43093685 Score: 308
Period size: 100 Copynumber: 1.9 Consensus size: 100
43093486 GTTGCAGAAA
* **
43093496 GATTAAACCATGGAAGCGACTTTCGAGGCTATTTGTTTGATAAGGTTTAACTGTCAGGTGGTTCA
1 GATTAAACCACGGAAGCGACTTTCGAGGCTATTTGTTTGATAAGGCCTAACTGTCAGGTGGTTCA
43093561 TGTGGTTAATTTACGATTAAGGAAGGTTCCAGACG
66 TGTGGTTAATTTACGATTAAGGAAGGTTCCAGACG
* * * * *
43093596 GATTAAACCACGGAAGCGACTTTCGGGGCTATTTGTTTGATAAGGCCTAATTTTTAGGTGGTTCC
1 GATTAAACCACGGAAGCGACTTTCGAGGCTATTTGTTTGATAAGGCCTAACTGTCAGGTGGTTCA
43093661 TGTGGTTAATTTACGATTAAGGAAG
66 TGTGGTTAATTTACGATTAAGGAAG
43093686 AATTGGTCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (100 bp):
GATTAAACCACGGAAGCGACTTTCGAGGCTATTTGTTTGATAAGGCCTAACTGTCAGGTGGTTCA
TGTGGTTAATTTACGATTAAGGAAGGTTCCAGACG
Found at i:43096264 original size:29 final size:28
Alignment explanation
Indices: 43096220--43096279 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
43096210 TTGCTGCCAG
*
43096220 ACTCTTGCTTGACGGAGAGTCATTACCAA
1 ACTCTTGCTTGACGGAGAGTCACTA-CAA
* * *
43096249 ACTCTTGTTTGGCGGATAGTCACTACAA
1 ACTCTTGCTTGACGGAGAGTCACTACAA
43096277 ACT
1 ACT
43096280 TTCGACTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (28 bp):
ACTCTTGCTTGACGGAGAGTCACTACAA
Found at i:43097790 original size:15 final size:15
Alignment explanation
Indices: 43097770--43097804 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
43097760 GGATGCAAAC
43097770 TCATAAATGGTTGAA
1 TCATAAATGGTTGAA
43097785 TCATAAATGGTTGAA
1 TCATAAATGGTTGAA
43097800 TCATA
1 TCATA
43097805 CACGCAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (15 bp):
TCATAAATGGTTGAA
Found at i:43107510 original size:20 final size:20
Alignment explanation
Indices: 43107465--43107511 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
43107455 CCACTCTCCT
* *
43107465 CCCCCTTGCACCGTACCCTT
1 CCCCCTCGCACCGTACCCTG
*
43107485 CTCCCTCGCACCGT-CCACTG
1 CCCCCTCGCACCGTACC-CTG
43107505 CCCCCTC
1 CCCCCTC
43107512 AACGCCTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.09, C:0.60, G:0.11, T:0.21
Consensus pattern (20 bp):
CCCCCTCGCACCGTACCCTG
Found at i:43107716 original size:6 final size:6
Alignment explanation
Indices: 43107705--43107731 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43107695 TAGGCTTAAC
43107705 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
43107732 AACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:43107770 original size:17 final size:16
Alignment explanation
Indices: 43107722--43107776 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
43107712 TTTATTTTTA
43107722 TTTTTATTTTAA-CTT
1 TTTTTATTTTAATCTT
* *
43107737 TTTTTAGTTCTATTCTT
1 TTTTTA-TTTTAATCTT
43107754 TTTTTATTTTAAATCTT
1 TTTTTATTTT-AATCTT
*
43107771 GTTTTA
1 TTTTTA
43107777 CAATTATGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 6 0.19
16 7 0.22
17 19 0.59
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTATTTTAATCTT
Found at i:43109370 original size:15 final size:15
Alignment explanation
Indices: 43109350--43109380 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43109340 TTCTTTTTAG
43109350 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
43109365 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
43109380 T
1 T
43109381 ATTTTATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:43114861 original size:17 final size:19
Alignment explanation
Indices: 43114834--43114871 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43114824 AGATACATTA
43114834 CATACAAGTCA-AACCTTT
1 CATACAAGTCAGAACCTTT
43114852 CATA-AAGTCATGAACCTTT
1 CATACAAGTCA-GAACCTTT
43114871 C
1 C
43114872 CATTGAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (19 bp):
CATACAAGTCAGAACCTTT
Found at i:43116884 original size:17 final size:17
Alignment explanation
Indices: 43116862--43116900 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
43116852 CTTTCTCTCC
*
43116862 TCTTTTCTCTTAAATTT
1 TCTTTTCTCTTAAAATT
43116879 TCTTTTCTCTTAAAATT
1 TCTTTTCTCTTAAAATT
43116896 TCTTT
1 TCTTT
43116901 CTTTCTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTTTTCTCTTAAAATT
Found at i:43120905 original size:28 final size:28
Alignment explanation
Indices: 43120865--43120919 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
43120855 GTGACATTGA
43120865 GGCCCAAAAGCATTCCTGGAGTAAACTT
1 GGCCCAAAAGCATTCCTGGAGTAAACTT
*
43120893 GGCCCAAGAGCATTCCTGGAGTAAACT
1 GGCCCAAAAGCATTCCTGGAGTAAACT
43120920 ATCTTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (28 bp):
GGCCCAAAAGCATTCCTGGAGTAAACTT
Found at i:43127715 original size:40 final size:40
Alignment explanation
Indices: 43127666--43127744 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
43127656 CAAAAGAAAG
43127666 TCCAACAACTCAATTACTAACTAAGATGAGTTTAATAAAT
1 TCCAACAACTCAATTACTAACTAAGATGAGTTTAATAAAT
* * * *
43127706 TCCAGCAACTCATTTATTAACTAAGATGAGTTTATTAAA
1 TCCAACAACTCAATTACTAACTAAGATGAGTTTAATAAA
43127745 ATTAAAGTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (40 bp):
TCCAACAACTCAATTACTAACTAAGATGAGTTTAATAAAT
Found at i:43130769 original size:23 final size:22
Alignment explanation
Indices: 43130726--43130769 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
43130716 TTTCAAGTCA
43130726 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
43130749 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
43130770 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:43130943 original size:23 final size:23
Alignment explanation
Indices: 43130871--43130943 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
43130861 AGTGCCACAT
*
43130871 TGATATGTAGTCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
43130894 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
43130917 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
43130940 TGAT
1 TGAT
43130944 CAATAACACT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:43131426 original size:30 final size:30
Alignment explanation
Indices: 43131392--43131450 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
43131382 TCCTTGACTC
43131392 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
43131422 AAACTTTTGCATATTTACACTTTTGCCCC
1 AAACTTTGGCAAAATTACAATTTTGCCCC
43131451 AAAGCTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:43134748 original size:27 final size:27
Alignment explanation
Indices: 43134718--43134868 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
43134708 ATATTGAGTC
* *
43134718 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
43134745 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43134772 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
43134800 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43134827 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
43134854 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43134869 GTACAATTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
27 83 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43134810 original size:55 final size:54
Alignment explanation
Indices: 43134718--43134868 Score: 169
Period size: 55 Copynumber: 2.8 Consensus size: 54
43134708 ATATTGAGTC
* * *
43134718 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
* ** ** *
43134772 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAAT
* **
43134827 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCT
43134869 GTACAATTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 37 0.45
55 45 0.55
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
Found at i:43151680 original size:23 final size:25
Alignment explanation
Indices: 43151647--43151696 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
43151637 ATTCTGATTT
43151647 AATTAGTAAATATATATT-TTTAAA
1 AATTAGTAAATATATATTATTTAAA
43151671 AATTA-TAAATATATATTATTTAAA
1 AATTAGTAAATATATATTATTTAAA
43151695 AA
1 AA
43151697 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTAGTAAATATATATTATTTAAA
Found at i:43153363 original size:3 final size:3
Alignment explanation
Indices: 43153338--43153529 Score: 92
Period size: 3 Copynumber: 64.3 Consensus size: 3
43153328 CATATCTTTG
* * * *
43153338 TTA TT- TTA TCA TTA TTT TTA TTA TTA GTA GTA TTA TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *** * * * *
43153382 TTA TTA ATA TTA TTA TTA TTA ACG TCA TCA TTA CTA -TA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
43153429 TCT- TTA TTA CTT- TTA TTA TTA TTA TTT TTG TTA TTA TTGA -TA TTA
1 T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
* * * * * * *
43153474 TTA CTA GTA TTA CTT- TTA TTA TTA ATA TTA TCA CTA CTA TCA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43153519 TTA TTTA TTA T
1 TTA -TTA TTA T
43153530 ATTCCTATAT
Statistics
Matches: 146, Mismatches: 30, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
2 11 0.08
3 125 0.86
4 10 0.07
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:43153751 original size:4 final size:4
Alignment explanation
Indices: 43153742--43153779 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
43153732 ATTTTATAAT
43153742 TTTA TTTA TTGT- TATTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA TTTA T
43153780 GTGCTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:43157709 original size:11 final size:11
Alignment explanation
Indices: 43157685--43157717 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
43157675 TACTTCACTT
*
43157685 GAAAA-AAAAC
1 GAAAAGAAAAA
43157695 GAAAAGAAAAA
1 GAAAAGAAAAA
43157706 GAAAAGAAAAA
1 GAAAAGAAAAA
43157717 G
1 G
43157718 GAGAGGCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:43158871 original size:131 final size:131
Alignment explanation
Indices: 43158633--43159335 Score: 936
Period size: 131 Copynumber: 5.4 Consensus size: 131
43158623 TACCAAGCCT
* * **
43158633 TATCTCCCTGAGCAACAGTAGAGTAGGTCGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * * *
43158698 AGCAGATCGAAGACAGCGGATCTTATCTT-CCTAAGGTAGTAGGAAGCATATTTAAGCCACCAGT
66 AGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAA-ATAGTAGGAAGCAGATTTAAGCCACCAGT
43158762 CC
130 CC
* *
43158764 TATCTCCCTGAGCACCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTGAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *
43158829 AGTAGATCGAAGACGGTGAATCTTGTCTTCCCGAAATGGTAGGAAGCAGATTTAAGGCACCAGTC
66 AGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAAATAGTAGGAAGCAGATTTAAGCCACCAGTC
43158894 C
131 C
** * * *
43158895 TATCTCTTTGAGCAGCAGTGGAGTAGTTTGAAA-ATTGTATATCTTATCTCCCTAAGCAGTAGCG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTT-AAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* * *
43158959 GAGCAGATTGAAGGCGGCGAATCTTGTCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACCAGT
65 GAGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAAATAGTAGGAAGCAGATTTAAGCCACCAGT
43159024 CC
130 CC
* * * *
43159026 TATCTCCCTGAGCACCAGTGGAGTAGGTTGAAGATTGTAGTTCTTATCTCCCTAAGTAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *
43159091 AGCAGATCGAAGACGACAAATCTTGTCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCACTAGTC
66 AGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAAATAGTAGGAAGCAGATTTAAGCCACCAGTC
43159156 C
131 C
* *
43159157 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGTTCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
43159222 AGCAGATCGAAGACGGCGAATCTTATCTTCCC-AAGGTAGTAGGGAAGCAGA--T-CG-CATCCA
66 AGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAA-ATAGTA-GGAAGCAGATTTAAGCCA-CCA
43159282 G-CC
128 GTCC
* **
43159285 TTATCTCCCTGAGCAGTAGTGGAGTAGGTTAAAGATTACAGATCTTATCTC
1 -TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTC
43159336 TCTGAAGTTA
Statistics
Matches: 508, Mismatches: 57, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
128 4 0.01
129 49 0.10
130 4 0.01
131 435 0.86
132 16 0.03
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCGAATCTTGTCTTCCCGAAATAGTAGGAAGCAGATTTAAGCCACCAGTC
C
Found at i:43159246 original size:44 final size:44
Alignment explanation
Indices: 43159067--43159275 Score: 119
Period size: 44 Copynumber: 4.8 Consensus size: 44
43159057 AGATTGTAGT
* *
43159067 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGACAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACTAA
* * ** * *
43159111 TCTTGTCTTCCC-GAG-A-TAGTAGGAAGCAGATTTAAG-CCACTAG
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGACTAA
* * * * * * * *
43159154 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG--TAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGACTA-A
* *
43159198 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACTAA
*
43159242 TCTTATCTTCCC-AAGGTAGTAG-GGAAGCAGATCG
1 TCTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATCG
43159276 CATCCAGCCT
Statistics
Matches: 125, Mismatches: 26, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
42 8 0.06
43 27 0.22
44 63 0.50
45 27 0.22
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACTAA
Found at i:43159398 original size:41 final size:41
Alignment explanation
Indices: 43159327--43159532 Score: 164
Period size: 44 Copynumber: 4.9 Consensus size: 41
43159317 AGATTACAGA
* * * * * *
43159327 TCTTATCTCTCTGAAGTTACTGTAGTGCAGATCACATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCAG
* * *
43159368 TCTTATCGCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC---A-AAACCAG
* ** *
43159412 TCTTATCTCCATGAAGTTGCAGTAGAGTGGATTAAAACCATAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACC--AG
* ** *
43159455 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCAG
* *
43159497 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-CAAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAA
43159533 GAATTCAATC
Statistics
Matches: 127, Mismatches: 30, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
40 3 0.02
41 58 0.46
42 3 0.02
43 2 0.02
44 61 0.48
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCAG
Found at i:43159417 original size:129 final size:128
Alignment explanation
Indices: 43159284--43159609 Score: 359
Period size: 129 Copynumber: 2.5 Consensus size: 128
43159274 CGCATCCAGC
* * ** *
43159284 CTTATCTCCCTGAGCAGTAGTGGAGTAGG-TTAAAGATTACAGATCTTATCTCTCTGAAGTTACT
1 CTTATCTCCCTGAGCAGCAGTAGAGT-GGATTAAA-ACCACAGATCTTATCTCTCTGAAGTTACA
*
43159348 GTAGTGCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAAT
64 GTAGAGCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAAT
* ** * *
43159413 CTTATCTCCATGAAGTTGCAGTAGAGTGGATTAAAACCATAGATCTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTG-AGCAGCAGTAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAG
* * * **
43159478 TAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAAAAGAATTCAAT
65 TAGAGCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAAT
* ** * * * * * * *
43159542 CCTATCTCCCTGAAGTTGTAATGGAGCGGATTAAAACCACAAATCTTAGAC-CTCTGAAGTTTCA
1 CTTATCTCCCTG-AGCAGCAGTAGAGTGGATTAAAACCACAGATCTTA-TCTCTCTGAAGTTACA
43159606 GTAG
64 GTAG
43159610 GTCAGATTAA
Statistics
Matches: 168, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
129 152 0.90
130 16 0.10
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (128 bp):
CTTATCTCCCTGAGCAGCAGTAGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGT
AGAGCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAAT
Found at i:43159427 original size:44 final size:44
Alignment explanation
Indices: 43159368--43159568 Score: 155
Period size: 44 Copynumber: 4.6 Consensus size: 44
43159358 TCACATCCAG
*
43159368 TCTTATCGCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * * * **
43159412 TCTTATCTCCATGAAGTTGCAGTAGAG-TG-GATTA-AAACCATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACC--A-A
* * * * *
43159456 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC----GCATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCAA
* **
43159497 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAAAAGAATTCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * *
43159541 TCCTATCTCCCTGAAGTTGTAATGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
43159569 GGATTAAAAC
Statistics
Matches: 122, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
40 1 0.01
41 33 0.27
42 3 0.02
43 2 0.02
44 82 0.67
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
Found at i:43159616 original size:129 final size:129
Alignment explanation
Indices: 43159326--43159616 Score: 372
Period size: 129 Copynumber: 2.3 Consensus size: 129
43159316 AAGATTACAG
* *
43159326 ATCTTATCTCTCTGAAGTTACTGTA-GTGCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAG
1 ATCTTAACTCTCTGAAGTTACAGTAGGT-CAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAG
* * * * *
43159390 TGGAGCAGACAAAAGAAACCAATCTTATCTCCATGAAGTTGCAGTAGAGTGGATTAAAACCATAG
65 TGGAGCAGACAAAAGAAACCAATCCTATCTCCATGAAGTTGCAATAGAGCGGATTAAAACCACAA
* * * *
43159455 ATCTTATCTCTCTGAAGTTGCAGTAGAG-CAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAG
1 ATCTTAACTCTCTGAAGTTACAGTAG-GTCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAG
* ** * * *
43159519 TGGAGTAGACAAAAGAATTCAATCCTATCTCCCTGAAGTTGTAATGGAGCGGATTAAAACCACAA
65 TGGAGCAGACAAAAGAAACCAATCCTATCTCCATGAAGTTGCAATAGAGCGGATTAAAACCACAA
*
43159584 ATCTTAGAC-CTCTGAAGTTTCAGTAGGTCAGAT
1 ATCTTA-ACTCTCTGAAGTTACAGTAGGTCAGAT
43159617 TAAATTTACC
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
128 1 0.01
129 138 0.98
130 1 0.01
131 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (129 bp):
ATCTTAACTCTCTGAAGTTACAGTAGGTCAGATCACATCCAGTCTTATCGCCCTGAAGTTGCAGT
GGAGCAGACAAAAGAAACCAATCCTATCTCCATGAAGTTGCAATAGAGCGGATTAAAACCACAA
Found at i:43160197 original size:22 final size:22
Alignment explanation
Indices: 43160172--43160242 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
43160162 TATCCTATCA
43160172 CCTCCTCTGCCTCGTCACGTCC
1 CCTCCTCTGCCTCGTCACGTCC
* * * *
43160194 CCTCCACTGCTCTAACATC-CTATCA
1 CCTCCTCTGC-CT--CGTCAC-GTCC
43160219 CCTCCTCTGCCTCGTCACGTCC
1 CCTCCTCTGCCTCGTCACGTCC
43160241 CC
1 CC
43160243 CCCACTGCTC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
22 16 0.44
23 3 0.08
24 3 0.08
25 14 0.39
ACGTcount: A:0.11, C:0.52, G:0.10, T:0.27
Consensus pattern (22 bp):
CCTCCTCTGCCTCGTCACGTCC
Found at i:43160232 original size:47 final size:47
Alignment explanation
Indices: 43160163--43160256 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
43160153 AGGCTGCCCT
*
43160163 ATCCTATCACCTCCTCTGCCTCGTCACGTCCCCTCCACTGCTCTAAC
1 ATCCTATCACCTCCTCTGCCTCGTCACGTCCCCCCCACTGCTCTAAC
43160210 ATCCTATCACCTCCTCTGCCTCGTCACGTCCCCCCCACTGCTCTAAC
1 ATCCTATCACCTCCTCTGCCTCGTCACGTCCCCCCCACTGCTCTAAC
43160257 CCTGCAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.15, C:0.50, G:0.09, T:0.27
Consensus pattern (47 bp):
ATCCTATCACCTCCTCTGCCTCGTCACGTCCCCCCCACTGCTCTAAC
Found at i:43161260 original size:25 final size:24
Alignment explanation
Indices: 43161232--43161300 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
43161222 TATTATTTAT
43161232 TATTATTTATCTTATTATATGTAAA
1 TATTATTTATCTTATTATATG-AAA
* * *
43161257 TATTCATTTGT-TTA-AATTTGAAA
1 TATT-ATTTATCTTATTATATGAAA
*
43161280 TA-TATTTATCTTATTGTATGA
1 TATTATTTATCTTATTATATGA
43161301 CTGATTATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
21 5 0.15
22 4 0.12
23 9 0.26
24 4 0.12
25 7 0.21
26 5 0.15
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (24 bp):
TATTATTTATCTTATTATATGAAA
Found at i:43161481 original size:9 final size:9
Alignment explanation
Indices: 43161463--43161507 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
43161453 ACATTTTATA
43161463 ATTTTATTT
1 ATTTTATTT
*
43161472 ATTTTCTTT
1 ATTTTATTT
43161481 ATTGTTA-TT
1 ATT-TTATTT
43161490 A-TTTATTT
1 ATTTTATTT
43161498 A-TTTATTT
1 ATTTTATTT
43161506 AT
1 AT
43161508 GTGCCTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 3 0.10
8 12 0.39
9 14 0.45
10 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:43179366 original size:64 final size:64
Alignment explanation
Indices: 43179297--43179419 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
43179287 TTTTTTGAAT
* * *
43179297 CAAGAAAA-TAAACATA-TTTAAAATAACATAAAAATGAC-AAAATAACACCAACTTATTCTTCA
1 CAAGAAAACAAAACATACTTAAAAACAACAT-AAAATG-CTAAAATAACACCAACTT-TTCTTCA
43179359 TG
63 TG
*
43179361 CAAGAAAACAAAACATACTTAAAAACAACATAAAATGCTAAAATAACACCAGCTTTTCT
1 CAAGAAAACAAAACATACTTAAAAACAACATAAAATGCTAAAATAACACCAACTTTTCT
43179420 AATGATTCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
64 13 0.25
65 28 0.54
66 11 0.21
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (64 bp):
CAAGAAAACAAAACATACTTAAAAACAACATAAAATGCTAAAATAACACCAACTTTTCTTCATG
Found at i:43185578 original size:18 final size:18
Alignment explanation
Indices: 43185551--43185585 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43185541 ATGATGTGCC
43185551 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
* *
43185569 AAACTGTTTTGATGCTT
1 AAACTATTTTCATGCTT
43185586 TTTGTTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:43189130 original size:129 final size:129
Alignment explanation
Indices: 43188883--43189131 Score: 295
Period size: 129 Copynumber: 1.9 Consensus size: 129
43188873 TACAGTCTTC
* * * *
43188883 GCTTTCGTGTTCTTTCAGTTCAACTAAAATGGGTTTGTCTATTTTTACTTTTTTTGTACTATTTG
1 GCTTTCGTGTCCTTTCAGTTCAACTAAAATGGGTTTATCTATTTTTACGTTTCTTGTACTATTTG
* * * * * **
43188948 ATTATTATTGATTGCCTTTTTTGTTGATTTTGCTGTTATTAGCTCTTTTCAAATTACAATATTT
66 ATTATTATTGACTACCTCTTTTGTTGATTTTACTGTTATTAGCTATTGGCAAATTACAATATTT
* * * * *
43189012 GCTTTTGTGTCCTTTCAGTTCAAATTTAAATTGGTTTATCTGTTTTTA-GTTTCTTGTACTATTT
1 GCTTTCGTGTCCTTTCAGTTC-AACTAAAATGGGTTTATCTATTTTTACGTTTCTTGTACTATTT
* * *
43189076 GATTCTTATTGACTA-CTCCTTTTGTTGATTTTACTGTTCTTTGCTATTGGCAAATT
65 GATTATTATTGACTACCT-CTTTTGTTGATTTTACTGTTATTAGCTATTGGCAAATT
43189132 GCACAACATT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
128 2 0.02
129 76 0.77
130 21 0.21
ACGTcount: A:0.18, C:0.13, G:0.14, T:0.55
Consensus pattern (129 bp):
GCTTTCGTGTCCTTTCAGTTCAACTAAAATGGGTTTATCTATTTTTACGTTTCTTGTACTATTTG
ATTATTATTGACTACCTCTTTTGTTGATTTTACTGTTATTAGCTATTGGCAAATTACAATATTT
Found at i:43192808 original size:12 final size:12
Alignment explanation
Indices: 43192791--43192832 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
43192781 AAAGCTCTGT
43192791 AAATATTTATAA
1 AAATATTTATAA
*
43192803 AAATA-TT-TAC
1 AAATATTTATAA
*
43192813 GAATATTTATAA
1 AAATATTTATAA
43192825 AAATATTT
1 AAATATTT
43192833 GTAGCTCGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:43193891 original size:26 final size:25
Alignment explanation
Indices: 43193820--43193892 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
43193810 TTTTCACCCT
* *
43193820 AATTTTACCCTAGTAAAATTTTGAC
1 AATTTTACCCTGGTAAAATTTCGAC
*
43193845 AATTTTACCC-GCGATATAATTTCGAC
1 AATTTTACCCTG-G-TAAAATTTCGAC
43193871 AATTTTACCCTTGGTAAAATTT
1 AATTTTACCC-TGGTAAAATTT
43193893 TGAGAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 11 0.28
26 27 0.68
27 1 0.03
28 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (25 bp):
AATTTTACCCTGGTAAAATTTCGAC
Found at i:43197344 original size:16 final size:16
Alignment explanation
Indices: 43197317--43197357 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43197307 CTTTGATCAG
43197317 TGAAAAAG-AAAAGTTA
1 TGAAAAAGTAAAA-TTA
43197333 -GAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
*
43197348 TGAAAGAGTA
1 TGAAAAAGTA
43197358 CATTTAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.20
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:43201086 original size:26 final size:26
Alignment explanation
Indices: 43201057--43201125 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
43201047 CAGCCCGACC
43201057 CACAGCTCGTGTGAGCAAGCCCATTT
1 CACAGCTCGTGTGAGCAAGCCCATTT
* * ** *
43201083 CACAACTCATGTGATTAGGCCCATTT
1 CACAGCTCGTGTGAGCAAGCCCATTT
43201109 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
43201126 TATATAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAAGCCCATTT
Found at i:43211043 original size:12 final size:12
Alignment explanation
Indices: 43211023--43211054 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
43211013 TGCCTTACAT
43211023 GGCCATGTGTTA
1 GGCCATGTGTTA
*
43211035 GGTCATGTGTTA
1 GGCCATGTGTTA
43211047 GGCCATGT
1 GGCCATGT
43211055 AACTCACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (12 bp):
GGCCATGTGTTA
Found at i:43213183 original size:30 final size:30
Alignment explanation
Indices: 43213144--43213220 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
43213134 CTGAGCCTGC
* ** *
43213144 GCCCTATACAGTAGTAGCGTGTGGGCCATA
1 GCCCAATACAGTAACAGAGTGTGGGCCATA
* *
43213174 GCCTAATACAGTAACAGAGTGTGGGCCTTA
1 GCCCAATACAGTAACAGAGTGTGGGCCATA
43213204 GCCCAATACAGTAACAG
1 GCCCAATACAGTAACAG
43213221 TGCAAATGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (30 bp):
GCCCAATACAGTAACAGAGTGTGGGCCATA
Found at i:43213357 original size:26 final size:26
Alignment explanation
Indices: 43213328--43213430 Score: 127
Period size: 26 Copynumber: 4.0 Consensus size: 26
43213318 ACACCAATAT
* *
43213328 CGCAGCAAAGCTACCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
*
43213354 CGCAGCAAAGCTGCCAGTAACAATAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* * * *
43213380 TGCAGCAGAA-TTGCAAGTATCAGTAA
1 CGCAGCA-AAGCTGCCAGTAACAGTAA
43213406 CGCAGCAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
43213431 TTTGTGGCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.03
26 59 0.94
27 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:43213641 original size:27 final size:27
Alignment explanation
Indices: 43213611--43213724 Score: 90
Period size: 27 Copynumber: 4.2 Consensus size: 27
43213601 CATCTCCTAA
*
43213611 GGGTATAACGGTCATTTTACCCTATAG
1 GGGTATAACGATCATTTTACCCTATAG
** * *
43213638 GGGTATTTCGATAATTTTACCC-ATCG
1 GGGTATAACGATCATTTTACCCTATAG
** * *
43213664 AGGGTATTTC-AGTCATTTTACCAT-TCGG
1 -GGGTATAACGA-TCATTTTACCCTAT-AG
*
43213692 GGGTATAACGATTATTTTACCCTATAG
1 GGGTATAACGATCATTTTACCCTATAG
43213719 GGGTAT
1 GGGTAT
43213725 TTCAATAATT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
26 4 0.06
27 61 0.90
28 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (27 bp):
GGGTATAACGATCATTTTACCCTATAG
Found at i:43213695 original size:54 final size:54
Alignment explanation
Indices: 43213624--43214007 Score: 407
Period size: 54 Copynumber: 7.1 Consensus size: 54
43213614 TATAACGGTC
* *
43213624 ATTTTACCCTATAG-GGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTC
1 ATTTTACCC-ATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
* ** * * *
43213678 ATTTTA-CCATTCGGGGGTATAACGATTATTTTACCCTATAG-GGGTATTTCAATA
1 ATTTTACCCA-TCGAGGGTATTTCGATAATTTTACCC-ATCGAGGGTATTTCAGTA
* ** *
43213732 ATTTTACCCATCAAGGGTATTTTAATAATTTTATCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
* * * * ** *
43213786 ATTTTAACCATCAAGGGTATTTCGGTAATTTAACCCATTTAGGGTATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
* * * *
43213840 ATTTTACCCATCGAGGGTATATCGATAATTTTACCCATTGAGGGTATTTTAGTC
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
* *
43213894 ATATTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTT-TGATA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAG-TA
* * * * * * *
43213948 ATTTTACTCATTGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
*
43214002 ACTTTA
1 ATTTTA
43214008 GTGGCCCATT
Statistics
Matches: 276, Mismatches: 47, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.00
53 8 0.03
54 260 0.94
55 7 0.03
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCAGTA
Found at i:43213733 original size:81 final size:80
Alignment explanation
Indices: 43213610--43214007 Score: 397
Period size: 81 Copynumber: 4.9 Consensus size: 80
43213600 TCATCTCCTA
* * * * *
43213610 AGGGTATAACGGTCATTTTACCCTATAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCA
1 AGGGTATATCGATAATTTTACCC-ATAGGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCA
*
43213675 GTCATTTTA-CCATTCG
65 GTAATTTTACCCA-TCG
* * * ** *
43213691 GGGGTATAACGATTATTTTACCCTATAGGGGTATTTCAATAATTTTACCCATCAAGGGTATTTTA
1 AGGGTATATCGATAATTTTACCC-ATAGGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCA
* *
43213756 ATAATTTTATCCATCG
65 GTAATTTTACCCATCG
* * * * **
43213772 AGGGTATTTC-AGTAATTTTAACCATCAAGGGTATTTCGGTAATTTAACCCATTTAGGGTATTTC
1 AGGGTATATCGA-TAATTTTACCCAT-AGGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTC
*
43213836 AGTCATTTTACCCATCG
64 AGTAATTTTACCCATCG
* ** * * *
43213853 AGGGTATATCGATAATTTTACCCATTGAGGGTATTTTAGTCATATTACCCATCGAGGGTATTTC-
1 AGGGTATATCGATAATTTTACCCATAG-GGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCA
43213917 GATAATTTTACCCATCG
65 G-TAATTTTACCCATCG
* * * * * *
43213934 AGGGTATTTTGATAATTTTACTCATTGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTCG
1 AGGGTATATCGATAATTTTACCCA-TAGGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCA
*
43213999 GTAACTTTA
65 GTAATTTTA
43214008 GTGGCCCATT
Statistics
Matches: 265, Mismatches: 44, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
80 4 0.02
81 254 0.96
82 7 0.03
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (80 bp):
AGGGTATATCGATAATTTTACCCATAGGGGTATTTCGGTAATTTTACCCATCAAGGGTATTTCAG
TAATTTTACCCATCG
Found at i:43213735 original size:27 final size:26
Alignment explanation
Indices: 43213624--43214007 Score: 249
Period size: 27 Copynumber: 14.2 Consensus size: 26
43213614 TATAACGGTC
43213624 ATTTTACCCTATAGGGGTATTTCGATA
1 ATTTTACCC-ATAGGGGTATTTCGATA
* *
43213651 ATTTTACCCATCGAGGGTATTTC-AGTC
1 ATTTTACCCATAG-GGGTATTTCGA-TA
* ** *
43213678 ATTTTA-CCATTCGGGGGTATAACGATT
1 ATTTTACCCA-T-AGGGGTATTTCGATA
*
43213705 ATTTTACCCTATAGGGGTATTTCAATA
1 ATTTTACCC-ATAGGGGTATTTCGATA
* **
43213732 ATTTTACCCATCAAGGGTATTTTAATA
1 ATTTTACCCAT-AGGGGTATTTCGATA
* *
43213759 ATTTTATCCATCGAGGGTATTTC-AGTA
1 ATTTTACCCATAG-GGGTATTTCGA-TA
* * *
43213786 ATTTTAACCATCAAGGGTATTTCGGTA
1 ATTTTACCCAT-AGGGGTATTTCGATA
* *
43213813 ATTTAACCCATTTA-GGGTATTTC-AGTC
1 ATTTTACCCA--TAGGGGTATTTCGA-TA
* *
43213840 ATTTTACCCATCGAGGGTATATCGATA
1 ATTTTACCCATAG-GGGTATTTCGATA
* * *
43213867 ATTTTACCCATTGAGGGTATTT-TAGTC
1 ATTTTACCCATAG-GGGTATTTCGA-TA
* *
43213894 ATATTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATAG-GGGTATTTCGATA
* *
43213921 ATTTTACCCATCGAGGGTATTTTGATA
1 ATTTTACCCATAG-GGGTATTTCGATA
* * * *
43213948 ATTTTACTCATTGGGGGTATTTTGGTA
1 ATTTTACCCA-TAGGGGTATTTCGATA
* *
43213975 ATTTTACCCATCAAGGGTATTTCGGTA
1 ATTTTACCCAT-AGGGGTATTTCGATA
*
43214002 ACTTTA
1 ATTTTA
43214008 GTGGCCCATT
Statistics
Matches: 288, Mismatches: 47, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
25 1 0.00
26 12 0.04
27 263 0.91
28 10 0.03
29 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (26 bp):
ATTTTACCCATAGGGGTATTTCGATA
Found at i:43216352 original size:25 final size:26
Alignment explanation
Indices: 43216319--43216374 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
43216309 AAAAATTTAA
*
43216319 CAAATTGACC-CCGGGTTAACTAGAT
1 CAAACTGACCTCCGGGTTAACTAGAT
**
43216344 CAAACTGACCTTTGGGTTAACTAGAT
1 CAAACTGACCTCCGGGTTAACTAGAT
43216370 CAAAC
1 CAAAC
43216375 CGTAATGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (26 bp):
CAAACTGACCTCCGGGTTAACTAGAT
Found at i:43217872 original size:16 final size:17
Alignment explanation
Indices: 43217851--43217884 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43217841 AATGAGATTA
43217851 AGAAAATT-ATTTAGTT
1 AGAAAATTAATTTAGTT
43217867 AGAAAATTAATTTAGTT
1 AGAAAATTAATTTAGTT
43217884 A
1 A
43217885 TTTCAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAGTT
Found at i:43223507 original size:18 final size:18
Alignment explanation
Indices: 43223484--43223521 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43223474 TGGTAGTCCT
43223484 CCACAACAGGTCAGTATG
1 CCACAACAGGTCAGTATG
43223502 CCACAACAGGTCAGTATG
1 CCACAACAGGTCAGTATG
43223520 CC
1 CC
43223522 CTCCCCTGGC
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:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (18 bp):
CCACAACAGGTCAGTATG
Found at i:43228748 original size:125 final size:125
Alignment explanation
Indices: 43228356--43228777 Score: 607
Period size: 125 Copynumber: 3.4 Consensus size: 125
43228346 CGTGCACGCA
* * * * *
43228356 AAGAATTTGTAAAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTAGTCTTGGAAGAAATAAT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGTCCTAGAAGAAATAAT
*
43228421 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTCTATGAG
66 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAG
* * * * *
43228481 AAGAATTTGTTAAATCGCGCCCACGTGAACACGCTTTTGCTACAG-TAGGTCCTA-AAAAAATTA
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTA-GTCCTAGAAGAAATAA
* * * *
43228544 TTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAAAAACGCTTCAATCAGGATGCTATT-TGAG
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAATCGCTTCTACCAGGATGCT-TTATGAG
* ** * *
43228607 AAGAATTTCTGAAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTTCGTCCTAGAAGAACTAAT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGTCCTAGAAGAAATAAT
43228672 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAG
66 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAG
43228732 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
43228778 AGCATGTTTG
Statistics
Matches: 259, Mismatches: 31, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
124 41 0.16
125 111 0.43
126 69 0.27
127 38 0.15
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (125 bp):
AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTAGTCCTAGAAGAAATAAT
TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAG
Found at i:43232470 original size:18 final size:18
Alignment explanation
Indices: 43232447--43232486 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43232437 GACTCGGAAA
* *
43232447 AGGATATATATAAGGGTT
1 AGGATACATATAAGGGCT
43232465 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
43232483 AGGA
1 AGGA
43232487 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:43233152 original size:7 final size:7
Alignment explanation
Indices: 43233140--43233176 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
43233130 TATACATAAC
43233140 ACTAATT
1 ACTAATT
43233147 ACTAATT
1 ACTAATT
43233154 ACTAATT
1 ACTAATT
43233161 ACTAATT
1 ACTAATT
43233168 ACTAATT
1 ACTAATT
43233175 AC
1 AC
43233177 CAATCGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (7 bp):
ACTAATT
Found at i:43244194 original size:22 final size:20
Alignment explanation
Indices: 43244159--43244200 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
43244149 TCATTGTTGA
*
43244159 GAAATTGATGAATTAGGCTT
1 GAAATTGATGAATTAAGCTT
43244179 GAAATTGATAGAAATTAAGCTT
1 GAAATTGAT-G-AATTAAGCTT
43244201 CGATCATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (20 bp):
GAAATTGATGAATTAAGCTT
Found at i:43249408 original size:27 final size:27
Alignment explanation
Indices: 43249369--43249620 Score: 264
Period size: 27 Copynumber: 9.4 Consensus size: 27
43249359 AGAGATCAAT
43249369 AAATGA-TCGAAATACCCCCATAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
43249396 AAATGACTAAAATACCCCCATGGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * * *
43249423 AAACGA-TCGAAATAACCCAATAGGATA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
43249450 AAATGATTGAAATACCCCCATAGGATA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
43249477 AAATGATTGAAATAACCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
43249504 AAATGA-TCGAAATA-CCCTATAGGGGTA
1 AAATGACT-GAAATACCCCCATA-GGGTA
* *
43249531 AAATGACCGAAATA-CCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
43249557 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
43249584 AAATAACTGATATACCCCTA-AGAGGTA
1 AAATGACTGAAATACCCCCATAG-GGTA
43249611 AAATGACTGA
1 AAATGACTGA
43249621 TATGATATGG
Statistics
Matches: 196, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
26 29 0.15
27 165 0.84
28 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:43249504 original size:81 final size:81
Alignment explanation
Indices: 43249369--43249586 Score: 305
Period size: 81 Copynumber: 2.7 Consensus size: 81
43249359 AGAGATCAAT
* *
43249369 AAATGATCGAAATACCCCCATAGGGTAAAATGACTAAAATACCCCCATGGGGTAAAACGATCGAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAACGATCGAA
43249434 ATAACCCAATA-GGATA
66 AT-ACCCAATAGGGATA
* * * * *
43249450 AAATGATTGAAATACCCCCATAGGATAAAATGATTGAAATAACCCCATAGGGTAAAATGATCGAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAACGATCGAA
* *
43249515 ATACCCTATAGGGGTA
66 ATACCCAATAGGGATA
* * *
43249531 AAATGACCGAAATA-CCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAA
43249587 TAACTGATAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 44 0.37
81 76 0.63
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAACGATCGAA
ATACCCAATAGGGATA
Found at i:43249789 original size:26 final size:26
Alignment explanation
Indices: 43249759--43249813 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
43249749 TGGAGGAAGT
* *
43249759 ATACTGTTACTGGCAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGCTGCG
43249785 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
43249811 ATA
1 ATA
43249814 TTAGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:43259909 original size:19 final size:18
Alignment explanation
Indices: 43259863--43259910 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
43259853 GATAGAATTT
*
43259863 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
43259882 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
43259900 TTGTATTAAAA
1 TTGTA-TAAAA
43259911 ATTTAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:43259969 original size:20 final size:21
Alignment explanation
Indices: 43259925--43259972 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
43259915 AAACATGTTA
43259925 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
43259947 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
43259967 ATTTTT
1 ATTTTT
43259973 GATAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:43264532 original size:20 final size:20
Alignment explanation
Indices: 43264503--43264542 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43264493 TTATAAAGTT
*
43264503 AATAATAAAATACCTTACAA
1 AATAACAAAATACCTTACAA
*
43264523 AATAACAAAATATCTTACAA
1 AATAACAAAATACCTTACAA
43264543 CTCATCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAACAAAATACCTTACAA
Found at i:43264720 original size:13 final size:13
Alignment explanation
Indices: 43264702--43264735 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
43264692 ATTTTGTTAT
43264702 TATCTTTACAAAA
1 TATCTTTACAAAA
43264715 TATCTTATTACAAAA
1 TATC-T-TTACAAAA
43264730 TATCTT
1 TATCTT
43264736 ACATAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.26
14 2 0.11
15 12 0.63
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
TATCTTTACAAAA
Found at i:43264727 original size:15 final size:15
Alignment explanation
Indices: 43264707--43264736 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43264697 GTTATTATCT
43264707 TTACAAAATATCTTA
1 TTACAAAATATCTTA
43264722 TTACAAAATATCTTA
1 TTACAAAATATCTTA
43264737 CATAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TTACAAAATATCTTA
Found at i:43273116 original size:41 final size:41
Alignment explanation
Indices: 43272958--43273114 Score: 212
Period size: 41 Copynumber: 3.8 Consensus size: 41
43272948 TTTTTAGAGT
43272958 AGCGCCGCTAATGCTCGAGGTTTTAGCGGCGTTTATGATTA
1 AGCGCCGCTAATGCTCGAGGTTTTAGCGGCGTTTATGATTA
43272999 AGCGCCGCTAATGCTC-AGGGTTTTAGCGGCGTTTATGATTA
1 AGCGCCGCTAATGCTCGA-GGTTTTAGCGGCGTTTATGATTA
* * * * *
43273040 AGTGCCGCTAATGCTTGAGGTTTTAGCGGCATTTTTGA-AA
1 AGCGCCGCTAATGCTCGAGGTTTTAGCGGCGTTTATGATTA
*
43273080 AGGCGCCACTAATGCTCG-GGTTTTTAGCGGCGTTT
1 A-GCGCCGCTAATGCTCGAGG-TTTTAGCGGCGTTT
43273115 TTTTGAAAGC
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
40 5 0.05
41 97 0.94
42 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (41 bp):
AGCGCCGCTAATGCTCGAGGTTTTAGCGGCGTTTATGATTA
Found at i:43273624 original size:21 final size:19
Alignment explanation
Indices: 43273598--43273644 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
43273588 GGGTTAGACG
*
43273598 TTAGGGGTTAGGAGTAGGGAT
1 TTAGGGGTTA-G-CTAGGGAT
*
43273619 TTAGGGTTTAGCTAGGGAT
1 TTAGGGGTTAGCTAGGGAT
43273638 TTAGGGG
1 TTAGGGG
43273645 CCTGGTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.57
20 1 0.04
21 9 0.39
ACGTcount: A:0.21, C:0.02, G:0.45, T:0.32
Consensus pattern (19 bp):
TTAGGGGTTAGCTAGGGAT
Found at i:43274911 original size:14 final size:15
Alignment explanation
Indices: 43274894--43274926 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43274884 GGGTTGGGAT
43274894 TTAAGGT-TTAGGGG
1 TTAAGGTGTTAGGGG
43274908 TTAA-GTGTTAGGGG
1 TTAAGGTGTTAGGGG
43274922 TTAAG
1 TTAAG
43274927 AGTTAGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.36
Consensus pattern (15 bp):
TTAAGGTGTTAGGGG
Found at i:43274931 original size:14 final size:14
Alignment explanation
Indices: 43274901--43274932 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
43274891 GATTTAAGGT
*
43274901 TTAGGGGTTAAGTG
1 TTAGGGGTTAAGAG
43274915 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
43274929 TTAG
1 TTAG
43274933 AGATTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.41, T:0.34
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:43279122 original size:43 final size:43
Alignment explanation
Indices: 43279056--43279141 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
43279046 AGTTCATTAG
* * *
43279056 AAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTACC
1 AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
*
43279099 AAGATTTACTTGATTAAGAAAATGCATTATATGTTTTATTACC
1 AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
43279142 TTGCATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (43 bp):
AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
Found at i:43279587 original size:38 final size:38
Alignment explanation
Indices: 43279517--43279592 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
43279507 GGGAAAAGCG
* *
43279517 TCGCTAAAAGAGATGATCTATAGCGCCATTTGTGGGAA
1 TCGCTAAAAGACATGATCTATAGAGCCATTTGTGGGAA
* *
43279555 TCGCTAAAAGTCATGATCTATAGTAG-CGTTTGTGGGAA
1 TCGCTAAAAGACATGATCTATAG-AGCCATTTGTGGGAA
43279593 AAGCGCCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 32 0.97
39 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (38 bp):
TCGCTAAAAGACATGATCTATAGAGCCATTTGTGGGAA
Found at i:43279665 original size:43 final size:43
Alignment explanation
Indices: 43279409--43279667 Score: 144
Period size: 43 Copynumber: 6.2 Consensus size: 43
43279399 GATATGTTTT
* * * * **
43279409 TAGCGGTGTTTGAGTGAAAAGCGCTGCTAAAGGTC-TG-TTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATT-TA
* * * * * *
43279451 TAGCAGCGTTTGTACGAAAAAGCGTCGTTAAAGATC-TG-TTCTA
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAAATCATGATT-TA
* * * *
43279494 TAGCGACGTTTGTGGGAAAAGCGTCGCTAAAAGA-GATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAA-ATCATGATTTA
* * * * *
43279537 TAGCGCCATTTGTGGG--AA---TCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATTTA
** * *
43279575 TAGTAGCGTTTGTGGGAAAAGCGCCGGTAAAAATTATGATTTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATTTA
* **
43279618 TAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCATGACTTT-
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGA-TTTA
43279661 TAGCGGC
1 TAGCGGC
43279668 ATTTATTTCT
Statistics
Matches: 168, Mismatches: 38, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
38 29 0.17
40 2 0.01
41 2 0.01
42 25 0.15
43 106 0.63
44 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATTTA
Found at i:43286651 original size:130 final size:130
Alignment explanation
Indices: 43286415--43286678 Score: 456
Period size: 130 Copynumber: 2.0 Consensus size: 130
43286405 ACTCGATCAA
*
43286415 CTCTTTGTGGATTCTGCACTTCATTCAATACAATTCAGGATTCTCTTAAACCCTTTCCTCTTGAT
1 CTCTTTGTAGATTCTGCACTTCATTCAATACAATTCAGGATTCTCTTAAACCCTTTCCTCTTGAT
* * *
43286480 TCATTATTTATGTTTATTTTTAGTATCAAATTTATTGTGTTTATGAAATCCATGAGAAACTAATC
66 TCATTACTTATGTTTATTTTTAGTATCAAATTTATTATGTTTATGAAATCCATGAGAAAATAATC
* * * *
43286545 CTCTTTGTAGATTTTGCACTTCATTCAATATAATTCAGGATTCTCTTAAACCCTTTTCTTTTGAT
1 CTCTTTGTAGATTCTGCACTTCATTCAATACAATTCAGGATTCTCTTAAACCCTTTCCTCTTGAT
43286610 TCATTACTTATGTTTATTTTTAGTATCAAATTTATTATGTTTATGAAATCCATGAGAAAATAATC
66 TCATTACTTATGTTTATTTTTAGTATCAAATTTATTATGTTTATGAAATCCATGAGAAAATAATC
43286675 CTCT
1 CTCT
43286679 CATGGGGGAT
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 126 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.46
Consensus pattern (130 bp):
CTCTTTGTAGATTCTGCACTTCATTCAATACAATTCAGGATTCTCTTAAACCCTTTCCTCTTGAT
TCATTACTTATGTTTATTTTTAGTATCAAATTTATTATGTTTATGAAATCCATGAGAAAATAATC
Found at i:43288434 original size:26 final size:27
Alignment explanation
Indices: 43288384--43288434 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
43288374 AGTTAATAAA
* *
43288384 TTCTCTTTGAGTTTTATTTTCAAGAAT
1 TTCTCTTTGAGTTTCATTTACAAGAAT
*
43288411 TTCT-TTTGAGTTTCATTTAGAAGA
1 TTCTCTTTGAGTTTCATTTACAAGA
43288435 GTTTTAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (27 bp):
TTCTCTTTGAGTTTCATTTACAAGAAT
Found at i:43291167 original size:21 final size:20
Alignment explanation
Indices: 43291141--43291188 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
43291131 CGTCAATTAT
*
43291141 TTAATTAC-AATAAATTAAA
1 TTAATTACAAAGAAATTAAA
43291160 TAGTAATT-CAAAGAAATTAAA
1 T--TAATTACAAAGAAATTAAA
43291181 TTAATTAC
1 TTAATTAC
43291189 TAAGTCATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (20 bp):
TTAATTACAAAGAAATTAAA
Found at i:43295518 original size:23 final size:23
Alignment explanation
Indices: 43295488--43295533 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
43295478 TCTTCGTCCG
43295488 AGGTAAGTTCGTAAGTAAATTAT
1 AGGTAAGTTCGTAAGTAAATTAT
43295511 AGGTAAGTTCGTAAGTAAATTAT
1 AGGTAAGTTCGTAAGTAAATTAT
43295534 TAAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (23 bp):
AGGTAAGTTCGTAAGTAAATTAT
Found at i:43301424 original size:25 final size:25
Alignment explanation
Indices: 43301389--43301463 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
43301379 TAGAGATTAT
* *
43301389 CGATTCTCAGCTCGTATGAGCTTAC
1 CGATTCACAGCTCGTATGAGCATAC
*
43301414 CGATTTACAGCTCGTGA-GAGCATAC
1 CGATTCACAGCTCGT-ATGAGCATAC
* *
43301439 CGATTCATAGCTCATATGAGCATAC
1 CGATTCACAGCTCGTATGAGCATAC
43301464 ATGTACAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (25 bp):
CGATTCACAGCTCGTATGAGCATAC
Done.