Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 39 of 221
Found at i:10763791 original size:185 final size:176
Alignment explanation
Indices: 10763574--10763910 Score: 487
Period size: 185 Copynumber: 1.9 Consensus size: 176
10763564 GTAAGTTATG
* * * * *
10763574 TGTATTATGTATTATGTATGTTATGCATAATATTAATTAAGCTGTGTAATATGTATTATGTACGT
1 TGTATTATGTATTATGTACGCTATACATAATATTAATTAAGCTGTGCAATATGTATTATGTACGC
10763639 TATGTATAATATTAATTAAGTTGTGTATAATGTAAGAAATGTATTATGTA-TGTTATGTATAAAA
66 TATGTATAATATTAATTAAGTTGTG--T-AT-T-----ATGTATTATGTACT-TTATGTATAAAA
*
10763703 TTAATTAAGTTGTGTATTATGTATGTTATGTATAATATTAATTAAGTTGTGTATTA
121 TTAATTAAGTTGTGTATTATGTAAGTTATGTATAATATTAATTAAGTTGTGTATTA
* * *
10763759 TGTATTATGTATTATGTACGCTATATATAATATTAATTAAGTTGTGCATTATGTATTATGTACGC
1 TGTATTATGTATTATGTACGCTATACATAATATTAATTAAGCTGTGCAATATGTATTATGTACGC
*
10763824 TATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACTTTATGTATAATATTAATTAAGT
66 TATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACTTTATGTATAAAATTAATTAAGT
10763889 TGTGTATTATGTAAGTTATGTA
131 TGTGTATTATGTAAGTTATGTA
10763911 AGAAATGTAT
Statistics
Matches: 141, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
176 54 0.38
177 1 0.01
181 1 0.01
182 2 0.01
183 1 0.01
185 82 0.58
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.48
Consensus pattern (176 bp):
TGTATTATGTATTATGTACGCTATACATAATATTAATTAAGCTGTGCAATATGTATTATGTACGC
TATGTATAATATTAATTAAGTTGTGTATTATGTATTATGTACTTTATGTATAAAATTAATTAAGT
TGTGTATTATGTAAGTTATGTATAATATTAATTAAGTTGTGTATTA
Found at i:10763909 original size:9 final size:9
Alignment explanation
Indices: 10763895--10764037 Score: 52
Period size: 9 Copynumber: 16.2 Consensus size: 9
10763885 AAGTTGTGTA
10763895 TTATGTAAG
1 TTATGTAAG
10763904 TTATGTAAG
1 TTATGTAAG
**
10763913 AAATGT-A-
1 TTATGTAAG
*
10763920 TTATATAAG
1 TTATGTAAG
*
10763929 TTGTGT-A-
1 TTATGTAAG
* *
10763936 TAATGTTAG
1 TTATGTAAG
**
10763945 TTATCAAAG
1 TTATGTAAG
10763954 TTATGTACTATG
1 TTATGTA--A-G
*
10763966 TAAT-TAA-
1 TTATGTAAG
*
10763973 TTATTTAAG
1 TTATGTAAG
*
10763982 TTGTGTAAG
1 TTATGTAAG
*
10763991 TTGTGT-A-
1 TTATGTAAG
10763998 TTATGTAAG
1 TTATGTAAG
*
10764007 TTAT-TATG
1 TTATGTAAG
10764015 TTATTATGTAAG
1 ---TTATGTAAG
10764027 TTATGTAAG
1 TTATGTAAG
10764036 TT
1 TT
10764038 TATATATGAT
Statistics
Matches: 97, Mismatches: 22, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
7 15 0.15
8 12 0.12
9 56 0.58
11 7 0.07
12 7 0.07
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:10763919 original size:25 final size:25
Alignment explanation
Indices: 10763891--10764036 Score: 92
Period size: 25 Copynumber: 5.9 Consensus size: 25
10763881 AATTAAGTTG
*
10763891 TGTATTATGTAAGTTATGTAAGAAA
1 TGTATTATGTAAGTTATGTAAGTAA
* *
10763916 TGTATTATATAAGTTGTGT-A-TAA
1 TGTATTATGTAAGTTATGTAAGTAA
**
10763939 TGTTAGTTATCAAAGTTATGTACTATGTAA
1 TG-TA-TTATGTAAGTTATGTA--A-GTAA
* * **
10763969 T-TAATTATTTAAGTTGTGTAAGTTG
1 TGT-ATTATGTAAGTTATGTAAGTAA
*
10763994 TGTATTATGTAAGTTAT-T-A-T-G
1 TGTATTATGTAAGTTATGTAAGTAA
10764015 T-TATTATGTAAGTTATGTAAGT
1 TGTATTATGTAAGTTATGTAAGT
10764037 TTATATATGA
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
20 15 0.16
21 3 0.03
22 2 0.02
23 6 0.06
24 4 0.04
25 44 0.46
26 2 0.02
28 15 0.16
29 1 0.01
30 4 0.04
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.47
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAAGTAA
Found at i:10763992 original size:37 final size:36
Alignment explanation
Indices: 10763951--10764033 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
10763941 TTAGTTATCA
*
10763951 AAGTTATGTACTATGTAA-TTAATTAT-TTAAGTTGTGT
1 AAGTTATGTACTATGTAAGTT-ATTATGTT-A-TTATGT
* *
10763988 AAGTTGTGTATTATGTAAGTTATTATGTTATTATGT
1 AAGTTATGTACTATGTAAGTTATTATGTTATTATGT
10764024 AAGTTATGTA
1 AAGTTATGTA
10764034 AGTTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 14 0.35
37 22 0.55
38 4 0.10
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.49
Consensus pattern (36 bp):
AAGTTATGTACTATGTAAGTTATTATGTTATTATGT
Found at i:10764065 original size:33 final size:30
Alignment explanation
Indices: 10763998--10764070 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 30
10763988 AAGTTGTGTA
*
10763998 TTATGTAAG-TTATTATGTTATTATGTAAG
1 TTATGTAAGTTTATTATGTTATTATATAAG
*
10764027 TTATGTAAGTTTATATATGATTTTATATATAAG
1 TTATGTAAGTTTAT-TATG-TTAT-TATATAAG
10764060 TTATGTAAGTT
1 TTATGTAAGTT
10764071 ATGCAAGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 9 0.24
30 4 0.11
31 4 0.11
32 3 0.08
33 18 0.47
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (30 bp):
TTATGTAAGTTTATTATGTTATTATATAAG
Found at i:10764073 original size:42 final size:42
Alignment explanation
Indices: 10764018--10764098 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
10764008 TATTATGTTA
* * *
10764018 TTATGTAAGTTATGTAAGTTTATATATGATTTTATATATAAG
1 TTATGTAAGTTATGCAAGTTTATATATAAGTTTATATATAAG
10764060 TTATGTAAGTTATGCAAGTTTATATATAAGTTTATATAT
1 TTATGTAAGTTATGCAAGTTTATATATAAGTTTATATAT
10764099 GTGTAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (42 bp):
TTATGTAAGTTATGCAAGTTTATATATAAGTTTATATATAAG
Found at i:10765655 original size:84 final size:84
Alignment explanation
Indices: 10765561--10765807 Score: 404
Period size: 84 Copynumber: 2.9 Consensus size: 84
10765551 ACGGTGCGGC
* *
10765561 ATTGGCAAACAATAATTCACTCTTGCGGCGCTTTCCTAAAAAACGCCACTAGAAGATTTTATTCC
1 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAGAAGATTTTATTCC
* *
10765626 AGTAGAGAAACGGCACTGT
66 AGTAGAGAAACGGCACCGA
*
10765645 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAATCGCCACTAGAAGATTTTATTCC
1 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAGAAGATTTTATTCC
**
10765710 AGTAGAGAAACGGTGCCGA
66 AGTAGAGAAACGGCACCGA
* *
10765729 ATTGGAAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTTATTCC
1 ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAGAAGATTTTATTCC
*
10765794 AGTACAGAAACGGC
66 AGTAGAGAAACGGC
10765808 GCCACTTTGG
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 151 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (84 bp):
ATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTAGAAGATTTTATTCC
AGTAGAGAAACGGCACCGA
Found at i:10766371 original size:89 final size:88
Alignment explanation
Indices: 10766268--10766526 Score: 362
Period size: 88 Copynumber: 2.9 Consensus size: 88
10766258 TATAAAGAAC
* * * *
10766268 TTATTTAATATATAAATTAAAAAGTACTAATTAGTCTAAATCTTAAACCCTAACACGACCTCAAA
1 TTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCCTAAC-CGACCTCAAA
10766333 TCCCTAACCCCTAACCCCTAAACT
65 TCCCTAACCCCTAACCCCTAAACT
* *
10766357 TTATTTAATATATAAATTAAAAAATACTAATTAATCAAAACCCTAAAACCTAAACTCGACC-CAA
1 TTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCCT-AAC-CGACCTCAA
10766421 ATCCCTAACCCCTAA-CCCTAAACT
64 ATCCCTAACCCCTAACCCCTAAACT
* * *
10766445 TTACTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCATAACCTAATCCT-AA
1 TTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCCTAACC-GA-CCTCAA
*
10766509 ATCCCTAACCCTTAACCC
64 ATCCCTAACCCCTAACCC
10766527 TTAACCCCTA
Statistics
Matches: 152, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
86 1 0.01
87 4 0.03
88 74 0.49
89 65 0.43
90 8 0.05
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (88 bp):
TTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCCTAACCGACCTCAAAT
CCCTAACCCCTAACCCCTAAACT
Found at i:10766531 original size:14 final size:14
Alignment explanation
Indices: 10766511--10766550 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
10766501 AATCCTAAAT
10766511 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
10766525 CCTTAACCCCTAAC
1 CCCTAACCCTTAAC
*
10766539 CCCTAAACCTTA
1 CCCTAACCCTTA
10766551 TTTAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:10766536 original size:21 final size:21
Alignment explanation
Indices: 10766511--10766550 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10766501 AATCCTAAAT
* *
10766511 CCCTAACCCTTAACCCTTAAC
1 CCCTAACCCCTAAACCTTAAC
10766532 CCCTAACCCCTAAACCTTA
1 CCCTAACCCCTAAACCTTA
10766551 TTTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAACCCCTAAACCTTAAC
Found at i:10766661 original size:12 final size:12
Alignment explanation
Indices: 10766644--10766669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10766634 CTCTTAACAT
10766644 CTAACCCCTAAC
1 CTAACCCCTAAC
10766656 CTAACCCCTAAC
1 CTAACCCCTAAC
10766668 CT
1 CT
10766670 TTAACTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:10766729 original size:14 final size:15
Alignment explanation
Indices: 10766710--10766743 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
10766700 CTTAAACCAG
10766710 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
10766724 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
10766739 AATCC
1 AATCC
10766744 ATAAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:10767563 original size:114 final size:114
Alignment explanation
Indices: 10767307--10767675 Score: 515
Period size: 114 Copynumber: 3.2 Consensus size: 114
10767297 CTGAGCATTA
* * * * * *
10767307 GCGGCGCCTCCTCAAAAACGCCGCTAAAGCCTTGAGAATTAGCGACGCTTTATTAAAAACGTCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGC
* * * * *
10767372 TAAATCCCCAAAAGCTAAGAAACCA-CGTCGTTGAGCTTAGGTTCTTTT
66 TAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
*
10767420 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAATGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGC
* *
10767485 TAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
* *
10767534 GCGGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGACGCTTACTTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGC
* * * * *
10767599 TAATTCCTCGAAATCTCAAAAAACAGTGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
* * *
10767648 ACGGCGCTTTCTTAAAAATGCCGCTAAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAA
10767676 TTGCCGAAAG
Statistics
Matches: 227, Mismatches: 28, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
113 78 0.34
114 149 0.66
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGC
TAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
Found at i:10767662 original size:73 final size:72
Alignment explanation
Indices: 10767579--10767747 Score: 221
Period size: 73 Copynumber: 2.3 Consensus size: 72
10767569 GCATTAGCGA
* * *
10767579 CGCTTACTTAAAAACGCCGCTAATTCCTCGAAATCTCAAAAAACAGTGTCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAATTCC-CGAAAGCTCAAAAAACAGCGTCGTTGGGCTTAGGTTT
10767644 TTTTACGG
65 TTTTACGG
* * * *
10767652 CGCTTTCTTAAAAATGCCGCTAAATTGCCGAAAGCTCAAAAAACGGCGTCGTTGGGTTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCT-AATTCCCGAAAGCTCAAAAAACAGCGTCGTTGGGCTTAGGTTT
**
10767717 TTTTGTGG
65 TTTTACGG
* *
10767725 CGCTTTCCTATAAACGCCGCTAA
1 CGCTTTCTTAAAAACGCCGCTAA
10767748 AGCCCTGAGC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
72 2 0.02
73 76 0.92
74 5 0.06
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (72 bp):
CGCTTTCTTAAAAACGCCGCTAATTCCCGAAAGCTCAAAAAACAGCGTCGTTGGGCTTAGGTTTT
TTTACGG
Found at i:10767842 original size:187 final size:187
Alignment explanation
Indices: 10767465--10767861 Score: 539
Period size: 187 Copynumber: 2.1 Consensus size: 187
10767455 GCATTAGCGA
* *
10767465 CGCTTTCTTAAAAATGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTT
10767530 TTTTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGACGCTTACTTAAAAACG
66 TTTTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGACGCTTACTTAAAAACG
* * * * * *
10767595 CCGCTAATTCCTCGAAATCTCAAAAAACAGTGTCGTTGGGCTTAGGTTTTTTTACGG
131 CCGCTAAATCCCCGAAAGCTCAAAAAACAGCGTCATTGGGCTTAGGTTATTTTACGG
** *
10767652 CGCTTTCTTAAAAATGCCGCTAAATTGCCGAAAGCTCAAAAAACGGCGTCGTTGGGTTTAGGTTT
1 CGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTT
* * * *
10767717 TTTTGTGGCGCTTTC-CTATAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTCT-CTTAAAAA
66 TTTTGCGGCGCTTTCTC-AAAAACACCGCTAAAGCCCTGAGCATTAGCGACGCT-TACTT-AAAA
* * * * *
10767780 ACGCTGCTAAATCCCCGAACGCTGAAAAAACGGCGTCATTGGGCTTAGG-TATTTTGCGG
128 ACGCCGCTAAATCCCCGAAAGCTCAAAAAACAGCGTCATTGGGCTTAGGTTATTTTACGG
** *
10767839 CGCTTTCTGGAAAACGCCGCTAA
1 CGCTTTCTTAAAAATGCCGCTAA
10767862 TGCTTATTTT
Statistics
Matches: 184, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
186 1 0.01
187 138 0.75
188 45 0.24
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (187 bp):
CGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTT
TTTTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGACGCTTACTTAAAAACG
CCGCTAAATCCCCGAAAGCTCAAAAAACAGCGTCATTGGGCTTAGGTTATTTTACGG
Found at i:10767855 original size:114 final size:114
Alignment explanation
Indices: 10767649--10767861 Score: 279
Period size: 115 Copynumber: 1.9 Consensus size: 114
10767639 GGTTTTTTTA
* * ** * *
10767649 CGGCGCTTTCTTAAAAATGCCGCTAAATTGCCGAAAGCTCAAAAAACGGCGTCGTTGGGTTTAGG
1 CGGCGCTCTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAGG
* *
10767714 TTTTTTTGTGGCGCTTTCCTATAAACGCCGCTAAAGCCCTGAGCATTAG
66 TTATTTTGCGGCGCTTTCCTATAAACGCCGCTAAAGCCCTGAGCATTAG
* * *
10767763 CGGCGCTCTCTTAAAAAACGCTGCTAAATCCCCGAACGCTGAAAAAACGGCGTCATTGGGCTTAG
1 CGGCGCTCTCTT-AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAG
10767828 G-TATTTTGCGGCGCTTT-CTGGA-AAACGCCGCTAA
65 GTTATTTTGCGGCGCTTTCCT--ATAAACGCCGCTAA
10767862 TGCTTATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
113 2 0.02
114 37 0.44
115 46 0.54
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (114 bp):
CGGCGCTCTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCATTGGGCTTAGG
TTATTTTGCGGCGCTTTCCTATAAACGCCGCTAAAGCCCTGAGCATTAG
Found at i:10779173 original size:29 final size:30
Alignment explanation
Indices: 10779131--10779187 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
10779121 TATACCACAT
* * *
10779131 TCAAACTTGTATGTGTATAATTGCACAAAA
1 TCAAAATTGTATGTATAGAATTGCACAAAA
*
10779161 TCAAAATT-TATGTATCGAATTGCACAA
1 TCAAAATTGTATGTATAGAATTGCACAA
10779188 TAAATTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (30 bp):
TCAAAATTGTATGTATAGAATTGCACAAAA
Found at i:10779285 original size:17 final size:17
Alignment explanation
Indices: 10779265--10779302 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10779255 AAATTTAATT
*
10779265 ATAAATGTTTATGGATG
1 ATAAATGATTATGGATG
*
10779282 ATAAATGATTATGTATG
1 ATAAATGATTATGGATG
10779299 ATAA
1 ATAA
10779303 TAAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (17 bp):
ATAAATGATTATGGATG
Found at i:10779948 original size:3 final size:3
Alignment explanation
Indices: 10779940--10779968 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10779930 GGAACTTTAA
10779940 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10779969 AAGGCGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10781890 original size:20 final size:20
Alignment explanation
Indices: 10781866--10781922 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
10781856 AAAAATTCAA
10781866 AAAAATTATAAAAATTATTTT
1 AAAAATTATAAAAATTA-TTT
*
10781887 AAAAATTAT-TAAATTA-TT
1 AAAAATTATAAAAATTATTT
* *
10781905 AGAAAGTATAAAAATTAT
1 AAAAATTATAAAAATTAT
10781923 AAAAGCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 9 0.30
19 6 0.20
20 6 0.20
21 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
AAAAATTATAAAAATTATTT
Found at i:10781898 original size:10 final size:9
Alignment explanation
Indices: 10781855--10781926 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
10781845 TTTAAAAAAT
10781855 TAAAAATTCA
1 TAAAAATT-A
*
10781865 AAAAAATTA
1 TAAAAATTA
10781874 TAAAAATTA
1 TAAAAATTA
10781883 TTTTAAAAATTA
1 ---TAAAAATTA
*
10781895 T-TAAATTA
1 TAAAAATTA
* *
10781903 TTAGAAAGTA
1 -TAAAAATTA
10781913 TAAAAATTA
1 TAAAAATTA
10781922 TAAAA
1 TAAAA
10781927 GCTATTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.12
9 23 0.46
10 12 0.24
12 9 0.18
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:10784990 original size:33 final size:32
Alignment explanation
Indices: 10784933--10784994 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
10784923 TAATTTTTTG
10784933 TTTTATATTTTTAAATTTATTTTAACAAAATA
1 TTTTATATTTTTAAATTTATTTTAACAAAATA
*
10784965 TTTTATAATTTTTGAATATTA-TTTAACAAA
1 TTTTAT-ATTTTTAAAT-TTATTTTAACAAA
10784995 GTTTCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 6 0.22
33 18 0.67
34 3 0.11
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTTATATTTTTAAATTTATTTTAACAAAATA
Found at i:10785419 original size:17 final size:18
Alignment explanation
Indices: 10785397--10785437 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
10785387 ACGTATTTAG
10785397 ATATATTTAAA-AAT-AGA
1 ATATATTTAAATAATGA-A
10785414 ATATA-TTAAATAATGAA
1 ATATATTTAAATAATGAA
10785431 ATATATT
1 ATATATT
10785438 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 14 0.67
18 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATATTTAAATAATGAA
Found at i:10785468 original size:18 final size:18
Alignment explanation
Indices: 10785441--10785477 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10785431 ATATATTATT
* *
10785441 TAAAATAATACATTAAAA
1 TAAAAAAATAAATTAAAA
10785459 TAAAAAAATAAATTAAAA
1 TAAAAAAATAAATTAAAA
10785477 T
1 T
10785478 TTGAGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAAAATAAATTAAAA
Found at i:10803077 original size:33 final size:33
Alignment explanation
Indices: 10803035--10803101 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
10803025 GAAAGAAAAA
10803035 TCAGTGGTGTTTTAGTATAATTGAGTAATTCAT
1 TCAGTGGTGTTTTAGTATAATTGAGTAATTCAT
10803068 TCAGTGGTGTTTTAGTATAATTGAGTAATTCAT
1 TCAGTGGTGTTTTAGTATAATTGAGTAATTCAT
10803101 T
1 T
10803102 TTATTCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (33 bp):
TCAGTGGTGTTTTAGTATAATTGAGTAATTCAT
Found at i:10803146 original size:12 final size:12
Alignment explanation
Indices: 10803129--10803153 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10803119 AGGCGGTGAC
10803129 CCTGTTACTTAA
1 CCTGTTACTTAA
10803141 CCTGTTACTTAA
1 CCTGTTACTTAA
10803153 C
1 C
10803154 ACAGAGGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CCTGTTACTTAA
Found at i:10805852 original size:27 final size:27
Alignment explanation
Indices: 10805821--10805998 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
10805811 TAAATTGTAC
10805821 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
10805848 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10805874 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
10805902 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
10805930 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10805957 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10805984 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10805999 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10805935 original size:82 final size:81
Alignment explanation
Indices: 10805822--10805977 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
10805812 AAATTGTACA
*
10805822 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
10805886 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10805903 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
10805968 TGCGAGTTGA
65 TGCGAATTGA
10805978 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10805989 original size:82 final size:81
Alignment explanation
Indices: 10805818--10805998 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
10805808 GATTAAATTG
*
10805818 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
10805883 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10805899 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
10805963 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10805981 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10805999 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:10807579 original size:29 final size:29
Alignment explanation
Indices: 10807538--10807673 Score: 146
Period size: 29 Copynumber: 4.6 Consensus size: 29
10807528 GGCTTCCACT
* *
10807538 TATAACATATTCCGCCACTAGGGCTTACA
1 TATAACAGATTCCGCCACTAGGGCTCACA
*
10807567 TATAATAGATTCCGCCACTAGGGCTCACA
1 TATAACAGATTCCGCCACTAGGGCTCACA
* * * *
10807596 TATAACATATTCAGCCACAAAGGCCTCCACA
1 TATAACAGATTCCGCCAC-TAGGGCT-CACA
** *
10807627 TATAACAGATTTTGCCACTAGGACTCACA
1 TATAACAGATTCCGCCACTAGGGCTCACA
* *
10807656 TATAACATATTCAGCCAC
1 TATAACAGATTCCGCCAC
10807674 AAACTATAAC
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
29 60 0.67
30 10 0.11
31 19 0.21
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (29 bp):
TATAACAGATTCCGCCACTAGGGCTCACA
Found at i:10807637 original size:60 final size:59
Alignment explanation
Indices: 10807538--10807676 Score: 190
Period size: 60 Copynumber: 2.4 Consensus size: 59
10807528 GGCTTCCACT
* * * * * *
10807538 TATAACATATTCCGCCAC-TAGGGCTTACATATAATAGATTCCGCCACTAGGGCTCACA
1 TATAACATATTCAGCCACAAAGGCCTCACATATAACAGATTCCGCCACTAGGACTCACA
**
10807596 TATAACATATTCAGCCACAAAGGCCTCCACATATAACAGATTTTGCCACTAGGACTCACA
1 TATAACATATTCAGCCACAAAGGCCT-CACATATAACAGATTCCGCCACTAGGACTCACA
10807656 TATAACATATTCAGCCACAAA
1 TATAACATATTCAGCCACAAA
10807677 CTATAACACC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 17 0.24
59 5 0.07
60 49 0.69
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (59 bp):
TATAACATATTCAGCCACAAAGGCCTCACATATAACAGATTCCGCCACTAGGACTCACA
Found at i:10818031 original size:33 final size:33
Alignment explanation
Indices: 10817992--10818061 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
10817982 TACATATTCA
* *
10817992 TCAAACACCACTTGAAAAGATTCTATATATATT
1 TCAAACACCACTTGAAAACATCCTATATATATT
10818025 TCAAACACCACTTGAAAACATCCTATATATATT
1 TCAAACACCACTTGAAAACATCCTATATATATT
10818058 TCAA
1 TCAA
10818062 CCACAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (33 bp):
TCAAACACCACTTGAAAACATCCTATATATATT
Found at i:10818383 original size:41 final size:41
Alignment explanation
Indices: 10818310--10818599 Score: 314
Period size: 41 Copynumber: 7.1 Consensus size: 41
10818300 GTCTAAACAA
* * * *
10818310 GGCACAAAAGTGC-ATTTAGGTGTACCGAAGTACAAATAGG
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * * *
10818350 GGCACATATGTGCAATTCAGGGGTACCGTAGTACAAAGAGT
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
*
10818391 GGCACATATGTGCAATTT-GGAGGTACCAAAGTACAAACAGG
1 GGCACATATGTGCAATTTAGG-GGTACCGAAGTACAAACAGG
* * * *
10818432 GGCACGTATGTGTAATTTAAGGGTACCAAAGTACAAACAGG
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * * * * *
10818473 GGCACGTATTTGCAATTCAGGGATACCAAACTACAAACAGG
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * * * *
10818514 AGCACATATGTGTAATTTAGGGGTACTGAAATACAAACAAG
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
* * *
10818555 GGCACATATGTGCAATTTAAGGGTATCGAAGTACAAACAAG
1 GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
10818596 GGCA
1 GGCA
10818600 TGTTTGTGCA
Statistics
Matches: 210, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
40 13 0.06
41 196 0.93
42 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (41 bp):
GGCACATATGTGCAATTTAGGGGTACCGAAGTACAAACAGG
Found at i:10818549 original size:123 final size:123
Alignment explanation
Indices: 10818304--10818612 Score: 353
Period size: 123 Copynumber: 2.5 Consensus size: 123
10818294 ACCGGAGTCT
* * * * *
10818304 AAACAA-GGCACAAAAGTGC-ATTT-AGGTGTACCGAAGTACAAATAGGGGCACATATGTGCAAT
1 AAACAAGGGCACATATGTGCAATTTAAGG-GTACCGAAGTACAAACAGGGGCACGTATTTGCAAT
* ** * *
10818366 TCAGGGGTACCGTAGTACAAAGAGTGGCACATATGTGCAATTTGGAGGTACCAAAGTAC
65 TCAGGGATACCAAACTACAAACAGTGGCACATATGTGCAATTTGGAGGTACCAAAGTAC
* * * *
10818425 AAACAGGGGCACGTATGTGTAATTTAAGGGTACCAAAGTACAAACAGGGGCACGTATTTGCAATT
1 AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCACGTATTTGCAATT
* *
10818490 CAGGGATACCAAACTACAAACAG-GAGCACATATGTGTAATTTAGG-GGTACTGAAA-TAC
66 CAGGGATACCAAACTACAAACAGTG-GCACATATGTGCAATTT-GGAGGTAC-CAAAGTAC
* * *
10818548 AAACAAGGGCACATATGTGCAATTTAAGGGTATCGAAGTACAAACAAGGGCATGT-TTGTGCAAT
1 AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCACGTATT-TGCAAT
10818612 T
65 T
10818613 AAACAATAAT
Statistics
Matches: 158, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
121 5 0.03
122 12 0.08
123 133 0.84
124 8 0.05
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (123 bp):
AAACAAGGGCACATATGTGCAATTTAAGGGTACCGAAGTACAAACAGGGGCACGTATTTGCAATT
CAGGGATACCAAACTACAAACAGTGGCACATATGTGCAATTTGGAGGTACCAAAGTAC
Found at i:10819383 original size:24 final size:24
Alignment explanation
Indices: 10819351--10819398 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10819341 GGAAGAAAAC
10819351 CAATTAGAAAGATGATACTATCTT
1 CAATTAGAAAGATGATACTATCTT
10819375 CAATTAGAAAGATGATACTATCTT
1 CAATTAGAAAGATGATACTATCTT
10819399 TACTTTGTTT
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:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
CAATTAGAAAGATGATACTATCTT
Found at i:10829394 original size:15 final size:16
Alignment explanation
Indices: 10829358--10829395 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
10829348 TTATATTGCA
10829358 TATATATATGTTAACT
1 TATATATATGTTAACT
*
10829374 TAATATATAT-TTAAGT
1 T-ATATATATGTTAACT
10829390 TATATA
1 TATATA
10829396 ATGATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TATATATATGTTAACT
Found at i:10833109 original size:20 final size:21
Alignment explanation
Indices: 10833068--10833125 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
10833058 GGCCTGGCCC
10833068 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA-CAAAA
10833090 ATTTATTTTAAAAATA-AAAA
1 ATTTATTTTAAAAATACAAAA
**
10833110 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
10833126 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 18 0.55
22 9 0.27
23 6 0.18
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTATTTTAAAAATACAAAA
Found at i:10833127 original size:11 final size:11
Alignment explanation
Indices: 10833107--10833144 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
10833097 TTAAAAATAA
10833107 AAAAAGTATTTT
1 AAAAA-TATTTT
10833119 AAAAATATTTT
1 AAAAATATTTT
10833130 AAAAATATTTT
1 AAAAATATTTT
10833141 AAAA
1 AAAA
10833145 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:10833150 original size:17 final size:17
Alignment explanation
Indices: 10833128--10833161 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10833118 TAAAAATATT
* *
10833128 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
10833145 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
10833162 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:10833155 original size:20 final size:20
Alignment explanation
Indices: 10833093--10833155 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
10833083 ACCAAAAATT
* *
10833093 TATTTTAAAAATAAAAAAAG
1 TATTTTAAAATTAAAAAAAA
***
10833113 TATTTTAAAAATATTTTAAAAA
1 TATTTT-AAAAT-TAAAAAAAA
10833135 TATTTTAAAATTAAAAAAAA
1 TATTTTAAAATTAAAAAAAA
10833155 T
1 T
10833156 TTAAAAAGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 13 0.39
21 9 0.27
22 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TATTTTAAAATTAAAAAAAA
Found at i:10833162 original size:29 final size:29
Alignment explanation
Indices: 10833119--10833181 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
10833109 AAAGTATTTT
* *
10833119 AAAAATATTTTAAAAATATTTTAAAATTA
1 AAAAAAATTTAAAAAATATTTTAAAATTA
*
10833148 AAAAAAATTTAAAAAGTATTTTAAAATTA
1 AAAAAAATTTAAAAAATATTTTAAAATTA
10833177 AAAAA
1 AAAAA
10833182 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAAAATTTAAAAAATATTTTAAAATTA
Found at i:10833168 original size:40 final size:41
Alignment explanation
Indices: 10833093--10833211 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
10833083 ACCAAAAATT
10833093 TATTTTAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAAATAAAAAAAG-ATTTTAAAAATATTTTAAAAA
*
10833135 TATTTTAAAATTAAAAAAA-A-TTTAAAAAGTATTTT--AAA
1 TATTTTAAAAATAAAAAAAGATTTTAAAAA-TATTTTAAAAA
* *
10833173 -A-TTAAAAAATAAAAAAATTTATTTT-AAAATATTTTAAAA
1 TATTTTAAAAATAAAAAAA--GATTTTAAAAATATTTTAAAA
10833212 TTAAAAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
36 14 0.21
37 1 0.01
38 9 0.13
39 13 0.19
40 12 0.18
42 18 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (41 bp):
TATTTTAAAAATAAAAAAAGATTTTAAAAATATTTTAAAAA
Found at i:10833189 original size:28 final size:27
Alignment explanation
Indices: 10833130--10833202 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 27
10833120 AAAATATTTT
10833130 AAAAATATTTTAAAATTAAAAAAAATTTA
1 AAAAATATTTTAAAATTAAAAAAAA--TA
*
10833159 AAAAGTATTTTAAAATTAAAAAATAA-A
1 AAAAATATTTTAAAATTAAAAAA-AATA
*
10833186 AAAATTTATTTTAAAAT
1 AAAA-ATATTTTAAAAT
10833203 ATTTTAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.12
28 11 0.28
29 22 0.55
30 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
AAAAATATTTTAAAATTAAAAAAAATA
Found at i:10833232 original size:39 final size:39
Alignment explanation
Indices: 10833099--10833234 Score: 122
Period size: 39 Copynumber: 3.5 Consensus size: 39
10833089 AATTTATTTT
* *
10833099 AAAAATAAAAAAA-GTATTTTAAAAA-TATTTTAAAAATATTTT
1 AAAAATAAAAAAATTTA-TTTAAAAAGTATTTT--AAA-A-TTA
*
10833141 AAAATTAAAAAAA---ATTTAAAAAGTATTTTAAAATTA
1 AAAAATAAAAAAATTTATTTAAAAAGTATTTTAAAATTA
*
10833177 AAAAATAAAAAAATTTATTTTAAAA-TATTTTAAAATTAA
1 AAAAATAAAAAAATTTATTTAAAAAGTATTTTAAAATT-A
* *
10833216 AAAAATAAATATATTTATT
1 AAAAATAAAAAAATTTATT
10833235 ATATCGGGCC
Statistics
Matches: 83, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
36 14 0.17
37 1 0.01
38 15 0.18
39 34 0.41
40 7 0.08
42 12 0.14
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (39 bp):
AAAAATAAAAAAATTTATTTAAAAAGTATTTTAAAATTA
Found at i:10836103 original size:27 final size:27
Alignment explanation
Indices: 10836037--10836121 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
10836027 GACCGAAATA
* * *
10836037 CCCTTGAAAGGTAAAATGAACGAAATA
1 CCCTTGTAAGGTAAAATGAACGTAATG
* * * *
10836064 CCCCTATATGGTAAAATGATCGTAATG
1 CCCTTGTAAGGTAAAATGAACGTAATG
* * *
10836091 CCCTTGTAGGGTAATATGACCGTAATG
1 CCCTTGTAAGGTAAAATGAACGTAATG
10836118 CCCT
1 CCCT
10836122 GGTGGGAATA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
CCCTTGTAAGGTAAAATGAACGTAATG
Found at i:10836213 original size:24 final size:24
Alignment explanation
Indices: 10836181--10836238 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
10836171 CTGTGGTTAA
10836181 ATGAATGATTTGTCTGTG-TTTGG
1 ATGAATGATTTGTCTGTGATTTGG
* *
10836204 TATGACTGATTTGTTTGTGATTTGG
1 -ATGAATGATTTGTCTGTGATTTGG
*
10836229 ATGATTGATT
1 ATGAATGATT
10836239 CTGAGCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (24 bp):
ATGAATGATTTGTCTGTGATTTGG
Found at i:10836345 original size:27 final size:26
Alignment explanation
Indices: 10836302--10836371 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
10836292 ATAGAGGAAG
**
10836302 TACTG-TACTGGTGGCTTGGCCATAT-A
1 TACTGTTACTGGCAGCTTGG-C-TATGA
* *
10836328 TACTGTTACTGGCAGCTTTGCTGTGA
1 TACTGTTACTGGCAGCTTGGCTATGA
*
10836354 TACTGTTGCTGGCAGCTT
1 TACTGTTACTGGCAGCTT
10836372 TGCTGCGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.05
26 24 0.65
27 11 0.30
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTGGCTATGA
Found at i:10836356 original size:26 final size:26
Alignment explanation
Indices: 10836327--10836383 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
10836317 TTGGCCATAT
*
10836327 ATACTGTTACTGGCAGCTTTGCTGTG
1 ATACTGTTACTGGCAGCTTTGCTGCG
*
10836353 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
10836379 ATACT
1 ATACT
10836384 ATTGATGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:10836392 original size:26 final size:26
Alignment explanation
Indices: 10836337--10836392 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
10836327 ATACTGTTAC
* * *
10836337 TGGCAGCTTTGCTGTGATACTGTTGC
1 TGGCAGCTTTGCTGCGATACTATTGA
10836363 TGGCAGCTTTGCTGCGATACTATTGA
1 TGGCAGCTTTGCTGCGATACTATTGA
10836389 TGGC
1 TGGC
10836393 TTTGTGCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTATTGA
Found at i:10836431 original size:32 final size:33
Alignment explanation
Indices: 10836386--10836573 Score: 242
Period size: 32 Copynumber: 5.8 Consensus size: 33
10836376 GCGATACTAT
*
10836386 TGATGGCTT-TGTGCCGATCATATTACCATTAC
1 TGATGGCTTGTGTGCCGATCATATTACTATTAC
* *
10836418 TGATGG-TTGTGTGCTGATCATATTACCATTAC
1 TGATGGCTTGTGTGCCGATCATATTACTATTAC
* * *
10836450 TGATGG-TTGTGTGCCTATTATATTACTACTAC
1 TGATGGCTTGTGTGCCGATCATATTACTATTAC
* *
10836482 TGATGGCTTTTGTGCCGATCATACTACTATTAC
1 TGATGGCTTGTGTGCCGATCATATTACTATTAC
* *
10836515 TAATGGC-TGTGTGCCGATCATATTACTACTAC
1 TGATGGCTTGTGTGCCGATCATATTACTATTAC
*
10836547 TGATGGCTT-TGTGCCAATCATATTACT
1 TGATGGCTTGTGTGCCGATCATATTACT
10836574 GTACTTGGGG
Statistics
Matches: 136, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
31 2 0.01
32 106 0.78
33 28 0.21
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (33 bp):
TGATGGCTTGTGTGCCGATCATATTACTATTAC
Found at i:10836526 original size:65 final size:65
Alignment explanation
Indices: 10836388--10836573 Score: 250
Period size: 65 Copynumber: 2.9 Consensus size: 65
10836378 GATACTATTG
* * * * * * *
10836388 ATGGCTTTGTGCCGATCATATTACCATTACTGATGG-TTGTGTGCTGATCATATTACCATTACTG
1 ATGGCTGTGTGCCGATCATATTACTACTACTGATGGCTTTTGTGCCGATCATATTACTATTACTA
* * * *
10836452 ATGGTTGTGTGCCTATTATATTACTACTACTGATGGCTTTTGTGCCGATCATACTACTATTACTA
1 ATGGCTGTGTGCCGATCATATTACTACTACTGATGGCTTTTGTGCCGATCATATTACTATTACTA
*
10836517 ATGGCTGTGTGCCGATCATATTACTACTACTGATGGC-TTTGTGCCAATCATATTACT
1 ATGGCTGTGTGCCGATCATATTACTACTACTGATGGCTTTTGTGCCGATCATATTACT
10836574 GTACTTGGGG
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 48 0.46
65 57 0.54
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (65 bp):
ATGGCTGTGTGCCGATCATATTACTACTACTGATGGCTTTTGTGCCGATCATATTACTATTACTA
Found at i:10836526 original size:97 final size:96
Alignment explanation
Indices: 10836380--10836573 Score: 273
Period size: 97 Copynumber: 2.0 Consensus size: 96
10836370 TTTGCTGCGA
* * * * *
10836380 TACTATTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGTTGTGTGCTGATCATATTACC
1 TACTACTGATGGCTTTGTGCCGATCATACTACCATTACTAATGGCTGTGTGCCGATCATATTACC
* * *
10836445 ATTACTGATGG-TTGTGTGCCTATTATATTAC
66 ACTACTGATGGCTT-TGTGCCAATCATATTAC
*
10836476 TACTACTGATGGCTTTTGTGCCGATCATACTACTATTACTAATGGCTGTGTGCCGATCATATTAC
1 TACTACTGATGGC-TTTGTGCCGATCATACTACCATTACTAATGGCTGTGTGCCGATCATATTAC
*
10836541 TACTACTGATGGCTTTGTGCCAATCATATTAC
65 CACTACTGATGGCTTTGTGCCAATCATATTAC
10836573 T
1 T
10836574 GTACTTGGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 12 0.14
97 72 0.84
98 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (96 bp):
TACTACTGATGGCTTTGTGCCGATCATACTACCATTACTAATGGCTGTGTGCCGATCATATTACC
ACTACTGATGGCTTTGTGCCAATCATATTAC
Found at i:10846751 original size:50 final size:50
Alignment explanation
Indices: 10846630--10846921 Score: 291
Period size: 50 Copynumber: 5.7 Consensus size: 50
10846620 GGTAAAAAGA
*
10846630 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* * *
10846686 TCCCATATAATACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
10846736 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * **
10846786 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * * **
10846836 TCCCATGTAAGATCATATCTGGGATATGACATTGGTA--GTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
10846885 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
10846922 TGTTATTATC
Statistics
Matches: 200, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 35 0.17
50 126 0.63
53 3 0.01
55 1 0.00
56 34 0.17
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:10850735 original size:23 final size:24
Alignment explanation
Indices: 10850682--10850735 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
10850672 GAAGTCTAAA
10850682 AAATAAAATAAAAACAAATAACAG
1 AAATAAAATAAAAACAAATAACAG
* ** *
10850706 AGA-AAAATAAAAGTAAA-AATAG
1 AAATAAAATAAAAACAAATAACAG
10850728 AAATAAAA
1 AAATAAAA
10850736 AATAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 6 0.25
23 16 0.67
24 2 0.08
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (24 bp):
AAATAAAATAAAAACAAATAACAG
Found at i:10864146 original size:28 final size:28
Alignment explanation
Indices: 10864095--10864176 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
10864085 CTGATACTGA
*
10864095 TTCTG-TAATGGGCTTAGG-TCCACCTGG
1 TTCTGTTAATGGGCTAAGGCT-CACCTGG
*
10864122 TTCTGTTAATGGTCTAAGGCTCACCTGG
1 TTCTGTTAATGGGCTAAGGCTCACCTGG
10864150 TTCTGTTAATGGGCTAAGGCTCACCTG
1 TTCTGTTAATGGGCTAAGGCTCACCTG
10864177 ATACTATGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
27 5 0.10
28 44 0.88
29 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (28 bp):
TTCTGTTAATGGGCTAAGGCTCACCTGG
Found at i:10870253 original size:18 final size:18
Alignment explanation
Indices: 10870232--10870269 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10870222 TTTATTTTTC
10870232 AATACTAATTTGACCCAA
1 AATACTAATTTGACCCAA
* *
10870250 AATACTTATTTTACCCAA
1 AATACTAATTTGACCCAA
10870268 AA
1 AA
10870270 ATTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (18 bp):
AATACTAATTTGACCCAA
Found at i:10870759 original size:18 final size:18
Alignment explanation
Indices: 10870713--10870764 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
10870703 AAATGTAACA
*
10870713 ACTAAATTAA-AAAAATT
1 ACTAAATTAATAAAAATG
* **
10870730 ATTAAAAAAATAAAAATG
1 ACTAAATTAATAAAAATG
10870748 ACTAAATTAATAGAAAA
1 ACTAAATTAATA-AAAA
10870765 AAAAGTTTTC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
ACTAAATTAATAAAAATG
Found at i:10876047 original size:61 final size:61
Alignment explanation
Indices: 10875972--10876111 Score: 210
Period size: 61 Copynumber: 2.3 Consensus size: 61
10875962 AAGAGAAGTA
** *
10875972 TACTAAATGTTAAGGAATGCCTTTGTGGTAAAACTCTGGACAGGAAAACATTTGTGGT-GAG
1 TACTAAATGTTAAGGAACACCTTTGGGGTAAAACTCTGGACAGGAAAACATTTGT-GTCGAG
* *
10876033 TACTAAATGTTAAGGAACACCTTTGGGGTAAAACTCTGGACAGGAAAGCCTTTGTGTCGAG
1 TACTAAATGTTAAGGAACACCTTTGGGGTAAAACTCTGGACAGGAAAACATTTGTGTCGAG
*
10876094 TATTAAATGTTAAGGAAC
1 TACTAAATGTTAAGGAAC
10876112 GTCTTTATGG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
60 2 0.03
61 70 0.97
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (61 bp):
TACTAAATGTTAAGGAACACCTTTGGGGTAAAACTCTGGACAGGAAAACATTTGTGTCGAG
Found at i:10877936 original size:7 final size:7
Alignment explanation
Indices: 10877866--10877935 Score: 86
Period size: 7 Copynumber: 10.0 Consensus size: 7
10877856 TAAAATTAAT
10877866 AATTGAG
1 AATTGAG
*
10877873 AATTGGG
1 AATTGAG
*
10877880 AATTTAG
1 AATTGAG
10877887 AATTGAG
1 AATTGAG
10877894 AATTGAG
1 AATTGAG
10877901 AATTGAG
1 AATTGAG
10877908 AATTGAG
1 AATTGAG
* *
10877915 GAGTGAG
1 AATTGAG
*
10877922 GATTGAG
1 AATTGAG
*
10877929 TATTGAG
1 AATTGAG
10877936 TTGAAAAGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (7 bp):
AATTGAG
Found at i:10888548 original size:18 final size:18
Alignment explanation
Indices: 10888522--10888583 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 18
10888512 TTATTATAAA
*
10888522 TTATGATAATTCCTATTT
1 TTATTATAATTCCTATTT
*
10888540 TTATTATAATT--TATATA
1 TTATTATAATTCCTAT-TT
*
10888557 TTGTTA-AATTCCTA-TT
1 TTATTATAATTCCTATTT
10888573 TTATTATAATT
1 TTATTATAATT
10888584 TACATACTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
16 13 0.37
17 10 0.29
18 12 0.34
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATTATAATTCCTATTT
Found at i:10888597 original size:33 final size:34
Alignment explanation
Indices: 10888529--10888598 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
10888519 AAATTATGAT
* * *
10888529 AATTCCTATTTTTATTATAATTTATATATTGTTA
1 AATTCCTATTTTTATTATAATTTACATACTATTA
10888563 AATTCCTA-TTTTATTATAATTTACATACTATTA
1 AATTCCTATTTTTATTATAATTTACATACTATTA
10888596 AAT
1 AAT
10888599 AAATATATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (34 bp):
AATTCCTATTTTTATTATAATTTACATACTATTA
Found at i:10896060 original size:16 final size:15
Alignment explanation
Indices: 10896035--10896086 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
10896025 TTAAATTATT
10896035 ATTTAATATAAAATA
1 ATTTAATATAAAATA
**
10896050 ATTTAAATATAATTTA
1 ATTT-AATATAAAATA
*
10896066 TTTTTAATATAAATATA
1 -ATTTAATATAAA-ATA
10896083 ATTT
1 ATTT
10896087 TCAATTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 4 0.14
16 19 0.68
17 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAATATAAAATA
Found at i:10899670 original size:25 final size:25
Alignment explanation
Indices: 10899630--10899716 Score: 102
Period size: 25 Copynumber: 3.5 Consensus size: 25
10899620 ATTTATCTGG
*
10899630 AAAGCCTTTGTAGTGAATTCTCTAA
1 AAAGCCTTTGTGGTGAATTCTCTAA
* *
10899655 AAAGCCTCTGTGGTGAATTCTCTAG
1 AAAGCCTTTGTGGTGAATTCTCTAA
* ** *
10899680 AAATCCTTTGTGGCAAATCCTCTAA
1 AAAGCCTTTGTGGTGAATTCTCTAA
*
10899705 AAAGCCTATGTG
1 AAAGCCTTTGTG
10899717 ACTACCTCAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (25 bp):
AAAGCCTTTGTGGTGAATTCTCTAA
Found at i:10905679 original size:20 final size:19
Alignment explanation
Indices: 10905654--10905779 Score: 81
Period size: 20 Copynumber: 6.3 Consensus size: 19
10905644 TTGTACGGGA
10905654 TTGCACTTCTGTGCCTCTGT
1 TTGCACTTC-GTGCCTCTGT
*
10905674 TTGCACTTTAGTGCCTCTGT
1 TTGCAC-TTCGTGCCTCTGT
** * *
10905694 TTATACTTCGATGTCTCTAT
1 TTGCACTTCG-TGCCTCTGT
* *
10905714 TTGCACTGCGGTGCCTCTGA
1 TTGCACTTC-GTGCCTCTGT
* * *
10905734 TTGCACAATCGTGCCTTTTT
1 TTGCAC-TTCGTGCCTCTGT
* *
10905754 TTACACATCAGTGCCTCTGT
1 TTGCACTTC-GTGCCTCTGT
10905774 TATGCA
1 T-TGCA
10905780 TTTATGATGC
Statistics
Matches: 79, Mismatches: 21, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
19 6 0.08
20 66 0.84
21 7 0.09
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.41
Consensus pattern (19 bp):
TTGCACTTCGTGCCTCTGT
Found at i:10910016 original size:70 final size:70
Alignment explanation
Indices: 10909898--10910034 Score: 238
Period size: 70 Copynumber: 2.0 Consensus size: 70
10909888 CAAACATACT
*
10909898 TGATTAAATTTCATATCAAAACATTCCCTAAATGATCACTTTGCAAACATGCCAACACATACCAC
1 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACATGCCAACACATACCAC
10909963 TTTGG
66 TTTGG
* * *
10909968 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGTAAACATGCTAGCACATACCAC
1 TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACATGCCAACACATACCAC
10910033 TT
66 TT
10910035 CGGCCATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (70 bp):
TGATTAAATTTCATATCAAAACATGCCCTAAATGATCACTTTGCAAACATGCCAACACATACCAC
TTTGG
Found at i:10911532 original size:29 final size:29
Alignment explanation
Indices: 10911496--10911586 Score: 137
Period size: 29 Copynumber: 3.1 Consensus size: 29
10911486 TTTTTAATCG
10911496 ATGGTCGAAACCATCCCTTTTCATATTCA
1 ATGGTCGAAACCATCCCTTTTCATATTCA
* * *
10911525 ATTGTCGAAGCCATCCCTTTTCATATTCG
1 ATGGTCGAAACCATCCCTTTTCATATTCA
**
10911554 ATGGTCGTCACCATCCCTTTTCATATTCA
1 ATGGTCGAAACCATCCCTTTTCATATTCA
10911583 ATGG
1 ATGG
10911587 GCGTCAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
ATGGTCGAAACCATCCCTTTTCATATTCA
Found at i:10913663 original size:19 final size:19
Alignment explanation
Indices: 10913641--10913679 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10913631 CACGGCCGTA
10913641 TGGAACCTCCAAGGCCATG
1 TGGAACCTCCAAGGCCATG
*
10913660 TGGAACCTCCAATGCCATG
1 TGGAACCTCCAAGGCCATG
10913679 T
1 T
10913680 AACTTTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (19 bp):
TGGAACCTCCAAGGCCATG
Found at i:10915875 original size:51 final size:51
Alignment explanation
Indices: 10915765--10915875 Score: 123
Period size: 51 Copynumber: 2.2 Consensus size: 51
10915755 AGGTTTGGTT
* * **
10915765 CACATAGTAGCCTGTACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
** * * * *
10915816 CATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATTCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
*
10915867 CGCATAGTA
1 CACATAGTA
10915876 CACATGCGAC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCATCCGATA
Found at i:10918594 original size:20 final size:20
Alignment explanation
Indices: 10918525--10918594 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
10918515 ATAACAGAAG
*
10918525 CACCGAAGTGCTAAAAAGGG-
1 CACCGAAGTGC-AAACAGGGA
* *
10918545 CA-CAAATGTGCAAACAGGGG
1 CACCGAA-GTGCAAACAGGGA
* * *
10918565 CACTGTAGTGCGAACAGGGA
1 CACCGAAGTGCAAACAGGGA
10918585 CACCGAAGTG
1 CACCGAAGTG
10918595 TATTCAAAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.26
20 27 0.71
21 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.11
Consensus pattern (20 bp):
CACCGAAGTGCAAACAGGGA
Found at i:10918625 original size:20 final size:20
Alignment explanation
Indices: 10918602--10918639 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10918592 GTGTATTCAA
* *
10918602 AGGCACCGAATTGCAAATAG
1 AGGCACCAAAGTGCAAATAG
10918622 AGGCACCAAAGTGCAAAT
1 AGGCACCAAAGTGCAAAT
10918640 CTAGTACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
AGGCACCAAAGTGCAAATAG
Found at i:10923898 original size:50 final size:50
Alignment explanation
Indices: 10923843--10923953 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 50
10923833 GAGAAAGAAA
*
10923843 GAAAATTGAAGAGAAAAGAGGAGAGGAAGAGGGCGAACGGCTAGGGTAGG
1 GAAAATTGAAGAGAAAAGAGGAGAGGAAGAGGGCGAACGGCTAGGATAGG
* *
10923893 GAAAATTGAAGAGAAAAGAGGAGAGGAAGAGGGTGAATGGCTAGGATAGG
1 GAAAATTGAAGAGAAAAGAGGAGAGGAAGAGGGCGAACGGCTAGGATAGG
10923943 GAAAAATTGAA
1 G-AAAATTGAA
10923954 TTAAAGGCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 48 0.84
51 9 0.16
ACGTcount: A:0.45, C:0.04, G:0.41, T:0.11
Consensus pattern (50 bp):
GAAAATTGAAGAGAAAAGAGGAGAGGAAGAGGGCGAACGGCTAGGATAGG
Found at i:10924905 original size:34 final size:34
Alignment explanation
Indices: 10924835--10924909 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
10924825 AATGCCAGTA
* ** *
10924835 ATCAGTAGGGCCTTTGCCCAATTTCAATAATAAT
1 ATCAGTAGGGCCTTGGCCCAATAACAATAACAAT
*
10924869 ATCAGTGGGGCCTTGGCCC-ATAACAATAACATAT
1 ATCAGTAGGGCCTTGGCCCAATAACAATAACA-AT
10924903 ATCAGTA
1 ATCAGTA
10924910 ATGTAGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 9 0.26
34 25 0.74
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (34 bp):
ATCAGTAGGGCCTTGGCCCAATAACAATAACAAT
Found at i:10925391 original size:27 final size:27
Alignment explanation
Indices: 10925369--10925758 Score: 442
Period size: 27 Copynumber: 14.4 Consensus size: 27
10925359 GAGGTATAAC
10925369 AGTCATTTTACCCTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
10925396 GGTCATTTTAACCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
10925423 AGTCATTTTATCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
10925450 AGTCATTTTACCCTATAGAGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
10925477 GGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* * **
10925504 AGCCATTTTACCTTATAAGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
10925531 AGTCATTTTA-CCTGATGCGGGTATTTT
1 AGTCATTTTACCCT-ATGGGGGTATTTT
* *
10925558 AGTCATTTTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* * * * * *
10925585 AATCATTCTATCTTATGAGGGCATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
10925612 AGTCATTTTACCCTATGAGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
*
10925639 GGTCATTTTACCCTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
10925666 TGTCATTTTATCTTATGGGGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
10925692 CGATCATTTTACCCTGTGGAGGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
* *
10925720 GGTCATTTTACCCTATGGAGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
10925747 GGTCATTTTACC
1 AGTCATTTTACC
10925759 TATTTTGGGG
Statistics
Matches: 310, Mismatches: 49, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
26 6 0.02
27 297 0.96
28 7 0.02
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTT
Found at i:10937250 original size:2 final size:2
Alignment explanation
Indices: 10937243--10937289 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
10937233 TTTGAATAAA
*
10937243 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10937285 TC TC T
1 TC TC T
10937290 TTTAAAACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:10941226 original size:23 final size:22
Alignment explanation
Indices: 10941183--10941240 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
10941173 AAAGGGTATC
* *
10941183 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
10941204 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
10941227 TGCATATCATATCT
1 TACAAATCATATCT
10941241 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:10941256 original size:21 final size:21
Alignment explanation
Indices: 10941219--10941273 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
10941209 AATCATATCT
10941219 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
10941238 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
10941259 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
10941274 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 11 0.33
21 22 0.67
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:10941886 original size:44 final size:44
Alignment explanation
Indices: 10941829--10942078 Score: 186
Period size: 44 Copynumber: 5.7 Consensus size: 44
10941819 ATGTGATCTA
* ** *
10941829 CTCCACTGTAACTTCAGATAGATAAGATCT-GTGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TAGTGGCTTTAATCCG
* * * *
10941873 TTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCG
* * *** * * *
10941917 CTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAG-TGGCTTTAATCCG
** * *
10941962 C-CTCACTGCAACTTCA-GGAGGATAAGACTT-GATTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTAG-TGGCTTTAATCCG
* * * *
10942006 CTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTATTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCG
*
10942050 CTCCACTACAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
10942079 CGCCATCTTC
Statistics
Matches: 166, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
43 5 0.03
44 125 0.75
45 34 0.20
46 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCG
Found at i:10942172 original size:50 final size:50
Alignment explanation
Indices: 10942118--10942274 Score: 154
Period size: 50 Copynumber: 3.1 Consensus size: 50
10942108 TCGGGGAAAC
* * * *
10942118 AAGATTCTCCATCGTGGCTTCAATCTGTTCCACTACACTGCCAGGGAAGT
1 AAGATTCGCCATTGTGGCTTCAATCTATTCCATTACACTGCCAGGGAAGT
* * * ** * * ** *
10942168 AAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTAGGGAAAT
1 AAGATTCGCCATTGTGGCTTCAATCTATTCCATTACACTGCCAGGGAAGT
* *
10942218 AAGATTCGCCATTGTAGCTTCAATCTATTCCATTACACCGCCAGAGG-AGT
1 AAGATTCGCCATTGTGGCTTCAATCTATTCCATTACACTGCCAG-GGAAGT
10942268 AAGATTC
1 AAGATTC
10942275 ACTGTCGTGG
Statistics
Matches: 81, Mismatches: 25, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
50 79 0.98
51 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
AAGATTCGCCATTGTGGCTTCAATCTATTCCATTACACTGCCAGGGAAGT
Found at i:10942238 original size:100 final size:100
Alignment explanation
Indices: 10942093--10942274 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 100
10942083 ATCTTCAGTA
* * * * *
10942093 TTTTAAATTGCAATGTCGGGGAAACAAGATTCTCCATCGTGGCTTCAATCTGTTCCACTACACTG
1 TTTTAAATTGCAATGTCAGGGAAACAAGATTCGCCATCGTAGCTTCAATCTATTCCACTACACCG
10942158 CCAG-GGAAGTAAGATTCGCCGTTGCGGCTTCAATC
66 CCAGAGG-AGTAAGATTCGCCGTTGCGGCTTCAATC
* * * * *
10942193 TTTTTAATTGCAATGTTAGGGAAATAAGATTCGCCATTGTAGCTTCAATCTATTCCATTACACCG
1 TTTTAAATTGCAATGTCAGGGAAACAAGATTCGCCATCGTAGCTTCAATCTATTCCACTACACCG
10942258 CCAGAGGAGTAAGATTC
66 CCAGAGGAGTAAGATTC
10942275 ACTGTCGTGG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 69 0.97
101 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (100 bp):
TTTTAAATTGCAATGTCAGGGAAACAAGATTCGCCATCGTAGCTTCAATCTATTCCACTACACCG
CCAGAGGAGTAAGATTCGCCGTTGCGGCTTCAATC
Found at i:10942363 original size:45 final size:45
Alignment explanation
Indices: 10942313--10942454 Score: 178
Period size: 45 Copynumber: 3.2 Consensus size: 45
10942303 TAATGCTAAA
* ** *
10942313 GAGATAAGACTTTGTGATTTTCAACCTATTTTACTGCTGATCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
**** *
10942358 GAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
* *
10942402 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACTAGA
1 GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
10942447 GAGATAGG
1 GAGATAGG
10942455 GCTGGGGTCA
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 36 0.45
45 44 0.55
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
GAGATAGGACTTTGTGATTTTCAACCTATTCCACTGCTGACCAGG
Found at i:10942582 original size:88 final size:88
Alignment explanation
Indices: 10942454--10942952 Score: 730
Period size: 88 Copynumber: 5.7 Consensus size: 88
10942444 AGAGAGATAG
* * * * * *
10942454 GGCTGGGGTCATCGATCTGTTTCACTGTCAGTGTAGGAAGGCTAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
10942519 TCCGCTGCAACTCAAGGAGGCAA
66 TCCGCTGCAACCCAAGGAGGCAA
* * *
10942542 GGCTAGTGTCTTCGATCTACTTCACTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
10942607 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAAGGAGGCAA
* * ** *
10942630 GGCTGGTGTCTTCGAACTACTTTGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
10942695 TCTGCTACAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAAGGAGGCAA
* * *
10942718 GGCTGGTGTCTTCGATATGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
10942783 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAAGGAGGCAA
*
10942806 GGCTGGTGT-TTTGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTTAACCTG
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTG
* *
10942870 CTCCGCTGCAACCTAAAGAGGCAA
65 CTCCGCTGCAACCCAAGGAGGCAA
**
10942894 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
10942953 CTGATCTACT
Statistics
Matches: 370, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
87 39 0.11
88 291 0.79
89 40 0.11
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAAGGAGGCAA
Found at i:10949670 original size:21 final size:20
Alignment explanation
Indices: 10949632--10949670 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10949622 TTTAAGATTG
*
10949632 CATATCTAGATTGCATATAT
1 CATATCTAGATTACATATAT
*
10949652 CATATCTAAGATTATATAT
1 CATATCT-AGATTACATAT
10949671 CCTTGAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (20 bp):
CATATCTAGATTACATATAT
Found at i:10953892 original size:22 final size:23
Alignment explanation
Indices: 10953864--10953912 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
10953854 CATTCGAAAA
10953864 TGAATGTGTTTT-CCACTAAGTT
1 TGAATGTGTTTTCCCACTAAGTT
10953886 TGAATGTGTTTTCCCACTAAGTT
1 TGAATGTGTTTTCCCACTAAGTT
10953909 TGAA
1 TGAA
10953913 ATAACTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (23 bp):
TGAATGTGTTTTCCCACTAAGTT
Found at i:10971155 original size:48 final size:48
Alignment explanation
Indices: 10971084--10971180 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
10971074 TATGAGTATG
10971084 TTTCTTGGATTATTATATAATAGTTACAACATTACTCATAGTGATAAC
1 TTTCTTGGATTATTATATAATAGTTACAACATTACTCATAGTGATAAC
10971132 TTTCTTGGATTATTATATAATAGTTACAACATTACTCATAGTGATAAC
1 TTTCTTGGATTATTATATAATAGTTACAACATTACTCATAGTGATAAC
10971180 T
1 T
10971181 ATGTATACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (48 bp):
TTTCTTGGATTATTATATAATAGTTACAACATTACTCATAGTGATAAC
Found at i:10971321 original size:24 final size:23
Alignment explanation
Indices: 10971290--10971362 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
10971280 AGACTGATGT
*
10971290 TGGGTATGCCACAATCTATGTAG
1 TGGGTATGCTACAATCTATGTAG
* *
10971313 TGGGATATGCTATAAAGACTGATGT--
1 TGGG-TATGCTA-CAA-TCT-ATGTAG
10971338 TGGGTATGCTACAATCTATGTAG
1 TGGGTATGCTACAATCTATGTAG
10971361 TG
1 TG
10971363 AGATATGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 4 0.10
22 2 0.05
23 8 0.21
24 13 0.33
25 6 0.15
26 2 0.05
27 4 0.10
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGGTATGCTACAATCTATGTAG
Found at i:10971345 original size:48 final size:48
Alignment explanation
Indices: 10971274--10971369 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
10971264 AAAGGTTGTA
*
10971274 CTATAAAGACTGATGTTGGGTATGCCACAATCTATGTAGTGGGATATG
1 CTATAAAGACTGATGTTGGGTATGCCACAATCTATGTAGTGAGATATG
*
10971322 CTATAAAGACTGATGTTGGGTATGCTACAATCTATGTAGTGAGATATG
1 CTATAAAGACTGATGTTGGGTATGCCACAATCTATGTAGTGAGATATG
10971370 ATTGATCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (48 bp):
CTATAAAGACTGATGTTGGGTATGCCACAATCTATGTAGTGAGATATG
Found at i:10975817 original size:20 final size:21
Alignment explanation
Indices: 10975777--10975821 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
10975767 AGTCCATAAA
10975777 ATCACATTTCATAATCTCAAT
1 ATCACATTTCATAATCTCAAT
10975798 ATCACATTTCATAA-CTCAAT
1 ATCACATTTCATAATCTCAAT
10975818 ATCA
1 ATCA
10975822 AATTCACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
ATCACATTTCATAATCTCAAT
Found at i:10975834 original size:37 final size:36
Alignment explanation
Indices: 10975793--10975884 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 36
10975783 TTTCATAATC
*
10975793 TCAATATCACATTTCAT-AACTCAATATCAAATTCACT
1 TCAATATC-CA-TTAATCAACTCAATATCAAATTCACT
* *
10975830 TCAATTATCTATTAATCAACTCAGTATCAAATTCACT
1 TCAA-TATCCATTAATCAACTCAATATCAAATTCACT
*
10975867 TCAATTATCTATTAATCA
1 TCAA-TATCCATTAATCA
10975885 TTCATTAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 4 0.08
37 42 0.84
38 4 0.08
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (36 bp):
TCAATATCCATTAATCAACTCAATATCAAATTCACT
Found at i:10987977 original size:56 final size:52
Alignment explanation
Indices: 10987881--10988077 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 52
10987871 ATTTGGGTAA
* * **
10987881 AGAGATCCCATGTAAGACCATGTTTGGGACATGGAATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAGA-CATG
10987937 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAC--G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATG
* *
10987987 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTAGCACCGAG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATG
* * *
10988037 AGAGGTCCC-CGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
10988078 TGTTATTATC
Statistics
Matches: 128, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
49 28 0.22
50 55 0.43
52 1 0.01
53 4 0.03
55 2 0.02
56 38 0.30
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (52 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACATG
Found at i:10988076 original size:99 final size:103
Alignment explanation
Indices: 10987889--10988077 Score: 260
Period size: 106 Copynumber: 1.8 Consensus size: 103
10987879 AAAGAGATCC
* * *
10987889 CATGTAAGACCATGTTTGGGACATGGAATTGGCATCCTTGAGATCATGAGAGGTCCCATGTAAGA
1 CATGTAAGACCATGTCTGGGACATGGAATTAGCATCC-TGAGA--ATGAGAGGTCCCACGTAAGA
*
10987954 CCATGTCTGGGACATGGCGTTGGCACCGAGACGAGAGGTCT
63 CCATGTCTGGGACATGACGTTGGCACCGAGACGAGAGGTCT
**
10987995 CATGTAAGACCATGTCTGGGACATGGCGTTAGCA-CC-GAG-ATGAGAGGTCCC-CGTAAGACCA
1 CATGTAAGACCATGTCTGGGACATGGAATTAGCATCCTGAGAATGAGAGGTCCCACGTAAGACCA
*
10988056 TGTCTGGGACATGACTTTGGCA
66 TGTCTGGGACATGACGTTGGCA
10988078 TGTTATTATC
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
99 29 0.38
100 12 0.16
103 3 0.04
105 2 0.03
106 30 0.39
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (103 bp):
CATGTAAGACCATGTCTGGGACATGGAATTAGCATCCTGAGAATGAGAGGTCCCACGTAAGACCA
TGTCTGGGACATGACGTTGGCACCGAGACGAGAGGTCT
Found at i:10998568 original size:28 final size:28
Alignment explanation
Indices: 10998478--10998549 Score: 135
Period size: 28 Copynumber: 2.6 Consensus size: 28
10998468 ATGATAGTAC
*
10998478 AGTGTGGGCCCTAGCCCGATACAGTAAT
1 AGTGTGGGCCTTAGCCCGATACAGTAAT
10998506 AGTGTGGGCCTTAGCCCGATACAGTAAT
1 AGTGTGGGCCTTAGCCCGATACAGTAAT
10998534 AGTGTGGGCCTTAGCC
1 AGTGTGGGCCTTAGCC
10998550 TATTACAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCGATACAGTAAT
Found at i:10998983 original size:26 final size:26
Alignment explanation
Indices: 10998906--10998992 Score: 111
Period size: 27 Copynumber: 3.3 Consensus size: 26
10998896 TTATAATAGA
* * *
10998906 CATTTTACCCTATGGGGGTATTTCAGC
1 CATTTTACCCT-TTGGGGTATTTCGGT
10998933 CATTTTACCCTTTGGGGGTATTTCGGT
1 CATTTTACCCTTT-GGGGTATTTCGGT
* *
10998960 CATTTCACCCTTTGGGGTATTTCGAT
1 CATTTTACCCTTTGGGGTATTTCGGT
10998986 CATTTTA
1 CATTTTA
10998993 TTGACCCCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 19 0.36
27 34 0.64
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (26 bp):
CATTTTACCCTTTGGGGTATTTCGGT
Found at i:11000071 original size:13 final size:13
Alignment explanation
Indices: 11000032--11000071 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
11000022 TTCGGCAAGC
*
11000032 AAAGAGAAAAGGG
1 AAAGAGAAAAGTG
11000045 AAAGAGAAAA-TG
1 AAAGAGAAAAGTG
*
11000057 AAATAGAAAAGTG
1 AAAGAGAAAAGTG
11000070 AA
1 AA
11000072 CAAACCCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (13 bp):
AAAGAGAAAAGTG
Found at i:11000748 original size:25 final size:24
Alignment explanation
Indices: 11000702--11000758 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
11000692 TCCTGTACAT
11000702 GTATGCTCATACGAGCTCTAAATCA
1 GTATGCTCATACGAGCTCTAAA-CA
** * *
11000727 GTATGCTTTTACGAGTTGTAAACA
1 GTATGCTCATACGAGCTCTAAACA
*
11000751 GTAAGCTC
1 GTATGCTC
11000759 CTTTGAGCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATGCTCATACGAGCTCTAAACA
Found at i:11000791 original size:25 final size:26
Alignment explanation
Indices: 11000763--11000828 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
11000753 AAGCTCCTTT
*
11000763 GAGCTGAAAAAT-GGTAAGCTCATGC
1 GAGCTGAAAAATCGGTAAGCTCATAC
** *
11000788 GAGCTG-AGTATCGGTAAGCTCATAT
1 GAGCTGAAAAATCGGTAAGCTCATAC
11000813 GAGCTG--AAATCGGTAA
1 GAGCTGAAAAATCGGTAA
11000829 CCCTAATGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 11 0.32
25 23 0.68
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (26 bp):
GAGCTGAAAAATCGGTAAGCTCATAC
Found at i:11017701 original size:21 final size:21
Alignment explanation
Indices: 11017677--11017729 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
11017667 AGACCAAGAT
11017677 ACACGACCATGTA-ACTGAGGG
1 ACACGACC-TGTAGACTGAGGG
*
11017698 ACAC-ACCTGTATGGCTGAGGG
1 ACACGACCTGTA-GACTGAGGG
11017719 ACACG-CCTGTA
1 ACACGACCTGTA
11017730 TGATAGGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 21 0.75
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (21 bp):
ACACGACCTGTAGACTGAGGG
Found at i:11017730 original size:21 final size:21
Alignment explanation
Indices: 11017691--11017731 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11017681 GACCATGTAA
11017691 CTGAGGGACACACCTGTATGG
1 CTGAGGGACACACCTGTATGG
*
11017712 CTGAGGGACACGCCTGTATG
1 CTGAGGGACACACCTGTATG
11017732 ATAGGGGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (21 bp):
CTGAGGGACACACCTGTATGG
Found at i:11023427 original size:29 final size:29
Alignment explanation
Indices: 11023385--11023442 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
11023375 AATACATGAA
11023385 GGGTTAGTCACAGAGAGGTTATGTCGAAT
1 GGGTTAGTCACAGAGAGGTTATGTCGAAT
11023414 GGGTTAGTCACAGAGAGGTTATGTCGAAT
1 GGGTTAGTCACAGAGAGGTTATGTCGAAT
11023443 CATGACTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (29 bp):
GGGTTAGTCACAGAGAGGTTATGTCGAAT
Found at i:11026658 original size:16 final size:16
Alignment explanation
Indices: 11026637--11026680 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
11026627 ACTATTGAAG
11026637 CATATGGAACCTTACT
1 CATATGGAACCTTACT
**
11026653 CATAT-GCTCTCTTACT
1 CATATGGAAC-CTTACT
11026669 CATATGGAACCT
1 CATATGGAACCT
11026681 GATGTGGTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (16 bp):
CATATGGAACCTTACT
Found at i:11032253 original size:26 final size:27
Alignment explanation
Indices: 11032218--11032268 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
11032208 ACCATAGCAC
11032218 AAATCAGTCATTTACCCTCGAGGGGCA
1 AAATCAGTCATTTACCCTCGAGGGGCA
* *
11032245 AAAT-AGTCATTTACCTTCTAGGGG
1 AAATCAGTCATTTACCCTCGAGGGG
11032269 AATTACGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTCGAGGGGCA
Found at i:11035081 original size:48 final size:46
Alignment explanation
Indices: 11034975--11035089 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 46
11034965 TCAAATTTGA
** *
11034975 AAAACTCTTTTAAATAATAATTTAATTTTTTTAATTATCTTTTTTT
1 AAAACTCTTTTAAATAATAATGAAATTTTTTTAATTATCTTTTTCT
*
11035021 AAAACTCTTTTAAATATTAATGAAATTCTGTTTTAATTAT-TATTTATCT
1 AAAACTCTTTTAAATAATAATGAAATT-T-TTTTAATTATCT-TTT-TCT
11035070 AAAACTC-TTTAAATTAATAA
1 AAAACTCTTTTAAA-TAATAA
11035090 CAATTATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
46 24 0.41
47 2 0.03
48 19 0.32
49 14 0.24
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (46 bp):
AAAACTCTTTTAAATAATAATGAAATTTTTTTAATTATCTTTTTCT
Found at i:11035096 original size:33 final size:34
Alignment explanation
Indices: 11035059--11035124 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
11035049 TGTTTTAATT
11035059 ATTATTT-ATCTAAAACTC-TTTAAATTAATAACA
1 ATTATTTAATCTAAAACTCTTTTAAA-TAATAACA
11035092 ATTATTTAATCTAAAACTCTTTTAAATAATAAC
1 ATTATTTAATCTAAAACTCTTTTAAATAATAAC
11035125 TAAATTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 7 0.23
34 18 0.58
35 6 0.19
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (34 bp):
ATTATTTAATCTAAAACTCTTTTAAATAATAACA
Found at i:11044837 original size:120 final size:120
Alignment explanation
Indices: 11044622--11045077 Score: 831
Period size: 120 Copynumber: 3.8 Consensus size: 120
11044612 TTCTTTTTAC
** *
11044622 ATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTGTATTAAATTATATATTTTTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
* * *
11044687 TGAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATT
66 TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
**
11044742 ATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
11044807 TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
66 TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
11044862 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
11044927 TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
66 TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
11044982 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
1 ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
*
11045047 TTAAATTATATTTAATAATAATTATGTTAAA
66 TTAAATTATATTTAATAATAATTATATTAAA
11045078 ATATGATTAA
Statistics
Matches: 329, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 329 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
ATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTA
TTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTGTATATT
Found at i:11044917 original size:54 final size:54
Alignment explanation
Indices: 11044859--11045037 Score: 164
Period size: 56 Copynumber: 3.1 Consensus size: 54
11044849 AGTATTGTAT
11044859 ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* ** * * *
11044913 ATTATATATTTTTATTAAATT-ATATTTAATAATAATT-ATATTAAATTATATTTTATAGTATTG
1 ATTAT-GA-TTTTAGAAAATTCATA--TAAGAATATTTAATATT-AA-GA-ATTTTAT--TA---
11044976 TA
54 -A
11044978 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 -ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
11045033 ATTAT
1 ATTAT
11045038 ATATTTTTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
54 10 0.10
55 5 0.05
56 15 0.15
57 11 0.11
58 1 0.01
59 9 0.09
61 9 0.09
62 1 0.01
63 11 0.11
64 15 0.15
65 5 0.05
66 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (54 bp):
ATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:11045317 original size:16 final size:16
Alignment explanation
Indices: 11045290--11045359 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
11045280 TTGATTTGCT
*
11045290 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
11045306 ATTACACATCTATTCC
1 ATTACACCTCTATTCC
*
11045322 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
11045338 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
11045354 AATACA
1 ATTACA
11045360 GCGAACTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:11045331 original size:32 final size:32
Alignment explanation
Indices: 11045290--11045354 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
11045280 TTGATTTGCT
11045290 ATTACGCCTCTATTCCATTACACATCTATTCC
1 ATTACGCCTCTATTCCATTACACATCTATTCC
* *
11045322 ATTACGCCTCTATTCCATTACGCCTCTATTCC
1 ATTACGCCTCTATTCCATTACACATCTATTCC
11045354 A
1 A
11045355 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.35, G:0.05, T:0.37
Consensus pattern (32 bp):
ATTACGCCTCTATTCCATTACACATCTATTCC
Found at i:11046433 original size:26 final size:26
Alignment explanation
Indices: 11046402--11046482 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
11046392 GTTTTAATAA
11046402 TAATTTAAATTCTATTTAATTATATT
1 TAATTTAAATTCTATTTAATTATATT
* * *
11046428 TAATTTAAAACTCT-TTTAAATA-ATGA
1 TAATTT-AAATTCTATTTAATTATAT-T
11046454 TAA-TTAAATTCTATTTCAATTATTATT
1 TAATTTAAATTCTATTT-AATTA-TATT
11046481 TA
1 TA
11046483 TCTAAAACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
24 6 0.14
25 7 0.16
26 20 0.47
27 8 0.19
28 2 0.05
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (26 bp):
TAATTTAAATTCTATTTAATTATATT
Found at i:11046450 original size:49 final size:47
Alignment explanation
Indices: 11046385--11046526 Score: 178
Period size: 52 Copynumber: 2.9 Consensus size: 47
11046375 TTGAATTTTA
*
11046385 AAAACTCGTTTT-AATAATAATTTAAATTCTATTTAATTATATTTAATTT
1 AAAACTC-TTTTAAATAATAA-TTAAATTCTATTTAATTATATTT-ATCT
11046434 AAAACTCTTTTAAATAATGATAATTAAATTCTATTTCAATTATTATTTATCT
1 AAAACTCTTTTAAAT-A--ATAATTAAATTCTATTT-AATTA-TATTTATCT
* *
11046486 AAAACTCTTTTAAATAATAACTAAATTCTATTTACTTATAT
1 AAAACTCTTTTAAATAATAATTAAATTCTATTTAATTATAT
11046527 GATAAGGAAT
Statistics
Matches: 84, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
47 3 0.04
48 8 0.10
49 26 0.31
50 1 0.01
51 14 0.17
52 27 0.32
53 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (47 bp):
AAAACTCTTTTAAATAATAATTAAATTCTATTTAATTATATTTATCT
Found at i:11046489 original size:52 final size:50
Alignment explanation
Indices: 11046385--11046526 Score: 177
Period size: 49 Copynumber: 2.9 Consensus size: 50
11046375 TTGAATTTTA
* *
11046385 AAAACTCGTTTT-AATAATA-ATTTAAATTCTATTTAATTATATTTAATTT
1 AAAACTC-TTTTAAATAATATAATTAAATTCTATTTAATTATATTTAATCT
11046434 AAAACTCTTTTAAATAATGATAATTAAATTCTATTTCAATTATTATTT-ATCT
1 AAAACTCTTTTAAATAAT-ATAATTAAATTCTATTT-AATTA-TATTTAATCT
* *
11046486 AAAACTCTTTTAAAT-A-ATAACTAAATTCTATTTACTTATAT
1 AAAACTCTTTTAAATAATATAATTAAATTCTATTTAATTATAT
11046527 GATAAGGAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
47 3 0.04
48 8 0.10
49 29 0.35
50 1 0.01
51 15 0.18
52 23 0.27
53 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (50 bp):
AAAACTCTTTTAAATAATATAATTAAATTCTATTTAATTATATTTAATCT
Found at i:11046590 original size:94 final size:95
Alignment explanation
Indices: 11046466--11046646 Score: 292
Period size: 94 Copynumber: 1.9 Consensus size: 95
11046456 ATTAAATTCT
* *
11046466 ATTTCAATTATTATTTATCTAAAACTCTTTTAAATAATAACTAAATTCTATTTACTTATATGATA
1 ATTTCAATTATTATTTATCTAAAACTCTTTTAAATAATAACTAAATTCTATCTACTCATATGATA
11046531 AGGAATATATCAAAT-CCTTTTGCTTTTGA
66 AGGAATATATCAAATCCCTTTTGCTTTTGA
* * * * *
11046560 ATTTTAATTATTCTTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATCTCCTCATCTGATA
1 ATTTCAATTATTATTTATCTAAAACTCTTTTAAATAATAACTAAATTCTATCTACTCATATGATA
11046625 AGGAATATATCAAATCCCTTTT
66 AGGAATATATCAAATCCCTTTT
11046647 TTTATCTCGT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 73 0.92
95 6 0.08
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.45
Consensus pattern (95 bp):
ATTTCAATTATTATTTATCTAAAACTCTTTTAAATAATAACTAAATTCTATCTACTCATATGATA
AGGAATATATCAAATCCCTTTTGCTTTTGA
Found at i:11052258 original size:28 final size:28
Alignment explanation
Indices: 11052216--11052338 Score: 160
Period size: 28 Copynumber: 4.4 Consensus size: 28
11052206 CTATTCAGTG
*
11052216 ACAGT-ACAGTGTGGGCCTTAGCCTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
11052243 ACAGTGACAGTATGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
**
11052271 GTAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
11052299 ACAG-AATCAATGCGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
11052327 ACAGTAACAGTG
1 ACAGTAACAGTG
11052339 CAATGCAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.09
28 73 0.89
29 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:11053187 original size:27 final size:27
Alignment explanation
Indices: 11052754--11053187 Score: 455
Period size: 27 Copynumber: 16.1 Consensus size: 27
11052744 GGGTATAATA
*
11052754 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
11052781 ATCATTTTACCCCATGGGGGTCATTTCG
1 GTCATTTTACCCTATGGGGGT-ATTTCG
* * *
11052809 GTCATTTCACCCTATCGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
11052836 ATCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * ** *
11052862 ATCATTCTACCCTATAAGGGTATTT-T
1 GTCATTTTACCCTATGGGGGTATTTCG
*
11052888 GTCATTTTACCCTATGAGGGGTATTTTG
1 GTCATTTTACCCTATG-GGGGTATTTCG
* *
11052916 GTCATTTTATCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
11052943 GTCATTTTATCCTATGGGGTTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * **
11052970 ATCATTTTACCCTATGAGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
11052997 GTTATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
11053024 GTTATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
11053051 GTC-TTTCTACCCTATGGGGGTA-TTCTG
1 GTCATTT-TACCCTATGGGGGTATTTC-G
* * * * *
11053078 ATAATTTTACCTTATAGAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
** *
11053106 GTCATTTTACCCTATAAGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
11053133 GTCATTTTACCCTAT-AGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
11053159 GTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
11053186 GT
1 GT
11053188 GTATATATCG
Statistics
Matches: 345, Mismatches: 52, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
26 66 0.19
27 218 0.63
28 59 0.17
29 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:11055396 original size:36 final size:36
Alignment explanation
Indices: 11055349--11055420 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
11055339 TTTTTAAAGG
11055349 GGGGTAAGGTAATATTTTCATAAATTGTAATTTCTT
1 GGGGTAAGGTAATATTTTCATAAATTGTAATTTCTT
11055385 GGGGTAAGGTAATATTTTCATAAATTGTAATTTCTT
1 GGGGTAAGGTAATATTTTCATAAATTGTAATTTCTT
11055421 TCTTAAGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (36 bp):
GGGGTAAGGTAATATTTTCATAAATTGTAATTTCTT
Found at i:11070724 original size:187 final size:180
Alignment explanation
Indices: 11070413--11070831 Score: 594
Period size: 187 Copynumber: 2.3 Consensus size: 180
11070403 AACCACATGT
* *
11070413 TGTGTTTTGAAGAAGAAAAATGGTGTTTGACAAGAGAGAAAAT-A-AGAGAAAAAATGGCAGCTG
1 TGTGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCCG
* * * * * * * *
11070476 ATAGTGGGGGAAAATGATTTTAAGTTGAAAGTGTTGTATGGGTTTACAAAAATTGCACAAAAGCA
66 ACAATGGGGGAAAATAATTTTAAGCTAAAAGTGTGGCATGGGTTTACAAAAATTACACAAAAGCA
* *
11070541 TGATTATAATCATGGTGATGGAAATTCTTGTAGATGAAATTAGCCAACCA
131 TGATTATAATCATGGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCA
* *
11070591 TGTGTTTTGAAGAAGAAAAATGGTGCTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGTAGCCG
1 TGTGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCCG
*
11070656 ACAATGGAGGGAAAAAAACAATAATTTTAAGCTAAAAGTGTGGCGTGGGTTTACAAAAATTACAC
66 ACAATGG-GGG-----AA-AATAATTTTAAGCTAAAAGTGTGGCATGGGTTTACAAAAATTACAC
11070721 AAAAGCATGATTATAATCATGGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCA
124 AAAAGCATGATTATAATCATGGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCA
*
11070778 TATGTTTTGAAGAA-AAAAAGTGGTGTTTGGCAAGAGAGAAAATGAGAGA-AAAAA
1 TGTGTTTTGAAGAAGAAAAA-TGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAA
11070832 TTTTGTTACA
Statistics
Matches: 214, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
178 41 0.19
179 1 0.00
180 22 0.10
181 3 0.01
186 12 0.06
187 135 0.63
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (180 bp):
TGTGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAGAAAAAATGGCAGCCG
ACAATGGGGGAAAATAATTTTAAGCTAAAAGTGTGGCATGGGTTTACAAAAATTACACAAAAGCA
TGATTATAATCATGGTAATGGAAATTCTTGTAGATGAAATGAGCCAACCA
Found at i:11077802 original size:16 final size:16
Alignment explanation
Indices: 11077777--11077814 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11077767 ATGTTCTAGA
11077777 AACCCCACATGTTTTC
1 AACCCCACATGTTTTC
*
11077793 AACCCTACATGTTTTC
1 AACCCCACATGTTTTC
*
11077809 GACCCC
1 AACCCC
11077815 GTATGATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.39, G:0.08, T:0.29
Consensus pattern (16 bp):
AACCCCACATGTTTTC
Found at i:11077843 original size:62 final size:62
Alignment explanation
Indices: 11077767--11077887 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 62
11077757 AAGAGAACTC
* *
11077767 ATGTTCTAGAAACCCCACATGTTTTCAACCCTACATGTTTTCGACCCCGTATGATTCCACTT
1 ATGTTCTAGAAACCCAACATGTTTTCAACCCTACATGTTTTCGACCCCATATGATTCCACTT
*
11077829 ATGTTCTAGAAACCCAACATGTTTTCAACCCTACATGTTTTCGACCCTATATGATTCCA
1 ATGTTCTAGAAACCCAACATGTTTTCAACCCTACATGTTTTCGACCCCATATGATTCCA
11077888 TAATGCCAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (62 bp):
ATGTTCTAGAAACCCAACATGTTTTCAACCCTACATGTTTTCGACCCCATATGATTCCACTT
Found at i:11077864 original size:16 final size:16
Alignment explanation
Indices: 11077839--11077877 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11077829 ATGTTCTAGA
*
11077839 AACCCAACATGTTTTC
1 AACCCTACATGTTTTC
11077855 AACCCTACATGTTTTC
1 AACCCTACATGTTTTC
*
11077871 GACCCTA
1 AACCCTA
11077878 TATGATTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.08, T:0.31
Consensus pattern (16 bp):
AACCCTACATGTTTTC
Found at i:11079462 original size:81 final size:81
Alignment explanation
Indices: 11079370--11079522 Score: 297
Period size: 81 Copynumber: 1.9 Consensus size: 81
11079360 TTTTTTTTCA
11079370 TTGATTTTTTTTCTTTTGTGTGCTTGAGCTTGTAAATATACAAGTGATTGGTTAGGAGCATGTAC
1 TTGATTTTTTTTCTTTTGTGTGCTTGAGCTTGTAAATATACAAGTGATTGGTTAGGAGCATGTAC
11079435 ATAGGTTGCTTGAAAG
66 ATAGGTTGCTTGAAAG
*
11079451 TTGATTTTTTTTCTTTTGTGTGCTTGAGCTTGTAGATATACAAGTGATTGGTTAGGAGCATGTAC
1 TTGATTTTTTTTCTTTTGTGTGCTTGAGCTTGTAAATATACAAGTGATTGGTTAGGAGCATGTAC
11079516 ATAGGTT
66 ATAGGTT
11079523 ACTTAAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (81 bp):
TTGATTTTTTTTCTTTTGTGTGCTTGAGCTTGTAAATATACAAGTGATTGGTTAGGAGCATGTAC
ATAGGTTGCTTGAAAG
Found at i:11085260 original size:40 final size:40
Alignment explanation
Indices: 11085223--11085354 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
11085213 GCTACTCGTT
* *
11085223 CAAATGCCTTCGGGACATAGCTC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
11085263 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
11085303 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
11085342 CAAATGCCTTCGG
1 CAAATGCCTTCGG
11085355 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.42
40 44 0.53
41 4 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:11085342 original size:79 final size:82
Alignment explanation
Indices: 11085223--11085407 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
11085213 GCTACTCGTT
* * * *
11085223 CAAATGCCTTCGGGACATAGCTC-GATTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
11085286 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
11085303 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
11085366 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
11085383 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
11085408 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 51 0.57
80 36 0.40
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Done.