Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 93 of 127
Found at i:17492569 original size:39 final size:38
Alignment explanation
Indices: 17492512--17492586 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 38
17492502 TTATCTTTTG
* *
17492512 ATTTTATTTTTTATATTTTGATT-TTTAGTTTTTTTATTT
1 ATTTTATTTTCTATATTTT-ATTATTTA-TTTATTTATTT
17492551 ATTTTATTTTACTA-ATTTTATTATTTATTTATTTAT
1 ATTTTATTTT-CTATATTTTATTATTTATTTATTTAT
17492587 ATTGAGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 11 0.34
39 19 0.59
40 2 0.06
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (38 bp):
ATTTTATTTTCTATATTTTATTATTTATTTATTTATTT
Found at i:17496070 original size:14 final size:14
Alignment explanation
Indices: 17496051--17496077 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17496041 CTTTATGAAT
17496051 ATTATTAAATTAAA
1 ATTATTAAATTAAA
17496065 ATTATTAAATTAA
1 ATTATTAAATTAA
17496078 TTTTAAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATTAAATTAAA
Found at i:17506907 original size:10 final size:10
Alignment explanation
Indices: 17506891--17506932 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
17506881 TTATCATACT
17506891 TATAAATATA
1 TATAAATATA
*
17506901 AATAAATATA
1 TATAAATATA
*
17506911 TATATATATA
1 TATAAATATA
*
17506921 TATATATATA
1 TATAAATATA
17506931 TA
1 TA
17506933 CAAACAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATAAATATA
Found at i:17506913 original size:4 final size:4
Alignment explanation
Indices: 17506891--17506932 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
17506881 TTATCATACT
* * *
17506891 TATA AATA TAAA TAAA TATA TATA TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
17506933 CAAACAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:17506931 original size:6 final size:6
Alignment explanation
Indices: 17506891--17506932 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
17506881 TTATCATACT
* * *
17506891 TATAAA TATAAA TAAATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA
17506933 CAAACAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:17510530 original size:23 final size:23
Alignment explanation
Indices: 17510482--17510530 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
17510472 AAAAATTTAT
*
17510482 TTTATTATAGGAAAAATTAATGC
1 TTTATTATAGGAAAAATTAATAC
*
17510505 TTTATT-TAAGGAAAAATTGATAC
1 TTTATTAT-AGGAAAAATTAATAC
17510528 TTT
1 TTT
17510531 TAATTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (23 bp):
TTTATTATAGGAAAAATTAATAC
Found at i:17510582 original size:58 final size:57
Alignment explanation
Indices: 17510505--17510779 Score: 296
Period size: 58 Copynumber: 4.8 Consensus size: 57
17510495 AAATTAATGC
* *
17510505 TTTATTTAAGGAAAAATTGATACTTTTAATTTTTTCTCAAATATTTTTTAAATATTTTT
1 TTTATTTAA-GAAAAATTGATACTTTCAACTTTTTCTCAAATATTTTTTAAATA-TTTT
* *
17510564 TTTATTTAAGAAAAATTGATA-TTTTAACTTTTTCTCAAACA-TTTTTAAATA--TT
1 TTTATTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAATATTTTTTAAATATTTT
*
17510617 TTTATTTAAGAAAAATTGATA-TTTCAACTTTTCCTCAAAATATTTTTTGAAATATTTT
1 TTTATTTAAGAAAAATTGATACTTTCAACTTTTTCTC-AAATATTTTTT-AAATATTTT
* * * * * *
17510675 TTTACTTAAGAAAAATTAATAC-TTCAACTTTTTCTTAAAAATATTTATAAAAATATTT
1 TTTATTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAATAT-TTTTTAAATAT-TTT
* * * *
17510733 TTTATTTATA-AAAAATTAATAC-TTCAACTTTTCCTTAAACATTTTTT
1 TTTATTTA-AGAAAAATTGATACTTTCAACTTTTTCTCAAATATTTTTT
17510780 TAACTTAAAA
Statistics
Matches: 191, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
53 36 0.19
54 4 0.02
55 5 0.03
56 15 0.08
57 32 0.17
58 89 0.47
59 10 0.05
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTATTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAATATTTTTTAAATATTTT
Found at i:17510658 original size:111 final size:114
Alignment explanation
Indices: 17510505--17510782 Score: 336
Period size: 111 Copynumber: 2.4 Consensus size: 114
17510495 AAATTAATGC
* * * *
17510505 TTTATTTAAGGAAAAATTGATACTTTTAATTTTTTCTC-AAATATTTTTTAAATATTTTTTTTAT
1 TTTATTTAA-GAAAAATTGATA-TTTCAACTTTTCCTCAAAATATTTTTTAAATA-TTTTTTTAC
* * * *
17510569 TTAAGAAAAATTGATATTTTAACTTTTTCTCAAACAT-TTT-T-AAATA-TT
63 TTAAGAAAAATTAATACTTCAACTTTTTCTCAAAAATATTTATAAAATATTT
17510617 TTTATTTAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTGAAATATTTTTTTACTT
1 TTTATTTAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTT-AAATATTTTTTTACTT
*
17510682 AAGAAAAATTAATACTTCAACTTTTTCTTAAAAATATTTATAAAAATATTT
65 AAGAAAAATTAATACTTCAACTTTTTCTCAAAAATATTTAT-AAAATATTT
* * *
17510733 TTTATTTATA-AAAAATTAATACTTCAACTTTTCCTTAAACAT-TTTTTTAA
1 TTTATTTA-AGAAAAATTGATATTTCAACTTTTCCTCAAA-ATATTTTTTAA
17510783 CTTAAAAAAA
Statistics
Matches: 145, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
110 12 0.08
111 63 0.43
112 17 0.12
113 1 0.01
115 7 0.05
116 42 0.29
117 3 0.02
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.50
Consensus pattern (114 bp):
TTTATTTAAGAAAAATTGATATTTCAACTTTTCCTCAAAATATTTTTTAAATATTTTTTTACTTA
AGAAAAATTAATACTTCAACTTTTTCTCAAAAATATTTATAAAATATTT
Found at i:17519803 original size:4 final size:4
Alignment explanation
Indices: 17519790--17519840 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
17519780 TATTTTTTTA
** *
17519790 TATT TA-T TATT TATT TATT TATT TATT TGGT TATT TATGC T-TT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT
17519837 TATT
1 TATT
17519841 AAATTTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 4 0.11
4 33 0.87
5 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:17520170 original size:20 final size:21
Alignment explanation
Indices: 17520137--17520180 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
17520127 ATTTATTTTG
17520137 AAACAAAAATAAAAAT-AATA
1 AAACAAAAATAAAAATAAATA
*
17520157 AAACAAATAA-AAAATTAAATA
1 AAACAAA-AATAAAAATAAATA
17520178 AAA
1 AAA
17520181 ATTGGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACAAAAATAAAAATAAATA
Found at i:17520819 original size:19 final size:22
Alignment explanation
Indices: 17520795--17520842 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
17520785 ATGAAAAATT
*
17520795 TAAAATA-AAAAA-TTT-TTAA
1 TAAAATAGAAAAAGTTTCTAAA
17520814 TAAAATTAGAAAAAGTTTCTAAA
1 TAAAA-TAGAAAAAGTTTCTAAA
17520837 TAAAAT
1 TAAAAT
17520843 TATAGAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 5 0.21
22 4 0.17
23 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAATAGAAAAAGTTTCTAAA
Found at i:17521768 original size:31 final size:30
Alignment explanation
Indices: 17521732--17521831 Score: 148
Period size: 31 Copynumber: 3.3 Consensus size: 30
17521722 TTCACACATG
* *
17521732 TTTTAACATTATAAAATAATCATTTTATCTT
1 TTTTAATATTATAAAATGATCATTTTA-CTT
17521763 TTTTAATATTATAAAATGATCATTTTACTT
1 TTTTAATATTATAAAATGATCATTTTACTT
*
17521793 TTTGTAATATTATAAAATGATTATTTTAC-T
1 TTT-TAATATTATAAAATGATCATTTTACTT
17521823 TTTTAATAT
1 TTTTAATAT
17521832 AAAAATTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
29 6 0.09
30 10 0.15
31 49 0.75
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTTAATATTATAAAATGATCATTTTACTT
Found at i:17521848 original size:16 final size:16
Alignment explanation
Indices: 17521827--17521860 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
17521817 TTTACTTTTT
17521827 AATATA-AAAATTATAA
1 AATATATAAAATTA-AA
17521843 AATATATAAAATTAAA
1 AATATATAAAATTAAA
17521859 AA
1 AA
17521861 AAATCATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATATAAAATTAAA
Found at i:17521862 original size:18 final size:16
Alignment explanation
Indices: 17521827--17521861 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17521817 TTTACTTTTT
*
17521827 AATATAAAAATTATAA
1 AATATAAAAATTAAAA
17521843 AATATATAAAATTAAAA
1 AATATA-AAAATTAAAA
17521860 AA
1 AA
17521862 AATCATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAAAATTAAAA
Found at i:17522059 original size:31 final size:31
Alignment explanation
Indices: 17522024--17522084 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
17522014 GTTTTGCTAA
* * *
17522024 CATTTGCCATCTTTTTTTTTTTTGAATAAAG
1 CATTTGCCATCTTCTTGTTGTTTGAATAAAG
*
17522055 CATTTGGCATCTTCTTGTTGTTTGAATAAA
1 CATTTGCCATCTTCTTGTTGTTTGAATAAA
17522085 TTGATTAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (31 bp):
CATTTGCCATCTTCTTGTTGTTTGAATAAAG
Found at i:17531409 original size:58 final size:58
Alignment explanation
Indices: 17531329--17531574 Score: 307
Period size: 58 Copynumber: 4.2 Consensus size: 58
17531319 AGCATTTTAA
* *
17531329 AAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAATGCTTTTTTG
1 AAATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAC-TTTTTG
* * * * *
17531387 AAATTTTTATTTCCAAGGAAAATTAATACTTTTAATTTTTCCTCAAAAATTCTTTTTG
1 AAATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTG
* * * * *
17531445 AACTCTTTATTTTCAAAGAAAATTGATACCTTCAACTTTTTCTCAAAAATACTTTTTG
1 AAATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTG
* * * *
17531503 AAATCTTTATTTTCAAGGAAAATTGATACTTTCAATTTTTCTTC-AAAATATTTTTTTG
1 AAATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-CTTTTTG
17531561 AAATTTTTACTTTT
1 AAATTTTTA-TTTT
17531575 ATTTTTTTGT
Statistics
Matches: 161, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
57 6 0.04
58 145 0.90
59 10 0.06
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (58 bp):
AAATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTG
Found at i:17531467 original size:116 final size:116
Alignment explanation
Indices: 17531334--17531562 Score: 338
Period size: 116 Copynumber: 2.0 Consensus size: 116
17531324 TTTAAAAATT
* * *
17531334 TTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAATGCTTTTTTGAAATTTTTATT
1 TTTATTTTCAAGAAAAATTGATACCTTCAACTTTTCCTCAAAAATAC-TTTTTGAAATCTTTATT
*
17531398 TCCAAGGAAAATTAATACTTTTAATTTTTCCTCAAAA-ATTCTTTTTGAACTC
65 TCCAAGGAAAATTAATACTTTCAATTTTTCCTCAAAATATT-TTTTTGAACTC
*
17531450 TTTATTTTCAA-AGAAAATTGATACCTTCAACTTTTTCTCAAAAATACTTTTTGAAATCTTTATT
1 TTTATTTTCAAGA-AAAATTGATACCTTCAACTTTTCCTCAAAAATACTTTTTGAAATCTTTATT
* * *
17531514 TTCAAGGAAAATTGATACTTTCAATTTTTCTTCAAAATATTTTTTTGAA
65 TCCAAGGAAAATTAATACTTTCAATTTTTCCTCAAAATATTTTTTTGAA
17531563 ATTTTTACTT
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
115 1 0.01
116 92 0.90
117 9 0.09
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.47
Consensus pattern (116 bp):
TTTATTTTCAAGAAAAATTGATACCTTCAACTTTTCCTCAAAAATACTTTTTGAAATCTTTATTT
CCAAGGAAAATTAATACTTTCAATTTTTCCTCAAAATATTTTTTTGAACTC
Found at i:17532741 original size:85 final size:85
Alignment explanation
Indices: 17532620--17532845 Score: 285
Period size: 85 Copynumber: 2.6 Consensus size: 85
17532610 ATGCAAGCTA
** * * * * *
17532620 AAATCCAGAAACGTAATGACCTGGATCGAACTGAAGTTTGAAATAAATAACTTGGACTGAA-CCG
1 AAATCCA-AAACAAAATGACTTGGATCGAACCGAAGTCTAAAAGAAATAACTTGGACT-AAGCCG
*
17532684 ATGAAGGATCTGGCATAGGTCG
64 AAGAAGGATCTGGCATAGGTCG
* *
17532706 AAATCCAAAACAAAATGACTTGGATTGAACCGAAGTCTAAAAGGAATAACTTGGACTAAGCCGAA
1 AAATCCAAAACAAAATGACTTGGATCGAACCGAAGTCTAAAAGAAATAACTTGGACTAAGCCGAA
17532771 GAAGGATCTGGCATAGGTCG
66 GAAGGATCTGGCATAGGTCG
* ** *
17532791 AAATCCAAAACAAAATGACTTGGATGGAACC-ATAGTCTAAACTAAGTAACTTGGA
1 AAATCCAAAACAAAATGACTTGGATCGAACCGA-AGTCTAAAAGAAATAACTTGGA
17532846 TGGAACCATA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
84 3 0.02
85 113 0.92
86 7 0.06
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (85 bp):
AAATCCAAAACAAAATGACTTGGATCGAACCGAAGTCTAAAAGAAATAACTTGGACTAAGCCGAA
GAAGGATCTGGCATAGGTCG
Found at i:17532846 original size:31 final size:31
Alignment explanation
Indices: 17532808--17532882 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
17532798 AAACAAAATG
17532808 ACTTGGATGGAACCATAGTCTAAACTAAGTA
1 ACTTGGATGGAACCATAGTCTAAACTAAGTA
*
17532839 ACTTGGATGGAACCATAGTCTGAACTAAGTA
1 ACTTGGATGGAACCATAGTCTAAACTAAGTA
*
17532870 ACTTGGATTGAAC
1 ACTTGGATGGAAC
17532883 TGAAGAAGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (31 bp):
ACTTGGATGGAACCATAGTCTAAACTAAGTA
Found at i:17532987 original size:85 final size:84
Alignment explanation
Indices: 17532844--17533000 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 84
17532834 AAGTAACTTG
* * * * * * *
17532844 GATGGAACCATAGTCTGAACTAAGTAACTTGGATTGAACTGAAGAAGGATTTGGCATAGGCCGAA
1 GATGGAACCAAAGTCTAAAATAAATAACTTGGACTGAACCGAAGAAAGATTTGGCATAGGCCGAA
17532909 ATCTAAAACAAAATAACCTA
66 ATC-AAAACAAAATAACCTA
*
17532929 GATGGAACCAAAGTTTAAAATAAATAACTTGGACTGAACCGAAGAAAGATTTGGCATAGGCCGAA
1 GATGGAACCAAAGTCTAAAATAAATAACTTGGACTGAACCGAAGAAAGATTTGGCATAGGCCGAA
17532994 ATCAAAA
66 ATCAAAA
17533001 TGACTTGGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 4 0.06
85 60 0.94
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (84 bp):
GATGGAACCAAAGTCTAAAATAAATAACTTGGACTGAACCGAAGAAAGATTTGGCATAGGCCGAA
ATCAAAACAAAATAACCTA
Found at i:17533248 original size:17 final size:17
Alignment explanation
Indices: 17533226--17533274 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
17533216 AAACAAATTC
17533226 GCAAGAATTGAAGATTT
1 GCAAGAATTGAAGATTT
17533243 GCAAGAATTGGAA-ATTT
1 GCAAGAATT-GAAGATTT
*
17533260 -CAAGAATTGGAGATT
1 GCAAGAATTGAAGATT
17533275 CATAAGACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.07
16 11 0.38
17 13 0.45
18 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
GCAAGAATTGAAGATTT
Found at i:17533265 original size:16 final size:18
Alignment explanation
Indices: 17533226--17533274 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 18
17533216 AAACAAATTC
17533226 GCAAGAATT-GAAGATTT
1 GCAAGAATTGGAAGATTT
17533243 GCAAGAATTGGAA-ATTT
1 GCAAGAATTGGAAGATTT
17533260 -CAAGAATTGG-AGATT
1 GCAAGAATTGGAAGATT
17533275 CATAAGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.03
16 13 0.43
17 13 0.43
18 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (18 bp):
GCAAGAATTGGAAGATTT
Found at i:17533347 original size:17 final size:17
Alignment explanation
Indices: 17533189--17533348 Score: 65
Period size: 17 Copynumber: 9.6 Consensus size: 17
17533179 AGGTTCAAAA
**
17533189 ATTCACAAGAATTTTAG
1 ATTCACAAGAATTGGAG
*** *
17533206 ATTCACAAGAA-AACAA
1 ATTCACAAGAATTGGAG
* *
17533222 ATTCGCAAGAATTGAAG
1 ATTCACAAGAATTGGAG
** *
17533239 ATTTGCAAGAATTGGAA
1 ATTCACAAGAATTGGAG
*
17533256 ATT-TCAAGAATTGGAG
1 ATTCACAAGAATTGGAG
* * **
17533272 ATTCATAAGACTTTCAG
1 ATTCACAAGAATTGGAG
*
17533289 ATTCACAAG-ATTAGAG
1 ATTCACAAGAATTGGAG
*** * ** *
17533305 ATGGGCAAGACTTTCAA
1 ATTCACAAGAATTGGAG
**
17533322 ATTTGCAAGAATTGGAG
1 ATTCACAAGAATTGGAG
17533339 ATTCACAAGA
1 ATTCACAAGA
17533349 CTTTCAGATT
Statistics
Matches: 102, Mismatches: 38, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
16 35 0.34
17 67 0.66
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (17 bp):
ATTCACAAGAATTGGAG
Found at i:17533357 original size:17 final size:17
Alignment explanation
Indices: 17533270--17533358 Score: 63
Period size: 17 Copynumber: 5.3 Consensus size: 17
17533260 CAAGAATTGG
*
17533270 AGATTCATAAGACTTTC
1 AGATTCACAAGACTTTC
**
17533287 AGATTCACAAGA-TTAG
1 AGATTCACAAGACTTTC
***
17533303 AGATGGGCAAGACTTTC
1 AGATTCACAAGACTTTC
* ** * **
17533320 AAATTTGCAAGAATTGG
1 AGATTCACAAGACTTTC
17533337 AGATTCACAAGACTTTC
1 AGATTCACAAGACTTTC
17533354 AGATT
1 AGATT
17533359 TGTAAGAATT
Statistics
Matches: 51, Mismatches: 20, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
16 11 0.22
17 40 0.78
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (17 bp):
AGATTCACAAGACTTTC
Found at i:17534728 original size:23 final size:24
Alignment explanation
Indices: 17534702--17534762 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
17534692 TGAGTATTCC
17534702 TTTTTTTTTTCAACTTTTTT-ATT
1 TTTTTTTTTTCAACTTTTTTGATT
* * *
17534725 TTTTATTTTTCAATTTTTTTGCTT
1 TTTTTTTTTTCAACTTTTTTGATT
17534749 TTTCATTTTTTTCA
1 TTT--TTTTTTTCA
17534763 CTTCATCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 18 0.58
24 5 0.16
26 8 0.26
ACGTcount: A:0.13, C:0.10, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTTTTTTTCAACTTTTTTGATT
Found at i:17534743 original size:17 final size:16
Alignment explanation
Indices: 17534723--17534760 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17534713 AACTTTTTTA
17534723 TTTTTT-ATTTTTCAAT
1 TTTTTTGATTTTTC-AT
*
17534739 TTTTTTGCTTTTTCAT
1 TTTTTTGATTTTTCAT
17534755 TTTTTT
1 TTTTTT
17534761 CACTTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTGATTTTTCAT
Found at i:17538949 original size:58 final size:58
Alignment explanation
Indices: 17538701--17539053 Score: 374
Period size: 58 Copynumber: 6.0 Consensus size: 58
17538691 TGCTTTTATG
* * * *
17538701 CAAGAAAAATTGTTACTTTCAACTTTTCCT--TAAA-CCTTTTTAAAATTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTGAAATCTTTATTTT
*
17538756 CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATGCCTTTTTTATTGAAAT-TTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CC---TTT-TTGAAATCTTTATTTT
* * * *
17538818 TAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACCTTTTTTGAAATTTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CC-TTTTTGAAATCTTTATTTT
* * * * *
17538878 CACGAAAAATTGATACTTTCAATTTTTCCTCAAAAATGCTTTTTGAACTCATTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTGAAATCTTTATTTT
* * *
17538936 CAAGAAAAATTGATACCTTCAACTTTTTCTCAAAAATAC-TTTTGAAAATCTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTG-AAATCTTTATTTT
** * ** *
17538994 TGAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTTGAAATTTTTACTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-ATCCTTTTTGAAATCTTTA-TTTT
17539054 ATTTTTTTGT
Statistics
Matches: 252, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
55 28 0.11
57 8 0.03
58 90 0.36
59 20 0.08
60 53 0.21
62 47 0.19
63 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTGAAATCTTTATTTT
Found at i:17539060 original size:26 final size:26
Alignment explanation
Indices: 17539031--17539080 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17539021 CCTCAAAATA
* *
17539031 TTTTTT-TTGAAATTTTTACTTTTAT
1 TTTTTTGTTCAAATTATTACTTTTAT
*
17539056 TTTTTTGTTCAAATTATTATTTTTA
1 TTTTTTGTTCAAATTATTACTTTTA
17539081 ATTATTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTTGTTCAAATTATTACTTTTAT
Found at i:17540512 original size:9 final size:10
Alignment explanation
Indices: 17540479--17540511 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
17540469 AAAATTATCT
17540479 TTTTAATAAA
1 TTTTAATAAA
17540489 TTTTAATAAA
1 TTTTAATAAA
17540499 -TTT-ATAAA
1 TTTTAATAAA
17540507 TTTTA
1 TTTTA
17540512 TTAAGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.24
9 6 0.29
10 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:17540995 original size:8 final size:8
Alignment explanation
Indices: 17540978--17541006 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
17540968 GTTTCTTTTT
17540978 AAAAAA-A
1 AAAAAACA
17540985 AAAAAACA
1 AAAAAACA
17540993 AAAAAACA
1 AAAAAACA
17541001 AAAAAA
1 AAAAAA
17541007 AGGGAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:17541994 original size:19 final size:18
Alignment explanation
Indices: 17541950--17541995 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
17541940 AAAACTAAAG
17541950 AAGAAT-AATAACAAAAA
1 AAGAATAAATAACAAAAA
*
17541967 AATATATAAATAACAAATAA
1 AAGA-ATAAATAACAAA-AA
17541987 AAGAATAAA
1 AAGAATAAA
17541996 AATATGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 2 0.08
19 14 0.58
20 5 0.21
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (18 bp):
AAGAATAAATAACAAAAA
Found at i:17542404 original size:22 final size:22
Alignment explanation
Indices: 17542379--17542425 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
17542369 TTAAAATCCA
*
17542379 AAATCTTAAAAATCAAAACCCT
1 AAATCCTAAAAATCAAAACCCT
*
17542401 AAATCCTAAAACTCAAAACCCT
1 AAATCCTAAAAATCAAAACCCT
17542423 AAA
1 AAA
17542426 ACCAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATCCTAAAAATCAAAACCCT
Found at i:17542476 original size:16 final size:17
Alignment explanation
Indices: 17542451--17542497 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
17542441 AAAACCCTCT
17542451 AAACCCTTC-AACCCTA
1 AAACCCTTCAAACCCTA
*
17542467 AAACCTTTCAAACCCTA
1 AAACCCTTCAAACCCTA
*
17542484 AAACCCTTTAAACC
1 AAACCCTTCAAACC
17542498 TTTCAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (17 bp):
AAACCCTTCAAACCCTA
Found at i:17542503 original size:42 final size:43
Alignment explanation
Indices: 17542417--17542503 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
17542407 TAAAACTCAA
**
17542417 AACCCTAAAACCAATCAAAACTTTAAAACCCTCTAAACCCTTC
1 AACCCTAAAACCAATCAAAACCCTAAAACCCTCTAAACCCTTC
** * *
17542460 AACCCTAAAACCTTTC-AAACCCTAAAACCCTTTAAACCTTTC
1 AACCCTAAAACCAATCAAAACCCTAAAACCCTCTAAACCCTTC
17542502 AA
1 AA
17542504 ACATTCGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 24 0.63
43 14 0.37
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (43 bp):
AACCCTAAAACCAATCAAAACCCTAAAACCCTCTAAACCCTTC
Found at i:17542612 original size:30 final size:29
Alignment explanation
Indices: 17542577--17542648 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
17542567 TTTGAAAATA
*
17542577 AAAAACCTTAAATCTAAAACCCTAAACCTT
1 AAAAACCTTAAAT-TAAAACCCTAAACCCT
* * **
17542607 TAAAACTTTAAAATTAAAACTTTAAACCCT
1 AAAAACCTT-AAATTAAAACCCTAAACCCT
17542637 AAAAACCTTAAA
1 AAAAACCTTAAA
17542649 CCCTAAACCT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 3 0.09
30 27 0.79
31 4 0.12
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAACCTTAAATTAAAACCCTAAACCCT
Found at i:17542650 original size:53 final size:53
Alignment explanation
Indices: 17542593--17542702 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
17542583 CTTAAATCTA
*
17542593 AAACCCTAAACCTTTAAAACTTTAAAATTAAAACTTTAAACCCTAAAAACCTT
1 AAACCCTAAACCTTTAAAACTCTAAAATTAAAACTTTAAACCCTAAAAACCTT
* * *
17542646 AAACCCTAAACCTTTAAAACTCTAAAATTGAAACTTTCAACCCTCAAAACCTT
1 AAACCCTAAACCTTTAAAACTCTAAAATTAAAACTTTAAACCCTAAAAACCTT
17542699 AAAC
1 AAAC
17542703 TACAAAACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.26
Consensus pattern (53 bp):
AAACCCTAAACCTTTAAAACTCTAAAATTAAAACTTTAAACCCTAAAAACCTT
Found at i:17542731 original size:15 final size:15
Alignment explanation
Indices: 17542713--17542940 Score: 92
Period size: 15 Copynumber: 15.3 Consensus size: 15
17542703 TACAAAACTC
17542713 AAAACCTTAAACCCT
1 AAAACCTTAAACCCT
* *
17542728 AAAACCTCCAAAACCTT
1 AAAACCT--TAAACCCT
*
17542745 AAAACTTTCCAAACCCT
1 AAAACCTT--AAACCCT
* *
17542762 AAAACCTCCAAACCTT
1 AAAACCT-TAAACCCT
17542778 AAAA-CTTCAAACCCT
1 AAAACCTT-AAACCCT
*
17542793 AAAATC-TAAATCCC-
1 AAAACCTTAAA-CCCT
*
17542807 AAAATC-TAAACCCT
1 AAAACCTTAAACCCT
17542821 -AAACCTTTAAACCCTT
1 AAAACC-TTAAACCC-T
*
17542837 AAAACCTCAAACTCC-
1 AAAACCTTAAAC-CCT
* *
17542852 AAAGCCTTAAAGCCTT
1 AAAACCTTAAA-CCCT
17542868 AAAA---T----CCT
1 AAAACCTTAAACCCT
17542876 AAAA-CTTGAAACCCT
1 AAAACCTT-AAACCCT
*
17542891 AAAAGCCTTAAA-ACT
1 AAAA-CCTTAAACCCT
*
17542906 CAAAACC-AAAACCCT
1 -AAAACCTTAAACCCT
*
17542921 AAAATCTTGAAACCCT
1 AAAACCTT-AAACCCT
17542937 AAAA
1 AAAA
17542941 TGATATCTTA
Statistics
Matches: 162, Mismatches: 22, Indels: 57
0.67 0.09 0.24
Matches are distributed among these distances:
8 6 0.04
10 1 0.01
13 8 0.05
14 21 0.13
15 53 0.33
16 39 0.24
17 34 0.21
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAACCTTAAACCCT
Found at i:17542748 original size:8 final size:8
Alignment explanation
Indices: 17542578--17542940 Score: 87
Period size: 8 Copynumber: 47.5 Consensus size: 8
17542568 TTGAAAATAA
17542578 AAAACCTT
1 AAAACCTT
*
17542586 -AAATC-T
1 AAAACCTT
*
17542592 AAAACCCT
1 AAAACCTT
17542600 -AAACCTTT
1 AAAACC-TT
*
17542608 AAAACTTT
1 AAAACCTT
17542616 AAAA--TT
1 AAAACCTT
*
17542622 AAAACTTT
1 AAAACCTT
* *
17542630 AAACCCTA
1 AAAACCTT
17542638 AAAACCTT
1 AAAACCTT
*
17542646 -AAACCCT
1 AAAACCTT
17542653 -AAACCTTT
1 AAAACC-TT
17542661 AAAA-CTCT
1 AAAACCT-T
17542669 AAAA--TT
1 AAAACCTT
* *
17542675 GAAACTTT
1 AAAACCTT
* * *
17542683 CAACCCTC
1 AAAACCTT
17542691 AAAACCTT
1 AAAACCTT
17542699 -AAA-C-T
1 AAAACCTT
* *
17542704 ACAAAACTC
1 A-AAACCTT
17542713 AAAACCTT
1 AAAACCTT
*
17542721 -AAACCCT
1 AAAACCTT
*
17542728 AAAACCTCC
1 AAAACCT-T
17542737 AAAACCTT
1 AAAACCTT
*
17542745 AAAACTTT
1 AAAACCTT
* *
17542753 CCAAACCCT
1 -AAAACCTT
*
17542762 AAAACCTC
1 AAAACCTT
*
17542770 CAAACCTT
1 AAAACCTT
17542778 AAAA-CTT
1 AAAACCTT
* *
17542785 CAAACCCT
1 AAAACCTT
*
17542793 AAAATC-T
1 AAAACCTT
* *
17542800 AAATCC-C
1 AAAACCTT
*
17542807 AAAATC-T
1 AAAACCTT
*
17542814 -AAACCCT
1 AAAACCTT
17542821 -AAACCTTT
1 AAAACC-TT
*
17542829 AAACCCTT
1 AAAACCTT
17542837 AAAACC-T
1 AAAACCTT
* *
17542844 CAAA-CTCC
1 AAAACCT-T
*
17542852 AAAGCCTT
1 AAAACCTT
*
17542860 AAAGCCTT
1 AAAACCTT
17542868 AAAATCC-T
1 AAAA-CCTT
17542876 AAAA-CTT
1 AAAACCTT
* *
17542883 GAAACCCT
1 AAAACCTT
17542891 AAAAGCCTT
1 AAAA-CCTT
*
17542900 AAAA-CTC
1 AAAACCTT
17542907 AAAACC--
1 AAAACCTT
*
17542913 AAAACCCT
1 AAAACCTT
*
17542921 AAAATCTT
1 AAAACCTT
* *
17542929 GAAACCCT
1 AAAACCTT
17542937 AAAA
1 AAAA
17542941 TGATATCTTA
Statistics
Matches: 256, Mismatches: 67, Indels: 64
0.66 0.17 0.17
Matches are distributed among these distances:
5 1 0.00
6 24 0.09
7 73 0.29
8 123 0.48
9 35 0.14
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (8 bp):
AAAACCTT
Found at i:17542761 original size:34 final size:31
Alignment explanation
Indices: 17542713--17542796 Score: 125
Period size: 34 Copynumber: 2.6 Consensus size: 31
17542703 TACAAAACTC
17542713 AAAACCTT-AAACCCTAAAACCTCCAAAACCTT
1 AAAA-CTTCAAACCCTAAAACCTCC-AAACCTT
17542745 AAAACTTTCCAAACCCTAAAACCTCCAAACCTT
1 AAAAC-TT-CAAACCCTAAAACCTCCAAACCTT
17542778 AAAACTTCAAACCCTAAAA
1 AAAACTTCAAACCCTAAAA
17542797 TCTAAATCCC
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
31 13 0.27
32 8 0.16
33 12 0.24
34 16 0.33
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (31 bp):
AAAACTTCAAACCCTAAAACCTCCAAACCTT
Found at i:17542773 original size:16 final size:16
Alignment explanation
Indices: 17542721--17542848 Score: 92
Period size: 17 Copynumber: 8.2 Consensus size: 16
17542711 TCAAAACCTT
17542721 AAACCCTAAAACCTCC
1 AAACCCTAAAACCTCC
* *
17542737 AAAACCTTAAAACTTTCC
1 -AAACCCTAAAAC-CTCC
17542755 AAACCCTAAAACCTCC
1 AAACCCTAAAACCTCC
* *
17542771 AAACCTTAAAA-CTTC
1 AAACCCTAAAACCTCC
*
17542786 AAACCCTAAAA--TCT
1 AAACCCTAAAACCTCC
*
17542800 AAATCCC-AAAA--TCT
1 AAA-CCCTAAAACCTCC
**
17542814 AAACCCT-AAACCTTT
1 AAACCCTAAAACCTCC
17542829 AAACCCTTAAAACCT-C
1 AAACCC-TAAAACCTCC
17542845 AAAC
1 AAAC
17542849 TCCAAAGCCT
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
13 6 0.06
14 14 0.15
15 24 0.26
16 18 0.19
17 28 0.30
18 3 0.03
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (16 bp):
AAACCCTAAAACCTCC
Found at i:17542896 original size:32 final size:31
Alignment explanation
Indices: 17542833--17542924 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 31
17542823 ACCTTTAAAC
* * *
17542833 CCTTAAAACCTCAAACTCCAAAGCCTTAAAG
1 CCTTAAAACCTAAAACTCCAAACCCTAAAAG
**
17542864 CCTTAAAATCCTAAAACTTGAAACCCTAAAAG
1 CCTTAAAA-CCTAAAACTCCAAACCCTAAAAG
*
17542896 CCTTAAAA-CTCAAAAC-CAAAACCCTAAAA
1 CCTTAAAACCT-AAAACTCCAAACCCTAAAA
17542925 TCTTGAAACC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
30 13 0.25
31 13 0.25
32 26 0.50
ACGTcount: A:0.48, C:0.29, G:0.04, T:0.18
Consensus pattern (31 bp):
CCTTAAAACCTAAAACTCCAAACCCTAAAAG
Found at i:17548850 original size:17 final size:17
Alignment explanation
Indices: 17548822--17548871 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17548812 ACAACAAAAC
17548822 AAAAAAA-A-AGAAA-G
1 AAAAAAATAGAGAAATG
17548836 AGAAAAAATAGAGAAATG
1 A-AAAAAATAGAGAAATG
* *
17548854 AAAAGAATAGAAAAATG
1 AAAAAAATAGAGAAATG
17548871 A
1 A
17548872 TTATGACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 1 0.03
15 6 0.20
16 1 0.03
17 20 0.67
18 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (17 bp):
AAAAAAATAGAGAAATG
Found at i:17548857 original size:15 final size:17
Alignment explanation
Indices: 17548837--17548871 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17548827 AAAAGAAAGA
*
17548837 GAAAA-AATAGAGAAAT
1 GAAAAGAATAGAAAAAT
17548853 GAAAAGAATAGAAAAAT
1 GAAAAGAATAGAAAAAT
17548870 GA
1 GA
17548872 TTATGACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (17 bp):
GAAAAGAATAGAAAAAT
Found at i:17550304 original size:28 final size:28
Alignment explanation
Indices: 17550255--17550329 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
17550245 TAAAAAACTC
* * **
17550255 AAGCCCAGTTTAGCTGATAGCCAAGCTT
1 AAGCCCAGATTATCTGGCAGCCAAGCTT
17550283 AAGCCCAGATTATCTGGCAGCCAAGCTT
1 AAGCCCAGATTATCTGGCAGCCAAGCTT
17550311 AAGCCCAGATTATCTGGCA
1 AAGCCCAGATTATCTGGCA
17550330 CTAAGGAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (28 bp):
AAGCCCAGATTATCTGGCAGCCAAGCTT
Found at i:17551004 original size:33 final size:33
Alignment explanation
Indices: 17550766--17551030 Score: 102
Period size: 33 Copynumber: 8.0 Consensus size: 33
17550756 TTAAACCCAG
* *
17550766 TTTACCTGGCACCCAGTGAAAATTTAAGCCCAAA
1 TTTAGCTGGCACCCAATGAAAATTTAAG-CCAAA
* * * * *
17550800 -TTAGCTAGTC-CTCAATGAAATTTTAAACCCAA
1 TTTAGCT-GGCACCCAATGAAAATTTAAGCCAAA
* * *
17550832 TTTA-CTTGGCACCTAACG-AAAGTTAAGCCCAAA
1 TTTAGC-TGGCACCCAATGAAAATTTAAG-CCAAA
* * * *
17550865 -TTGGCTGGTACCCAAT-AAACTTTTAAGCTCAGA
1 TTTAGCTGGCACCCAATGAAA-ATTTAAGC-CAAA
** *
17550898 -TTATTTGGCACACC-ATCAAAAGATTTTAAGTCC-AA
1 TTTAGCTGGCAC-CCAAT-GAAA-A-TTTAAG-CCAAA
*** * * *
17550933 TTTAGCTGGCATTTAATGAAATTTTAAACTC-AG
1 TTTAGCTGGCACCCAATGAAAATTTAAGC-CAAA
*
17550966 CTTAGCTGGCACCCAATGAAAATTTAAGCCAAA
1 TTTAGCTGGCACCCAATGAAAATTTAAGCCAAA
**
17550999 TTTAGCAT-GCACCCAATGAAGTTTTAAGCCAA
1 TTTAGC-TGGCACCCAATGAAAATTTAAGCCAA
17551031 GCCCAGTTTA
Statistics
Matches: 164, Mismatches: 48, Indels: 39
0.65 0.19 0.16
Matches are distributed among these distances:
32 28 0.17
33 106 0.65
34 5 0.03
35 7 0.04
36 17 0.10
37 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (33 bp):
TTTAGCTGGCACCCAATGAAAATTTAAGCCAAA
Found at i:17551017 original size:66 final size:65
Alignment explanation
Indices: 17550751--17551025 Score: 202
Period size: 66 Copynumber: 4.1 Consensus size: 65
17550741 GGCCCTAATA
* * *
17550751 AAATTTTAAACCCAGTTTACCTGGCACCCAGTGAAAATTTAAGCCCAAATTAGCTAGTC-CTCAA
1 AAATTTTAAACCCAGTTTA-CTGGCACCCAATGAAAATTTAAGCCCAAATTAGCT-GGCACCCAA
17550815 TG
64 TG
* * * * * *
17550817 AAATTTTAAACCCAATTTACTTGGCACCTAACG-AAAGTTAAGCCCAAATTGGCTGGTACCCAAT
1 AAATTTTAAACCCAGTTTAC-TGGCACCCAATGAAAATTTAAGCCCAAATTAGCTGGCACCCAAT
17550881 -
65 G
* * * * * * * *
17550881 AAACTTTTAAGCTCAGATTATTTGGCACACC-ATCAAAAGATTTTAAGTCCAATTTAGCTGGCAT
1 AAA-TTTTAAACCCAGTTTA-CTGGCAC-CCAAT-GAAA-A-TTTAAGCCCAAATTAGCTGGCAC
**
17550945 TTAATG
60 CCAATG
* *
17550951 AAATTTTAAACTCAGCTTAGCTGGCACCCAATGAAAATTTAAG-CCAAATTTAGCAT-GCACCCA
1 AAATTTTAAACCCAGTTTA-CTGGCACCCAATGAAAATTTAAGCCCAAA-TTAGC-TGGCACCCA
17551014 ATG
63 ATG
*
17551017 AAGTTTTAA
1 AAATTTTAA
17551026 GCCAAGCCCA
Statistics
Matches: 161, Mismatches: 35, Indels: 26
0.73 0.16 0.12
Matches are distributed among these distances:
64 4 0.02
65 48 0.30
66 54 0.34
67 4 0.02
68 6 0.04
69 42 0.26
70 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (65 bp):
AAATTTTAAACCCAGTTTACTGGCACCCAATGAAAATTTAAGCCCAAATTAGCTGGCACCCAATG
Found at i:17551170 original size:36 final size:37
Alignment explanation
Indices: 17551130--17551393 Score: 192
Period size: 36 Copynumber: 7.4 Consensus size: 37
17551120 TCAGTTATTT
* *
17551130 TTTATTTTCTAACTTGCAATGTTGTCCTAG-TCATTC
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
* * * **
17551166 TTTATTTTC-AACTTGCAATGTTGTCC-CGATC-GCC
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
* * * *
17551200 TTTTACTTTTC-GACTTGCGATATTATCCCAG-TCATTT
1 -TTTA-TTTTCTGACTTGCGATGTTGTCCTAGATCATTC
* * *
17551237 TTTATTTTTTGACTTACGATGTTGT-CTCGATCATTC
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
* * * *
17551273 TTTATTTTTTGACTTGCGATGTTATCC-CGATCGTTC
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
* *
17551309 TTTATTTTCTGACTTGTG-TGTTGTCCTAG-TTATTC
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
** * * *
17551344 TTTATTTT-TGACTTATGGTGTTGTCCT-TATCATTA
1 TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
*
17551379 TTTATTTTTTGACTT
1 TTTATTTTCTGACTT
17551394 ATAGTGTCAT
Statistics
Matches: 185, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
34 10 0.05
35 69 0.37
36 104 0.56
37 2 0.01
ACGTcount: A:0.16, C:0.18, G:0.14, T:0.52
Consensus pattern (37 bp):
TTTATTTTCTGACTTGCGATGTTGTCCTAGATCATTC
Found at i:17551279 original size:107 final size:105
Alignment explanation
Indices: 17551115--17551386 Score: 280
Period size: 107 Copynumber: 2.6 Consensus size: 105
17551105 ACTTATGGTG
* * * * *
17551115 TTATCTCAGTTATTTTTTATTTTCTAACTTGCAATGTTGTCCTAGTCATTCTTTATTTTCAACTT
1 TTATCCCAGTTATTTTTTATTTTTTGACTTACGATGTTGTCCTA-TCATTCTTTATTTTCAACTT
*
17551180 GCAATGTTGTCCCGATCGC-CTTTTACTTTTC-GACTTGCGATA
65 GCAATGTTATCCCGATCGCTC-TTTA-TTTTCTGACTTGCG-TA
* * **
17551222 TTATCCCAGTCATTTTTTATTTTTTGACTTACGATGTTGTCTCGATCATTCTTTATTTTTTGACT
1 TTATCCCAGTTATTTTTTATTTTTTGACTTACGATGTTGTC-CTATCATTCTTTA-TTTTCAACT
* * * *
17551287 TGCGATGTTATCCCGATCGTTCTTTATTTTCTGACTTGTGTG
64 TGCAATGTTATCCCGATCGCTCTTTATTTTCTGACTTGCGTA
* * * * * *
17551329 TTGTCCTAGTTATTCTTTA-TTTTTGACTTATGGTGTTGTCCTTATCATTATTTATTTT
1 TTATCCCAGTTATTTTTTATTTTTTGACTTACGATGTTGTCC-TATCATTCTTTATTTT
17551387 TTGACTTATA
Statistics
Matches: 138, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
105 5 0.04
106 29 0.21
107 66 0.48
108 37 0.27
109 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.53
Consensus pattern (105 bp):
TTATCCCAGTTATTTTTTATTTTTTGACTTACGATGTTGTCCTATCATTCTTTATTTTCAACTTG
CAATGTTATCCCGATCGCTCTTTATTTTCTGACTTGCGTA
Found at i:17551395 original size:36 final size:36
Alignment explanation
Indices: 17551231--17551997 Score: 240
Period size: 36 Copynumber: 21.4 Consensus size: 36
17551221 ATTATCCCAG
* * *
17551231 TCATTTTTTATTTTTTGACTTACGATGTTGT-CTCGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCT-GA
** * * *
17551267 TCATTCTTTATTTTTTGACTTGCGATGTTATCCCGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * *
17551303 TCGTTCTTTATTTTCTGACTTGT-GTGTTGTCCT-A
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* *
17551337 GTTATTCTTTA-TTTTTGACTTATGGTGTTGTCCTTA
1 -TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * ** *
17551373 TCATTATTTATTTTTTGACTTATAGTGTCAT-TTGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * * * *
17551408 GTCGTTATTTATTTTTTGACCTGTGGTATTGT-CTCGA
1 -TCATTCTTTATTTTTTGACTTATGGTGTTGTCCT-GA
* *** * * *
17551445 TCGTTCTTTATTTTCAAACTT-TCAGTGTTGTCCCGG
1 TCATTCTTTATTTTTTGACTTAT-GGTGTTGTCCTGA
* * * **
17551481 TTATTTTTTATTTTTTGACTTATAGTGTCAT-CTGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * *** * ** *
17551516 GTCATTCTTTATTTTCTAACTTGCAGTATTGTTTTGG
1 -TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
** *** * **
17551553 TCATTCTTTATTTTTAAACTTACAATATCATCCTGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
** * * **** ****
17551589 TTGTTTTTTAGTTCCCAACTTGCAATGTTGTCCTGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * * * *
17551625 TTATTTTTTA-TTTTTGACTTGTAGTGTTAT-CTCGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCT-GA
* *** * * * *
17551660 TCATTCTTTATTTTTGGACTTGCAGTATTATCCCCGG
1 TCATTCTTTATTTTTTGACTTATGGTGTTGT-CCTGA
* * * **
17551697 TCATTCTTTGTTTCTTGACTTGA-AGTGTTGTCCCAA
1 TCATTCTTTATTTTTTGACTT-ATGGTGTTGTCCTGA
* * * ** * *
17551733 TCGTTCTTTA--TTCTGACTTACGGCATTGTCTTAA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* *
17551767 TCATTCTTTATTTTTTGACTTATGATGTCAT-TAC-GA
1 TCATTCTTTATTTTTTGACTTATGGTGT--TGTCCTGA
*** ** ** *
17551803 TCATTCTTT-TTTTTTTTTTTACAGTGTCATCCCGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * *
17551838 TCGTTCTTTATTTTTTGACTTACGGTGTTAT-CTCGA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCT-GA
* * *
17551874 TCATTCTTTATTTTTTGACTTACT-TTGTTATCCCGA
1 TCATTCTTTATTTTTTGACTTA-TGGTGTTGTCCTGA
* ** * * *
17551910 TCGTTCTTTATTTTCAGACTTACGGTCTTGTCCTGG
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
* * **
17551946 TCATTCTTTATTTTTTAACTTACGGTGTTGTCCCAA
1 TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
17551982 TCATT-TCTTATTTTTT
1 TCATTCT-TTATTTTTT
17551998 AAATTGCAAT
Statistics
Matches: 545, Mismatches: 156, Indels: 60
0.72 0.20 0.08
Matches are distributed among these distances:
33 1 0.00
34 39 0.07
35 85 0.16
36 384 0.70
37 34 0.06
38 2 0.00
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (36 bp):
TCATTCTTTATTTTTTGACTTATGGTGTTGTCCTGA
Found at i:17551545 original size:108 final size:108
Alignment explanation
Indices: 17551379--17551573 Score: 273
Period size: 108 Copynumber: 1.8 Consensus size: 108
17551369 CTTATCATTA
* * * * **
17551379 TTTATTTTTTGACTTATAGTGTCATTTGAGTCGTTATTTATTTTTTGACCTGTGGTATTGTCTCG
1 TTTATTTTTTGACTTATAGTGTCATCTGAGTCATTATTTATTTTCTAACCTGCAGTATTGTCTCG
*
17551444 ATCGTTCTTTATTTTCAAACTTTCAGTGTTGTCCCGGTTATTT
66 ATCATTCTTTATTTTCAAACTTTCAGTGTTGTCCCGGTTATTT
* * * *
17551487 TTTATTTTTTGACTTATAGTGTCATCTGAGTCATTCTTTATTTTCTAACTTGCAGTATTGTTTTG
1 TTTATTTTTTGACTTATAGTGTCATCTGAGTCATTATTTATTTTCTAACCTGCAGTATTGTCTCG
* *
17551552 GTCATTCTTTATTTTTAAACTT
66 ATCATTCTTTATTTTCAAACTT
17551574 ACAATATCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 74 1.00
ACGTcount: A:0.17, C:0.13, G:0.14, T:0.55
Consensus pattern (108 bp):
TTTATTTTTTGACTTATAGTGTCATCTGAGTCATTATTTATTTTCTAACCTGCAGTATTGTCTCG
ATCATTCTTTATTTTCAAACTTTCAGTGTTGTCCCGGTTATTT
Found at i:17551841 original size:393 final size:393
Alignment explanation
Indices: 17551093--17551968 Score: 853
Period size: 393 Copynumber: 2.2 Consensus size: 393
17551083 TTAGCAGTCA
* * * * *
17551093 TTTTATTTTTTGACTTATGGTGTTATCTCAGTTATTTTTTATTTTCTAACTTGCAATGTTGTCCT
1 TTTTATTTTTTGACTTAT-GTGTTATCTGAGTCATTCTTTATTTTCTAACTTGCAGTATTGTCCT
* * * * ** ** * *
17551158 AGTCATTCTTTA-TTTTCAACTTGCAATGTTGTCCCGATCGCCTTTTACTTTTCGACTTGCGATA
65 GGTCATTCTTTATTTTTAAACTTACAATATCATCCCGATCGCCTTTTACTTCCCAACTTGCAATA
* *
17551222 TTATCCCAGTCATTTTTTATTTTTTGACTTACGATGTTGTCTCGATCATTCTTTATTTTTTGACT
130 TTATCCCAGTCATTTTTTATTTTTTGACTTACGATGTTATCTCGATCATTCTTTATTTTTGGACT
* * * * * * *
17551287 TGCGATGTTATCCCGATCGTTCTTTATTTTCTGACTTGTGTGTTGTCCTAGTTATTCTTTATTTT
195 TGCGATATTATCCCGATCATTCTTTATTTTCTGACTTGAGTGTTGTCCCAATCATTCTTTATTTC
* ** * *
17551352 TGACTTATGGTGTTGTCCTTATCATTATTTATTTTTTGACTTATAGTGTCATTTGAGTCGTTATT
260 TGACTTACGGCATTGTCCTTATCATTATTTATTTTTTGACTTATAGTGTCATTCGAGTCATTATT
*** ** * * * *
17551417 TATTTTTTGACCTGTGGTATTGTCTCGATCGTTCTTTATTTTCAAACTTTCAGTGTTGTCCCGGT
325 TATTTTTTGACCTACAGTATCATCCCGATCGTTCTTTATTTTCAAACTTACAGTGTTATCCCGAT
*
17551482 TATT
390 CATT
* **
17551486 TTTTATTTTTTGACTTATAGTGTCATCTGAGTCATTCTTTATTTTCTAACTTGCAGTATTGTTTT
1 TTTTATTTTTTGACTTAT-GTGTTATCTGAGTCATTCTTTATTTTCTAACTTGCAGTATTGTCCT
* * ** * *
17551551 GGTCATTCTTTATTTTTAAACTTACAATATCATCCTGATTGTTTTTTAGTTCCCAACTTGCAATG
65 GGTCATTCTTTATTTTTAAACTTACAATATCATCCCGATCGCCTTTTACTTCCCAACTTGCAATA
* * *
17551616 TTGT-CCTGATTATTTTTTA-TTTTTGACTT--GTAGTGTTATCTCGATCATTCTTTATTTTTGG
130 TTATCCCAG-TCATTTTTTATTTTTTGACTTACG-A-TGTTATCTCGATCATTCTTTATTTTTGG
* * *
17551677 ACTTGC-AGTATTATCCCCGGTCATTCTTT-GTTTCTTGACTTGAAGTGTTGTCCCAATCGTTCT
192 ACTTGCGA-TATTAT-CCCGATCATTCTTTATTTTC-TGACTTG-AGTGTTGTCCCAATCATTCT
*
17551740 TTA-TTCTGACTTACGGCATTGT-CTTAATCATTCTTTATTTTTTGACTTAT-GATGTCATTACG
253 TTATTTCTGACTTACGGCATTGTCCTT-ATCATTATTTATTTTTTGACTTATAG-TGTCATT-CG
* **** * *** *
17551802 A-TCATTCTTT-TTTTTTTTTTTACAGTGTCATCCCGATCGTTCTTTATTTTTTGACTTACGGTG
315 AGTCATTATTTATTTTTTGACCTACAGTATCATCCCGATCGTTCTTTATTTTCAAACTTACAGTG
*
17551865 TTATCTCGATCATT
380 TTATCCCGATCATT
* * * * * * *
17551879 CTTTATTTTTTGACTTACTTTGTTATCCCGA-TCGTTCTTTATTTTC-AGACTTACGGTCTTGTC
1 TTTTATTTTTTGACTTA-TGTGTTAT-CTGAGTCATTCTTTATTTTCTA-ACTTGCAGTATTGTC
*
17551942 CTGGTCATTCTTTATTTTTTAACTTAC
63 CTGGTCATTCTTTATTTTTAAACTTAC
17551969 GGTGTTGTCC
Statistics
Matches: 391, Mismatches: 78, Indels: 28
0.79 0.16 0.06
Matches are distributed among these distances:
391 1 0.00
392 3 0.01
393 243 0.62
394 124 0.32
395 20 0.05
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (393 bp):
TTTTATTTTTTGACTTATGTGTTATCTGAGTCATTCTTTATTTTCTAACTTGCAGTATTGTCCTG
GTCATTCTTTATTTTTAAACTTACAATATCATCCCGATCGCCTTTTACTTCCCAACTTGCAATAT
TATCCCAGTCATTTTTTATTTTTTGACTTACGATGTTATCTCGATCATTCTTTATTTTTGGACTT
GCGATATTATCCCGATCATTCTTTATTTTCTGACTTGAGTGTTGTCCCAATCATTCTTTATTTCT
GACTTACGGCATTGTCCTTATCATTATTTATTTTTTGACTTATAGTGTCATTCGAGTCATTATTT
ATTTTTTGACCTACAGTATCATCCCGATCGTTCTTTATTTTCAAACTTACAGTGTTATCCCGATC
ATT
Found at i:17551911 original size:107 final size:105
Alignment explanation
Indices: 17551631--17551923 Score: 268
Period size: 107 Copynumber: 2.8 Consensus size: 105
17551621 CTGATTATTT
*** * * *
17551631 TTTATTTTTGACTTGTAGTGTTATCTCGATCATTCTTTATTTTTGGACTTGC-AGTATTATCCCC
1 TTTATTTTTGACTTACGGTGTTATCTCGATCATTCTTTATTTTTTGACTTACTA-TGTTAT-CCC
* **
17551695 GGTCATTCTTTGTTTCTTGACTTGAAGTGTTGTCCCAATCGTTC
64 GATCATTCTTT-TTT-TTGACTTGAAGTGTCATCCCAATCGTTC
* ** * ** * **
17551739 TTTA-TTCTGACTTACGGCATTGTCTTAATCATTCTTTATTTTTTGACTTA-TGATGTCATTACG
1 TTTATTTTTGACTTACGGTGTTATCTCGATCATTCTTTATTTTTTGACTTACT-ATGTTATCCCG
*** * *
17551802 ATCATTCTTTTTTTTTTTTTTACAGTGTCATCCCGATCGTTC
65 ATCATTCTTTTTTTTGACTTGA-AGTGTCATCCCAATCGTTC
*
17551844 TTTATTTTTTGACTTACGGTGTTATCTCGATCATTCTTTATTTTTTGACTTACTTTGTTATCCCG
1 TTTA-TTTTTGACTTACGGTGTTATCTCGATCATTCTTTATTTTTTGACTTACTATGTTATCCCG
* *
17551909 ATCGTTCTTTATTTT
65 ATCATTCTTTTTTTT
17551924 CAGACTTACG
Statistics
Matches: 144, Mismatches: 35, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
104 5 0.03
105 23 0.16
106 11 0.08
107 99 0.69
108 6 0.04
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (105 bp):
TTTATTTTTGACTTACGGTGTTATCTCGATCATTCTTTATTTTTTGACTTACTATGTTATCCCGA
TCATTCTTTTTTTTGACTTGAAGTGTCATCCCAATCGTTC
Found at i:17552978 original size:13 final size:13
Alignment explanation
Indices: 17552960--17552986 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17552950 TCTACCTCAC
17552960 CAATAAAAGGCCA
1 CAATAAAAGGCCA
17552973 CAATAAAAGGCCA
1 CAATAAAAGGCCA
17552986 C
1 C
17552987 CACCAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (13 bp):
CAATAAAAGGCCA
Found at i:17554128 original size:20 final size:20
Alignment explanation
Indices: 17554082--17554129 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
17554072 AAACTACTTG
* * *
17554082 ATGTTAACTACTGTTGATCG
1 ATGTTGACTACTATTGATCA
**
17554102 ACATTGACTACTATTGATCA
1 ATGTTGACTACTATTGATCA
17554122 ATGTTGAC
1 ATGTTGAC
17554130 CAATGTTGAC
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTTGACTACTATTGATCA
Found at i:17554176 original size:4 final size:4
Alignment explanation
Indices: 17554163--17554215 Score: 65
Period size: 4 Copynumber: 13.0 Consensus size: 4
17554153 ATCAAAAAAC
17554163 ATTT -TTT ATTT ATTT ATTCT A-TT ATTT ATTT ATTT ATTT ATTTT ATGTT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT A-TTT AT-TT
17554212 ATTT
1 ATTT
17554216 TTTGTATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 5 0.11
4 29 0.66
5 10 0.23
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:17554655 original size:3 final size:3
Alignment explanation
Indices: 17554647--17554730 Score: 132
Period size: 3 Copynumber: 27.7 Consensus size: 3
17554637 AAAATAATTA
*
17554647 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
17554693 AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17554731 ATTTTTATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 73 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17554974 original size:8 final size:9
Alignment explanation
Indices: 17554925--17554984 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
17554915 TCCAAACCTT
17554925 AAAACCCTC
1 AAAACCCTC
*
17554934 AAAACTCTTC
1 AAAAC-CCTC
* *
17554944 TAAACCTTC
1 AAAACCCTC
17554953 --AACCCTC
1 AAAACCCTC
*
17554960 GAAACCCT-
1 AAAACCCTC
17554968 AAAACCCTC
1 AAAACCCTC
17554977 AAAACCCT
1 AAAACCCT
17554985 TAAATCGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.14
8 7 0.16
9 23 0.53
10 7 0.16
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAACCCTC
Found at i:17554975 original size:17 final size:17
Alignment explanation
Indices: 17554953--17555001 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
17554943 CTAAACCTTC
17554953 AACCCTCGAAACCCTAA
1 AACCCTCGAAACCCTAA
* *
17554970 AACCCTCAAAACCCTTA
1 AACCCTCGAAACCCTAA
17554987 AA---TCGAAACCCTAA
1 AACCCTCGAAACCCTAA
17555001 A
1 A
17555002 CCTTCAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.39
17 17 0.61
ACGTcount: A:0.45, C:0.37, G:0.04, T:0.14
Consensus pattern (17 bp):
AACCCTCGAAACCCTAA
Found at i:17555180 original size:8 final size:8
Alignment explanation
Indices: 17555103--17555447 Score: 65
Period size: 8 Copynumber: 45.2 Consensus size: 8
17555093 TTTACAATCC
17555103 AAACCCTA
1 AAACCCTA
*
17555111 AAACCTCCA
1 AAACC-CTA
17555120 AAA-CCTA
1 AAACCCTA
*
17555127 AAA-CTTA
1 AAACCCTA
*
17555134 AAAGCCTA
1 AAACCCTA
*
17555142 AAATCC--
1 AAACCCTA
*
17555148 AAACCTTA
1 AAACCCTA
*
17555156 AAATCC--
1 AAACCCTA
17555162 AAA-CC-A
1 AAACCCTA
17555168 AAACCCTA
1 AAACCCTA
17555176 AAACCCTTA
1 AAACCC-TA
*
17555185 AAACCC-C
1 AAACCCTA
*
17555192 AAACCTTA
1 AAACCCTA
*
17555200 AAACCTTTA
1 AAACC-CTA
*
17555209 AAACCC-C
1 AAACCCTA
*
17555216 AAACCTTA
1 AAACCCTA
* *
17555224 AAACCTTT
1 AAACCCTA
***
17555232 AAATTTTA
1 AAACCCTA
*
17555240 AAA-CCTCG
1 AAACCCT-A
17555248 AAACCCTA
1 AAACCCTA
*
17555256 AAACTC-A
1 AAACCCTA
* *
17555263 AAATCTTA
1 AAACCCTA
*
17555271 AAA-CTTA
1 AAACCCTA
*
17555278 AAACCTTA
1 AAACCCTA
*
17555286 AAATCC--
1 AAACCCTA
*
17555292 AAATCCTA
1 AAACCCTA
*
17555300 AAATCC--
1 AAACCCTA
*
17555306 AAA-CCTT
1 AAACCCTA
*
17555313 AAACCCTCC
1 AAACCCT-A
17555322 AAACCCTA
1 AAACCCTA
17555330 AAACCCTTA
1 AAACCC-TA
*
17555339 AAA-TCTCA
1 AAACCCT-A
17555347 AAACTCC-A
1 AAAC-CCTA
*
17555355 AAGCCCTA
1 AAACCCTA
* *
17555363 AAGCCTTA
1 AAACCCTA
*
17555371 AAACCTTA
1 AAACCCTA
* *
17555379 AAA-TCTG
1 AAACCCTA
*
17555386 AAACCTTA
1 AAACCCTA
*
17555394 AAACTC-A
1 AAACCCTA
17555401 AAA-CC-A
1 AAACCCTA
*
17555407 AAACCTTA
1 AAACCCTA
*
17555415 AAA-TCTA
1 AAACCCTA
*
17555422 AAATCCTA
1 AAACCCTA
* * *
17555430 AAATCTTG
1 AAACCCTA
17555438 AAACCCTA
1 AAACCCTA
17555446 AA
1 AA
17555448 TCTAACACAA
Statistics
Matches: 252, Mismatches: 55, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
5 4 0.02
6 24 0.10
7 55 0.22
8 132 0.52
9 36 0.14
10 1 0.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (8 bp):
AAACCCTA
Found at i:17555188 original size:9 final size:9
Alignment explanation
Indices: 17555167--17555234 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
17555157 AATCCAAACC
17555167 AAAACCC-T
1 AAAACCCTT
17555175 AAAACCCTT
1 AAAACCCTT
17555184 AAAACCC--
1 AAAACCCTT
*
17555191 CAAA-CCTT
1 AAAACCCTT
*
17555199 AAAACCTTT
1 AAAACCCTT
17555208 AAAACCC--
1 AAAACCCTT
*
17555215 CAAA-CCTT
1 AAAACCCTT
*
17555223 AAAACCTTT
1 AAAACCCTT
17555232 AAA
1 AAA
17555235 TTTTAAAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
6 4 0.09
7 6 0.13
8 13 0.28
9 23 0.50
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAACCCTT
Found at i:17555196 original size:24 final size:24
Alignment explanation
Indices: 17555168--17555234 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
17555158 ATCCAAACCA
* *
17555168 AAACCCTAAAACCCTTAAAACCCC
1 AAACCTTAAAACCTTTAAAACCCC
17555192 AAACCTTAAAACCTTTAAAACCCC
1 AAACCTTAAAACCTTTAAAACCCC
17555216 AAACCTTAAAACCTTTAAA
1 AAACCTTAAAACCTTTAAA
17555235 TTTTAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (24 bp):
AAACCTTAAAACCTTTAAAACCCC
Found at i:17555272 original size:31 final size:31
Alignment explanation
Indices: 17555192--17555274 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
17555182 TTAAAACCCC
* * *
17555192 AAACCTTAAAACCTTTAAAACCCCAAACCTTA
1 AAACCTCAAAATC-TTAAAACCCCAAACCCTA
** * *
17555224 AAACCTTTAAATTTTAAAACCTCGAAACCCTA
1 AAACCTCAAAATCTTAAAACC-CCAAACCCTA
17555256 AAA-CTCAAAATCTTAAAAC
1 AAACCTCAAAATCTTAAAAC
17555275 TTAAAACCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 21 0.50
32 21 0.50
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (31 bp):
AAACCTCAAAATCTTAAAACCCCAAACCCTA
Found at i:17555335 original size:17 final size:16
Alignment explanation
Indices: 17555303--17555336 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17555293 AATCCTAAAA
*
17555303 TCCAAACCTTAAACCC
1 TCCAAACCTAAAACCC
17555319 TCCAAACCCTAAAACCC
1 TCCAAA-CCTAAAACCC
17555336 T
1 T
17555337 TAAAATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (16 bp):
TCCAAACCTAAAACCC
Found at i:17555404 original size:15 final size:15
Alignment explanation
Indices: 17555103--17555405 Score: 89
Period size: 15 Copynumber: 20.3 Consensus size: 15
17555093 TTTACAATCC
*
17555103 AAACCCTAAAACCTCCA
1 AAACCTTAAAA-CT-CA
*
17555120 AAACC-TAAAACTTA
1 AAACCTTAAAACTCA
*
17555134 AAAGCC-TAAAA-TCC
1 AAA-CCTTAAAACTCA
*
17555148 AAACCTTAAAA-TCC
1 AAACCTTAAAACTCA
*
17555162 AAACC--AAAACCCTA
1 AAACCTTAAAACTC-A
* *
17555176 AAACCCTTAAAACCCC
1 AAA-CCTTAAAACTCA
17555192 AAACCTTAAAA--C-
1 AAACCTTAAAACTCA
* * *
17555204 ---CTTTAAAACCCC
1 AAACCTTAAAACTCA
**
17555216 AAACCTTAAAACCTTT
1 AAACCTTAAAA-CTCA
** *
17555232 AAATTTTAAAACCTCG
1 AAACCTTAAAA-CTCA
*
17555248 AAACCCTAAAACTCA
1 AAACCTTAAAACTCA
* *
17555263 AAATCTTAAAACTTA
1 AAACCTTAAAACTCA
17555278 AAACCTTAAAA-TCCA
1 AAACCTTAAAACT-CA
* *
17555293 AATCC-TAAAA-TCC
1 AAACCTTAAAACTCA
* *
17555306 AAACCTTAAACCCTCC
1 AAACCTTAAA-ACTCA
* *
17555322 AAACCCTAAAACCCTTA
1 AAACCTTAAAA--CTCA
* *
17555339 AAATCTCAAAACTCCA
1 AAACCTTAAAACT-CA
* * * *
17555355 AAGCCCTAAAGCCTTA
1 AAACCTTAAA-ACTCA
*
17555371 AAACCTTAAAA-TCTG
1 AAACCTTAAAACTC-A
17555386 AAACCTTAAAACTCA
1 AAACCTTAAAACTCA
17555401 AAACC
1 AAACC
17555406 AAAACCTTAA
Statistics
Matches: 214, Mismatches: 48, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
9 7 0.03
11 1 0.00
12 4 0.02
13 9 0.04
14 36 0.17
15 74 0.35
16 59 0.28
17 24 0.11
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (15 bp):
AAACCTTAAAACTCA
Found at i:17555473 original size:17 final size:18
Alignment explanation
Indices: 17555438--17555478 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17555428 TAAAATCTTG
*
17555438 AAACCCTAAATCTAACAC
1 AAACCATAAATCTAACAC
17555456 AAACCATAAATC-AACAC
1 AAACCATAAATCTAACAC
17555473 ATAACC
1 A-AACC
17555479 CCCTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.15
Consensus pattern (18 bp):
AAACCATAAATCTAACAC
Found at i:17556239 original size:24 final size:24
Alignment explanation
Indices: 17556223--17556270 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17556213 AAATTATTAT
17556223 TAAATTTCAATTCGAAACTATTTC
1 TAAATTTCAATTCGAAACTATTTC
*
17556247 TAAATTTCAATTCAAAACTATTTC
1 TAAATTTCAATTCGAAACTATTTC
17556271 ATCCAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATTTCAATTCGAAACTATTTC
Found at i:17563891 original size:23 final size:21
Alignment explanation
Indices: 17563865--17563917 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
17563855 AATTTATCAG
*
17563865 TTGATTATTTAATGATATAATAA
1 TTGATTATATAA--ATATAATAA
* *
17563888 TTGATTATATAAATGTAATAT
1 TTGATTATATAAATATAATAA
17563909 TTGATTATA
1 TTGATTATA
17563918 AATGTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (21 bp):
TTGATTATATAAATATAATAA
Found at i:17563912 original size:21 final size:19
Alignment explanation
Indices: 17563882--17563924 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
17563872 TTTAATGATA
17563882 TAATAATTGATTATATAAATG
1 TAATAATTGA-T-TATAAATG
*
17563903 TAATATTTGATTATAAATG
1 TAATAATTGATTATAAATG
17563922 TAA
1 TAA
17563925 GTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 1 0.05
21 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (19 bp):
TAATAATTGATTATAAATG
Found at i:17564186 original size:13 final size:13
Alignment explanation
Indices: 17564168--17564192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17564158 AGATTTTGAA
17564168 ATATTTAAGTTTC
1 ATATTTAAGTTTC
17564181 ATATTTAAGTTT
1 ATATTTAAGTTT
17564193 ATTGTGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATATTTAAGTTTC
Found at i:17564748 original size:8 final size:8
Alignment explanation
Indices: 17564735--17564771 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
17564725 TTTTTATTTA
17564735 TATATATT
1 TATATATT
*
17564743 TATATAAT
1 TATATATT
17564751 TATATATT
1 TATATATT
*
17564759 TAAATATT
1 TATATATT
17564767 TATAT
1 TATAT
17564772 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:17564775 original size:14 final size:16
Alignment explanation
Indices: 17564735--17564789 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
17564725 TTTTTATTTA
*
17564735 TATATATTTATATAAT
1 TATATATTTAAATAAT
17564751 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
* *
17564766 T-TATATTTAAAAAAA
1 TATATATTTAAATAAT
17564781 TATAT-TTTA
1 TATATATTTA
17564790 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:17564791 original size:21 final size:22
Alignment explanation
Indices: 17564765--17564816 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
17564755 TATTTAAATA
17564765 TTTATATTTAAAAA-AATATAT
1 TTTATATTTAAAAATAATATAT
17564786 TTTATATTTAAAAATAATATAT
1 TTTATATTTAAAAATAATATAT
17564808 TATTA-ATTT
1 T-TTATATTT
17564817 TGAATCAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.48
22 12 0.41
23 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTTAAAAATAATATAT
Found at i:17565456 original size:22 final size:22
Alignment explanation
Indices: 17565416--17565457 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17565406 AAAGAATTAT
*
17565416 AAATTTTTTTTCTATTTCATAA
1 AAATTTTTTTTCTAATTCATAA
17565438 AAATTATTTTTTC-AATTCAT
1 AAATT-TTTTTTCTAATTCAT
17565458 TTACTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATTTTTTTTCTAATTCATAA
Found at i:17565863 original size:3 final size:3
Alignment explanation
Indices: 17565855--17565891 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17565845 AAGCTAAACC
17565855 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17565892 TATGATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17566653 original size:3 final size:3
Alignment explanation
Indices: 17566612--17566636 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17566602 AATTTTTTAA
17566612 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17566637 TGTTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17566716 original size:20 final size:20
Alignment explanation
Indices: 17566661--17566725 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
17566651 ATTGATTTTG
17566661 AATAAATATATTT-AA-AC-
1 AATAAATATATTTAAATACA
17566678 AATAAA-A-ATTATAATAATACA
1 AATAAATATATT-T-A-AATACA
17566699 AATAAATATATTTAAATA-A
1 AATAAATATATTTAAATACA
17566718 AA-AAATAT
1 AATAAATAT
17566726 GATTATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
15 3 0.08
16 2 0.05
17 6 0.15
18 6 0.15
19 5 0.12
20 6 0.15
21 7 0.17
22 2 0.05
23 3 0.08
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAATATATTTAAATACA
Found at i:17566722 original size:37 final size:36
Alignment explanation
Indices: 17566661--17566775 Score: 131
Period size: 37 Copynumber: 3.1 Consensus size: 36
17566651 ATTGATTTTG
* *
17566661 AATAAATATATTTAAACAATAAAAATTATAATAATACA
1 AATAAATATATTTAAATAA-AAAAA-TATAATTATACA
* **
17566699 AATAAATATATTTAAATAAAAAAATATGATTATTTA
1 AATAAATATATTTAAATAAAAAAATATAATTATACA
* * *
17566735 AATAAAATTTATTTGAATAACAAAATATAATTATACA
1 AAT-AAATATATTTAAATAAAAAAATATAATTATACA
17566772 AATA
1 AATA
17566776 TATCGTAACT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 12 0.18
37 35 0.54
38 18 0.28
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (36 bp):
AATAAATATATTTAAATAAAAAAATATAATTATACA
Found at i:17566723 original size:18 final size:18
Alignment explanation
Indices: 17566664--17566763 Score: 62
Period size: 18 Copynumber: 5.4 Consensus size: 18
17566654 GATTTTGAAT
*
17566664 AAATATATTTAAACAATAA
1 AAATATATTTAAATAA-AA
*
17566683 AAAT-TA-TAATAATACAAA
1 AAATATATTTA-AATA-AAA
17566701 TAAATATATTTAAATAAAA
1 -AAATATATTTAAATAAAA
**
17566720 AAATATGA-TTATTTAAATA
1 AAATAT-ATTTAAATAAA-A
* * *
17566739 AAATTTATTTGAATAACA
1 AAATATATTTAAATAAAA
17566757 AAATATA
1 AAATATA
17566764 ATTATACAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
17 2 0.03
18 28 0.45
19 24 0.39
20 6 0.10
21 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (18 bp):
AAATATATTTAAATAAAA
Found at i:17569248 original size:16 final size:15
Alignment explanation
Indices: 17569227--17569288 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
17569217 AATATATACA
*
17569227 TAAAAATTAATTTTTT
1 TAAAAATT-ATATTTT
17569243 TAAAAAATTATATTTT
1 T-AAAAATTATATTTT
* *
17569259 TAAAATTTATAATTTA
1 TAAAAATTAT-ATTTT
17569275 TATAAAATT-TATTT
1 TA-AAAATTATATTT
17569289 ATATTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 12 0.31
16 15 0.38
17 12 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAAAATTATATTTT
Found at i:17571641 original size:33 final size:33
Alignment explanation
Indices: 17571576--17571641 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
17571566 AATTGCTGAA
* * *
17571576 CAAAATAAGAAAAAAAGATAAAGAGATGTTTAT
1 CAAAATAAAAAAAAAAGAAAAAGAAATGTTTAT
*
17571609 CAAAATAAAAAAAAAATTAAAAAGAAAT-TTTAT
1 CAAAATAAAAAAAAAA-GAAAAAGAAATGTTTAT
17571642 TTTTTATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.23
Consensus pattern (33 bp):
CAAAATAAAAAAAAAAGAAAAAGAAATGTTTAT
Found at i:17573440 original size:61 final size:61
Alignment explanation
Indices: 17573309--17573447 Score: 158
Period size: 61 Copynumber: 2.3 Consensus size: 61
17573299 AGCATTTATA
* * **
17573309 AGAA-TATTTATGTAATTATAGTATGAAGGGTGTTATAGTAATTTTAATTAATTATGTTAGG
1 AGAAGTATTT-TGTAATTATAGTATGAAGGGTATTATAGTAATTTTAATTAATTATGGTAAC
* * *
17573370 A-AAGCTATTTTGTAATTATGGTAT-AAGGGATATTATAGTAGTTTTATTTAATTATGGTAAC
1 AGAAG-TATTTTGTAATTATAGTATGAAGGG-TATTATAGTAATTTTAATTAATTATGGTAAC
17573431 AGAAGTATTTTTGTAAT
1 AGAAGTA-TTTTGTAAT
17573448 CATGATAAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
60 7 0.11
61 42 0.64
62 17 0.26
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (61 bp):
AGAAGTATTTTGTAATTATAGTATGAAGGGTATTATAGTAATTTTAATTAATTATGGTAAC
Found at i:17583418 original size:16 final size:16
Alignment explanation
Indices: 17583397--17583429 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17583387 ATAAACTTAA
*
17583397 ACTTAGTAAAATGAAG
1 ACTTAGTAAAATAAAG
17583413 ACTTAGTAAAATAAAG
1 ACTTAGTAAAATAAAG
17583429 A
1 A
17583430 ACAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (16 bp):
ACTTAGTAAAATAAAG
Found at i:17587073 original size:8 final size:8
Alignment explanation
Indices: 17587057--17587113 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
17587047 ATATTATATT
17587057 AATTAATA
1 AATTAATA
*
17587065 AATTCATA
1 AATTAATA
17587073 AATTAA-A
1 AATTAATA
*
17587080 AATAAAT-
1 AATTAATA
* * *
17587087 ATTTTATT
1 AATTAATA
17587095 AATTAATA
1 AATTAATA
17587103 AATTAATA
1 AATTAATA
17587111 AAT
1 AAT
17587114 AAAAAATTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
7 10 0.26
8 28 0.74
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
AATTAATA
Found at i:17587080 original size:38 final size:38
Alignment explanation
Indices: 17587036--17587120 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
17587026 CAATAAACAT
*
17587036 ATTAAAAATAAATATTATATTAATTAATAAATTCATAA
1 ATTAAAAATAAATATTATATTAATTAATAAATTAATAA
*
17587074 ATTAAAAATAAATATTTTATTAATTAATAAATTAATAA
1 ATTAAAAATAAATATTATATTAATTAATAAATTAATAA
*
17587112 ATAAAAAAT
1 ATTAAAAAT
17587121 TTTATTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (38 bp):
ATTAAAAATAAATATTATATTAATTAATAAATTAATAA
Found at i:17587173 original size:22 final size:21
Alignment explanation
Indices: 17587141--17587184 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
17587131 GTTTTTAAAA
**
17587141 TTTAAATAATTTATTAAATAT
1 TTTAAATAATTTAAAAAATAT
17587162 TTTATAATAATTTAAAAAATAT
1 TTTA-AATAATTTAAAAAATAT
17587184 T
1 T
17587185 CATCGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAATAATTTAAAAAATAT
Found at i:17587184 original size:29 final size:29
Alignment explanation
Indices: 17587123--17587183 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
17587113 TAAAAAATTT
*
17587123 TATTAAAAGTTTTTAAAATTTAAATAATT
1 TATTAAAAGTTTTTAAAATTTAAATAATA
*
17587152 TATTAAATA-TTTTATAATAATTTAAAAAATA
1 TATTAAA-AGTTTT-TAA-AATTTAAATAATA
17587183 T
1 T
17587184 TCATCGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 11 0.41
30 4 0.15
31 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TATTAAAAGTTTTTAAAATTTAAATAATA
Found at i:17590494 original size:18 final size:16
Alignment explanation
Indices: 17590456--17590509 Score: 90
Period size: 16 Copynumber: 3.2 Consensus size: 16
17590446 AAAATATATA
17590456 CTTCCAAATGATGTTT
1 CTTCCAAATGATGTTT
17590472 CTTCCAAATGATGTTCCT
1 CTTCCAAATGATGTT--T
17590490 CTTCCAAATGATGTTT
1 CTTCCAAATGATGTTT
17590506 CTTC
1 CTTC
17590510 TTTGTATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 20 0.56
18 16 0.44
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
CTTCCAAATGATGTTT
Found at i:17603419 original size:15 final size:15
Alignment explanation
Indices: 17603401--17603434 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17603391 TCCCACCTTT
17603401 TTTCATCCATTTAGC
1 TTTCATCCATTTAGC
**
17603416 TTTCATTTATTTAGC
1 TTTCATCCATTTAGC
17603431 TTTC
1 TTTC
17603435 TTCCTTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTCATCCATTTAGC
Found at i:17608393 original size:15 final size:14
Alignment explanation
Indices: 17608342--17608391 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
17608332 TTATTTTAAC
*
17608342 ATATTTTAGTTATT
1 ATATTTTAGTTGTT
17608356 ATATTTT-GTTGTT
1 ATATTTTAGTTGTT
* *
17608369 ATATATTATTTGTT
1 ATATTTTAGTTGTT
17608383 AATATTTTA
1 -ATATTTTA
17608392 TTATTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 12 0.40
15 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (14 bp):
ATATTTTAGTTGTT
Found at i:17609050 original size:21 final size:21
Alignment explanation
Indices: 17609017--17609079 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
17609007 ACAACATTTT
* *
17609017 TTGAGTTGAAAGCTGTTGTGA
1 TTGAGCTGGAAGCTGTTGTGA
*
17609038 TTGAGCTGGAAGCTGTTGTGT
1 TTGAGCTGGAAGCTGTTGTGA
*
17609059 TTGAACTGGAAGCTGTTGTGA
1 TTGAGCTGGAAGCTGTTGTGA
17609080 GGTCTTGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.08, G:0.35, T:0.37
Consensus pattern (21 bp):
TTGAGCTGGAAGCTGTTGTGA
Found at i:17611362 original size:20 final size:21
Alignment explanation
Indices: 17611323--17611362 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17611313 GATACTTATT
**
17611323 AGAAATGAAAACAACGAACAA
1 AGAAATGAAAACAAAAAACAA
17611344 AGAAATG-AAACAAAAAACA
1 AGAAATGAAAACAAAAAACA
17611363 TAAGTGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.70, C:0.12, G:0.12, T:0.05
Consensus pattern (21 bp):
AGAAATGAAAACAAAAAACAA
Found at i:17616201 original size:30 final size:32
Alignment explanation
Indices: 17616136--17616206 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
17616126 GGGTAGATTG
* ** *
17616136 AAATTTTTCGTTTTTGAACTCTCAAGCTGGAA
1 AAATTTTTTGTTTCAGAACTCTCAACCTGGAA
17616168 AAATTTTTTGTTTCAGAACTCTC-ACCT-GAA
1 AAATTTTTTGTTTCAGAACTCTCAACCTGGAA
17616198 AAATTTTTT
1 AAATTTTTT
17616207 TCCTCTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 12 0.34
31 3 0.09
32 20 0.57
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (32 bp):
AAATTTTTTGTTTCAGAACTCTCAACCTGGAA
Found at i:17616450 original size:16 final size:17
Alignment explanation
Indices: 17616423--17616455 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
17616413 TCTGATTTTC
17616423 GTTTTGGTTTTTTGTTT
1 GTTTTGGTTTTTTGTTT
17616440 GTTTT-GTTTTTTGTTT
1 GTTTTGGTTTTTTGTTT
17616456 TGGTTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (17 bp):
GTTTTGGTTTTTTGTTT
Found at i:17616457 original size:17 final size:17
Alignment explanation
Indices: 17616418--17616464 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
17616408 TTCTGTCTGA
17616418 TTTTCGTTTTGGTTTTTTG
1 TTTT-GTTTT-GTTTTTTG
17616437 -TTTGTTTTGTTTTTTG
1 TTTTGTTTTGTTTTTTG
*
17616453 TTTTGGTTTGTT
1 TTTTGTTTTGTT
17616465 AAATATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 15 0.58
18 3 0.12
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.77
Consensus pattern (17 bp):
TTTTGTTTTGTTTTTTG
Found at i:17622019 original size:3 final size:3
Alignment explanation
Indices: 17622011--17622056 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
17622001 CATTTTTTAA
*
17622011 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATAT ATAT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT
17622057 TTTCTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 30 0.77
4 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17622846 original size:24 final size:24
Alignment explanation
Indices: 17622819--17622865 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
17622809 TTGACCCGTA
*
17622819 ACTCGATCCGGGATCCATGAATCT
1 ACTCGATCCGGGATCCACGAATCT
17622843 ACTCGATCCGGGATCCACGAATC
1 ACTCGATCCGGGATCCACGAATC
17622866 GACCCGACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (24 bp):
ACTCGATCCGGGATCCACGAATCT
Found at i:17628539 original size:57 final size:57
Alignment explanation
Indices: 17628447--17628561 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
17628437 AAAGGTTTCA
** *
17628447 CGCCTTACTCTGTACCAGTCTACCAAACCCGTTATCTTTCCGTAAATAATGTTACAT
1 CGCCTTACTCTGTACCAGTCTACCAAACCAATTATCTTTCCGTAAACAATGTTACAT
*
17628504 CGCCTTACTCTGTACCAGTCTACCAAACCAATTATCTTTTCGTAAACAATGTTACAT
1 CGCCTTACTCTGTACCAGTCTACCAAACCAATTATCTTTCCGTAAACAATGTTACAT
17628561 C
1 C
17628562 AATCCCTCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (57 bp):
CGCCTTACTCTGTACCAGTCTACCAAACCAATTATCTTTCCGTAAACAATGTTACAT
Found at i:17639510 original size:3 final size:3
Alignment explanation
Indices: 17639502--17639527 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17639492 CTACTGATAT
17639502 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17639528 TTTGCATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17643382 original size:22 final size:21
Alignment explanation
Indices: 17643356--17643404 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
17643346 GTTTCAAGTT
*
17643356 TTTTTTTTCGATCTCTTCCTCTC
1 TTTTTTATCGATCT-TT-CTCTC
17643379 TTTTTTCATCGATCTTTCTCTC
1 TTTTTT-ATCGATCTTTCTCTC
17643401 TTTT
1 TTTT
17643405 CTTACAGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 8 0.33
24 7 0.29
ACGTcount: A:0.06, C:0.27, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTTATCGATCTTTCTCTC
Found at i:17643611 original size:7 final size:6
Alignment explanation
Indices: 17643591--17643623 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17643581 TGAATCGAAT
*
17643591 AAAAGA AAAAGA AAAAGG AAAA-A AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
17643624 ATAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:17643952 original size:47 final size:46
Alignment explanation
Indices: 17643791--17643964 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 46
17643781 ATTTAAAAGG
* * * * * ***
17643791 CTCCTCTGAGCATAGGCACAACAATTTAAAAAAAAATAAAAAAAAA
1 CTCCTCTAAGCAGAGACTCAACAATTTTAAAAATTTTAAAAAAAAA
** * * * *
17643837 CTTTTCTAAGTAGAGACTTAACAATTTTTAAAAATTTT-AAAAGAAG
1 CTCCTCTAAGCAGAGACTCAACAA-TTTTAAAAATTTTAAAAAAAAA
* *
17643883 TTCCTCTAAGCAGA-AGTTCAACAACTTTTAAAAATTTTAAAAAAAAA
1 CTCCTCTAAGCAGAGA-CTCAACAA-TTTTAAAAATTTTAAAAAAAAA
17643930 CTCCTCTAAGCAGAGACTCAACAATTTTAAAAATT
1 CTCCTCTAAGCAGAGACTCAACAATTTTAAAAATT
17643965 CATCTTGAAA
Statistics
Matches: 99, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
45 1 0.01
46 62 0.63
47 35 0.35
48 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (46 bp):
CTCCTCTAAGCAGAGACTCAACAATTTTAAAAATTTTAAAAAAAAA
Found at i:17643963 original size:46 final size:47
Alignment explanation
Indices: 17643827--17643964 Score: 165
Period size: 46 Copynumber: 3.0 Consensus size: 47
17643817 TAAAAAAAAA
** * * *
17643827 TAAAAAAAAACTTTTCTAAGTAGAGACTTAACAATTTTTAAAAATTT
1 TAAAAAAAAACTCCTCTAAGCAGAGACTCAACAACTTTTAAAAATTT
* ** *
17643874 T-AAAAGAAGTTCCTCTAAGCAGA-AGTTCAACAACTTTTAAAAATTT
1 TAAAAAAAAACTCCTCTAAGCAGAGA-CTCAACAACTTTTAAAAATTT
17643920 TAAAAAAAAACTCCTCTAAGCAGAGACTCAACAA-TTTTAAAAATT
1 TAAAAAAAAACTCCTCTAAGCAGAGACTCAACAACTTTTAAAAATT
17643965 CATCTTGAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
45 1 0.01
46 46 0.61
47 27 0.36
48 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (47 bp):
TAAAAAAAAACTCCTCTAAGCAGAGACTCAACAACTTTTAAAAATTT
Found at i:17644204 original size:104 final size:104
Alignment explanation
Indices: 17644006--17644235 Score: 269
Period size: 104 Copynumber: 2.2 Consensus size: 104
17643996 CAATAACTTT
* * *
17644006 AAAATCTCATCTTGAAAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGA
1 AAAATCTCATCTTAAAAAAAGCTCCTCTTAGCAAAGGCTCAACAACTTTAAAAATCTCAACTTGA
* *
17644071 AAAATGCTCATCTCAGTAGAAGCTCAACAACTTGAAAAA
66 AAAATGCTCAGCTCAATAGAAGCTCAACAACTTGAAAAA
* * *
17644110 AAAATCTTATCTTAAAAAAAGTTTCT-TTCAGCAAAGGCTCAACAACTTTAAAAATCTCAACTTG
1 AAAATCTCATCTTAAAAAAAGCTCCTCTT-AGCAAAGGCTCAACAACTTTAAAAATCTCAACTTG
* * *
17644174 AAAAA-GACTTC-GCTCAATAGAGGCTTAACAACTT----TA
65 AAAAATG-C-TCAGCTCAATAGAAGCTCAACAACTTGAAAAA
17644210 AAAATCTCATCTTGAAAAAAA-CTCCT
1 AAAATCTCATCTT-AAAAAAAGCTCCT
17644236 TTCAATAGAG
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
100 16 0.15
101 7 0.06
103 3 0.03
104 80 0.74
105 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (104 bp):
AAAATCTCATCTTAAAAAAAGCTCCTCTTAGCAAAGGCTCAACAACTTTAAAAATCTCAACTTGA
AAAATGCTCAGCTCAATAGAAGCTCAACAACTTGAAAAA
Found at i:17644204 original size:154 final size:152
Alignment explanation
Indices: 17643982--17644270 Score: 391
Period size: 154 Copynumber: 1.9 Consensus size: 152
17643972 AAAAAACTCA
* * * * * * *
17643982 TTTCAGCAGAGGTTCAATAACTTTAAAATCTCATCTTGAAAAAAGCTCCTCTTAGCAGAGGCTCA
1 TTTCAGCAAAGGCTCAACAACTTTAAAATCTCAACTTGAAAAAAGCTCCGCTCAACAGAGGCTCA
** *
17644047 ACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTCAGTAGAAGCTCAACAACTTGAAAAAAA
66 ACAACTTTAAAAATCTCATCTTGAAAAAAACTCATCTCAATAGAAGCTCAACAACTT-AAAAAAA
17644112 AATCTTATCTTAAAAAAAGTTTC
130 AATCTTATCTTAAAAAAAGTTTC
* *
17644135 TTTCAGCAAAGGCTCAACAACTTTAAAAATCTCAACTTG-AAAAAGACTTCGCTCAATAGAGGCT
1 TTTCAGCAAAGGCTCAACAACTTT-AAAATCTCAACTTGAAAAAAG-CTCCGCTCAACAGAGGCT
* * * * *
17644199 TAACAACTTTAAAAATCTCATCTTGAAAAAAACTCCTTTCAATAGAGGTTCAACAACTTAAAAAA
64 CAACAACTTTAAAAATCTCATCTTGAAAAAAACTCATCTCAATAGAAGCTCAACAACTTAAAAAA
17644264 AAATCTT
129 AAATCTT
17644271 TTGAAAAAGG
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
153 40 0.34
154 77 0.66
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (152 bp):
TTTCAGCAAAGGCTCAACAACTTTAAAATCTCAACTTGAAAAAAGCTCCGCTCAACAGAGGCTCA
ACAACTTTAAAAATCTCATCTTGAAAAAAACTCATCTCAATAGAAGCTCAACAACTTAAAAAAAA
ATCTTATCTTAAAAAAAGTTTC
Found at i:17644241 original size:50 final size:50
Alignment explanation
Indices: 17643923--17644263 Score: 314
Period size: 50 Copynumber: 6.8 Consensus size: 50
17643913 AAAATTTTAA
* * * *
17643923 AAAAAAACTCCTCTAAGCAGAGACTCAACAATTTTAAAAAT-TCATCTTG
1 AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* * *
17643972 -AAAAAACTCATTTCAGCAGAGGTTCAATAACTTT-AAAATCTCATCTTG
1 AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
*
17644020 AAAAAAGCTCCTCTT-AGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
1 AAAAAAACTCCT-TTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
** * * * * * *
17644070 AAAAATGCTCATCTCAGTAGAAGCTCAACAACTTGAAAAAAAAATCTTATCTT-
1 AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTT----TAAAAATCTCATCTTG
* * * *
17644123 AAAAAAAGTTTCTTTCAGCAAAGGCTCAACAACTTTAAAAATCTCAACTTG
1 AAAAAAA-CTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* * ** ** *
17644174 AAAAAGACTTCGCTCAATAGAGGCTTAACAACTTTAAAAATCTCATCTTG
1 AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
** * *
17644224 AAAAAAACTCCTTTCAATAGAGGTTCAACAACTTAAAAAA
1 AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTTTAAAAA
17644264 AAATCTTTTG
Statistics
Matches: 235, Mismatches: 46, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
47 5 0.02
48 35 0.15
49 28 0.12
50 123 0.52
51 6 0.03
53 5 0.02
54 33 0.14
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (50 bp):
AAAAAAACTCCTTTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
Found at i:17655912 original size:6 final size:6
Alignment explanation
Indices: 17655901--17655929 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17655891 TAATTAAAGA
17655901 AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAAT
17655930 AGAAAGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:17656093 original size:60 final size:58
Alignment explanation
Indices: 17655964--17656168 Score: 270
Period size: 60 Copynumber: 3.4 Consensus size: 58
17655954 TCTTGTGTAG
*
17655964 GAAAAATTGATACTTTCAACTTTTCC-CTAAAATTA-TTTTTCGAAAATTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAATTATTTTTTTGAAAA-TTT-ATTTTCAA
* * *
17656023 GAAAAATTGATACTTTAAACTTTTCCTCAAAAATATATTTTTTTGAAACTTTATTTCCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAAT-TATTTTTTTGAAAATTTATTTTCAA
* * *
17656083 GAAAAATTGATATTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAA--TTATTTTTTTGAAAATTTATTTTCAA
17656143 GAAAAATTGATACTTTCAACTTTTCC
1 GAAAAATTGATACTTTCAACTTTTCC
17656169 CTAAAGATAT
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
59 29 0.22
60 85 0.66
61 6 0.05
62 9 0.07
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAATTATTTTTTTGAAAATTTATTTTCAA
Found at i:17656192 original size:60 final size:59
Alignment explanation
Indices: 17655964--17656194 Score: 263
Period size: 60 Copynumber: 3.9 Consensus size: 59
17655954 TCTTGTGTAG
** *
17655964 GAAAAATTGATACTTTCAACTTTTCC-CTAAAAT-TATTTTTCGAAAATTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAATATATTTTTTTAAAAATTT-ATTTTCAA
* * * *
17656023 GAAAAATTGATACTTTAAACTTTTCCTCAAAAATATATTTTTTTGAAACTTTATTTCCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAATATATTTTTTTAAAAATTTATTTTCAA
* * * * *
17656083 GAAAAATTGATATTTTCAACTTTTCCTCAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAT-ATATTTTTTTAAAAATTTATTTTCAA
17656143 GAAAAATTGATACTTTCAACTTTTCC-CTAAAGATAT-TTTCTTTTAAAAATTT
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAA-ATATATTT-TTTTAAAAATTT
17656195 TTTATTTTTA
Statistics
Matches: 149, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
59 34 0.23
60 100 0.67
61 15 0.10
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAATATATTTTTTTAAAAATTTATTTTCAA
Found at i:17656268 original size:30 final size:29
Alignment explanation
Indices: 17656212--17656268 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
17656202 TTATTTAAAG
*
17656212 AAAATAAAATAAAATAAAAGTGAAAAACA
1 AAAATAAAATAAAATAAAAGTAAAAAACA
*
17656241 AAAATAAAAATAAGAT-AAAGATAAAAAA
1 AAAAT-AAAATAAAATAAAAG-TAAAAAA
17656269 ATATTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (29 bp):
AAAATAAAATAAAATAAAAGTAAAAAACA
Found at i:17656296 original size:4 final size:4
Alignment explanation
Indices: 17656289--17656326 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
17656279 AATCTAATCT
* *
17656289 AATA AATA AATG AATA AATA AATA AAAA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
17656327 AAGAATTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:17657355 original size:14 final size:14
Alignment explanation
Indices: 17657333--17657463 Score: 59
Period size: 15 Copynumber: 8.6 Consensus size: 14
17657323 AAAAAAATAA
17657333 AAATAATAATAAAT
1 AAATAATAATAAAT
*
17657347 AAATTATAATATATAAT
1 AAATAAT-A-ATA-AAT
* *
17657364 AAATATAGAACTATAT
1 AAATA-ATAA-TAAAT
17657380 AAATAA-AATACATAT
1 AAATAATAATA-A-AT
* * *
17657395 AAATATTAACAGAAA
1 AAATAATAATA-AAT
* *
17657410 AAAAAAAAATAAAT
1 AAATAATAATAAAT
*
17657424 AAATAAGTAAAAATAT
1 AAATAA-TAATAA-AT
17657440 ACATATAATAAT-AAT
1 A-A-ATAATAATAAAT
17657455 AAATAATAA
1 AAATAATAA
17657464 AATACATAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 25
0.67 0.14 0.19
Matches are distributed among these distances:
13 9 0.10
14 16 0.18
15 24 0.28
16 19 0.22
17 14 0.16
18 5 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:17657357 original size:17 final size:18
Alignment explanation
Indices: 17657327--17657473 Score: 59
Period size: 16 Copynumber: 8.4 Consensus size: 18
17657317 TACAAGAAAA
17657327 AAATAAA-A-ATAATAAT
1 AAATAAATATATAATAAT
17657343 AAATAAAT-TATAAT-AT
1 AAATAAATATATAATAAT
*
17657359 ATAATAAATATAGAACTATAT
1 A-AATAAATATATAA-TA-AT
*
17657380 AAATAAAATACATATAAATATT
1 AAAT-AAAT--ATAT-AATAAT
*
17657402 AACAGAAA-A-A-AA-AA-
1 AA-ATAAATATATAATAAT
*
17657416 AAATAAATAAATAAGTAA-
1 AAATAAATATATAA-TAAT
* *
17657434 AAATATACATATAATAAT
1 AAATAAATATATAATAAT
17657452 -AATAAATA-ATAA-AAT
1 AAATAAATATATAATAAT
*
17657467 ACATAAA
1 AAATAAA
17657474 ATACACAAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 38
0.67 0.08 0.25
Matches are distributed among these distances:
13 4 0.04
14 3 0.03
15 5 0.05
16 23 0.23
17 21 0.21
18 18 0.18
19 2 0.02
20 3 0.03
21 7 0.07
22 6 0.06
23 6 0.06
24 2 0.02
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAATATATAATAAT
Found at i:17657468 original size:27 final size:27
Alignment explanation
Indices: 17657415--17657476 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
17657405 AGAAAAAAAA
*
17657415 AAAATAAATAAATAAGTAAAAATATACAT
1 AAAAT-AAT-AATAAATAAAAATATACAT
*
17657444 ATAATAATAATAAATAATAAA-ATACAT
1 AAAATAATAATAAATAA-AAATATACAT
17657471 AAAATA
1 AAAATA
17657477 CACAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.66
28 6 0.21
29 4 0.14
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAATAATAATAAATAAAAATATACAT
Found at i:17657474 original size:39 final size:39
Alignment explanation
Indices: 17657381--17657474 Score: 88
Period size: 39 Copynumber: 2.4 Consensus size: 39
17657371 GAACTATATA
*
17657381 AATAAAATACATATAAATATTAACAGAAAAAAAAAAAAT
1 AATAAAATACATAAAAATATTAACAGAAAAAAAAAAAAT
* * *
17657420 AA-ATAAATA-AGTAAAAATA-T-ACATATAATAATAATAAAT
1 AATA-AAATACA-TAAAAATATTAACAGA-AA-AAAAAAAAAT
17657459 AATAAAATACATAAAA
1 AATAAAATACATAAAA
17657475 TACACAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
37 4 0.09
38 5 0.11
39 34 0.76
40 2 0.04
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (39 bp):
AATAAAATACATAAAAATATTAACAGAAAAAAAAAAAAT
Found at i:17658769 original size:23 final size:22
Alignment explanation
Indices: 17658733--17658775 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17658723 AAGGAGAAGG
*
17658733 AAAAAGAAAGAAAAAAAATAGA
1 AAAAAGAAAAAAAAAAAATAGA
*
17658755 AAAATAGAAAAAAAAAGAATA
1 AAAA-AGAAAAAAAAAAAATA
17658776 TTAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAAATAGA
Found at i:17662962 original size:24 final size:26
Alignment explanation
Indices: 17662935--17662989 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
17662925 TTTGTTTAAC
*
17662935 AAAAA-TATTTTTAAAAAAT-AAAAA
1 AAAAATTATTTCTAAAAAATGAAAAA
* *
17662959 AAAAATTATTTCTAGAAAATGAAAAT
1 AAAAATTATTTCTAAAAAATGAAAAA
17662985 AAAAA
1 AAAAA
17662990 CAAAAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 12 0.46
26 9 0.35
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAAATTATTTCTAAAAAATGAAAAA
Found at i:17663772 original size:10 final size:10
Alignment explanation
Indices: 17663757--17663786 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17663747 TTAACCTAAC
17663757 AAATATATAT
1 AAATATATAT
17663767 AAATATATAT
1 AAATATATAT
*
17663777 ATATATATAT
1 AAATATATAT
17663787 TATGAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATATATAT
Found at i:17667207 original size:64 final size:61
Alignment explanation
Indices: 17667071--17667236 Score: 221
Period size: 64 Copynumber: 2.7 Consensus size: 61
17667061 TCTTGTACAG
** * *
17667071 GGAAAATTGATACTTTCAACTTTTCCCTGAAAA--TATTTTTTTTGAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAACTTTAATTTCAA
*
17667130 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATCTTTTTTTTTTTGAAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAAAT-TTTTTTTTTTTG-AAACTTT-AATTTCAA
*
17667194 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTT
17667237 ATTTTTATTT
Statistics
Matches: 95, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
59 30 0.32
60 1 0.01
62 10 0.11
63 16 0.17
64 38 0.40
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (61 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAAATTTTTTTTTTTTGAAACTTTAATTTCAA
Found at i:17667296 original size:18 final size:17
Alignment explanation
Indices: 17667273--17667394 Score: 65
Period size: 18 Copynumber: 7.2 Consensus size: 17
17667263 AATAAAAGTG
17667273 AAAATAAATAAAGATAAA
1 AAAATAAATAAA-ATAAA
*
17667291 AAAATAAAGAAAAGTAAA
1 AAAATAAATAAAA-TAAA
*
17667309 ACAA-AAATAAAAATAAA
1 AAAATAAAT-AAAATAAA
* * *
17667326 ATAA-AGATAAAA-AGA
1 AAAATAAATAAAATAAA
* * * *
17667341 ATATTAAATAAACCTAAT
1 AAAATAAATAAA-ATAAA
**
17667359 CTAATAAA-AAAATAAA
1 AAAATAAATAAAATAAA
*
17667375 AAAACAAATAAAA-AAA
1 AAAATAAATAAAATAAA
17667391 AAAA
1 AAAA
17667395 CCTGGAGCGG
Statistics
Matches: 80, Mismatches: 18, Indels: 14
0.71 0.16 0.12
Matches are distributed among these distances:
15 5 0.06
16 25 0.31
17 21 0.26
18 29 0.36
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAATAAATAAAATAAA
Found at i:17667337 original size:22 final size:21
Alignment explanation
Indices: 17667252--17667352 Score: 60
Period size: 22 Copynumber: 4.6 Consensus size: 21
17667242 TATTTTAAGA
* * *
17667252 AAATAGAACAAAATAAAAGTGA
1 AAATAAAATAAAATAAAAAT-A
*
17667274 AAAT-AAATAAAGATAAAAAAA
1 AAATAAAATAAA-ATAAAAATA
* *
17667295 TAAAGAAAAGTAAAACAAAAATAA
1 -AAATAAAA-TAAAATAAAAAT-A
*
17667319 AAATAAAATAAAGATAAAAAGA
1 AAATAAAATAAA-ATAAAAATA
* *
17667341 ATATTAAATAAA
1 AAATAAAATAAA
17667353 CCTAATCTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
21 6 0.10
22 28 0.46
23 22 0.36
24 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAATAAAATAAAATAAAAATA
Done.