Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_pilon, whole genome shotgun sequence
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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1720055 original size:24 final size:24
Alignment explanation
Indices: 1720028--1720077 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1720018 TGGTGGTTGA
*
1720028 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1720052 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1720076 TT
1 TT
1720078 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1725724 original size:421 final size:421
Alignment explanation
Indices: 1724934--1725782 Score: 1671
Period size: 421 Copynumber: 2.0 Consensus size: 421
1724924 ATTTAGACCT
*
1724934 TACCTAATAGGCACTAAAGTTATTGTTCACACTGATCATTCGGCTATAAAATACTTAGTGAACAA
1 TACCTGATAGGCACTAAAGTTATTGTTCACACTGATCATTCGGCTATAAAATACTTAGTGAACAA
1724999 AAAGGATGCCAAGCCTAGACTTATTAGGTGGATCTTACTTTTGCAAGAATTTGAATTAGAGGTGG
66 AAAGGATGCCAAGCCTAGACTTATTAGGTGGATCTTACTTTTGCAAGAATTTGAATTAGAGGTGG
1725064 TAGATAGAAAAGGAACTGAAAATCAAGTTGTTGATCACTTATCTAGGCTAGAGAATAATTTTGAA
131 TAGATAGAAAAGGAACTGAAAATCAAGTTGTTGATCACTTATCTAGGCTAGAGAATAATTTTGAA
1725129 TGCCATGACAATGTAGATATCCAAGAGGAATTTCCTGATGAGAAAATTTTATATGCCACGGCAAT
196 TGCCATGACAATGTAGATATCCAAGAGGAATTTCCTGATGAGAAAATTTTATATGCCACGGCAAT
*
1725194 CCCGTGGTACGCTGACCTTGTTAATTTTCTTGTTAGTGGAATTGTGCCTTTTGATTTGAATAGTC
261 CCCGTGGTACGCTGACCTTGTTAATTTTCTTATTAGTGGAATTGTGCCTTTTGATTTGAATAGTC
1725259 AGGATAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGGGATGAGCCATATCTGTTCAAG
326 AGGATAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGGGATGAGCCATATCTGTTCAAG
1725324 CATTGTGTTGATCAGCTCATTAGACGATGTG
391 CATTGTGTTGATCAGCTCATTAGACGATGTG
1725355 TACCTGATAGGCACTAAAGTTATTGTTCACACTGATCATTCGGCTATAAAATACTTAGTGAACAA
1 TACCTGATAGGCACTAAAGTTATTGTTCACACTGATCATTCGGCTATAAAATACTTAGTGAACAA
1725420 AAAGGATGCCAAGCCTAGACTTATTAGGTGGATCTTACTTTTGCAAGAATTTGAATTAGAGGTGG
66 AAAGGATGCCAAGCCTAGACTTATTAGGTGGATCTTACTTTTGCAAGAATTTGAATTAGAGGTGG
1725485 TAGATAGAAAAGGAACTGAAAATCAAGTTGTTGATCACTTATCTAGGCTAGAGAATAATTTTGAA
131 TAGATAGAAAAGGAACTGAAAATCAAGTTGTTGATCACTTATCTAGGCTAGAGAATAATTTTGAA
1725550 TGCCATGACAATGTAGATATCCAAGAGGAATTTCCTGATGAGAAAATTTTATATGCCACGGCAAT
196 TGCCATGACAATGTAGATATCCAAGAGGAATTTCCTGATGAGAAAATTTTATATGCCACGGCAAT
1725615 CCCGTGGTACGCTGACCTTGTTAATTTTCTTATTAGTGGAATTGTGCCTTTTGATTTGAATAGTC
261 CCCGTGGTACGCTGACCTTGTTAATTTTCTTATTAGTGGAATTGTGCCTTTTGATTTGAATAGTC
*
1725680 AGGCTAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGGGATGAGCCATATCTGTTCAAG
326 AGGATAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGGGATGAGCCATATCTGTTCAAG
1725745 CATTGTGTTGATCAGCTCATTAGACGATGTG
391 CATTGTGTTGATCAGCTCATTAGACGATGTG
1725776 TACCTGA
1 TACCTGA
1725783 AGAGGAGCAA
Statistics
Matches: 425, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
421 425 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (421 bp):
TACCTGATAGGCACTAAAGTTATTGTTCACACTGATCATTCGGCTATAAAATACTTAGTGAACAA
AAAGGATGCCAAGCCTAGACTTATTAGGTGGATCTTACTTTTGCAAGAATTTGAATTAGAGGTGG
TAGATAGAAAAGGAACTGAAAATCAAGTTGTTGATCACTTATCTAGGCTAGAGAATAATTTTGAA
TGCCATGACAATGTAGATATCCAAGAGGAATTTCCTGATGAGAAAATTTTATATGCCACGGCAAT
CCCGTGGTACGCTGACCTTGTTAATTTTCTTATTAGTGGAATTGTGCCTTTTGATTTGAATAGTC
AGGATAAAAAGAAGTTCAAGCACGATGCAAGGCACTATTTTTGGGATGAGCCATATCTGTTCAAG
CATTGTGTTGATCAGCTCATTAGACGATGTG
Found at i:1727347 original size:19 final size:21
Alignment explanation
Indices: 1727310--1727352 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1727300 TAACTTTTTC
*
1727310 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
1727330 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
1727350 TTT
1 TTT
1727353 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:1730663 original size:23 final size:24
Alignment explanation
Indices: 1730637--1730685 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1730627 TGGTGGTTGA
*
1730637 TTTAATGGT-TGTTTGAA-TTTATT
1 TTTAATGGTATATTT-AAGTTTATT
1730660 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAAGTTTATT
1730684 TT
1 TT
1730686 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTAATGGTATATTTAAGTTTATT
Found at i:1732187 original size:3 final size:3
Alignment explanation
Indices: 1732181--1732246 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
1732171 CATTTATTAT
* *
1732181 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TTAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* *
1732226 TAG T-A TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1732247 GGAAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 3 0.06
3 48 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1732457 original size:39 final size:39
Alignment explanation
Indices: 1732413--1732945 Score: 646
Period size: 39 Copynumber: 13.7 Consensus size: 39
1732403 AGGTTGAATA
* *
1732413 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
* * *
1732452 AGTTCTTCAGATTATGAAC-TCATTTTTTCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
*
1732491 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
* * * *
1732530 AGTTCTTCAAATTATTAAC-TCATTCTTTCTCTTCAGACA
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
* *
1732569 AGTTCTTCAGATTATGGAC-TCATTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
* * *
1732608 AGTTCTTCAGATTATAAACTCCTTCTTCCTCTTCAAACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
* * * *
1732647 AGTTCTTTAGATTATGAACTCCTTTTTCCTCTTCATACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
1732686 AGTTCTTCAGATTATGAAC-TCATTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
* *
1732725 AGTTCTTCAGATTATGAACTTCTTTTTCCTCTTCAGTCG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
* * *
1732764 AGTTCTTCAGATTATGAAC-TCATTTTTCATATTCAGACG
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
* * * * * *
1732803 AGTTTTTCAAATTATGAAATCCTTTTTTCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
*
1732842 AGTTCTTCAGATTATGAAC-TCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTTC-TTCTTCCTCTTCAGACG
* * *
1732881 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTTAGACG
1 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
* *
1732920 AGTTCTTTAGATTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTTCTTCT
1732946 GGAAATGTTT
Statistics
Matches: 430, Mismatches: 54, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
38 7 0.02
39 417 0.97
40 6 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
Found at i:1732529 original size:78 final size:78
Alignment explanation
Indices: 1732413--1732945 Score: 746
Period size: 78 Copynumber: 6.8 Consensus size: 78
1732403 AGGTTGAATA
* * * * *
1732413 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGACGAGTTCTTCAGATTATGAACTCATTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
*
1732478 TTCTCTTCAGATG
66 TTCTCTTCAGACG
* * *
1732491 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAAATTATTAACTCATTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
*
1732556 TTCTCTTCAGACA
66 TTCTCTTCAGACG
* * * * * *
1732569 AGTTCTTCAGATTATGGACTCATTCTTCCTCTTCAGATGAGTTCTTCAGATTATAAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* *
1732634 TCCTCTTCAAACG
66 TTCTCTTCAGACG
* *
1732647 AGTTCTTTAGATTATGAACTCCTTTTTCCTCTTCATACGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
*
1732712 TCCTCTTCAGACG
66 TTCTCTTCAGACG
* *
1732725 AGTTCTTCAGATTATGAACTTCTTTTTCCTCTTCAGTCGAGTTCTTCAGATTATGAACTCATT-T
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
*
1732789 TTCATATTCAGACG
66 TTC-TCTTCAGACG
* * * * *
1732803 AGTTTTTCAAATTATGAAATCCTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTC-TTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
1732867 TTCCTCTTCAGACG
66 TT-CTCTTCAGACG
* * *
1732881 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTTAGACGAGTTCTTTAGATTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
1732946 GGAAATGTTT
Statistics
Matches: 405, Mismatches: 46, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
77 5 0.01
78 396 0.98
79 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (78 bp):
AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
TTCTCTTCAGACG
Found at i:1732619 original size:117 final size:116
Alignment explanation
Indices: 1732413--1732945 Score: 717
Period size: 117 Copynumber: 4.6 Consensus size: 116
1732403 AGGTTGAATA
* * * *
1732413 AGTTCTTCAGACTATGAACTTC-TTCTTCCTCTTTAGACGAGTTCTTCAGATTATGAACTCATTT
1 AGTTCTTCAGATTATGAAC-TCATT-TTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTC
* *
1732477 TTTCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
64 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
* * * *
1732530 AGTTCTTCAAATTATTAACTCATTCTTTCTCTTCAGACAAGTTCTTCAGATTATGGACTCATTCT
1 AGTTCTTCAGATTATGAACTCATT-TTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * *
1732595 TCCTCTTCAGATGAGTTCTTCAGATTATAAACTCCTTCTTCCTCTTCAAACG
65 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
* * *
1732647 AGTTCTTTAGATTATGAACTCCTTTTTCCTCTTCATACGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGATTATGAACTCATTTTT-CTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * *
1732712 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTTCTTTTTCCTCTTCAGTCG
65 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
* * * * * *
1732764 AGTTCTTCAGATTATGAACTCATTTTTCATATTCAGACGAGTTTTTCAAATTATGAAATCCTTTT
1 AGTTCTTCAGATTATGAACTCATTTTTC-TCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * *
1732829 TTCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTTTCCTCTTCAGACG
65 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
* * * *
1732881 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTTAGACGAGTTCTTTAGATTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCATTTTT-CTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
1732946 GGAAATGTTT
Statistics
Matches: 367, Mismatches: 45, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
116 6 0.02
117 360 0.98
118 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (116 bp):
AGTTCTTCAGATTATGAACTCATTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCTT
CCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
Found at i:1733102 original size:45 final size:45
Alignment explanation
Indices: 1732994--1733382 Score: 428
Period size: 45 Copynumber: 8.6 Consensus size: 45
1732984 TTGTTATTTC
* *
1732994 AAAACATC-TGGCACTGAAGGTCTTATGGATGGCCTGAAGGACTTTTTG
1 AAAACATCAT-GCACTGAAGGTCTTATGGATGACCCGAAGG-C--TTTG
* *
1733042 AAAACATCCTGCACTGTAGGT-TATATGGATGACCCGAAGGCTTTG
1 AAAACATCATGCACTGAAGGTCT-TATGGATGACCCGAAGGCTTTG
* * **
1733087 AAATCATCATGCACTGAAGGTCTTATAGATGTGCCGAAGGCTTTTG
1 AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGC-TTTG
** *
1733133 AAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTG
1 AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTG
* * *
1733178 AAAACATCCTGCA-TTATAGGTCTTATGGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGA-AGGTCTTATGGATGACCCGAAGGCTTTG
* ** *
1733223 AAAATATTC-TGCACTGAAGGTCTTACAGATGACCTGAAGGCTTTG
1 AAAACA-TCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTG
* * *
1733268 AAAACATCCTGCATTGTAGGTCTTATGGATGACCC-AGAGGCTTTG
1 AAAACATCATGCACTGAAGGTCTTATGGATGACCCGA-AGGCTTTG
* * * * *
1733313 AAAACAACTTGCACTGTATGTCTTATGGATGACCTGAAGGCTTTG
1 AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTG
1733358 AAAACATCATGCACTGAAGGTCTTA
1 AAAACATCATGCACTGAAGGTCTTA
1733383 CAGATGTGGG
Statistics
Matches: 290, Mismatches: 41, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
44 5 0.02
45 203 0.70
46 46 0.16
47 2 0.01
48 33 0.11
49 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTG
Found at i:1733342 original size:135 final size:136
Alignment explanation
Indices: 1732994--1733389 Score: 489
Period size: 135 Copynumber: 2.9 Consensus size: 136
1732984 TTGTTATTTC
** * **
1732994 AAAACATC-TGGCACTGAAGGTCTTATGGATGGCCTGAAGGACTTTTTGAAAACATCCTGCACTG
1 AAAACATCAT-GCACTGAAGGTCTTACAGATGACCCAAAGG-C--TTTGAAAACATCCTGCACTG
* *
1733058 TAGGT-TATATGGATGACCCGAAGGCTTTG-AAATCATCATGCACTGAAGGTCTTATAGATGTGC
62 TAGGTCT-TATGGATGACCCGAAGGCTTTGAAAAT-ATCATGCACTGAAGGTCTTACAGATGTAC
1733121 CGAAGGCTTTTG
125 CGAAGGCTTTTG
* *
1733133 AAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTGAAAACATCCTGCATTATAGG
1 AAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTGAAAACATCCTGCACTGTAGG
*
1733198 TCTTATGGATGACCCGAAGGTTTTGAAAATATTC-TGCACTGAAGGTCTTACAGATG-ACCTGAA
66 TCTTATGGATGACCCGAAGGCTTTGAAAATA-TCATGCACTGAAGGTCTTACAGATGTACC-GAA
1733261 GGC-TTTG
129 GGCTTTTG
* * * ** * * * *
1733268 AAAACATCCTGCATTGTAGGTCTTATGGATGACCCAGAGGCTTTGAAAACAACTTGCACTGTATG
1 AAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTGAAAACATCCTGCACTGTAGG
* *
1733333 TCTTATGGATGACCTGAAGGCTTTGAAAACATCATGCACTGAAGGTCTTACAGATGT
66 TCTTATGGATGACCCGAAGGCTTTGAAAATATCATGCACTGAAGGTCTTACAGATGT
1733390 GGGAAATAGT
Statistics
Matches: 226, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
134 2 0.01
135 110 0.49
136 72 0.32
137 7 0.03
138 1 0.00
139 33 0.15
140 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (136 bp):
AAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGGCTTTGAAAACATCCTGCACTGTAGG
TCTTATGGATGACCCGAAGGCTTTGAAAATATCATGCACTGAAGGTCTTACAGATGTACCGAAGG
CTTTTG
Found at i:1734046 original size:22 final size:22
Alignment explanation
Indices: 1734018--1734094 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
1734008 AATAAAGCTT
1734018 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1734040 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
1734062 TCATCTTTGAAGAATA-AATCTA
1 TCATCTTTGAA-AAGAGAATCTA
*
1734084 TTATCTTTGAA
1 TCATCTTTGAA
1734095 GAATGTAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 47 0.94
23 3 0.06
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1734548 original size:54 final size:54
Alignment explanation
Indices: 1734466--1734627 Score: 288
Period size: 54 Copynumber: 3.0 Consensus size: 54
1734456 ATAATCACTG
*
1734466 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
*
1734520 GTTCGTAAAACATTTGACAACACATTCATCATTTCTTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
* *
1734574 ATTCATAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
1734628 TTCTCAATCA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTATGGCTTCTGCCCAGAT
Found at i:1735624 original size:75 final size:75
Alignment explanation
Indices: 1735501--1735752 Score: 362
Period size: 75 Copynumber: 3.4 Consensus size: 75
1735491 ATAAGATGAT
* * * *
1735501 ATGGGCCTTCAGCATGCCCCAACATTTGTTGATACAAATGTTCAAAACACATCAACATTCATGAT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGAT
* *
1735566 TCTAATTAAA
66 TCTGATTGAA
* *
1735576 ATGGGCTTTCAGCATGCCCTAACATTTGCTGATAAAAACGTTCAAAACACATCAACATTCCT-AT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGA-
1735640 TTCTGATTGAA
65 TTCTGATTGAA
* * * *
1735651 ATGGGCTTTCATCATGCCCTAACATTTACTGATACAAACGTTCAAAATACATCAACATTCCTGAT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGAT
*
1735716 TTTGATTGAA
66 TCTGATTGAA
*
1735726 ATGGGCTTTTAGCATGCCCCAACATTT
1 ATGGGCTTTCAGCATGCCCCAACATTT
1735753 TTTCATATTG
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
74 1 0.01
75 157 0.99
76 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGAT
TCTGATTGAA
Found at i:1736740 original size:40 final size:40
Alignment explanation
Indices: 1736685--1736764 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1736675 TTTCTTGATT
1736685 CCAGAATCTCAAGAACGTCTTTAGGATGTGCGGTGCTTCA
1 CCAGAATCTCAAGAACGTCTTTAGGATGTGCGGTGCTTCA
1736725 CCAGAATCTCAAGAACGTCTTTAGGATGTGCGGTGCTTCA
1 CCAGAATCTCAAGAACGTCTTTAGGATGTGCGGTGCTTCA
1736765 TCAAGAGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (40 bp):
CCAGAATCTCAAGAACGTCTTTAGGATGTGCGGTGCTTCA
Found at i:1740332 original size:42 final size:43
Alignment explanation
Indices: 1740285--1740366 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 43
1740275 TACATCAAAT
1740285 AAAACTTTACATATAGGG-ATAA-ATTTCACTCCTAACTTCAAC
1 AAAACTTTACATATAGGGTATAACATTT-ACTCCTAACTTCAAC
*
1740327 AAAACTTTACATATAGGGTATAACCTTTACTCCTAACTTC
1 AAAACTTTACATATAGGGTATAACATTTACTCCTAACTTC
1740367 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 18 0.49
43 16 0.43
44 3 0.08
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (43 bp):
AAAACTTTACATATAGGGTATAACATTTACTCCTAACTTCAAC
Found at i:1741002 original size:18 final size:20
Alignment explanation
Indices: 1740969--1741008 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1740959 TCTTGATCAT
*
1740969 AAAACTTTTTCCATTT-ATG
1 AAAACTTTTTCAATTTGATG
1740988 AAAACTTTTT-AATTTGATG
1 AAAACTTTTTCAATTTGATG
1741007 AA
1 AA
1741009 CACTCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (20 bp):
AAAACTTTTTCAATTTGATG
Found at i:1742434 original size:2 final size:2
Alignment explanation
Indices: 1742427--1742460 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1742417 AATGAAGTAA
1742427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1742461 AACAGGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1742606 original size:14 final size:13
Alignment explanation
Indices: 1742589--1742634 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1742579 AATATTAGTG
1742589 AATAAAACATAAAT
1 AATAAAA-ATAAAT
1742603 AATAACAAATAAAT
1 AATAA-AAATAAAT
*
1742617 AA-ATAAATAAAT
1 AATAAAAATAAAT
1742629 -ATAAAA
1 AATAAAA
1742635 TACTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 11 0.39
13 1 0.04
14 13 0.46
15 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:1742994 original size:34 final size:35
Alignment explanation
Indices: 1742956--1743028 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
1742946 GTTAATGACA
*
1742956 AAATTATAAAAAAATAAAATTTGGAGACCAAATT-
1 AAATTATAAAAAAATAAAATTTAGAGACCAAATTG
** * * *
1742990 AAATTATTCAGAAATATAATTTAGTGACCAAATTG
1 AAATTATAAAAAAATAAAATTTAGAGACCAAATTG
1743025 AAAT
1 AAAT
1743029 AACTCCAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (35 bp):
AAATTATAAAAAAATAAAATTTAGAGACCAAATTG
Found at i:1744032 original size:3 final size:3
Alignment explanation
Indices: 1744024--1744105 Score: 101
Period size: 3 Copynumber: 27.3 Consensus size: 3
1744014 AATTATTTAT
* * *
1744024 TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1744072 TAA TAA TAA AAA TTA TTA TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1744106 GTAAAAATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1746246 original size:14 final size:14
Alignment explanation
Indices: 1746227--1746256 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1746217 AACAACTAAC
1746227 ATAAAGAATTTTGG
1 ATAAAGAATTTTGG
1746241 ATAAAGAATTTTGG
1 ATAAAGAATTTTGG
1746255 AT
1 AT
1746257 TCTAAGGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (14 bp):
ATAAAGAATTTTGG
Found at i:1749347 original size:28 final size:29
Alignment explanation
Indices: 1749272--1749642 Score: 222
Period size: 30 Copynumber: 12.6 Consensus size: 29
1749262 TTAATTTTAC
1749272 ATCTTAACATTAAAAATATATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTTTT
*
1749302 ATAC-TAACTTATTAAATATATTTTATTTTT
1 AT-CTTAACTTA-AAAATATATTTTATTTTT
* *
1749332 GTCTTAA-TCT-AAAATATATTTTATTCTT
1 ATCTTAACT-TAAAAATATATTTTATTTTT
* * *
1749360 ATTTTAAATTAAAAATATATTTTAGTCTTT
1 ATCTTAACTTAAAAATATATTTTA-TTTTT
*
1749390 ATCTTAACTTAAAAATATATAATTTATTCTT
1 ATCTTAACTTAAAAATATAT--TTTATTTTT
* * * * *
1749421 ATCTTAACTTATTACATAAATTATATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTTTT
* * * * *
1749451 AACTTAAATTATTAAATATATTCTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTTTT
* * * * * *
1749481 ACCTTAAAATTATTAAATATAATTAATTCTT
1 ATCTT-AACTTA-AAAATATATTTTATTTTT
* *
1749512 ATTTTAACTTAAAACATATCTTTT-TGTTCTT
1 ATCTTAACTTAAAA-ATATATTTTAT-TT-TT
**
1749543 ATCTTAACTTAAAAA-ATATTTTCGTTTT
1 ATCTTAACTTAAAAATATATTTTATTTTT
*
1749571 AAC-T-AC--AAAAATATATTTTATTTTT
1 ATCTTAACTTAAAAATATATTTTATTTTT
* * **
1749596 ATCTTAGC-TACAAAAAATATTACATTTTT
1 ATCTTAACTTA-AAAATATATTTTATTTTT
* * *
1749625 ACCTTAAATTTAAAATAT
1 ATCTTAACTTAAAAATAT
1749643 CATCAGAATA
Statistics
Matches: 271, Mismatches: 49, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
24 5 0.02
25 13 0.05
26 3 0.01
27 2 0.01
28 27 0.10
29 56 0.21
30 100 0.37
31 55 0.20
32 10 0.04
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTTTT
Found at i:1749355 original size:58 final size:59
Alignment explanation
Indices: 1749272--1749599 Score: 214
Period size: 61 Copynumber: 5.6 Consensus size: 59
1749262 TTAATTTTAC
* *
1749272 ATCTTAACATTAAAAATATATTTTATTTTTATACTAACTTATTAAATATATTTTA-TTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTTAT-CTAACTTATTAAATATATTTTAGTCTTT
* * * *
1749332 GTCTTAA-TCT-AAAATATATTTTATTCTTATTTTAAATTA-AAAATATATTTTAGTCTTT
1 ATCTTAACT-TAAAAATATATTTTATTCTTA-TCTAACTTATTAAATATATTTTAGTCTTT
* * * *
1749390 ATCTTAACTTAAAAATATATAATTTATTCTTATCTTAACTTATTACATAAATTATATTC-TT
1 ATCTTAACTTAAAAATATAT--TTTATTCTTATC-TAACTTATTAAATATATTTTAGTCTTT
* * * * * * * * *
1749451 AACTTAAATTATTAAATATATTCTATTCTTACCTTAAAATTATTAAATATAATTAATTC-TT
1 ATCTTAACTTA-AAAATATATTTTATTCTTATC-T-AACTTATTAAATATATTTTAGTCTTT
* * * * *
1749512 ATTTTAACTTAAAACATATCTTTTTGTTCTTATCTTAACTTA--AAAAATATTTTCGT-TTT
1 ATCTTAACTTAAAA-ATAT-ATTTTATTCTTATC-TAACTTATTAAATATATTTTAGTCTTT
* *
1749571 AAC-T-AC--AAAAATATATTTTATTTTTATCT
1 ATCTTAACTTAAAAATATATTTTATTCTTATCT
1749600 TAGCTACAAA
Statistics
Matches: 210, Mismatches: 44, Indels: 36
0.72 0.15 0.12
Matches are distributed among these distances:
52 1 0.00
53 11 0.05
54 4 0.02
55 4 0.02
57 14 0.07
58 37 0.18
59 24 0.11
60 21 0.10
61 63 0.30
62 31 0.15
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (59 bp):
ATCTTAACTTAAAAATATATTTTATTCTTATCTAACTTATTAAATATATTTTAGTCTTT
Found at i:1749426 original size:31 final size:29
Alignment explanation
Indices: 1749272--1749601 Score: 237
Period size: 30 Copynumber: 11.2 Consensus size: 29
1749262 TTAATTTTAC
*
1749272 ATCTTAACATTAAAAATATATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
* *
1749302 ATAC-TAACTTATTAAATATATTTTATTTTT
1 AT-CTTAACTTA-AAAATATATTTTATTCTT
*
1749332 GTCTTAA-TCT-AAAATATATTTTATTCTT
1 ATCTTAACT-TAAAAATATATTTTATTCTT
* * *
1749360 ATTTTAAATTAAAAATATATTTTAGTCTTT
1 ATCTTAACTTAAAAATATATTTTATTC-TT
1749390 ATCTTAACTTAAAAATATATAATTTATTCTT
1 ATCTTAACTTAAAAATATAT--TTTATTCTT
* * * *
1749421 ATCTTAACTTATTACATAAATTATATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * * *
1749451 AACTTAAATTATTAAATATATTCTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * * * *
1749481 ACCTTAAAATTATTAAATATAATTAATTCTT
1 ATCTT-AACTTA-AAAATATATTTTATTCTT
* * *
1749512 ATTTTAACTTAAAACATATCTTTTTGTTCTT
1 ATCTTAACTTAAAA-ATAT-ATTTTATTCTT
*
1749543 ATCTTAACTTAAAAA-ATA--TT-TTCGT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
1749568 -T-TTAACTACAAAAATATATTTTATTTTT
1 ATCTTAACT-TAAAAATATATTTTATTCTT
1749596 ATCTTA
1 ATCTTA
1749602 GCTACAAAAA
Statistics
Matches: 243, Mismatches: 37, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.02
24 6 0.02
25 7 0.03
26 2 0.01
27 2 0.01
28 25 0.10
29 26 0.11
30 98 0.40
31 59 0.24
32 12 0.05
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:1749487 original size:91 final size:91
Alignment explanation
Indices: 1749353--1749522 Score: 209
Period size: 91 Copynumber: 1.9 Consensus size: 91
1749343 AAATATATTT
** * * * *
1749353 TATTCTTATTTTAAATTAAAAATATATTTTAGTCTTTATCTT-AACTTAAAAATATATAATTTAT
1 TATTCTTAACTTAAATTAAAAATATATTCTAGTCTTTACCTTAAAATTAAAAA-ATATAATTAAT
1749417 TCTTATCTTAACTTATTACATAAATTA
65 TCTTATCTTAACTTATTACATAAATTA
* * **
1749444 TATTCTTAACTTAAATTATTAAATATATTCTATTC-TTACCTTAAAATTATTAAATATAATTAAT
1 TATTCTTAACTTAAATTA-AAAATATATTCTAGTCTTTACCTTAAAATTAAAAAATATAATTAAT
*
1749508 TCTTATTTTAACTTA
65 TCTTATCTTAACTTA
1749523 AAACATATCT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
91 46 0.70
92 20 0.30
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (91 bp):
TATTCTTAACTTAAATTAAAAATATATTCTAGTCTTTACCTTAAAATTAAAAAATATAATTAATT
CTTATCTTAACTTATTACATAAATTA
Found at i:1749622 original size:29 final size:30
Alignment explanation
Indices: 1749573--1749630 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1749563 TTCGTTTTAA
** *
1749573 CTACAAAAATATATTTTATTTTTATCTTAG
1 CTACAAAAATATATTACATTTTTACCTTAG
1749603 CTACAAAAA-ATATTACATTTTTACCTTA
1 CTACAAAAATATATTACATTTTTACCTTA
1749631 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.45
Consensus pattern (30 bp):
CTACAAAAATATATTACATTTTTACCTTAG
Found at i:1749752 original size:29 final size:29
Alignment explanation
Indices: 1749647--1749810 Score: 133
Period size: 29 Copynumber: 5.7 Consensus size: 29
1749637 AAATATCATC
* *
1749647 AGAATAAAATATAAATATTTAAGTTAAGATA
1 AGAATAAAATAT--ATTTTTAAATTAAGATA
* * *
1749678 ATAATAAATTATATTTTTCTAATTTAAGATA
1 AGAATAAAATATA-TTTT-TAAATTAAGATA
* * * *
1749709 ATATTAGAATA-ATTTTTAAATTAAAATA
1 AGAATAAAATATATTTTTAAATTAAGATA
* *
1749737 AGAATAAAATATATTTTTACATTAACATA
1 AGAATAAAATATATTTTTAAATTAAGATA
*
1749766 AGAATAAAATATA--TTT-AA-TAAGTTA
1 AGAATAAAATATATTTTTAAATTAAGATA
*
1749791 AG-ATAAAAAATATTTTTAAA
1 AGAATAAAATATATTTTTAAA
1749811 GGTAAGATGT
Statistics
Matches: 109, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
24 9 0.08
25 7 0.06
26 4 0.04
27 5 0.05
28 18 0.17
29 33 0.30
30 4 0.04
31 29 0.27
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
AGAATAAAATATATTTTTAAATTAAGATA
Found at i:1749816 original size:24 final size:26
Alignment explanation
Indices: 1749771--1749835 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 26
1749761 ACATAAGAAT
*
1749771 AAAATATATTTAATAAGTTAAGATAA
1 AAAATATATTTAATAAGGTAAGATAA
* **
1749797 AAAATAT-TTTTA-AAGGTAAGATGT
1 AAAATATATTTAATAAGGTAAGATAA
1749821 AAAAT-TAATTTAATA
1 AAAATAT-ATTTAATA
1749836 TGTGAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.03
24 14 0.45
25 8 0.26
26 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (26 bp):
AAAATATATTTAATAAGGTAAGATAA
Found at i:1750808 original size:21 final size:21
Alignment explanation
Indices: 1750759--1750808 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1750749 TTTTTTTGCT
*
1750759 TTGTAGTTATCGTCACCGTTG
1 TTGTTGTTATCGTCACCGTTG
* * **
1750780 CTGCTGTTATCGTCGTCGTTG
1 TTGTTGTTATCGTCACCGTTG
1750801 TTGTTGTT
1 TTGTTGTT
1750809 GTGGTCACTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.08, C:0.18, G:0.26, T:0.48
Consensus pattern (21 bp):
TTGTTGTTATCGTCACCGTTG
Found at i:1752890 original size:18 final size:18
Alignment explanation
Indices: 1752863--1752897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1752853 TGCCAATAAT
* *
1752863 TAGAAGTTTTATTTCACA
1 TAGAAATTTTATATCACA
1752881 TAGAAATTTTATATCAC
1 TAGAAATTTTATATCAC
1752898 TCTCCAACGT
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:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
TAGAAATTTTATATCACA
Found at i:1756626 original size:14 final size:14
Alignment explanation
Indices: 1756607--1756643 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1756597 AATTTGCAAA
1756607 CTTACAAGGAAATC
1 CTTACAAGGAAATC
1756621 CTTACAAGGAAATC
1 CTTACAAGGAAATC
*
1756635 CTCACAAGG
1 CTTACAAGG
1756644 TAGATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (14 bp):
CTTACAAGGAAATC
Found at i:1757182 original size:65 final size:64
Alignment explanation
Indices: 1757029--1757208 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 64
1757019 TTGGACCCTT
* * *
1757029 AGTGCATCGGTGCACTAAGAGCGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCATG
1 AGTGCATCGATGCA-TAATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCATG
* ** * * * *
1757093 AGTGCATCTATGCATGGCTGGTGCATCGATGTATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGATGCAT-AATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-A
1757156 TG
63 TG
1757158 AGTGCATCGATGCATAATATGTGCATC-AGTGCATAAAATGCATTCGATGTT
1 AGTGCATCGATGCATAATA-GTGCATCGA-TGCATAAAATGCATTCGATGTT
1757209 CAATTTATTC
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
63 1 0.01
64 41 0.44
65 49 0.52
66 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATAATAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCATG
Found at i:1759639 original size:23 final size:23
Alignment explanation
Indices: 1759613--1759689 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
1759603 GATGCATTGA
1759613 TGCACATTCAAGGCGTGCATCGG
1 TGCACATTCAAGGCGTGCATCGG
* * * *
1759636 TGCACCTTC-ATG-GTGTATCGA
1 TGCACATTCAAGGCGTGCATCGG
*
1759657 TGCACATTCAAGGCATGCATCGG
1 TGCACATTCAAGGCGTGCATCGG
*
1759680 TGCACCTTCA
1 TGCACATTCA
1759690 TGGTGTATCG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 23 0.55
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (23 bp):
TGCACATTCAAGGCGTGCATCGG
Found at i:1759660 original size:21 final size:21
Alignment explanation
Indices: 1759631--1759704 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
1759621 CAAGGCGTGC
*
1759631 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* * *
1759652 ATCGATGCACATTCAAGGCATGC
1 ATCGATGCACCTTCATGG--TGT
*
1759675 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
1759696 ATCGATGCA
1 ATCGATGCA
1759705 TATTCAAAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 25 0.60
23 17 0.40
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Found at i:1759676 original size:44 final size:44
Alignment explanation
Indices: 1759611--1759729 Score: 193
Period size: 44 Copynumber: 2.7 Consensus size: 44
1759601 TCGATGCATT
*
1759611 GATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGTATC
1759655 GATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGTATC
* * *
1759699 GATGCATATTCAAAGGGATGCATCGATGCAC
1 GATGCACATTC-AAGGCATGCATCGGTGCAC
1759730 TGATAAGTGT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
44 53 0.76
45 17 0.24
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (44 bp):
GATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGTATC
Found at i:1759710 original size:21 final size:21
Alignment explanation
Indices: 1759611--1759710 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
1759601 TCGATGCATT
* *
1759611 GATGCACATTCAAGGCGTGCATC
1 GATGCACATTC-ATG-GTGTATC
* *
1759634 GGTGCACCTTCATGGTGTATC
1 GATGCACATTCATGGTGTATC
* *
1759655 GATGCACATTCAAGGCATGCATC
1 GATGCACATTCATGG--TGTATC
* *
1759678 GGTGCACCTTCATGGTGTATC
1 GATGCACATTCATGGTGTATC
*
1759699 GATGCATATTCA
1 GATGCACATTCA
1759711 AAGGGATGCA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
21 32 0.53
22 2 0.03
23 26 0.43
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (21 bp):
GATGCACATTCATGGTGTATC
Found at i:1759740 original size:44 final size:44
Alignment explanation
Indices: 1759611--1759749 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 44
1759601 TCGATGCATT
* * * *
1759611 GATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATC
1 GATGCATATTCAAGGCATGCATCGATGCACCTTCATAGTGTATC
* * *
1759655 GATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGTATC
1 GATGCATATTCAAGGCATGCATCGATGCACCTTCATAGTGTATC
* *
1759699 GATGCATATTCAAAGGGATGCATCGATGCA-C-TGATAAGTGTATC
1 GATGCATATTC-AAGGCATGCATCGATGCACCTTCAT-AGTGTATC
1759743 GATGCAT
1 GATGCAT
1759750 GAAGCAAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 3 0.03
44 68 0.78
45 16 0.18
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
GATGCATATTCAAGGCATGCATCGATGCACCTTCATAGTGTATC
Found at i:1763599 original size:22 final size:21
Alignment explanation
Indices: 1763557--1763596 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1763547 GAGCTTATTT
*
1763557 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1763578 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1763597 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1765662 original size:65 final size:64
Alignment explanation
Indices: 1765540--1765747 Score: 176
Period size: 65 Copynumber: 3.2 Consensus size: 64
1765530 TGCACTAAGA
*
1765540 GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGAATTCAATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
* * * *
1765604 GTGCATCGATGTATCAAATGCATTCAATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGA
1 GTGCATCGATGCATAAAATGAATTCAATG-TTTCA-AAATAGC-CTGAGTGCATCGATGCAT-GG
*
1765667 AT-
62 CTG
* * * ** *
1765669 GTGCATC-AGTGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGA
1 GTGCATCGA-TGCATAAAATGAATTCAATGTTTCAAAATA-GCC-TGAGTGCATCGATGCATGG-
*
1765731 TTG
62 CTG
*
1765734 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1765748 CACTCTGAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 43 0.36
65 63 0.53
66 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGAATTCAATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
Found at i:1766244 original size:57 final size:56
Alignment explanation
Indices: 1766151--1766379 Score: 280
Period size: 57 Copynumber: 4.0 Consensus size: 56
1766141 CAGAACCATA
* * * * *
1766151 CAACCCCGTCACGAATAGTAAGGCCTTGAGCCCAAAGCTAAGGAACCTGTAAGTATT
1 CAACCCCATCACGAACAGTAAGGCC-TGAGCACAAAGCCAAGGAACCTGCAAGTATT
1766208 CAACCCCATCACGAACAGTAAGGTCCTGAGCACAAAGCCAAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGG-CCTGAGCACAAAGCCAAGGAACCTGCAAGTATT
* * * * **
1766265 CAACCCCATCATGAACAGTAAGGCTCTCAACATAAAGCTGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGC-CTGAGCACAAAGCCAAGGAACCTGCAAGTATT
* * *
1766322 CAACCCCGTCACAAACAGTAAGG-CTCGTAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCCT-G-AGCACAAAGCCAAGGAACCTGCAAGTATT
1766379 C
1 C
1766380 TTCCTCCAAC
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
55 2 0.01
56 1 0.01
57 145 0.97
58 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (56 bp):
CAACCCCATCACGAACAGTAAGGCCTGAGCACAAAGCCAAGGAACCTGCAAGTATT
Found at i:1773237 original size:19 final size:20
Alignment explanation
Indices: 1773192--1773237 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1773182 AAGGGGGTTT
*
1773192 AGAAAAAATAAATTGAAATA
1 AGAAAAAATAAATTGAAACA
*
1773212 AGTAAAAAT-AA-TGAAAACA
1 AGAAAAAATAAATTG-AAACA
1773231 AGAAAAA
1 AGAAAAA
1773238 TAGATAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.55
20 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (20 bp):
AGAAAAAATAAATTGAAACA
Found at i:1773875 original size:18 final size:18
Alignment explanation
Indices: 1773852--1773896 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1773842 GCTTGAGATA
*
1773852 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAC
*
1773870 ACCTAAAGGAAATAAAAC
1 ACCTAAAGAAAATAAAAC
*
1773888 ACATAAAGA
1 ACCTAAAGA
1773897 TAATCATAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.13, G:0.09, T:0.13
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAC
Found at i:1777243 original size:31 final size:31
Alignment explanation
Indices: 1777201--1777260 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1777191 AACTTAAATG
* *
1777201 AGTTTTGCAATAATGAGATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
*
1777232 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATAATGAAATTTAAATAATT
1777261 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:1777750 original size:20 final size:20
Alignment explanation
Indices: 1777702--1777763 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1777692 AACTTAAATC
*
1777702 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1777722 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1777740 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1777759 AAAAT
1 AAAAT
1777764 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1777760 original size:26 final size:24
Alignment explanation
Indices: 1777731--1777791 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 24
1777721 TAAAATTTTA
*
1777731 ATAATATATAAAATAATTTATATGAT
1 ATAATATATAAAATAATCTATA--AT
*
1777757 ATAA-A-ATTAAAT-ATCTATAAT
1 ATAATATATAAAATAATCTATAAT
1777778 ATAATAT-TAAAATA
1 ATAATATATAAAATA
1777792 TTAATAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 6 0.21
24 6 0.21
25 1 0.03
26 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATATATAAAATAATCTATAAT
Found at i:1777782 original size:35 final size:37
Alignment explanation
Indices: 1777708--1777827 Score: 111
Period size: 40 Copynumber: 3.1 Consensus size: 37
1777698 AATCAAAATA
* * *
1777708 ATTAAAATAAATATAAAATTTTAATAATATATAAAATAAT
1 ATTAATATTAATATAAAA--TTAAT-ATATATAATATAAT
* *
1777748 -TT-ATA-TGATATAAAATTAAATATCTATAATATAAT
1 ATTAATATTAATATAAAATT-AATATATATAATATAAT
1777783 ATTAAAATATTAATAGTAAAATTAATATATATAATATAAT
1 ATT--AATATTAATA-TAAAATTAATATATATAATATAAT
1777823 ATTAA
1 ATTAA
1777828 AAAAATAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
35 14 0.21
36 5 0.08
37 8 0.12
38 4 0.06
39 5 0.08
40 23 0.35
41 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (37 bp):
ATTAATATTAATATAAAATTAATATATATAATATAAT
Found at i:1777796 original size:14 final size:14
Alignment explanation
Indices: 1777775--1777868 Score: 69
Period size: 14 Copynumber: 7.2 Consensus size: 14
1777765 AAATATCTAT
1777775 AATA-TAATATTAA
1 AATATTAATATTAA
*
1777788 AATATTAATAGT-A
1 AATATTAATATTAA
*
1777801 AA-ATTAATATATAT
1 AATATTAATAT-TAA
1777815 AATA-TAATATTAA
1 AATATTAATATTAA
* * *
1777828 AAAAATAATATT-T
1 AATATTAATATTAA
1777841 AAT-TT-AT-TTAA
1 AATATTAATATTAA
*
1777852 AAAATTAATATTAA
1 AATATTAATATTAA
1777866 AAT
1 AAT
1777869 TAAAATCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.03
11 4 0.07
12 10 0.16
13 17 0.28
14 27 0.44
15 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (14 bp):
AATATTAATATTAA
Found at i:1777812 original size:20 final size:20
Alignment explanation
Indices: 1777736--1777827 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
1777726 TTTTAATAAT
* *
1777736 ATATAAAA-TAATTTATATG
1 ATATAAAATTAATATATATA
*
1777755 ATATAAAATTAAATATCTATA
1 ATATAAAATT-AATATATATA
* *
1777776 ATATAATATTAAAATAT-TA
1 ATATAAAATTAATATATATA
1777795 ATAGTAAAATTAATATATATA
1 ATA-TAAAATTAATATATATA
*
1777816 ATATAATATTAA
1 ATATAAAATTAA
1777828 AAAAATAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.22
20 26 0.43
21 21 0.35
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAAAATTAATATATATA
Found at i:1777837 original size:40 final size:41
Alignment explanation
Indices: 1777758--1777837 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
1777748 TTATATGATA
* * *
1777758 TAAAATTAAATATCTATAATATAATATTAAAATATTAATAG
1 TAAAATTAAATATATATAATATAATATTAAAAAAATAATAG
1777799 TAAAATT-AATATATATAATATAATATTAAAAAAATAATA
1 TAAAATTAAATATATATAATATAATATTAAAAAAATAATA
1777838 TTTAATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 29 0.81
41 7 0.19
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (41 bp):
TAAAATTAAATATATATAATATAATATTAAAAAAATAATAG
Found at i:1777838 original size:26 final size:26
Alignment explanation
Indices: 1777778--1777862 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
1777768 TATCTATAAT
* * *
1777778 ATAATATTAAAATATTAATAGTAAAATTA
1 ATAATA-TATAATA-TAATATTAAAA-AA
1777807 AT-ATATATAATATAATATTAAAAAA
1 ATAATATATAATATAATATTAAAAAA
* *
1777832 ATAATATTTAAT-TTAT-TTAAAAAA
1 ATAATATATAATATAATATTAAAAAA
*
1777856 TTAATAT
1 ATAATAT
1777863 TAAAATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
24 14 0.29
25 6 0.12
26 18 0.37
27 6 0.12
28 3 0.06
29 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
ATAATATATAATATAATATTAAAAAA
Found at i:1777891 original size:35 final size:35
Alignment explanation
Indices: 1777689--1777902 Score: 87
Period size: 35 Copynumber: 6.2 Consensus size: 35
1777679 AAATATATAT
* *
1777689 TTAAACTT-AAATCAAA-ATAAT-TAAAATAAATA
1 TTAAAATTAAAATCAAATATAATATAAAATTAATA
** * *
1777721 -TAAAATTTTAAT-AATATATAAAAT-AATTTATATGA
1 TTAAAATTAAAATCAA-ATATAATATAAAATTA-AT-A
1777756 TATAAAATTAAATATCTATAATATAATATTAAAATATTAATA
1 T-TAAAATTAAA-ATC-A-AATATAATA-T-AAA-ATTAATA
* * *
1777798 GTAAAATT--AAT-ATATATAATATAATATTAA-A
1 TTAAAATTAAAATCAAATATAATATAAAATTAATA
* ** * * *
1777829 --AAAA-TAATATTTAATTTATTTAAAAAATTAATA
1 TTAAAATTAAAATCAAATATA-ATATAAAATTAATA
1777862 TTAAAATTAAAATCAAATATAATATAAAATTAA-A
1 TTAAAATTAAAATCAAATATAATATAAAATTAATA
1777896 TATAAAA
1 T-TAAAA
1777903 CCTCTTTGAA
Statistics
Matches: 132, Mismatches: 25, Indels: 47
0.65 0.12 0.23
Matches are distributed among these distances:
28 1 0.01
29 4 0.03
30 2 0.02
31 13 0.10
32 18 0.14
33 11 0.08
34 6 0.05
35 28 0.21
36 11 0.08
37 8 0.06
38 4 0.03
39 1 0.01
40 8 0.06
41 9 0.07
42 1 0.01
43 4 0.03
44 3 0.02
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (35 bp):
TTAAAATTAAAATCAAATATAATATAAAATTAATA
Found at i:1777897 original size:12 final size:12
Alignment explanation
Indices: 1777852--1777902 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1777842 ATTTATTTAA
1777852 AAAATT-AATATT
1 AAAATTAAATA-T
1777864 AAAATTAAA-AT
1 AAAATTAAATAT
*
1777875 CAAA-TATAATAT
1 AAAATTA-AATAT
1777887 AAAATTAAATAT
1 AAAATTAAATAT
1777899 AAAA
1 AAAA
1777903 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1778047 original size:12 final size:13
Alignment explanation
Indices: 1778030--1778059 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1778020 TTCTCTCTAA
1778030 AAATAATAG-TTT
1 AAATAATAGTTTT
1778042 AAATAATAGTTTT
1 AAATAATAGTTTT
1778055 AAATA
1 AAATA
1778060 TTAAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
AAATAATAGTTTT
Found at i:1781086 original size:39 final size:39
Alignment explanation
Indices: 1781025--1781110 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
1781015 ATCCAACGAT
* *
1781025 TCTAATTACTCAATTAGTTGGGTCCGTATATCC-CTCGAG
1 TCTAATTAATCAATTAGTTGGGTCCGTATA-CCGATCGAG
* *
1781064 TCTAATTAATCAGTTA-TGTGGGTTCGTATACCGATCGAG
1 TCTAATTAATCAATTAGT-TGGGTCCGTATACCGATCGAG
1781103 TCTAATTA
1 TCTAATTA
1781111 GAAAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.07
39 38 0.93
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (39 bp):
TCTAATTAATCAATTAGTTGGGTCCGTATACCGATCGAG
Found at i:1787158 original size:3 final size:3
Alignment explanation
Indices: 1787152--1787188 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1787142 GACGACGACA
* *
1787152 ATG ATG ATG ATG ATG GTG ATG GTG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1787189 GAGTGACAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1788407 original size:24 final size:24
Alignment explanation
Indices: 1788380--1788426 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1788370 CTCGTATAAA
*
1788380 TTGCACTGAAGTGCCACGTAGAAT
1 TTGCACCGAAGTGCCACGTAGAAT
*
1788404 TTGCACCGAAGTGCCGCGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
1788427 ATACACCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (24 bp):
TTGCACCGAAGTGCCACGTAGAAT
Found at i:1788439 original size:23 final size:24
Alignment explanation
Indices: 1788387--1788442 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1788377 AAATTGCACT
* *
1788387 GAAGTGCCACGTAGAATTTGCACC
1 GAAGTGCCACGTAGAATATACACC
*
1788411 GAAGTGCCGCGTAGAA-ATACACC
1 GAAGTGCCACGTAGAATATACACC
*
1788434 GTAGTGCCA
1 GAAGTGCCA
1788443 TATAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (24 bp):
GAAGTGCCACGTAGAATATACACC
Found at i:1789670 original size:266 final size:267
Alignment explanation
Indices: 1789195--1789735 Score: 978
Period size: 266 Copynumber: 2.0 Consensus size: 267
1789185 AGAATAGGCT
*
1789195 ATTTTCACCAGAAATTCATCAATACTTGACCCAAATTTTCATGTATAAAACCCTTATTATGCTAT
1 ATTTTCACCAGAAATTCATCAATAATTGACCCAAATTTTCATGTATAAAACCCTTATTATGCTAT
1789260 CAAACTCAACTATAACCACTATAACTAATTTATAGCATTCCAACACCTTATAATCTCCCATATTT
66 CAAACTCAACTATAACCACTATAACTAATTTATAGCATTCCAACACCTTATAATCTCCCATATTT
*
1789325 CATTAAAGTTCTTAGAACTAAAAATCTTACCGCATTTTCCATGTTATCCAAACTTAATTCTAACT
131 CATCAAAGTTCTTAGAACTAAAAATCTTACCGCATTTTCCATGTTATCCAAACTTAATTCTAACT
*
1789390 TTTATAACTTCTTATTCTCGTAGATGACAAGTCAAATTCAACCTCCAATTTCATTTAAACCATCT
196 CTTATAACTTCTTATTCTCGTAGATGACAAGTCAAATTCAACCTCCAATTTCATTTAAACCATCT
1789455 TATTCAA
261 TATTCAA
1789462 ATTTTCACC-GAAAATTCATCAATAATTGACCCAAATTTTCATGTATAAAACCCTTATTATGCTA
1 ATTTTCACCAG-AAATTCATCAATAATTGACCCAAATTTTCATGTATAAAACCCTTATTATGCTA
*
1789526 TCAAACTCAACTATAACCACTAT-ACTAATTTCTAGCATTCCAACACCTTATAATCTCCCATATT
65 TCAAACTCAACTATAACCACTATAACTAATTTATAGCATTCCAACACCTTATAATCTCCCATATT
* **
1789590 TCATCAAAGTTCTTAGAACTAAGAATCTTACTTCATTTTCCATGTTATCCAAACTTAATTCTAAC
130 TCATCAAAGTTCTTAGAACTAAAAATCTTACCGCATTTTCCATGTTATCCAAACTTAATTCTAAC
* *
1789655 TCTTATAACTTCTTATTCTCGTAGATGGCAAGTTAAATTCAACCTCCAATTTCATTTAAACCATC
195 TCTTATAACTTCTTATTCTCGTAGATGACAAGTCAAATTCAACCTCCAATTTCATTTAAACCATC
1789720 TTATTCAA
260 TTATTCAA
1789728 ATTTTCAC
1 ATTTTCAC
1789736 TTAAATGCTT
Statistics
Matches: 264, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
266 180 0.68
267 84 0.32
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (267 bp):
ATTTTCACCAGAAATTCATCAATAATTGACCCAAATTTTCATGTATAAAACCCTTATTATGCTAT
CAAACTCAACTATAACCACTATAACTAATTTATAGCATTCCAACACCTTATAATCTCCCATATTT
CATCAAAGTTCTTAGAACTAAAAATCTTACCGCATTTTCCATGTTATCCAAACTTAATTCTAACT
CTTATAACTTCTTATTCTCGTAGATGACAAGTCAAATTCAACCTCCAATTTCATTTAAACCATCT
TATTCAA
Found at i:1794784 original size:16 final size:16
Alignment explanation
Indices: 1794763--1794795 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1794753 ACCACTATAG
1794763 ACTCTGGTTTATGCCT
1 ACTCTGGTTTATGCCT
1794779 ACTCTGGTTTATGCCT
1 ACTCTGGTTTATGCCT
1794795 A
1 A
1794796 GAATCGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (16 bp):
ACTCTGGTTTATGCCT
Found at i:1795731 original size:23 final size:23
Alignment explanation
Indices: 1795705--1795769 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
1795695 AACTCGTATA
*
1795705 AATTGCACTGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1795728 AATTTGCACCGAAGTGCCGCGTAG
1 AA-TTGCACCGAAGTGCCACGTAG
* *
1795752 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1795770 TATAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 15 0.42
24 21 0.58
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1798822 original size:16 final size:16
Alignment explanation
Indices: 1798780--1798822 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
1798770 ATTATTTTTC
*
1798780 AAAAAATCATATATAA
1 AAAAAATTATATATAA
*
1798796 AATAAATATTATATATTA
1 AA-AAA-ATTATATATAA
1798814 AAAAAATTA
1 AAAAAATTA
1798823 CCTTACAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.26
17 6 0.26
18 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTATATATAA
Found at i:1811678 original size:29 final size:29
Alignment explanation
Indices: 1811657--1811765 Score: 155
Period size: 29 Copynumber: 3.8 Consensus size: 29
1811647 GGATGCGGAT
*
1811657 TAAATCCCATTCAAAAATAGGACGAGGAA
1 TAAATCCCATGCAAAAATAGGACGAGGAA
* * *
1811686 TAAATCCCATGCAGAAATAGGACAAGAAA
1 TAAATCCCATGCAAAAATAGGACGAGGAA
* *
1811715 TAAATCCCATCCAGAAATAGGACGAGGAA
1 TAAATCCCATGCAAAAATAGGACGAGGAA
*
1811744 TAAATCCCATGCAAAAACAGGA
1 TAAATCCCATGCAAAAATAGGA
1811766 ATGCATCAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (29 bp):
TAAATCCCATGCAAAAATAGGACGAGGAA
Found at i:1812461 original size:22 final size:22
Alignment explanation
Indices: 1812422--1812465 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1812412 GTCAATGGTC
*
1812422 AGGCCGGTCAAATAGTTGGGTT
1 AGGCCGGTCAAAGAGTTGGGTT
* *
1812444 AGGCCGGTCAACGGGTTGGGTT
1 AGGCCGGTCAAAGAGTTGGGTT
1812466 TGTCAATGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.41, T:0.25
Consensus pattern (22 bp):
AGGCCGGTCAAAGAGTTGGGTT
Found at i:1818602 original size:29 final size:28
Alignment explanation
Indices: 1818556--1818664 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 28
1818546 AAATGAAGAT
*
1818556 TAAATCCCAT-TAAAAAACAAGACGAGGAA
1 TAAATCCCATGT-AGAAACAAGA-GAGGAA
* *
1818585 TAAATCTCATGTAGAAACAGGA-ATGGAAA
1 TAAATCCCATGTAGAAACAAGAGA-GG-AA
* *
1818614 TAAATCCCATGCAGAAACAGGATG-GAGAA
1 TAAATCCCATGTAGAAACAAGA-GAG-GAA
1818643 TAAATCCCATGTAGAAACAAGA
1 TAAATCCCATGTAGAAACAAGA
1818665 ATGTATCAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.01
28 2 0.03
29 62 0.93
30 2 0.03
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.17
Consensus pattern (28 bp):
TAAATCCCATGTAGAAACAAGAGAGGAA
Found at i:1818621 original size:58 final size:58
Alignment explanation
Indices: 1818556--1818667 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
1818546 AAATGAAGAT
* * *
1818556 TAAATCCCATTAAAAAACAAGAC-GAGGAATAAATCTCATGTAGAAACAGGAATGGAAA
1 TAAATCCCATGAAAAAACAAGACGGA-GAATAAATCCCATGTAGAAACAAGAATGGAAA
* * * *
1818614 TAAATCCCATGCAGAAACAGGATGGAGAATAAATCCCATGTAGAAACAAGAATG
1 TAAATCCCATGAAAAAACAAGACGGAGAATAAATCCCATGTAGAAACAAGAATG
1818668 TATCAATGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 44 0.96
59 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (58 bp):
TAAATCCCATGAAAAAACAAGACGGAGAATAAATCCCATGTAGAAACAAGAATGGAAA
Found at i:1821025 original size:7 final size:7
Alignment explanation
Indices: 1821013--1821058 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
1821003 TCATTTGTCC
1821013 TTTCCTT
1 TTTCCTT
1821020 TTTCCTT
1 TTTCCTT
1821027 TTTCCTT
1 TTTCCTT
1821034 TTTCCTT
1 TTTCCTT
1821041 TTTCCTT
1 TTTCCTT
1821048 TTTCCTT
1 TTTCCTT
1821055 TTTC
1 TTTC
1821059 AAAACTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:1821418 original size:21 final size:21
Alignment explanation
Indices: 1821376--1821419 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1821366 AATATGTAAA
*
1821376 TCACATTGCGATTTTACGAAT
1 TCACATTGCGATTTTACAAAT
* *
1821397 TCACGTTGCGATTTTCCAAAT
1 TCACATTGCGATTTTACAAAT
1821418 TC
1 TC
1821420 GCAACGCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (21 bp):
TCACATTGCGATTTTACAAAT
Found at i:1821443 original size:20 final size:20
Alignment explanation
Indices: 1821418--1821464 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1821408 TTTTCCAAAT
1821418 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
1821438 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
1821458 TCACAAC
1 TCGCAAC
1821465 ACATAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:1821486 original size:20 final size:20
Alignment explanation
Indices: 1821461--1821503 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1821451 CTGTAAATCA
*
1821461 CAACACATAAGTCAAATTCG
1 CAACACAGAAGTCAAATTCG
1821481 CAACACAGAAGTCAAATTCG
1 CAACACAGAAGTCAAATTCG
1821501 CAA
1 CAA
1821504 AGAGCGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (20 bp):
CAACACAGAAGTCAAATTCG
Found at i:1821707 original size:20 final size:20
Alignment explanation
Indices: 1821682--1821724 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1821672 CTGTAAATCA
*
1821682 CAACACATAAGTCAAATTCG
1 CAACACAGAAGTCAAATTCG
1821702 CAACACAGAAGTCAAATTCG
1 CAACACAGAAGTCAAATTCG
1821722 CAA
1 CAA
1821725 AGAGCGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.16
Consensus pattern (20 bp):
CAACACAGAAGTCAAATTCG
Found at i:1821909 original size:22 final size:22
Alignment explanation
Indices: 1821879--1821926 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1821869 CTACGACGAC
* * *
1821879 ATCCGTCCCCATCTCTGGCGAA
1 ATCCATCCCAATCTCCGGCGAA
1821901 ATCCATCCCAATCTCCGGCGAA
1 ATCCATCCCAATCTCCGGCGAA
1821923 ATCC
1 ATCC
1821927 GTCTATCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCCATCCCAATCTCCGGCGAA
Found at i:1822332 original size:20 final size:20
Alignment explanation
Indices: 1822293--1822332 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1822283 GAAAATCGCA
* *
1822293 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTAAGTTTC
1822313 GCGTTGCGATTTTAAGTTTC
1 GCGTTGCGATTTTAAGTTTC
1822333 AGAAACTATT
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:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGTTGCGATTTTAAGTTTC
Found at i:1823930 original size:21 final size:21
Alignment explanation
Indices: 1823887--1823936 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1823877 GTTAGGGGAG
* *
1823887 TTGCGTGATGAGGTCAATGCT
1 TTGCGTGAGGAGGTCAATACT
**
1823908 TTGCGTGAGGAGGTCGGTACT
1 TTGCGTGAGGAGGTCAATACT
*
1823929 TTACGTGA
1 TTGCGTGA
1823937 AGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (21 bp):
TTGCGTGAGGAGGTCAATACT
Found at i:1823977 original size:21 final size:21
Alignment explanation
Indices: 1823953--1824002 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1823943 TGGTGCATGG
*
1823953 CGTGATGAGGTA-CGGTGTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
1823974 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
1823995 CGCGATGA
1 CGTGATGA
1824003 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:1824292 original size:42 final size:42
Alignment explanation
Indices: 1824245--1824357 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
1824235 TCAGACGTCA
* * * * * *
1824245 TTCAAGAGGGCTCTCCTATCGTTCAAGAGGCTATTATCATCC
1 TTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTATCATCC
* *
1824287 TTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCG
1 TTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTATCATCC
* *
1824329 TTCAAGAGGTCCCTCCCACCGTTCGAGAG
1 TTCAAGAGGCCCCTCCCACCGTTCAAGAG
1824358 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCACTATCATCC
Found at i:1824311 original size:21 final size:21
Alignment explanation
Indices: 1824287--1824357 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
1824277 ATTATCATCC
1824287 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
** *
1824308 TTCAAGAGGCCCCTATCATCG
1 TTCAAGAGGCCCCTCCCACCG
*
1824329 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
1824350 TTCGAGAG
1 TTCAAGAG
1824358 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:1825772 original size:64 final size:64
Alignment explanation
Indices: 1825701--1825849 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
1825691 GAATTGATGT
* *
1825701 ATTTGTAAAAGTAGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTG
* * ***
1825765 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTACTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTG
1825829 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
1825850 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAATTG
Found at i:1826185 original size:18 final size:18
Alignment explanation
Indices: 1826162--1826197 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1826152 AAGTCGGTTG
1826162 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
1826180 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
1826198 CCTTTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:1826698 original size:40 final size:40
Alignment explanation
Indices: 1826612--1826699 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
1826602 TTGCGAAATT
* * *
1826612 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAATTCG
1 AAAA-TCGAGTTGCGAATTCGAAAATCGAGTCGCAAATTCG
* *
1826653 AAAATCGAGTTGCGAATTC-AGAAATTGAGTCGCAAATTTG
1 AAAATCGAGTTGCGAATTCGA-AAATCGAGTCGCAAATTCG
*
1826693 TAAATCG
1 AAAATCG
1826700 CAACGCGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.03
40 35 0.88
41 4 0.10
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (40 bp):
AAAATCGAGTTGCGAATTCGAAAATCGAGTCGCAAATTCG
Found at i:1826749 original size:20 final size:20
Alignment explanation
Indices: 1826621--1826772 Score: 117
Period size: 20 Copynumber: 7.6 Consensus size: 20
1826611 TAAAATTCGT
* *
1826621 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGGAAATCGA
* *
1826641 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGGAAATCGA
** *
1826661 GTTGCGAATTCAGAAATTGA
1 GTTGCGAATTTGGAAATCGA
* * *
1826681 GTCGCAAATTTGTAAATCGCA
1 GTTGCGAATTTGGAAATCG-A
** * *
1826702 -ACGCGAATTTGTAAATCGT
1 GTTGCGAATTTGGAAATCGA
** *
1826721 GTTAAGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGA
* *
1826741 GTTGCGAATTTAGAAATCGC
1 GTTGCGAATTTGGAAATCGA
1826761 GTTGCGAATTTG
1 GTTGCGAATTTG
1826773 ACTTCTATGT
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 107 0.99
21 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGA
Found at i:1829712 original size:15 final size:17
Alignment explanation
Indices: 1829687--1829718 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1829677 ACACACTACT
1829687 TTTATCATTTTT-TTAA
1 TTTATCATTTTTATTAA
1829703 TTTA-CATTTTTATTAA
1 TTTATCATTTTTATTAA
1829719 GCTTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATCATTTTTATTAA
Found at i:1830876 original size:229 final size:231
Alignment explanation
Indices: 1830474--1830919 Score: 878
Period size: 229 Copynumber: 1.9 Consensus size: 231
1830464 GGGGTGTGTG
1830474 AAGATAGTCTCTTCTTCCTTAGCTGTAGCTGCTAAACGAGACTTGTTATAGAAATTGTTTGATTT
1 AAGATAGTCTCTTCTTCCTTAGCTGTAGCTGCTAAACGAGACTTGTTATAGAAATTGTTTGATTT
1830539 GTGCTATTTGGGTTGCTTGGTATTCTTTTTTGTTGATTGTTGGCTCTTGGCTACCTTTGTTGTGG
66 GTGCTATTTGGGTTGCTTGGTATTCTTTTTTGTTGATTGTTGGCTCTTGGCTACCTTTGTTGTGG
1830604 TAGGACTGTTTGTTTTTTTAGGTTTATACAGGTTTATATGTCACGGTTGTACATGAGTAGTTCTT
131 TAGGACTGTTTGTTTTTTTAGGTTTATACAGGTTTATATGTCACGGTTGTACATGAGTAGTTCTT
1830669 TTGG-TGAATATATTATTCATTCCAGAAAAAATATA
196 TTGGATGAATATATTATTCATTCCAGAAAAAATATA
1830704 AAGATAGTCTCTTCTTCCTTAGCTGTAGCTGCT-AACGAGACTTGTTATAGAAATTGTTTGATTT
1 AAGATAGTCTCTTCTTCCTTAGCTGTAGCTGCTAAACGAGACTTGTTATAGAAATTGTTTGATTT
1830768 GTGCTATTTGGGTTGCTTGGTATTCTTTTTTGTTGATTGTTGGCTCTTGGCTACCTTTGTTGTGG
66 GTGCTATTTGGGTTGCTTGGTATTCTTTTTTGTTGATTGTTGGCTCTTGGCTACCTTTGTTGTGG
1830833 TAGGACTGTTTGTTTTTTTAGGTTTATACAGGTTTATATGTCACGGTTGTACATGAGTAGTTCTT
131 TAGGACTGTTTGTTTTTTTAGGTTTATACAGGTTTATATGTCACGGTTGTACATGAGTAGTTCTT
1830898 TTGGATGAATATATTATTCATT
196 TTGGATGAATATATTATTCATT
1830920 TATCCAGAAA
Statistics
Matches: 215, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 165 0.77
230 50 0.23
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (231 bp):
AAGATAGTCTCTTCTTCCTTAGCTGTAGCTGCTAAACGAGACTTGTTATAGAAATTGTTTGATTT
GTGCTATTTGGGTTGCTTGGTATTCTTTTTTGTTGATTGTTGGCTCTTGGCTACCTTTGTTGTGG
TAGGACTGTTTGTTTTTTTAGGTTTATACAGGTTTATATGTCACGGTTGTACATGAGTAGTTCTT
TTGGATGAATATATTATTCATTCCAGAAAAAATATA
Found at i:1834055 original size:20 final size:19
Alignment explanation
Indices: 1834013--1834078 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
1834003 GGAACACTTA
*
1834013 GTGCATTGGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
*
1834032 GTGCATCGGTGCAGTAAGGG
1 GTGCATCGGTGCACTAA-GG
1834052 GTGCATCGGTGCACTAAGG
1 GTGCATCGGTGCACTAAGG
1834071 GTGCATCG
1 GTGCATCG
1834079 ATGTGTGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (19 bp):
GTGCATCGGTGCACTAAGG
Found at i:1836777 original size:21 final size:21
Alignment explanation
Indices: 1836752--1836816 Score: 53
Period size: 24 Copynumber: 3.0 Consensus size: 21
1836742 ATCGGTTCAT
1836752 CTTCATGATGTATCGATGCA-
1 CTTCATGATGTATCGATGCAG
* *
1836772 CATTCAAAGGGATGCATCGATGCAG
1 C-TTC--A-TGATGTATCGATGCAG
1836797 CTTCAT-AGTGTATCGATGCA
1 CTTCATGA-TGTATCGATGCA
1836817 TTATGCACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 1 0.03
23 1 0.03
24 16 0.46
25 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (21 bp):
CTTCATGATGTATCGATGCAG
Found at i:1836809 original size:45 final size:44
Alignment explanation
Indices: 1836719--1836816 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
1836709 GGCAGTTTGC
* * *
1836719 ATCGATGCACATTCAAGGAGTGCATCGGTTCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCAGCTTCATGATGT
1836763 ATCGATGCACATTCAAAGG-GATGCATCGATGCAGCTTCAT-AGTGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGATGCAGCTTCATGA-TGT
1836808 ATCGATGCA
1 ATCGATGCA
1836817 TTATGCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 16 0.33
45 32 0.67
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCAGCTTCATGATGT
Found at i:1842640 original size:64 final size:65
Alignment explanation
Indices: 1842572--1842759 Score: 172
Period size: 65 Copynumber: 2.9 Consensus size: 65
1842562 TGGACTAAGG
* * *
1842572 GTGCATCAATACGTGAAAT-ACATTCGATGTTTCAA-ACA-AGCCT-GAGTGCATCGATGCATGG
1 GTGCATCAATACATAAAATCA-ATTCGATGTTTCAATA-ATA-CATGGAGTGCATCGATGCATGG
*
1842633 TTT
63 TAT
** * *
1842636 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTAT
1 GTGCATCAATACATAAAATCAATTCGATGTTTCAATAATACATGGAGTGCATCGATGCATGGTAT
* * * * * *
1842701 GTGCATCAGTACATAAAAGCTATTCGATG-TTCAATTAAAATAAGG-GTGCATCGATGCAT
1 GTGCATCAATACATAAAATCAATTCGATGTTTCAA-TAATACATGGAGTGCATCGATGCAT
1842760 TGATTTATGC
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
64 48 0.47
65 55 0.53
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCAATACATAAAATCAATTCGATGTTTCAATAATACATGGAGTGCATCGATGCATGGTAT
Found at i:1842697 original size:65 final size:63
Alignment explanation
Indices: 1842615--1842778 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 63
1842605 AAACAAGCCT
* *
1842615 GAGTGCATCGATGCATGGTTTGTGCATCGGTGCATAAAATCAATTCGATGTT-TTAATAATACAT
1 GAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGCAATTCGATGTTATTAA-AATA-A-
1842679 G
63 G
* * *
1842680 GAGTGCATCGATGCATGGTATGTGCATCAGTACATAAAAGCTATTCGATGTTCAATTAAAATAAG
1 GAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGCAATTCGATGTT--ATTAAAATAAG
* *
1842745 G-GTGCATCGATGCATTGATTTATGCATCGGTACA
1 GAGTGCATCGATGCA-TGGTTTGTGCATCGGTACA
1842779 CTTACCTGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
64 13 0.15
65 64 0.74
66 1 0.01
67 4 0.05
68 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (63 bp):
GAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGCAATTCGATGTTATTAAAATAAG
Found at i:1844006 original size:25 final size:25
Alignment explanation
Indices: 1843972--1844041 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
1843962 CATATGAGTA
1843972 GTCATGAAAATTTATTGGACAAAAT
1 GTCATGAAAATTTATTGGACAAAAT
* *
1843997 GTCATGAAAA-TGA-T-GAAAACAAT
1 GTCATGAAAATTTATTGGACAA-AAT
1844020 G--ATGAAAATTTATTGGACAAAA
1 GTCATGAAAATTTATTGGACAAAA
1844042 CCAGAAACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 7 0.19
22 6 0.16
23 8 0.22
24 6 0.16
25 10 0.27
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (25 bp):
GTCATGAAAATTTATTGGACAAAAT
Found at i:1844565 original size:7 final size:7
Alignment explanation
Indices: 1844553--1844602 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
1844543 AGAAGGAGTT
1844553 AAAAGAA
1 AAAAGAA
1844560 AAAAG-A
1 AAAAGAA
*
1844566 ATAAGAA
1 AAAAGAA
1844573 AAAAGAA
1 AAAAGAA
1844580 AAAAG-A
1 AAAAGAA
1844586 AAAAG-A
1 AAAAGAA
1844592 AAAAGAA
1 AAAAGAA
1844599 AAAA
1 AAAA
1844603 ATGAGGCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 17 0.44
7 22 0.56
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:1844566 original size:20 final size:20
Alignment explanation
Indices: 1844553--1844602 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1844543 AGAAGGAGTT
*
1844553 AAAAGAAAAAAGAATAAGAA
1 AAAAGAAAAAAGAAGAAGAA
*
1844573 AAAAGAAAAAAGAAAAAG-A
1 AAAAGAAAAAAGAAGAAGAA
1844592 AAAAGAAAAAA
1 AAAAGAAAAAA
1844603 ATGAGGCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAGAAGAAGAA
Found at i:1844571 original size:13 final size:12
Alignment explanation
Indices: 1844553--1844602 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 12
1844543 AGAAGGAGTT
1844553 AAAAGAAAAAAG
1 AAAAGAAAAAAG
1844565 AATAAGAAAAAAG
1 AA-AAGAAAAAAG
*
1844578 AAAAAAGAAAAAG
1 AAAAGA-AAAAAG
1844591 AAAAAGAAAAAA
1 -AAAAGAAAAAA
1844603 ATGAGGCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 5 0.15
13 23 0.70
14 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:1844581 original size:6 final size:6
Alignment explanation
Indices: 1844553--1844601 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
1844543 AGAAGGAGTT
*
1844553 AAAAGAA AAAAGA ATAAGAA AAAAGAA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAG-A AAAAGA AAAAG-A AAAAG-A AAAAGA AAAAGA AAAAGA AAAA
1844602 AATGAGGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
6 22 0.56
7 17 0.44
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:1856910 original size:21 final size:19
Alignment explanation
Indices: 1856884--1856930 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1856874 ATTTAAACTA
1856884 AATCCTAAAAATAAAAAGAT
1 AATCCTAAAAA-AAAAAGAT
*
1856904 AATTCCT-AAAAACAAAGAT
1 AA-TCCTAAAAAAAAAAGAT
1856923 AATCCTAA
1 AATCCTAA
1856931 TTCGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.21
Consensus pattern (19 bp):
AATCCTAAAAAAAAAAGAT
Found at i:1868255 original size:171 final size:173
Alignment explanation
Indices: 1867968--1868312 Score: 667
Period size: 171 Copynumber: 2.0 Consensus size: 173
1867958 TACTTCATTG
1867968 AAATATTCCTTGATTTTTTTAATTGAGTTTACCTAACTTGATAAATACACTTTGTTAAGATTTTG
1 AAATATTCCTTGA-TTTTTTAATTGAGTTTACCTAACTTGATAAATACACTTTGTTAAGATTTTG
1868033 AGCCTTGATAAGCATGCTTCTTAATCTTTTGTGCTCTTTTTGTTGTTTGAGTGTGTCAAATTAAT
65 AGCCTTGATAAGCATGCTTCTTAATCTTTTGTGCTCTTTTTGTTGTTTGAGTGTGTCAAATTAAT
1868098 CTTGAAAATCTAGAACTTGT-GCATGATACATTTTGACACTACA
130 CTTGAAAATCTAGAACTTGTGGCATGATACATTTTGACACTACA
1868141 AAATATTCCTTGA-TTTTTAATTGAGTTTACCTAACTTGATAAATACACTTTGTTAAGATTTTGA
1 AAATATTCCTTGATTTTTTAATTGAGTTTACCTAACTTGATAAATACACTTTGTTAAGATTTTGA
1868205 GCCTTGATAAGCATGCTTCTTAATCTTTTGTGCTCTTTTTGTTGTTTGAGTGTGTCAAATTAATC
66 GCCTTGATAAGCATGCTTCTTAATCTTTTGTGCTCTTTTTGTTGTTTGAGTGTGTCAAATTAATC
1868270 TTGAAAATCTAGAACTTGTGGCATGATACATTTTGACACTACA
131 TTGAAAATCTAGAACTTGTGGCATGATACATTTTGACACTACA
1868313 TATGAAATTT
Statistics
Matches: 171, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
171 135 0.79
172 23 0.13
173 13 0.08
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (173 bp):
AAATATTCCTTGATTTTTTAATTGAGTTTACCTAACTTGATAAATACACTTTGTTAAGATTTTGA
GCCTTGATAAGCATGCTTCTTAATCTTTTGTGCTCTTTTTGTTGTTTGAGTGTGTCAAATTAATC
TTGAAAATCTAGAACTTGTGGCATGATACATTTTGACACTACA
Found at i:1868359 original size:15 final size:16
Alignment explanation
Indices: 1868339--1868370 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1868329 TTTCACCTAA
1868339 TCTTAAACCC-AGCTC
1 TCTTAAACCCGAGCTC
1868354 TCTTAAACCCGAGCTC
1 TCTTAAACCCGAGCTC
1868370 T
1 T
1868371 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.25, C:0.38, G:0.09, T:0.28
Consensus pattern (16 bp):
TCTTAAACCCGAGCTC
Found at i:1868499 original size:18 final size:18
Alignment explanation
Indices: 1868476--1868515 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1868466 ATTTAAATGG
* *
1868476 AAAAAAATTAGAAAAGTT
1 AAAAAAATAAAAAAAGTT
*
1868494 AAAAAAATAAAAAAATTT
1 AAAAAAATAAAAAAAGTT
1868512 AAAA
1 AAAA
1868516 GTTGAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAAAATAAAAAAAGTT
Found at i:1868505 original size:25 final size:25
Alignment explanation
Indices: 1868476--1868533 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1868466 ATTTAAATGG
1868476 AAAAAAATTAGAAAAGTTAAAAAAAT
1 AAAAAAATT-GAAAAGTTAAAAAAAT
* * *
1868502 AAAAAAATTTAAAAGTTGAAAAATT
1 AAAAAAATTGAAAAGTTAAAAAAAT
1868527 AAAAAAA
1 AAAAAAA
1868534 GAACGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (25 bp):
AAAAAAATTGAAAAGTTAAAAAAAT
Found at i:1868541 original size:19 final size:18
Alignment explanation
Indices: 1868519--1868562 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
1868509 TTTAAAAGTT
1868519 GAAAAATTAAAAAAAGAAC
1 GAAAAATTAAAAAAA-AAC
*
1868538 GAAAAA-TATAAAAAAAC
1 GAAAAATTAAAAAAAAAC
1868555 GAAAAATT
1 GAAAAATT
1868563 GTTTGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 6 0.26
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (18 bp):
GAAAAATTAAAAAAAAAC
Found at i:1870239 original size:31 final size:31
Alignment explanation
Indices: 1870200--1870271 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1870190 GTATTTTCTC
*
1870200 AATTTAATGAATTTAATATTCATTAAATGAT
1 AATTTAATGAATTTAATATTAATTAAATGAT
*
1870231 GATTTAATGAATTTAATATTAATTAAATGAT
1 AATTTAATGAATTTAATATTAATTAAATGAT
1870262 AATTTAATGA
1 AATTTAATGA
1870272 TAGATAAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (31 bp):
AATTTAATGAATTTAATATTAATTAAATGAT
Found at i:1870254 original size:11 final size:11
Alignment explanation
Indices: 1870200--1870273 Score: 52
Period size: 11 Copynumber: 7.1 Consensus size: 11
1870190 GTATTTTCTC
1870200 AATTTAATG--
1 AATTTAATGAT
1870209 AATTTAAT-ATT
1 AATTTAATGA-T
* *
1870220 CATTAAATGAT
1 AATTTAATGAT
*
1870231 GATTTAATG--
1 AATTTAATGAT
1870240 AATTTAAT-ATT
1 AATTTAATGA-T
*
1870251 AATTAAATGAT
1 AATTTAATGAT
1870262 AATTTAATGAT
1 AATTTAATGAT
1870273 A
1 A
1870274 GATAAGCATG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
9 15 0.30
11 33 0.66
12 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (11 bp):
AATTTAATGAT
Found at i:1871481 original size:24 final size:24
Alignment explanation
Indices: 1871454--1871501 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1871444 TGCATGACAT
1871454 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
1871478 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
1871502 GCATGAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:1871924 original size:61 final size:61
Alignment explanation
Indices: 1871836--1871950 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
1871826 GAAGGTGGAT
* * * *
1871836 ACGACCTTATGTATCATGTCCGAATTAGCACTATAGTGTAAGCATAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATATCAGAATTAGCACTATAGCGTAAGCATAGTGCAGGTGGTGGGC
* * * * *
1871897 ACGACCTTATGTGTTATATCAGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCATATCAGAATTAGCACTATAGCGTAAGCATAGTGCAGGT
1871951 TTAGCACTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATCATATCAGAATTAGCACTATAGCGTAAGCATAGTGCAGGTGGTGGGC
Found at i:1872147 original size:46 final size:46
Alignment explanation
Indices: 1872060--1872246 Score: 297
Period size: 45 Copynumber: 4.1 Consensus size: 46
1872050 GTAGGCATGC
* *
1872060 AAATAAGCTTACAAGCTTATGGAAT-AATGGTAAGTATATTGGTAA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
*
1872105 AAATAAGCTTACGAGCATATGGGATAAATGGTAAGTATATTGGTAA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
*
1872151 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTATATTGGT-A
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
* *
1872196 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTCTATTGATAA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
1872242 GAAAT
1 -AAAT
1872247 TTTATATTTG
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
45 64 0.49
46 63 0.48
47 4 0.03
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
Found at i:1872154 original size:21 final size:21
Alignment explanation
Indices: 1872085--1872154 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
1872075 CTTATGGAAT
1872085 AATGGTAAGTATATTGGTAAA
1 AATGGTAAGTATATTGGTAAA
* * * *
1872106 AATAAGCTTACGAGCATA-TGGGATA
1 AAT--G-GTA--AGTATATTGGTAAA
1872131 AATGGTAAGTATATTGGTAAA
1 AATGGTAAGTATATTGGTAAA
1872152 AAT
1 AAT
1872155 AAGCTTATGA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 5 0.14
21 11 0.31
22 2 0.06
23 2 0.06
24 2 0.06
25 8 0.23
26 5 0.14
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (21 bp):
AATGGTAAGTATATTGGTAAA
Found at i:1872170 original size:91 final size:92
Alignment explanation
Indices: 1872060--1872246 Score: 297
Period size: 91 Copynumber: 2.0 Consensus size: 92
1872050 GTAGGCATGC
1872060 AAATAAGCTTACAAGCTTATGGAAT-AATGGTAAGTATATTGGTAAAAATAAGCTTACGAGCATA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGT-AAAATAAGCTTACGAGCATA
*
1872124 TGGGATAAATGGTAAGTATATTGGTAA-
65 TGGGATAAATGGTAAGTATATTGATAAG
** * *
1872151 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATAT
*
1872216 GGGATAAATGGTAAGTCTATTGATAAG
66 GGGATAAATGGTAAGTATATTGATAAG
1872243 AAAT
1 AAAT
1872247 TTTATATTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
91 66 0.75
92 22 0.25
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (92 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATAT
GGGATAAATGGTAAGTATATTGATAAG
Found at i:1872648 original size:21 final size:21
Alignment explanation
Indices: 1872622--1872664 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1872612 TGTAGCAGTT
*
1872622 ACTGTAGCA-GTGCATCGGTAC
1 ACTGTAG-AGGTGCATCGATAC
1872643 ACTGTAGAGGTGCATCGATAC
1 ACTGTAGAGGTGCATCGATAC
1872664 A
1 A
1872665 TATTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (21 bp):
ACTGTAGAGGTGCATCGATAC
Found at i:1877469 original size:20 final size:20
Alignment explanation
Indices: 1877446--1877495 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
1877436 AAAATTTCAG
*
1877446 AAAAATCGAAAA-AAATAGAA
1 AAAAATC-AAAACAAAGAGAA
* *
1877466 AAAAGTCAAAACAAAGGGAA
1 AAAAATCAAAACAAAGAGAA
1877486 AAAAAT-AAAA
1 AAAAATCAAAA
1877496 AACTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.08
Consensus pattern (20 bp):
AAAAATCAAAACAAAGAGAA
Found at i:1879187 original size:10 final size:10
Alignment explanation
Indices: 1879172--1879201 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1879162 CCAACCCCTT
1879172 TTTATTTTTA
1 TTTATTTTTA
1879182 TTTATTTTTA
1 TTTATTTTTA
1879192 TTTATTTTTA
1 TTTATTTTTA
1879202 CAACAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:1883144 original size:77 final size:79
Alignment explanation
Indices: 1883059--1883205 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 79
1883049 AAATAAAATT
* *
1883059 TTATTTAATTAATT-CAAATTAAATAT-ACATT-AAAGACTTATAATCTGAATTACAATC-TTTA
1 TTATTTAATT-ATTCCAAATTAAACATCA-ATTAAAAGACTTATAATCTAAATTACAATCTTTTA
1883120 ATGTTTATTTAAAAAC
64 ATGTTTATTTAAAAAC
* * * * *
1883136 TTATTTAATTATTCCGAATTATACATCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTTAAT
1 TTATTTAATTATTCCAAATTAAACATCAATTAAAAGACTTATAATCTAAATTACAATCTTTTAAT
1883201 GTTTA
66 GTTTA
1883206 CTTACTATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
76 3 0.05
77 22 0.37
78 23 0.39
79 11 0.19
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (79 bp):
TTATTTAATTATTCCAAATTAAACATCAATTAAAAGACTTATAATCTAAATTACAATCTTTTAAT
GTTTATTTAAAAAC
Found at i:1887039 original size:21 final size:21
Alignment explanation
Indices: 1886986--1887082 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 21
1886976 AACAATTTTC
* * *
1886986 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCCT
* *
1887007 TTCATGAAAAGGTTAAGCCCT
1 TTCATCAAAAGGTTAAGTCCT
* *
1887028 TTCATCAAAAGGATAAGTCTT
1 TTCATCAAAAGGTTAAGTCCT
* *
1887049 TTAATCAAAAGGTTAAGTTCT
1 TTCATCAAAAGGTTAAGTCCT
* *
1887070 TTAATCGAAAGGT
1 TTCATCAAAAGGT
1887083 CTTAACCTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCCT
Found at i:1887505 original size:3 final size:3
Alignment explanation
Indices: 1887499--1887541 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1887489 ATAATAATAT
*
1887499 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1887542 CTCGGATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1897963 original size:20 final size:21
Alignment explanation
Indices: 1897925--1897963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1897915 ACATAAGGTC
*
1897925 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
1897946 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
1897964 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:1902935 original size:21 final size:21
Alignment explanation
Indices: 1902882--1902951 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1902872 TCCTTTCATG
* *
1902882 AAAAGGTTAAGAACTTTCATC
1 AAAAGGTTAAGTACTTTAATC
** **
1902903 AAAAGGAGAAGTTTTTTAATC
1 AAAAGGTTAAGTACTTTAATC
* *
1902924 AAAAGGTTAAGTCCTTTCATC
1 AAAAGGTTAAGTACTTTAATC
*
1902945 GAAAGGT
1 AAAAGGT
1902952 CTTAACCTCT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
AAAAGGTTAAGTACTTTAATC
Found at i:1903034 original size:21 final size:21
Alignment explanation
Indices: 1903009--1903049 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1902999 GGGCAATTAG
1903009 ACACAAGTTACAAG-ACACAAC
1 ACACAAGTTAC-AGCACACAAC
1903030 ACACAAGTTACAGCACACAA
1 ACACAAGTTACAGCACACAA
1903050 GTTTAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.51, C:0.29, G:0.10, T:0.10
Consensus pattern (21 bp):
ACACAAGTTACAGCACACAAC
Found at i:1919988 original size:30 final size:31
Alignment explanation
Indices: 1919954--1920011 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
1919944 TGACTAATCA
*
1919954 TTTTAACTAAC-TTGATTCT-TTTTGTCTTC
1 TTTTTACTAACATTGATTCTATTTTGTCTTC
*
1919983 TTTTTACTAACATTGATTTTATTTTGTCT
1 TTTTTACTAACATTGATTCTATTTTGTCT
1920012 GGTCTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (31 bp):
TTTTTACTAACATTGATTCTATTTTGTCTTC
Found at i:1921922 original size:9 final size:10
Alignment explanation
Indices: 1921899--1921961 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
1921889 AAAAGAAAGG
1921899 GAGAAAAAAA
1 GAGAAAAAAA
1921909 GAGAAAAATAA
1 GAGAAAAA-AA
*
1921920 GAAAAAAGAAA
1 GAGAAAA-AAA
* *
1921931 AAGAGAAAAA
1 GAGAAAAAAA
1921941 GA-AAAAAAA
1 GAGAAAAAAA
1921950 GA-AAAAAGAA
1 GAGAAAAA-AA
1921960 GA
1 GA
1921962 AAGAAAACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 13 0.30
10 16 0.36
11 14 0.32
12 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
GAGAAAAAAA
Found at i:1921928 original size:7 final size:7
Alignment explanation
Indices: 1921913--1921968 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
1921903 AAAAAAGAGA
1921913 AAAATAAG
1 AAAA-AAG
1921921 AAAAAAG
1 AAAAAAG
1921928 AAAAAGAG
1 AAAAA-AG
*
1921936 AAAAAGAA
1 AAAAA-AG
1921944 AAAAAAG
1 AAAAAAG
1921951 AAAAAAG
1 AAAAAAG
*
1921958 AAGAAAG
1 AAAAAAG
1921965 AAAA
1 AAAA
1921969 CATATCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
7 25 0.58
8 18 0.42
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:1921931 original size:24 final size:23
Alignment explanation
Indices: 1921904--1921968 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
1921894 AAAGGGAGAA
*
1921904 AAAAAGAGAAAAATAAGAAAAAAG
1 AAAAAGAGAAAAAGAA-AAAAAAG
1921928 AAAAAGAGAAAAAGAAAAAAAAG
1 AAAAAGAGAAAAAGAAAAAAAAG
1921951 AAAAA-AGAAGAAAGAAAA
1 AAAAAGAGAA-AAAGAAAA
1921969 CATATCAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 4 0.10
23 20 0.51
24 15 0.38
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAGAGAAAAAGAAAAAAAAG
Found at i:1921946 original size:30 final size:32
Alignment explanation
Indices: 1921905--1921965 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 32
1921895 AAGGGAGAAA
*
1921905 AAAAGAGAAAAATAAGAAAAAAGAA-AAAGAG
1 AAAAGAGAAAAAAAAGAAAAAAGAAGAAAGAG
1921936 AAAA-AGAAAAAAAAGAAAAAAGAAGAAAGA
1 AAAAGAGAAAAAAAAGAAAAAAGAAGAAAGA
1921966 AAACATATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (32 bp):
AAAAGAGAAAAAAAAGAAAAAAGAAGAAAGAG
Found at i:1924170 original size:2 final size:2
Alignment explanation
Indices: 1924157--1924215 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1924147 ATCCTTTCAA
*
1924157 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1924199 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1924216 AATACCTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.