Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 15 of 328
Found at i:4604298 original size:43 final size:44
Alignment explanation
Indices: 4604104--4604608 Score: 291
Period size: 43 Copynumber: 11.6 Consensus size: 44
4604094 ATTCACAAGC
* * * *
4604104 CTTAAACCCCTAAACAGTAGGGTAACAG-GCTGAAGATTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATC-GAAGA-TGACAGAT
* * * *
4604149 CTTAACCCCCTAAGTAGTAGGGAAACAGATCGAAGACGA-AGGGT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACA-GAT
* * * *
4604193 CTTAAACCCCTAATCAGTAGGGTAACAGACCGAA-TTG-CAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
* * * *
4604235 ATTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGA-AGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
* * **
4604278 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGA-TGGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
* * * *
4604321 CTTTAACCCCCTAAGCAGTAGGGTAACA-AGTCGAA-TTTACAAAC
1 C-TTAACCCCCTAAGCAGTAGGGTAACAGA-TCGAAGATGACAGAT
* * * *
4604365 CTTAAACCCCTAAGCAGTAGGGTAACAG-GCTGAAGATTTACAAAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATC-GAAGA-TGACAGAT
* * * * * * * *
4604410 CTTAACCCCCTAACCATTAGGGTAACAGGTTGAA-TTTACAAAC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
* * * * * * * **
4604453 CTTATCTCCCTAAGTAGTAGTGG-AGCAAATCAAAGACGA-AGGGC
1 CTTAACCCCCTAAGCAGTAG-GGTAACAGATCGAAGATGACA-GAT
* * * *
4604497 CTTAACCCCCTAAGCAATAGGGTAACAG-GCTGAA-TTTACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATC-GAAGATGACAGAT
* * * * ** **
4604540 CTTAACCCCCTAAGTAGTAGGGAAACAGATCAAAAATGATGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
* *
4604584 CTTAACCCTCTAAGTAGTAGGGTAA
1 CTTAACCCCCTAAGCAGTAGGGTAA
4604609 TAGGCTGGAA
Statistics
Matches: 350, Mismatches: 89, Indels: 43
0.73 0.18 0.09
Matches are distributed among these distances:
42 30 0.09
43 139 0.40
44 116 0.33
45 64 0.18
46 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (44 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGATCGAAGATGACAGAT
Found at i:4604614 original size:87 final size:87
Alignment explanation
Indices: 4604278--4604615 Score: 329
Period size: 87 Copynumber: 3.9 Consensus size: 87
4604268 AGATGAAGAT
* * *
4604278 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGG
1 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAATGATGGGCCTTAACCCCCTAAGCAGTAGG
*
4604343 GTAACAAG-TCGAATTTACAAAC
66 GTAACAGGCT-GAATTTACAAAC
* * * * * * * ***** * *
4604365 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAAATCTTAACCCCCTAACCATTAG
1 CTTAACCCCCTAAGCAGTAGGGAAACA-GATCAAAAATGATGGGCCTTAACCCCCTAAGCAGTAG
*
4604430 GGTAACAGGTTGAATTTACAAAC
65 GGTAACAGGCTGAATTTACAAAC
* * * * * * * * *
4604453 CTTATCTCCCTAAGTAGTAGTGG-AGCAAATCAAAGACGAAGGGCCTTAACCCCCTAAGCAATAG
1 CTTAACCCCCTAAGCAGTAG-GGAAACAGATCAAAAATGATGGGCCTTAACCCCCTAAGCAGTAG
* *
4604517 GGTAACAGGCTGAATTTACAGAT
65 GGTAACAGGCTGAATTTACAAAC
* * *
4604540 CTTAACCCCCTAAGTAGTAGGGAAACAGATCAAAAATGATGGGCCTTAACCCTCTAAGTAGTAGG
1 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAATGATGGGCCTTAACCCCCTAAGCAGTAGG
*
4604605 GTAATAGGCTG
66 GTAACAGGCTG
4604616 GAAATCAAAT
Statistics
Matches: 195, Mismatches: 52, Indels: 8
0.76 0.20 0.03
Matches are distributed among these distances:
86 2 0.01
87 129 0.66
88 61 0.31
89 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (87 bp):
CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAATGATGGGCCTTAACCCCCTAAGCAGTAGG
GTAACAGGCTGAATTTACAAAC
Found at i:4604891 original size:68 final size:67
Alignment explanation
Indices: 4604802--4605207 Score: 523
Period size: 68 Copynumber: 6.0 Consensus size: 67
4604792 AAGAGTCTCA
** * * *
4604802 TCTCCTTGAAATTGTAG-TGGAGTGGCTAAAAGCCACAGCAGATCTCCTTGAAGATTCAGTGGAT
1 TCTCCTTGAAA-TGGCGTTGGAGCGGCTAAAAGCCA-AGCAGATCTCCTTAAAGTTTCAGTGGAT
4604866 CCTTT
64 -CTTT
* * * **
4604871 T-TCCTTGAAATGGTGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAG--TCAGCAGATC
1 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCCA-AGCAGATCTCCTTAAAGTTTCAGTGGATC
*
4604933 TCT
65 TTT
* * *
4604936 TCTCCCTGAAATGGCGTTGGAGTGGCTAAAAGCCGAAGCAGATCTCTTTAAAGTTTCAGTGGATC
1 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCC-AAGCAGATCTCCTTAAAGTTTCAGTGGATC
4605001 TTT
65 TTT
**
4605004 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGATTGAAGCAGATCTCCTTAAAGTTTCAGTGGAT
1 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAG--CCAAGCAGATCTCCTTAAAGTTTCAGTGGAT
4605069 CTTT
64 CTTT
*
4605073 TCTCCTTGAAATGGCGTTGGAGCAGCTAAAAGCCGAAGCAGATCTCCTTAAAGTTTCAGTGGATC
1 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCC-AAGCAGATCTCCTTAAAGTTTCAGTGGATC
4605138 TTT
65 TTT
* * *
4605141 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAGTGAATC
1 TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCCA-AGCAGATCTCCTTAAAGTTTCAGTGGATC
4605206 TT
65 TT
4605208 GGCTCTCCGA
Statistics
Matches: 300, Mismatches: 28, Indels: 19
0.86 0.08 0.05
Matches are distributed among these distances:
65 4 0.01
66 50 0.17
67 5 0.02
68 177 0.59
69 64 0.21
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (67 bp):
TCTCCTTGAAATGGCGTTGGAGCGGCTAAAAGCCAAGCAGATCTCCTTAAAGTTTCAGTGGATCT
TT
Found at i:4605115 original size:137 final size:135
Alignment explanation
Indices: 4604826--4605207 Score: 531
Period size: 137 Copynumber: 2.8 Consensus size: 135
4604816 TAGTGGAGTG
* * *
4604826 GCTAAAAGCC-ACAGCAGATCTCCTTGAAGATTCAGTGGATCCTTTT-TCCTTGAAATGGTGTTG
1 GCTAAAAGCCGA-AGCAGATCTCCTTAAAGTTTCAGTGGAT-CTTTTCTCCTTGAAATGGCGTTG
** *
4604889 GAGCGGCTAAAAGCCACAA-CAGATCTCCTTGAAG--TCAGCAGATCTCTTCTCCCTGAAATGGC
64 GAGCGGCTAAAAG--ACAAGCAGATCTCCTTGAAGTTTCAGTGGATCTTTTCTCCCTGAAATGGC
**
4604951 GTTGGAGTG
127 GTTGGAGCA
*
4604960 GCTAAAAGCCGAAGCAGATCTCTTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGTTGGA
1 GCTAAAAGCCGAAGCAGATCTCCTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGTTGGA
* * *
4605025 GCGGCTAAAAGATTGAAGCAGATCTCCTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGT
66 GCGGCTAAAAGA--CAAGCAGATCTCCTTGAAGTTTCAGTGGATCTTTTCTCCCTGAAATGGCGT
4605090 TGGAGCA
129 TGGAGCA
4605097 GCTAAAAGCCGAAGCAGATCTCCTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGTTGGA
1 GCTAAAAGCCGAAGCAGATCTCCTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGTTGGA
* * *
4605162 GCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAGTGAATCTT
66 GCGGCTAAAAGACA-AGCAGATCTCCTTGAAGTTTCAGTGGATCTT
4605208 GGCTCTCCGA
Statistics
Matches: 222, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
132 1 0.00
133 5 0.02
134 66 0.30
135 16 0.07
136 28 0.13
137 106 0.48
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (135 bp):
GCTAAAAGCCGAAGCAGATCTCCTTAAAGTTTCAGTGGATCTTTTCTCCTTGAAATGGCGTTGGA
GCGGCTAAAAGACAAGCAGATCTCCTTGAAGTTTCAGTGGATCTTTTCTCCCTGAAATGGCGTTG
GAGCA
Found at i:4605348 original size:45 final size:45
Alignment explanation
Indices: 4605298--4605408 Score: 136
Period size: 44 Copynumber: 2.5 Consensus size: 45
4605288 GATTTGGCTT
* *
4605298 CCTGAAGTTGCAGTGAAGCAGATTTGAAGTCACCAGTCTTATCTC
1 CCTGAAGTTGCAGTGAAGCAGAGTTGAAGTCACAAGTCTTATCTC
* *
4605343 CCTGAAGTTGCAGT-AGAGCAG-GTTGAAGTTATAAGTCTTATCTC
1 CCTGAAGTTGCAGTGA-AGCAGAGTTGAAGTCACAAGTCTTATCTC
* * *
4605387 CCTGAATTTACAGTGGAGCAGA
1 CCTGAAGTTGCAGTGAAGCAGA
4605409 CTGGAGATAG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
44 37 0.66
45 19 0.34
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (45 bp):
CCTGAAGTTGCAGTGAAGCAGAGTTGAAGTCACAAGTCTTATCTC
Found at i:4613243 original size:6 final size:6
Alignment explanation
Indices: 4613232--4613258 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4613222 CTAAATTAAT
4613232 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
4613259 CAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:4613841 original size:9 final size:9
Alignment explanation
Indices: 4613817--4613915 Score: 81
Period size: 9 Copynumber: 10.4 Consensus size: 9
4613807 ATTAAGATTA
4613817 AATTTTAAAT
1 AATTTT-AAT
* *
4613827 ATTTTTATT
1 AATTTTAAT
4613836 AATTTTAAT
1 AATTTTAAT
*
4613845 AATTTTAGT
1 AATTTTAAT
*
4613854 AATTTCTTAT
1 AATTT-TAAT
4613864 AATTCTTAAT
1 AATT-TTAAT
*
4613874 ATTTTTAAAT
1 AATTTT-AAT
*
4613884 AATTTTCTAT
1 AATTTT-AAT
*
4613894 ATTTTTAAT
1 AATTTTAAT
*
4613903 AATTTTTAT
1 AATTTTAAT
4613912 AATT
1 AATT
4613916 ATTTGAAAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
9 37 0.53
10 32 0.46
11 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (9 bp):
AATTTTAAT
Found at i:4613841 original size:19 final size:18
Alignment explanation
Indices: 4613817--4613908 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 18
4613807 ATTAAGATTA
* *
4613817 AATTTTAAATATTTTTATT
1 AATTTT-AATAATTTTAGT
4613836 AATTTTAATAATTTTAGT
1 AATTTTAATAATTTTAGT
* *
4613854 AATTTCTTATAATTCTTAAT
1 AATTT-TAATAATT-TTAGT
*
4613874 ATTTTTAAATAATTTTCTA-T
1 AATTTT-AATAA-TTT-TAGT
*
4613894 ATTTTTAATAATTTT
1 AATTTTAATAATTTT
4613909 TATAATTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.02
18 18 0.29
19 19 0.31
20 20 0.32
21 4 0.06
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (18 bp):
AATTTTAATAATTTTAGT
Found at i:4613873 original size:29 final size:28
Alignment explanation
Indices: 4613817--4613908 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
4613807 ATTAAGATTA
4613817 AATTTTAAAT-ATTTTTATTAATTTTAAT
1 AATTTTAAATAATTTTTA-TAATTTTAAT
*
4613845 AATTTT-AGTAATTTCTTATAATTCTTAAT
1 AATTTTAAATAATTT-TTATAATT-TTAAT
* *
4613874 ATTTTTAAATAATTTTCTATATTTTTAAT
1 AATTTTAAATAATTTT-TATAATTTTAAT
4613903 AATTTT
1 AATTTT
4613909 TATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
27 2 0.04
28 15 0.28
29 24 0.44
30 13 0.24
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
AATTTTAAATAATTTTTATAATTTTAAT
Found at i:4613909 original size:20 final size:19
Alignment explanation
Indices: 4613828--4613909 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
4613818 ATTTTAAATA
*
4613828 TTTTTATTAATTTTAATAAT
1 TTTTTA-TATTTTTAATAAT
*
4613848 TTTAGTA-ATTTCTT-ATAAT
1 TTT-TTATATTT-TTAATAAT
* *
4613867 TCTTAATATTTTTAAATAAT
1 TTTTTATATTTTT-AATAAT
*
4613887 TTTCTATATTTTTAATAAT
1 TTTTTATATTTTTAATAAT
4613906 TTTT
1 TTTT
4613910 ATAATTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
18 3 0.06
19 23 0.48
20 20 0.42
21 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTTATATTTTTAATAAT
Found at i:4614592 original size:19 final size:19
Alignment explanation
Indices: 4614570--4614635 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
4614560 GTTTTCGTCG
*
4614570 GAAATGGTAATTTTTGTGA
1 GAAATGGTAATTTTTGTCA
* *
4614589 GAAATGATTAGTTTTTGTCA
1 GAAATG-GTAATTTTTGTCA
* * *
4614609 AAAACGGTAATTTGTGTCA
1 GAAATGGTAATTTTTGTCA
4614628 GAAATGGT
1 GAAATGGT
4614636 TGGAAACAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 22 0.61
20 14 0.39
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (19 bp):
GAAATGGTAATTTTTGTCA
Found at i:4614601 original size:39 final size:39
Alignment explanation
Indices: 4614558--4614633 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
4614548 ATTCCCAAAC
** * * *
4614558 TAGTTTTCGTCGGAAATGGTAATTTTTGTGAGAAATGAT
1 TAGTTTTCGTCAAAAACGGTAATTTGTGTCAGAAATGAT
*
4614597 TAGTTTTTGTCAAAAACGGTAATTTGTGTCAGAAATG
1 TAGTTTTCGTCAAAAACGGTAATTTGTGTCAGAAATG
4614634 GTTGGAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (39 bp):
TAGTTTTCGTCAAAAACGGTAATTTGTGTCAGAAATGAT
Found at i:4623772 original size:7 final size:7
Alignment explanation
Indices: 4623760--4623792 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4623750 AACCTAACCC
*
4623760 AAAAAAA
1 AAAAAAG
4623767 AAAAAAG
1 AAAAAAG
4623774 AAAAAAG
1 AAAAAAG
4623781 AAAAAAG
1 AAAAAAG
4623788 AAAAA
1 AAAAA
4623793 CCTAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:4623802 original size:24 final size:23
Alignment explanation
Indices: 4623774--4623820 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
4623764 AAAAAAAAAG
*
4623774 AAAAAAGAAAAAAGAAAAACCTAAC
1 AAAAAA-AAACAA-AAAAACCTAAC
4623799 AAAAAAAAACTAAAAAAACCTA
1 AAAAAAAAAC-AAAAAAACCTA
4623821 GCCACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.77, C:0.13, G:0.04, T:0.06
Consensus pattern (23 bp):
AAAAAAAAACAAAAAAACCTAAC
Found at i:4623863 original size:12 final size:12
Alignment explanation
Indices: 4623846--4623887 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
4623836 TCCCACTTGC
4623846 CCCATTTTTCCT
1 CCCATTTTTCCT
4623858 CCCATTTTTCCT
1 CCCATTTTTCCT
4623870 CCCATTTTTCCT
1 CCCATTTTTCCT
4623882 CCCATT
1 CCCATT
4623888 GTCTACCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.48
Consensus pattern (12 bp):
CCCATTTTTCCT
Found at i:4624344 original size:29 final size:29
Alignment explanation
Indices: 4624288--4624344 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4624278 TCTCTTCTTT
* *
4624288 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
4624317 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
4624345 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:4624605 original size:11 final size:11
Alignment explanation
Indices: 4624587--4624616 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4624577 GTGTATATTG
4624587 TATATATTATA
1 TATATATTATA
*
4624598 TTTATATTATA
1 TATATATTATA
4624609 TATATATT
1 TATATATT
4624617 CTAATGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:4636355 original size:6 final size:6
Alignment explanation
Indices: 4636336--4636369 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
4636326 AAGGCATCTT
4636336 AAAA-A AAAAG- AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
4636370 GAGAGGGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:4638141 original size:46 final size:46
Alignment explanation
Indices: 4638091--4638266 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
4638081 TGGTTGAGCA
4638091 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4638137 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
4638182 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4638230 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4638267 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4638247 original size:93 final size:93
Alignment explanation
Indices: 4638088--4638259 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
4638078 GGATGGTTGA
* *
4638088 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4638153 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
4638181 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4638246 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
4638260 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:4639783 original size:14 final size:14
Alignment explanation
Indices: 4639764--4639791 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4639754 GGCTGAAGGG
4639764 CAGCGCCGACTGAA
1 CAGCGCCGACTGAA
4639778 CAGCGCCGACTGAA
1 CAGCGCCGACTGAA
4639792 AACCCACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (14 bp):
CAGCGCCGACTGAA
Found at i:4645225 original size:46 final size:45
Alignment explanation
Indices: 4645174--4645344 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
4645164 GGTTGAGCAT
4645174 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
4645219 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAG
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
* * *
4645263 GC-ATCCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 CCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
4645308 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4645345 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 29 0.28
44 3 0.03
45 3 0.03
46 62 0.60
47 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4649854 original size:14 final size:14
Alignment explanation
Indices: 4649835--4649863 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4649825 CGCTGAGGTA
4649835 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4649849 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4649863 T
1 T
4649864 CATCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4650183 original size:14 final size:14
Alignment explanation
Indices: 4650164--4650192 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4650154 CGCTGAGGTA
4650164 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4650178 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4650192 T
1 T
4650193 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4650185 original size:163 final size:162
Alignment explanation
Indices: 4649777--4651889 Score: 2827
Period size: 163 Copynumber: 13.5 Consensus size: 162
4649767 CAAATTCTAC
*
4649777 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACGCGCTGAGGTATTTTCAA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
*
4649842 TTTCTGTTTTTCAATTTCTGTTCATCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 TTTCTGTTTTTCAATTTCTGTTCGTC----AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
4649907 TCAGGACACGTTGAGGTAATTTTAATTTCTGTTCAT
127 TCAGGACACGTTGAGGTAATTTTAATTTCTGTTCAT
* * *
4649943 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGTATTTTTAA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
4650008 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
66 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
4650073 GACACGTTGAGGTAATTTTAATTTCTGTTCAT
131 GACACGTTGAGGTAATTTTAATTTCTGTTCAT
* *
4650105 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGTATTTTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
4650170 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
*
4650235 GGACACATTGAGGTAATTTTAATTTCTGTTCAT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
*
4650268 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
4650333 ATTTCTG-TTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * *
4650397 AGACACGTTGAGGTAATTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
* *
4650429 C-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGTTGAGGTAATTTCA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCTCACACGCTGAGGTATTTTCA
* **
4650490 ATTTCTG-TTTTC-A------------AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* *
4650541 AGACACGTTGAGGT-ATTTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTT-AATTTCTGTTCAT
* * * * *
4650573 CAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTCTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
* ***
4650638 ATTTCTGTCTTTCAA---------AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
4650694 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
* *
4650727 CAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGTA-TTTCAA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
4650790 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
66 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
4650855 GACA--TTGAGGTAATTTTAATTTCTGTTCAT
131 GACACGTTGAGGTAATTTTAATTTCTGTTCAT
*
4650885 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
4650950 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * *
4651015 AGACACGTTGAGGTAATTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
* *
4651047 C--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGTTGAGGTAATTTCA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCTCACACGCTGAGGTATTTTCA
* **
4651107 ATTTCTG-TTTTC-A------------AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* *
4651158 AGACACGTTGAGGT-ATTTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTT-AATTTCTGTTCAT
* * * * *
4651190 CAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTATTCTCAA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
* **
4651255 TTTCTGTCTTTCAA----------AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
66 TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
4651310 GACACGTTGAGGTAATTTTAATTTCTGTTCAT
131 GACACGTTGAGGTAATTTTAATTTCTGTTCAT
* * * *
4651342 CAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGTTCACGCGCTGAGGTATTTTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
4651407 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
*
4651472 GGACACATTGAGGTAATTTTAATTTCTGTTCAT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
*
4651505 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCA
1 C-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCA
4651570 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * *
4651635 AGACACGTTGAGGTAATTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTTAATTTCTGTTCAT
* *
4651667 C-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGTTGAGGTAATTTCA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGCTCACACGCTGAGGTATTTTCA
* **
4651728 ATTTCTG-TTTTC-A------------AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 ATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * *
4651779 AGACATGTTGAGGT-ATTTTCAATTTCTGTT-TT
130 GGACACGTTGAGGTAATTTT-AATTTCTGTTCAT
* * * *
4651811 CAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTATTCTCAA
1 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
*
4651876 TTTCTGTCTTTCAA
66 TTTCTGTTTTTCAA
4651890 AAAAAAAAAT
Statistics
Matches: 1791, Mismatches: 95, Indels: 139
0.88 0.05 0.07
Matches are distributed among these distances:
142 4 0.00
143 70 0.04
144 126 0.07
145 74 0.04
146 37 0.02
147 44 0.02
148 30 0.02
149 6 0.00
150 1 0.00
151 76 0.04
152 50 0.03
153 135 0.08
154 7 0.00
155 1 0.00
156 7 0.00
157 58 0.03
158 51 0.03
159 80 0.04
160 132 0.07
161 78 0.04
162 160 0.09
163 476 0.27
166 88 0.05
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (162 bp):
CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACACGCTGAGGTATTTTCAA
TTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
GACACGTTGAGGTAATTTTAATTTCTGTTCAT
Found at i:4650345 original size:13 final size:13
Alignment explanation
Indices: 4650327--4650354 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4650317 CGCTGAGGTA
4650327 TTTTCAATTTCTG
1 TTTTCAATTTCTG
4650340 TTTTCAATTTCTG
1 TTTTCAATTTCTG
4650353 TT
1 TT
4650355 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:4650458 original size:72 final size:74
Alignment explanation
Indices: 4650341--4651928 Score: 1628
Period size: 72 Copynumber: 20.7 Consensus size: 74
4650331 CAATTTCTGT
*
4650341 TTTCAATTTCTGTTCGTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC
1 TTTCAATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACAC
4650403 GTTGAGGTAA
65 GTTGAGGTAA
4650413 TTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
4650476 TTGAGGTAA
66 TTGAGGTAA
* **
4650485 TTTCAATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
*
4650548 TTGAGGTAT
66 TTGAGGTAA
* *
4650557 TTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCAC
1 TTTCAATTTCTGTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CAC
* *
4650621 ATGCTGAGGT-A
63 ACGTTGAGGTAA
*
4650632 TTCTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGG
1 TT-TCAATTTCTGT-TTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGC
4650696 ACACGTTGAGGTAA
61 ACACGTTGAGGTAA
* * *
4650710 TTTTAATTTCTGTTCATCAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGTCTC-AGCTCAC
1 TTTCAATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CAC
* *
4650773 GCGCTGAGGT-A
63 ACGTTGAGGTAA
4650784 TTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTCAATTTCTG-TTTTCAA------------AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
4650849 CCTC-AGGACA--TTGAGGTAA
53 CCTCAAGCACACGTTGAGGTAA
* * *
4650868 TTTTAATTTCTGTTCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTC-AGCTCA
1 TTTCAATTTCTGTT-TTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CA
* *
4650932 CACGCTGAGGTAT
62 CACGTTGAGGTAA
4650945 TTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTCAATTTCTG-TTTTCAA------------AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
4651010 CCTCAAG-ACACGTTGAGGTAA
53 CCTCAAGCACACGTTGAGGTAA
4651031 TTTCAATTTCTGTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
4651093 TTGAGGTAA
66 TTGAGGTAA
* **
4651102 TTTCAATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
*
4651165 TTGAGGTAT
66 TTGAGGTAA
* *
4651174 TTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CACA
* *
4651238 TGCTGAGGT-A
64 CGTTGAGGTAA
*
4651248 TTCTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGA
1 TT-TCAATTTCTGT-TTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCA
4651312 CACGTTGAGGTAA
62 CACGTTGAGGTAA
* * * *
4651325 TTTTAATTTCTGTTCATCAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTC-AGTTCA
1 TTTCAATTTCTGTT-TTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CA
* * *
4651389 CGCGCTGAGGTAT
62 CACGTTGAGGTAA
4651402 TTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTCAATTTCTG-TTTTCAA------------AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
4651467 CCTC-AGGACACATTGAGGTAA
53 CCTCAAGCACACGTTGAGGTAA
* * *
4651488 TTTTAATTTCTGTTCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTC-AGCTCA
1 TTTCAATTTCTGTT-TTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CA
* *
4651552 CACGCTGAGGTAT
62 CACGTTGAGGTAA
4651565 TTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTCAATTTCTG-TTTTCAA------------AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
4651630 CCTCAAG-ACACGTTGAGGTAA
53 CCTCAAGCACACGTTGAGGTAA
4651651 TTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
4651714 TTGAGGTAA
66 TTGAGGTAA
* ** *
4651723 TTTCAATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACATG
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
*
4651786 TTGAGGTAT
66 TTGAGGTAA
*
4651795 TTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-AGTTCACA
1 TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--CACA
* *
4651859 TGCTGAGGT-A
64 CGTTGAGGTAA
*
4651869 TTCTCAATTTCTGTCTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGC
1 TT-TCAATTTCTGT-TTTC-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
4651929 TTCAGATCAC
Statistics
Matches: 1312, Mismatches: 100, Indels: 199
0.81 0.06 0.12
Matches are distributed among these distances:
71 73 0.06
72 361 0.28
73 139 0.11
74 61 0.05
75 139 0.11
76 58 0.04
77 97 0.07
78 48 0.04
79 40 0.03
81 34 0.03
83 8 0.01
84 15 0.01
85 16 0.01
86 76 0.06
87 34 0.03
88 109 0.08
89 4 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (74 bp):
TTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGCACACG
TTGAGGTAA
Found at i:4650803 original size:14 final size:14
Alignment explanation
Indices: 4650784--4650811 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4650774 CGCTGAGGTA
4650784 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
4650798 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
4650812 CGTCAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTCAATTTCTGTT
Found at i:4650963 original size:14 final size:14
Alignment explanation
Indices: 4650944--4650972 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4650934 CGCTGAGGTA
4650944 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4650958 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4650972 T
1 T
4650973 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4651063 original size:617 final size:620
Alignment explanation
Indices: 4649871--4651933 Score: 3717
Period size: 617 Copynumber: 3.3 Consensus size: 620
4649861 GTTCATCAAA
* ** *
4649871 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATTTT-AATTT
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTTCAATTT
* * * * **
4649935 CTGTTCATCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGT
65 CTGTT-TTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGT
* * * ***
4650000 ATTTTTAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTG
129 ATTCTCAATTTCTGTCTTTCAA---------AAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
4650065 AGCCTCAGGACACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAATCAACTCATATTGCGAG
185 AGCCTCAGGACACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAAT-AACTCATATTGCGAG
4650130 AGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCG
249 AGGTGAGTTGAGTCTCAGCTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCG
4650195 TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACATTGAGGTAATTTTAATTT
314 TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-ACATTGAGGTAATTTTAATTT
4650260 CTGTTCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGG
378 CTGTTCATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGG
4650325 TATTTTCAATTTCTG-TTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTT
443 TATTTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTT
4650389 GAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAG
508 GAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAG
4650454 GTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
573 GTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
4650502 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
*
4650567 TGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTA
66 TGTTTTC-AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTA
4650632 TTCTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
130 TTCTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
4650697 CACGTTGAGGTAATTTTAATTTCTGTTCATC-AAAAAATAACTCATATTGCGAGAGGTGAGTTGA
195 CACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAATAACTCATATTGCGAGAGGTGAGTTGA
4650761 GTCTCAGCTCACGCGCTGAGGTA-TTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAAC
260 GTCTCAGCTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAAC
4650825 TCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACATTGAGGTAATTTTAATTTCTGTTCATCAAA
325 TCATATTGCGAGAGGTGAGTTGAGCCTCAGGAACATTGAGGTAATTTTAATTTCTGTTCATCAAA
4650889 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAATTT
390 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAATTT
4650954 CTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
455 CTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
4651019 ACGTTGAGGTAATTTCAATTTCTGTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
520 ACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
4651083 TCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
585 TCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
4651119 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
*
4651184 TGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGAGGTAT
66 TGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTAT
4651249 TCTCAATTTCTGTCTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
131 TCTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
4651313 ACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGA
196 ACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAA-TAACTCATATTGCGAGAGGTGAGTTGA
*
4651378 GTCTCAGTTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAAC
260 GTCTCAGCTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAAC
4651443 TCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACATTGAGGTAATTTTAATTTCTGTTCATCAA
325 TCATATTGCGAGAGGTGAGTTGAGCCTCAGGA-ACATTGAGGTAATTTTAATTTCTGTTCATCAA
4651508 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAATT
389 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAATT
4651573 TCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA
454 TCTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA
4651638 CACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
519 CACGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
4651703 CTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
584 CTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
*
4651740 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
4651805 TGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTAT
66 TGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTAT
* *
4651870 TCTCAATTTCTGTCTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCTTCAG
131 TCTCAATTTCTGTCTTTC--AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
4651934 ATCACACACT
Statistics
Matches: 1398, Mismatches: 22, Indels: 31
0.96 0.02 0.02
Matches are distributed among these distances:
615 76 0.05
616 82 0.06
617 293 0.21
618 162 0.12
619 72 0.05
620 241 0.17
621 224 0.16
622 72 0.05
624 41 0.03
630 7 0.01
631 128 0.09
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (620 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
TGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGTTCACATGCTGAGGTAT
TCTCAATTTCTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
ACGTTGAGGTAATTTTAATTTCTGTTCATCAAAAAAATAACTCATATTGCGAGAGGTGAGTTGAG
TCTCAGCTCACGCGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTTCGTCAAAATCAACT
CATATTGCGAGAGGTGAGTTGAGCCTCAGGAACATTGAGGTAATTTTAATTTCTGTTCATCAAAA
AAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGCTCACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
CGTTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CAAGACACGTTGAGGTAATTTCAATTTCTGTTTTC
Found at i:4651420 original size:14 final size:14
Alignment explanation
Indices: 4651401--4651429 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4651391 CGCTGAGGTA
4651401 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4651415 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4651429 T
1 T
4651430 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4651583 original size:14 final size:14
Alignment explanation
Indices: 4651564--4651592 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4651554 CGCTGAGGTA
4651564 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4651578 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
4651592 T
1 T
4651593 CGTCAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:4652327 original size:44 final size:45
Alignment explanation
Indices: 4652244--4652342 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
4652234 TGAAGCTGTT
* *
4652244 AATCTTATAT-TTCTGAAGTCACAGTAAAGCAGATCGAAGCTACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* * ** *
4652288 AATCTTATATCCT-TGAAGTTACATTAAAGTGGATTGAAGCCACA
1 AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
* *
4652332 AAGCATATATC
1 AATCTTATATC
4652343 AGAAGATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (45 bp):
AATCTTATATCCTCTGAAGTCACAGTAAAGCAGATCGAAGCCACA
Found at i:4652693 original size:35 final size:35
Alignment explanation
Indices: 4652654--4652724 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
4652644 CACTTGCCTC
*
4652654 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
*
4652689 TTCCCATTCTCCCATGCTGTCTGCCACCAACACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
4652724 T
1 T
4652725 CACACACTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.46, G:0.10, T:0.25
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
Found at i:4653122 original size:11 final size:11
Alignment explanation
Indices: 4653106--4653142 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
4653096 ATTAAAACAT
4653106 AAAAAATATAC
1 AAAAAATATAC
4653117 AAAAAATATAC
1 AAAAAATATAC
4653128 AAAAAAATATAC
1 -AAAAAATATAC
4653140 AAA
1 AAA
4653143 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATATAC
Found at i:4653132 original size:12 final size:12
Alignment explanation
Indices: 4653106--4653142 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
4653096 ATTAAAACAT
4653106 AAAAAATATAC-
1 AAAAAATATACA
4653117 AAAAAATATACA
1 AAAAAATATACA
4653129 AAAAAATATACA
1 AAAAAATATACA
4653141 AA
1 AA
4653143 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATATACA
Found at i:4653258 original size:11 final size:11
Alignment explanation
Indices: 4653242--4653276 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4653232 CCGGATTCCC
4653242 CTCCCTTCTCT
1 CTCCCTTCTCT
4653253 CTCCCTTCTCT
1 CTCCCTTCTCT
4653264 CTTCCC-TCTCT
1 C-TCCCTTCTCT
4653275 CT
1 CT
4653277 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:4653762 original size:3 final size:3
Alignment explanation
Indices: 4653754--4653801 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
4653744 TGCATTTCAA
4653754 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4653801 T
1 T
4653802 GAAATACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4653911 original size:3 final size:3
Alignment explanation
Indices: 4653903--4653965 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
4653893 TGTGTTTCAA
4653903 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4653951 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
4653966 ATATCCTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4654238 original size:33 final size:30
Alignment explanation
Indices: 4654180--4654252 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
4654170 TAATATTATG
*
4654180 TATATATTTTAATATTATCAGTTATATATA
1 TATATATTTTAATACTATCAGTTATATATA
* *
4654210 CTATATGATTTCTAATACTATTATTTATATATA
1 -TATAT-ATTT-TAATACTATCAGTTATATATA
4654243 TATATATTTT
1 TATATATTTT
4654253 TCTTAGTACC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 9 0.24
32 9 0.24
33 18 0.49
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TATATATTTTAATACTATCAGTTATATATA
Found at i:4658432 original size:13 final size:13
Alignment explanation
Indices: 4658414--4658440 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4658404 TTTTTTCCTT
4658414 AAATCCATATTAA
1 AAATCCATATTAA
4658427 AAATCCATATTAA
1 AAATCCATATTAA
4658440 A
1 A
4658441 CCCTTTTTTT
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATCCATATTAA
Found at i:4662289 original size:25 final size:24
Alignment explanation
Indices: 4662260--4662335 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
4662250 CCTTTTGTCC
4662260 TTTTTCTGATTTTTTATTATTTGTTT
1 TTTTTCT-ATTTTTTATTATTTG-TT
*
4662286 TTTTTCT-TTCTTTATTATTTGTT
1 TTTTTCTATTTTTTATTATTTGTT
** *
4662309 TTTTTAAATTTTATTATTATTTATT
1 TTTTTCTATTTT-TTATTATTTGTT
4662334 TT
1 TT
4662336 ATAATATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 7 0.16
24 16 0.37
25 13 0.30
26 7 0.16
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTCTATTTTTTATTATTTGTT
Found at i:4662344 original size:25 final size:25
Alignment explanation
Indices: 4662297--4662346 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4662287 TTTTCTTTCT
* *
4662297 TTATTATTTGTTTTTTTAAATTTTA
1 TTATTATTTGATTTTATAAATTTTA
4662322 TTATTATTT-ATTTTATAATATTTTA
1 TTATTATTTGATTTTATAA-ATTTTA
4662347 AATGTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
TTATTATTTGATTTTATAAATTTTA
Found at i:4664883 original size:22 final size:21
Alignment explanation
Indices: 4664836--4664883 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
4664826 TTAACCTCAC
*
4664836 TCTTTTTCATATTTTAAATAA
1 TCTTTTTCATATATTAAATAA
* * *
4664857 CCTTTTTCATCTATTAAGTAA
1 TCTTTTTCATATATTAAATAA
4664878 TTCTTT
1 -TCTTT
4664884 CAATGTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (21 bp):
TCTTTTTCATATATTAAATAA
Found at i:4665108 original size:19 final size:20
Alignment explanation
Indices: 4665086--4665134 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4665076 TTTAACTTTT
*
4665086 TCTTT-ATGTTTTAAGTAAC
1 TCTTTCATGTTTTAAATAAC
* *
4665105 TCTTTCATATTTTAAATAAT
1 TCTTTCATGTTTTAAATAAC
4665125 TCTTTCATGT
1 TCTTTCATGT
4665135 ATTACTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (20 bp):
TCTTTCATGTTTTAAATAAC
Found at i:4672398 original size:22 final size:22
Alignment explanation
Indices: 4672368--4672410 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4672358 AGATATAAAC
*
4672368 TATTTTAAAT-TCTTTTATTATG
1 TATTGTAAATCTC-TTTATTATG
4672390 TATTGTAAATCTCTTTATTAT
1 TATTGTAAATCTCTTTATTAT
4672411 CATTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTGTAAATCTCTTTATTATG
Found at i:4676668 original size:13 final size:13
Alignment explanation
Indices: 4676647--4676678 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4676637 CCATATCCCT
*
4676647 CTCACAAAATTTC
1 CTCAAAAAATTTC
4676660 CTCAAAAAATTTC
1 CTCAAAAAATTTC
4676673 CTCAAA
1 CTCAAA
4676679 TTTATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (13 bp):
CTCAAAAAATTTC
Found at i:4677245 original size:5 final size:5
Alignment explanation
Indices: 4677237--4677263 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4677227 AAATTAAAAT
4677237 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
4677264 AAAATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:4679398 original size:12 final size:12
Alignment explanation
Indices: 4679383--4679429 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
4679373 TTATATTTTT
4679383 ATATTAATAATA
1 ATATTAATAATA
* *
4679395 ATATTAATATTTTT
1 ATATTAATA--ATA
4679409 ATATTAATAATA
1 ATATTAATAATA
4679421 ATATTAATA
1 ATATTAATA
4679430 TCAATCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTAATAATA
Found at i:4679404 original size:6 final size:6
Alignment explanation
Indices: 4679383--4679430 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
4679373 TTATATTTTT
* * *
4679383 ATATTA ATAATA ATATTA ATATTTTT ATATTA ATAATA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATA--TTA ATATTA ATATTA ATATTA ATAT
4679431 CAATCAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:4679406 original size:26 final size:26
Alignment explanation
Indices: 4679375--4679430 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
4679365 ATTTTAATTT
4679375 ATATTTTTATATTAATAATAATATTA
1 ATATTTTTATATTAATAATAATATTA
4679401 ATATTTTTATATTAATAATAATATTA
1 ATATTTTTATATTAATAATAATATTA
4679427 ATAT
1 ATAT
4679431 CAATCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTTTTATATTAATAATAATATTA
Found at i:4679414 original size:14 final size:14
Alignment explanation
Indices: 4679358--4679417 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
4679348 ATAATATATT
4679358 TTAATATATTTTA-A
1 TTAATAT-TTTTATA
*
4679372 TTTATATTTTTATA
1 TTAATATTTTTATA
* *
4679386 TTAATA--ATAATA
1 TTAATATTTTTATA
4679398 TTAATATTTTTATA
1 TTAATATTTTTATA
4679412 TTAATA
1 TTAATA
4679418 ATAATATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.27
13 5 0.14
14 22 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATATTTTTATA
Found at i:4681161 original size:29 final size:32
Alignment explanation
Indices: 4681085--4681152 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
4681075 GACATTATTT
* *
4681085 TTTAAATAATTATAAAAATATTATAGAAAATTA
1 TTTAAA-AACTATTAAAATATTATAGAAAATTA
4681118 TTTAAAAACTATTAAAAT-TTATA-AAAATT-
1 TTTAAAAACTATTAAAATATTATAGAAAATTA
4681147 TTTAAA
1 TTTAAA
4681153 CTGTATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 6 0.18
30 6 0.18
31 5 0.15
32 10 0.30
33 6 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
TTTAAAAACTATTAAAATATTATAGAAAATTA
Found at i:4683277 original size:30 final size:31
Alignment explanation
Indices: 4683241--4683325 Score: 129
Period size: 34 Copynumber: 2.7 Consensus size: 31
4683231 CCCCCCCAAA
4683241 AAAAACCTAACCCAAAAAAAAAAG-AAAAAG
1 AAAAACCTAACCCAAAAAAAAAAGAAAAAAG
4683271 AAAAACCTAACCCCCAAAAAAAAGAAGAAAAAAG
1 AAAAACCTAA--CCCAAAAAAAA-AAGAAAAAAG
4683305 AAAAACCTAA-CCAAAAAAAAA
1 AAAAACCTAACCCAAAAAAAAA
4683326 TAAAAAACCT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
30 11 0.22
31 10 0.20
32 11 0.22
33 3 0.06
34 16 0.31
ACGTcount: A:0.72, C:0.19, G:0.06, T:0.04
Consensus pattern (31 bp):
AAAAACCTAACCCAAAAAAAAAAGAAAAAAG
Found at i:4684106 original size:37 final size:37
Alignment explanation
Indices: 4684064--4684165 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
4684054 CTAATATTTT
4684064 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
4684101 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
4684144 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
4684166 CCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:4685854 original size:12 final size:12
Alignment explanation
Indices: 4685834--4685869 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4685824 ATTCATTTAA
4685834 CATTCATGCATT
1 CATTCATGCATT
*
4685846 CATTTATGCATT
1 CATTCATGCATT
*
4685858 CATTCATTCATT
1 CATTCATGCATT
4685870 GCATATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:4692851 original size:70 final size:69
Alignment explanation
Indices: 4692732--4693152 Score: 358
Period size: 70 Copynumber: 6.2 Consensus size: 69
4692722 GAGTTAAACC
* **
4692732 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTTGGGGCACGC
1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
4692796 TGAGGTA
63 TGAGGTA
* * * * *
4692803 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTG
4692868 AGGTA
65 AGGTA
* *
4692873 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCT
1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
4692937 GAGGTA
64 GAGGTA
* * * ** ** *
4692943 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTT-A-----A--GC-CTTTTA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
*
4692999 --AA
66 GGTA
** **** * *
4693001 TTTT-TTTTTCAAA-----ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
4693060 GGTA
66 GGTA
* *
4693064 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
4693129 TGAGGTA
63 TGAGGTA
*
4693136 TTTTCAATTTCTGTTTT
1 TTTTCAATTTTTGTTTT
4693153 CAATTTACGT
Statistics
Matches: 276, Mismatches: 49, Indels: 51
0.73 0.13 0.14
Matches are distributed among these distances:
52 24 0.09
53 1 0.00
57 3 0.01
58 5 0.02
60 5 0.02
61 5 0.02
63 5 0.02
65 3 0.01
67 1 0.00
68 26 0.09
69 3 0.01
70 90 0.33
71 41 0.15
72 64 0.23
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (69 bp):
TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
GGTA
Found at i:4693132 original size:72 final size:71
Alignment explanation
Indices: 4693006--4693534 Score: 275
Period size: 75 Copynumber: 7.2 Consensus size: 71
4692996 TTAAATTTTT
** * *
4693006 TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
*
4693071 TTTTTG
66 TTTCTG
* *
4693077 TGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCA
1 T-TTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
4693142 ATTTCTG
65 ATTTCTG
* * * * ** * *** *** * ***
4693149 TTTTCAATTT--ACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTGGGTTGA-ACCTTT
1 TTTTCAATTTCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-C-AG-GGCACGCTGAGGTATTT
*
4693207 T-AATTTCTACT
62 TCAATTTCT--G
** * *
4693218 TTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTT
1 TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCAC--GCTGAGGTATTTT
4693282 CAATTTCTG
63 CAATTTCTG
* ** ** * * *
4693291 TCTTTCAAAAAAAAAAAATTCAACTCATATTATGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
1 T-TTTC---------AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
4693356 GTATTTTCAATTTCTG
56 GTATTTTCAATTTCTG
** * *
4693372 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
1 -TTTTC---AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
4693437 TCAATTTCTG
62 TCAATTTCTG
* ** * * * * *
4693447 TTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCAAACGCCGAGGTATT
1 TTTTC---AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGC--ACGCTGAGGTATT
*
4693512 TTCAATTTCCG
61 TTCAATTTCTG
4693523 TTTTTCAATTTC
1 -TTTTCAATTTC
4693535 TGCCTTTCAA
Statistics
Matches: 348, Mismatches: 77, Indels: 63
0.71 0.16 0.13
Matches are distributed among these distances:
66 5 0.01
67 12 0.03
68 9 0.03
69 15 0.04
70 3 0.01
71 11 0.03
72 67 0.19
73 10 0.03
74 62 0.18
75 68 0.20
76 21 0.06
77 4 0.01
81 26 0.07
82 1 0.00
83 33 0.09
84 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (71 bp):
TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
TTTCTG
Found at i:4693493 original size:74 final size:75
Alignment explanation
Indices: 4693223--4693910 Score: 370
Period size: 79 Copynumber: 8.5 Consensus size: 75
4693213 CTACTTTTTC
* *
4693223 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-T-ACACGCTGAGGTATTTTCAATT
4693287 TCTGTCTTTCAAAAAAAA
64 TCTGT-TTTC-----AAA
** ** * *
4693305 AAAATTCAACTCATATTATGAGAAATGAGTTGAGCCTCAAG-ACATGCTGAGGTATTTTCAATTT
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTATTTTCAATTT
4693369 CTGTTTTTCAAA
65 CTG-TTTTCAAA
*
4693381 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTATTTTCAATTTC
*
4693445 TGTTGTCAAA
66 TGTTTTCAAA
* * * * *
4693455 AAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCAAACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT-ACACGCTGAGGTATTTTCAATTT
*
4693520 CCGTTTTTCAATTTCTGCCTTTCA
65 CTG-TTTTCAA------------A
** * * * * * * * *
4693544 AAAAAAAAATCA-ACT-C-ATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTAT
1 AAAATCAACTCATATTGCGAGA--G-GTGAGTTGAG-----CCTCAGG-T-ACACGCTGAGGTAT
4693605 TTTCAATTTCTGTCTTTCAAA
56 TTTCAATTTCTGT-TTTCAAA
* * *
4693626 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT-ACACGCTGAGGTA--TTTTCAAT
* *
4693691 TTATATTTTTCAAA
63 TTCT-GTTTTCAAA
* * * * **
4693705 AAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTCACATG-TCGAGGTATTTTCAAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT-ACACGCT-GAGGTATTTTCAATT
4693769 TCTGTTTTTCAGATTCTGTTTTCA
64 TCTG-TTTTCA-A----------A
* * *
4693793 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCT-CACGTGCTGAGCTATTTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TACAC--GCTGAGGTATTTTCAAT
4693856 TTCTGTTTTTCTTTTTCAAA
63 TTCTG-------TTTTCAAA
4693876 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
4693911 TTTTTAATTT
Statistics
Matches: 476, Mismatches: 71, Indels: 116
0.72 0.11 0.17
Matches are distributed among these distances:
74 44 0.09
75 55 0.12
76 29 0.06
77 35 0.07
78 3 0.01
79 64 0.13
80 1 0.00
81 30 0.06
82 23 0.05
83 36 0.08
84 31 0.07
85 2 0.00
86 4 0.01
87 2 0.00
88 56 0.12
89 18 0.04
93 4 0.01
94 39 0.08
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCTGAGGTATTTTCAATTTC
TGTTTTCAAA
Found at i:4693606 original size:94 final size:94
Alignment explanation
Indices: 4693452--4693624 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 94
4693442 TTCTGTTGTC
* * *
4693452 AAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCAAACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCAAACGCCGAGCTATTTTCAA
*
4693517 TTTCCGTTTTTCAATTTCTGCCTTTCAAA
66 TTTCCGTCTTTCAATTTCTGCCTTTCAAA
* * ** *
4693546 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-TCAAACGCCGAGCTATTTTCA
*
4693610 ATTTCTGTCTTTCAA
65 ATTTCCGTCTTTCAA
4693625 AAAAATCAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
93 2 0.03
94 66 0.97
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (94 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCAAACGCCGAGCTATTTTCAA
TTTCCGTCTTTCAATTTCTGCCTTTCAAA
Found at i:4693853 original size:88 final size:83
Alignment explanation
Indices: 4693619--4694122 Score: 257
Period size: 88 Copynumber: 6.0 Consensus size: 83
4693609 AATTTCTGTC
* * * * ** *
4693619 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACA-CACTGAGGTATT
1 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTATT
* ** * *
4693683 TT----TTCAATTTATATT
65 TTCAAAATCTGTTTTTCTT
* * * *
4693698 TTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTT
4693763 TCAAAATCTGTTTTTCAGATT
66 TCAAAATCTGTTTTTC---TT
*** * *
4693784 CTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTG-CTGAGCTA
1 -T-TTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTA
**
4693848 TTTTCAATTTCTGTTTTTCTT
63 TTTTCAAAATCTGTTTTTCTT
* ** * * * **
4693869 TTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAG-CT--TTTTA-ATTTCTGCGAGAG
1 TTTCAAAAAAA-TCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTA-
* * *
4693930 TTGAGTT--GAGTCTTTTAATTTCTGTT
63 TT---TTCAAAATCTGTT--TTTC--TT
* * * * *
4693956 TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG-TCACATATCGAGGTATT
1 TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-CGGCTCACATGTCGAGCTATT
*
4694018 TTCAAAATCTGCTTTTCAAGTT
65 TTCAAAATCTGTTTTTC---TT
* * **
4694040 AAGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCG-CTGAGCT
1 ---TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCT
**
4694104 ATTTTCAATTTCTGTTTTT
62 ATTTTCAAAATCTGTTTTT
4694123 AATGTCTGTT
Statistics
Matches: 328, Mismatches: 61, Indels: 62
0.73 0.14 0.14
Matches are distributed among these distances:
79 57 0.17
80 2 0.01
81 7 0.02
82 2 0.01
83 26 0.08
84 60 0.18
85 20 0.06
86 4 0.01
87 17 0.05
88 73 0.22
89 60 0.18
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (83 bp):
TTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTT
TCAAAATCTGTTTTTCTT
Found at i:4693928 original size:30 final size:30
Alignment explanation
Indices: 4693892--4693953 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4693882 CAACTCATAT
4693892 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
4693922 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
4693952 TG
1 TG
4693954 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:4694006 original size:256 final size:247
Alignment explanation
Indices: 4693350--4694122 Score: 864
Period size: 250 Copynumber: 3.1 Consensus size: 247
4693340 CTCAAGACAT
*
4693350 GCTGAGGTATTTTCAATTTCTG---TT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
1 GCTGAGCTATTTTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * * * * * *
4693411 GAGCCTCAG--GACACGCTGAGGTA--ATTTCAATTTCT-GTTGTCAAAAAAATCAACTCGTATT
66 GAGCTTCAGATCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCATATT
* * * * * ** * *
4693471 GTGAGAGGCGAGTTGAGCCT-CAGGTCAAACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTC
130 GCGAGAGGTGAGTTGAGCCTCCA-GTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTC
4693535 TGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
194 TG--TTTC----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
4693595 GCTGAGCTATTTTCAATTTCTG----TCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
1 GCTGAGCTATTTTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
4693656 GAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATT
66 GAGCTTCAGATCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCATATT
* **
4693721 GCGAGATGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTC-AGATTC
130 GCGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAG-TTC
* *
4693785 TGTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGT
194 TG-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
4693839 GCTGAGCTATTTTCAATTTCTGTTTTTCTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGA
1 GCTGAGCTATTTTCAATTTCTGTTTTTC--TTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGA
* * * * * * *
4693904 GTTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAAT
63 GTTGAGC--TTCAGA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAAT
* * *
4693966 CAACTCATATTGCGAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCT
119 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTT
**
4694031 TTTCAAGTTAAGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
184 TTTCAAGTTCTGTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
4694096 GCTGAGCTATTTTCAATTTCTGTTTTT
1 GCTGAGCTATTTTCAATTTCTGTTTTT
4694123 AATGTCTGTT
Statistics
Matches: 457, Mismatches: 44, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
244 68 0.15
245 66 0.14
247 12 0.03
248 2 0.00
249 15 0.03
250 83 0.18
251 30 0.07
252 1 0.00
253 3 0.01
254 2 0.00
255 5 0.01
256 73 0.16
257 79 0.17
258 13 0.03
259 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (247 bp):
GCTGAGCTATTTTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCTTCAGATCACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCATATTG
CGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAGTTCTG
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
Found at i:4694872 original size:31 final size:31
Alignment explanation
Indices: 4694778--4694871 Score: 129
Period size: 31 Copynumber: 3.0 Consensus size: 31
4694768 AGCCCCCCCA
4694778 AAAAAACCTAACCCTAAAAAAAAAGAAAAAAG
1 AAAAAACCTAACCC-AAAAAAAAAGAAAAAAG
4694810 -AAAAACCTAACCCCCAAAAAAAGAAGAAAAAAG
1 AAAAAACCTAA--CCCAAAAAAA-AAGAAAAAAG
*
4694843 AAAAAACCTAA-CCAAAAAAAAATAAAAAA
1 AAAAAACCTAACCCAAAAAAAAAGAAAAAA
4694872 ACCTAGCCAC
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
30 8 0.14
31 19 0.33
32 7 0.12
33 13 0.23
34 10 0.18
ACGTcount: A:0.72, C:0.17, G:0.05, T:0.05
Consensus pattern (31 bp):
AAAAAACCTAACCCAAAAAAAAAGAAAAAAG
Found at i:4695656 original size:37 final size:37
Alignment explanation
Indices: 4695614--4695715 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
4695604 CTAATATTTT
4695614 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
4695651 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
4695694 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
4695716 CCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:4697395 original size:26 final size:28
Alignment explanation
Indices: 4697349--4697415 Score: 106
Period size: 26 Copynumber: 2.5 Consensus size: 28
4697339 TTAAAGACAC
4697349 TATTATAAATATAATAAATATTTTATTA
1 TATTATAAATATAATAAATATTTTATTA
4697377 TATTATAAA-A-AATAAATATTTTATTA
1 TATTATAAATATAATAAATATTTTATTA
4697403 TA-T-TAAATATAAT
1 TATTATAAATATAAT
4697416 TTTTAAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.11
25 2 0.05
26 21 0.57
27 1 0.03
28 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTATAAATATAATAAATATTTTATTA
Found at i:4698533 original size:11 final size:12
Alignment explanation
Indices: 4698517--4698545 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4698507 TTTTTGTATG
4698517 AAAAAACAAA-A
1 AAAAAACAAATA
4698528 AAAAAACAAATA
1 AAAAAACAAATA
4698540 AAAAAA
1 AAAAAA
4698546 GCTTTATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAACAAATA
Found at i:4699070 original size:22 final size:23
Alignment explanation
Indices: 4699043--4699085 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4699033 TTATAATCAA
4699043 ATATAAACACATAATT-TTATTT
1 ATATAAACACATAATTATTATTT
* *
4699065 ATATAAATATATAATTATTAT
1 ATATAAACACATAATTATTAT
4699086 ATTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAACACATAATTATTATTT
Found at i:4705809 original size:9 final size:10
Alignment explanation
Indices: 4705785--4705852 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
4705775 TTTATATTTT
4705785 TAAAAAATTA
1 TAAAAAATTA
*
4705795 TAAAAACTTA
1 TAAAAAATTA
*
4705805 TAAAAAA-AA
1 TAAAAAATTA
*
4705814 CTAATAAATTA
1 -TAAAAAATTA
4705825 TAAACAAATGTA
1 TAAA-AAAT-TA
4705837 T-AAAAATGTA
1 TAAAAAAT-TA
4705847 TAAAAA
1 TAAAAA
4705853 TATATATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
9 1 0.02
10 32 0.68
11 11 0.23
12 3 0.06
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.26
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:4705810 original size:20 final size:19
Alignment explanation
Indices: 4705709--4705872 Score: 77
Period size: 20 Copynumber: 8.4 Consensus size: 19
4705699 TAAAAAACAT
*
4705709 TAAAAAAATATAAAAATT-
1 TAAAAAATTATAAAAATTA
* * *
4705727 TATAAATATCATAATAACTTA
1 TA-AAAAATTATAA-AAATTA
* *
4705748 TAAAATAATTCTAAAAATCA
1 TAAAA-AATTATAAAAATTA
* * * * *
4705768 T-AAAGATT-TTATATTTT
1 TAAAAAATTATAAAAATTA
4705785 TAAAAAATTATAAAAACTTA
1 TAAAAAATTATAAAAA-TTA
*
4705805 TAAAAAA-AACTAATAAATTA
1 TAAAAAATTA-TAA-AAATTA
4705825 TAAACAAATGTATAAAAATGTA
1 TAAA-AAAT-TATAAAAAT-TA
**
4705847 T-AAAAATATATATGAATTA
1 TAAAAAAT-TATAAAAATTA
4705866 TAAAAAA
1 TAAAAAA
4705873 AATCAGTTCC
Statistics
Matches: 107, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.05
18 11 0.10
19 18 0.17
20 47 0.44
21 19 0.18
22 6 0.06
23 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTA
Found at i:4710872 original size:23 final size:23
Alignment explanation
Indices: 4710842--4710900 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
4710832 ACAAACTAGA
4710842 CCCATACCCCCACTACAACAAGC
1 CCCATACCCCCACTACAACAAGC
*
4710865 CCCATACCCCCACTACCACAAGC
1 CCCATACCCCCACTACAACAAGC
*
4710888 CCCATACCGCCAC
1 CCCATACCCCCAC
4710901 AGTCCTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.56, G:0.05, T:0.08
Consensus pattern (23 bp):
CCCATACCCCCACTACAACAAGC
Found at i:4723057 original size:71 final size:71
Alignment explanation
Indices: 4722936--4723069 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
4722926 GTTTTCCAAG
* * *
4722936 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
4723001 GTTTCA
66 GTTTCA
* * *
4723007 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
4723070 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:4723076 original size:160 final size:160
Alignment explanation
Indices: 4722722--4723228 Score: 946
Period size: 160 Copynumber: 3.2 Consensus size: 160
4722712 CAATTTCTGT
4722722 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
1 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
4722787 TCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACGTTGAGGTAATTTCAATTTATGTTTCAAAA
66 TCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAA
*
4722850 ATCAACTCATATTGCGAGAAGTGAGTTAAG
131 ATCAACTCATATTGCGAGAAGTGAGTTGAG
4722880 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
1 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
4722945 TCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAA
66 TCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAA
4723010 ATCAACTCATATTGCGAGAAGTGAGTTGAG
131 ATCAACTCATATTGCGAGAAGTGAGTTGAG
4723040 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
1 CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
* *
4723105 TCACATTGCGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTAATTTCAATTTATGTTTCAAAA
66 TCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAA
*
4723170 ATCAACTCATATTGCGAGAAGTGAGTTGAA
131 ATCAACTCATATTGCGAGAAGTGAGTTGAG
* *
4723200 CCTCGGGGCACGCTGAGGTAATTTCAATT
1 CCTCAGGGCACGCTGAGGTATTTTCAATT
4723229 CCTATTAAAT
Statistics
Matches: 341, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
158 96 0.28
160 245 0.72
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (160 bp):
CCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGC
TCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTATGTTTCAAAA
ATCAACTCATATTGCGAGAAGTGAGTTGAG
Found at i:4723217 original size:71 final size:71
Alignment explanation
Indices: 4723096--4723345 Score: 286
Period size: 74 Copynumber: 3.5 Consensus size: 71
4723086 GTTTTCCAAG
* * * * *
4723096 AAAATCAGCTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACATGTTGAGGTAATTTCAATT-TA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTCTA
4723160 TGTTTCA
66 T-TTTCA
* * * *
4723167 AAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTCAATT-CT
* *
4723232 ATTAAATCT
65 ATT--TTCA
* * * * *
4723241 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGCGTCACGCTAAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTC-AATTCT
4723306 ATTTTCA
65 ATTTTCA
* *
4723313 AAATTCAATTCATATTGCGAGAGGTGAGTTGAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
4723346 TCTTTTTAAT
Statistics
Matches: 152, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
71 53 0.35
72 34 0.22
73 3 0.02
74 58 0.38
75 4 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCTGAGGTAATTTCAATTCTA
TTTTCA
Found at i:4723497 original size:13 final size:13
Alignment explanation
Indices: 4723479--4723503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4723469 TGAGTTGAGC
4723479 CTTTTAATTTCTG
1 CTTTTAATTTCTG
4723492 CTTTTAATTTCT
1 CTTTTAATTTCT
4723504 ATGTTTCAAA
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:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTTAATTTCTG
Found at i:4723511 original size:68 final size:68
Alignment explanation
Indices: 4723293--4723547 Score: 217
Period size: 67 Copynumber: 3.8 Consensus size: 68
4723283 ACGCTAAGGT
* * *
4723293 ATTTTCAAATTCTATTTTCAAA--ATTCAATTCATATTGCGAGAGGTGAGTTGAGTCTTTTTAAT
1 ATTTTCAATTTCTATTTTCAAATTATT-AACTCATATTGCGAGAGGTGAGTTGAG-CCTTTTAAT
4723356 TTCT-
64 TTCTG
* * * *
4723360 ATTTTCAATTTCTGTTTT----TAATCAACTCATATTGCGAGAGGTGAGTTGAACC-TTTAATTT
1 ATTTTCAATTTCTATTTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT
*
4723420 CAG
66 CTG
* * * *
4723423 TTTTTCGAA-ATCTACTTTTCAAATTATTAACTCATGTTGCGAAAGGTGAGTTGAGCCTTTTAAT
1 ATTTTC-AATTTCTA-TTTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAAT
4723487 TTCTG
64 TTCTG
* * ** * **
4723492 CTTTT-AATTTCTATGTTTCAAA-AACCAACCCATATTGCGAGAAATGAGTTGAGCCT
1 ATTTTCAATTTCTAT-TTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCT
4723548 CAGTTCACAT
Statistics
Matches: 150, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
62 9 0.06
63 9 0.06
64 31 0.21
65 2 0.01
67 45 0.30
68 40 0.27
69 14 0.09
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (68 bp):
ATTTTCAATTTCTATTTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT
CTG
Found at i:4724149 original size:24 final size:24
Alignment explanation
Indices: 4724117--4724237 Score: 133
Period size: 23 Copynumber: 5.2 Consensus size: 24
4724107 AAATCCAATA
* *
4724117 CCCATTACAAACTAGACCCATACC
1 CCCACTACAAACAAGACCCATACC
*
4724141 CCCACTACAAACTAGACCCATACC
1 CCCACTACAAACAAGACCCATACC
*
4724165 CCCACTAC-AACAAGCCCCATACC
1 CCCACTACAAACAAGACCCATACC
* *
4724188 CCCACTAC-CACAAGCCCCATACC
1 CCCACTACAAACAAGACCCATACC
* *
4724211 CCCACCAC-AACAA-TCCCATACC
1 CCCACTACAAACAAGACCCATACC
*
4724233 GCCAC
1 CCCAC
4724238 AGTCCTCGTA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
22 12 0.13
23 46 0.52
24 31 0.35
ACGTcount: A:0.35, C:0.50, G:0.04, T:0.11
Consensus pattern (24 bp):
CCCACTACAAACAAGACCCATACC
Found at i:4724183 original size:23 final size:23
Alignment explanation
Indices: 4724133--4724237 Score: 140
Period size: 23 Copynumber: 4.6 Consensus size: 23
4724123 ACAAACTAGA
* *
4724133 CCCATACCCCCACTACAAACTAGA
1 CCCATACCCCCACTAC-AACAAGC
4724157 CCCATACCCCCACTACAACAAGC
1 CCCATACCCCCACTACAACAAGC
*
4724180 CCCATACCCCCACTACCACAAGC
1 CCCATACCCCCACTACAACAAGC
* *
4724203 CCCATACCCCCACCACAACAA-T
1 CCCATACCCCCACTACAACAAGC
*
4724225 CCCATACCGCCAC
1 CCCATACCCCCAC
4724238 AGTCCTCGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
22 12 0.16
23 46 0.62
24 16 0.22
ACGTcount: A:0.33, C:0.53, G:0.04, T:0.10
Consensus pattern (23 bp):
CCCATACCCCCACTACAACAAGC
Found at i:4724804 original size:15 final size:15
Alignment explanation
Indices: 4724771--4724800 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4724761 TCCTCTGCCC
4724771 TCTCCCTCTCTCCTT
1 TCTCCCTCTCTCCTT
4724786 TCTCCC-CTCTCCTT
1 TCTCCCTCTCTCCTT
4724800 T
1 T
4724801 TCTCTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCCCTCTCTCCTT
Found at i:4724810 original size:22 final size:22
Alignment explanation
Indices: 4724758--4724810 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4724748 GGCCGGAGCC
* *
4724758 CTCTCCTCTGCCCTCTCCCTCT
1 CTCTCTTCTCCCCTCTCCCTCT
* *
4724780 CTC-CTTTCTCCCCTCTCCTTTT
1 CTCTC-TTCTCCCCTCTCCCTCT
4724802 CTCTCTTCT
1 CTCTCTTCT
4724811 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.00, C:0.53, G:0.02, T:0.45
Consensus pattern (22 bp):
CTCTCTTCTCCCCTCTCCCTCT
Found at i:4725290 original size:24 final size:22
Alignment explanation
Indices: 4725263--4725324 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 22
4725253 TACATATTAC
*
4725263 TAATATTGTTACTATTATTTTTAT
1 TAATATTATTA-TATTATTTTT-T
4725287 TAATA-TATTA-ATTATTTTTT
1 TAATATTATTATATTATTTTTT
4725307 TAAGTATTATTATTATTA
1 TAA-TATTATTA-TATTA
4725325 ATGGTTGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 5 0.15
23 4 0.12
24 9 0.27
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (22 bp):
TAATATTATTATATTATTTTTT
Found at i:4725300 original size:21 final size:21
Alignment explanation
Indices: 4725275--4725323 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
4725265 ATATTGTTAC
4725275 TATTATTTTTATTAA-TA-TAT
1 TATTATTTTT-TTAAGTATTAT
4725295 TAATTATTTTTTTAAGTATTAT
1 T-ATTATTTTTTTAAGTATTAT
4725317 TATTATT
1 TATTATT
4725324 AATGGTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTTTTTTAAGTATTAT
Found at i:4725383 original size:13 final size:14
Alignment explanation
Indices: 4725359--4725389 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4725349 ATTATTATCA
4725359 ATATTAATATATGT
1 ATATTAATATATGT
4725373 ATATT-ATATATGT
1 ATATTAATATATGT
4725386 ATAT
1 ATAT
4725390 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:4725942 original size:15 final size:13
Alignment explanation
Indices: 4725912--4725969 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
4725902 TCATGTATAT
4725912 TATTATATATGTA
1 TATTATATATGTA
*
4725925 TATTGTATATGTTCA
1 TATTATATATG-T-A
* *
4725940 TATTAAATATAT-
1 TATTATATATGTA
4725952 TATGTATATATGTA
1 TAT-TATATATGTA
4725966 TATT
1 TATT
4725970 TCTCACGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 3 0.09
13 18 0.51
14 5 0.14
15 9 0.26
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (13 bp):
TATTATATATGTA
Found at i:4729854 original size:2 final size:2
Alignment explanation
Indices: 4729847--4729892 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4729837 AAATATCTAC
4729847 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4729889 AG AG
1 AG AG
4729893 GGGATTCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4732700 original size:2 final size:2
Alignment explanation
Indices: 4732693--4732728 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4732683 ATTTTATTCT
4732693 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4732729 AAAGGGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4738017 original size:152 final size:152
Alignment explanation
Indices: 4737837--4738138 Score: 550
Period size: 152 Copynumber: 2.0 Consensus size: 152
4737827 TTACCACTAA
*
4737837 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTTA
1 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
* *
4737902 GATATAATTTCAAAATTAATAGAAATATTCCATATGCAAAAAAAACGAACACAAGTCCTAAAACA
66 GATATAATTTCAAAATTAATAGAAATATTCCATATACAAAAAAAAAGAACACAAGTCCTAAAACA
4737967 CACAACCAGAACACCTAACCAC
131 CACAACCAGAACACCTAACCAC
4737989 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
1 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
* * *
4738054 TATATAATTTCAAAATTAATGGAAATATTCCATATACAAAAAAAAAGAACACAAGTCCTCAAACA
66 GATATAATTTCAAAATTAATAGAAATATTCCATATACAAAAAAAAAGAACACAAGTCCTAAAACA
4738119 CACAACCAGAACACCTAACC
131 CACAACCAGAACACCTAACC
4738139 GTTGAACCAG
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 144 1.00
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (152 bp):
ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
GATATAATTTCAAAATTAATAGAAATATTCCATATACAAAAAAAAAGAACACAAGTCCTAAAACA
CACAACCAGAACACCTAACCAC
Found at i:4741355 original size:11 final size:11
Alignment explanation
Indices: 4741339--4741368 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4741329 TAGTGTATAA
4741339 AGAGATTTGGC
1 AGAGATTTGGC
4741350 AGAGATTTGGC
1 AGAGATTTGGC
4741361 AGAGATTT
1 AGAGATTT
4741369 ATGCCTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (11 bp):
AGAGATTTGGC
Found at i:4744620 original size:36 final size:35
Alignment explanation
Indices: 4744566--4744634 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
4744556 AAATAGTATT
* * *
4744566 ATTATTTTTATGTATTAAACCAATAATTTATATTTA
1 ATTATTATTATATATTAAA-CAATAATTCATATTTA
* *
4744602 ATTATTATTATATTTTAAACTATAATTCATATT
1 ATTATTATTATATATTAAACAATAATTCATATT
4744635 AAAAGTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 12 0.43
36 16 0.57
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (35 bp):
ATTATTATTATATATTAAACAATAATTCATATTTA
Found at i:4751966 original size:13 final size:13
Alignment explanation
Indices: 4751948--4751972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4751938 AATAATAATC
4751948 TCATGTATCCATG
1 TCATGTATCCATG
4751961 TCATGTATCCAT
1 TCATGTATCCAT
4751973 TATCCAAAAT
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
TCATGTATCCATG
Found at i:4755224 original size:39 final size:39
Alignment explanation
Indices: 4755180--4755256 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
4755170 AATCAAAAAT
4755180 TTATTTTAATATAATATTTATAGTATTATGCATACTTTA
1 TTATTTTAATATAATATTTATAGTATTATGCATACTTTA
*
4755219 TTATTTTAATATAATATTTATAGTATTATGCGTACTTT
1 TTATTTTAATATAATATTTATAGTATTATGCATACTTT
4755257 TATTTGGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (39 bp):
TTATTTTAATATAATATTTATAGTATTATGCATACTTTA
Found at i:4761694 original size:23 final size:23
Alignment explanation
Indices: 4761649--4761694 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4761639 ATATTTTTCA
* *
4761649 TTTAATAATTTTAAAATAGTTAT
1 TTTAATAATATTAAAATAATTAT
4761672 TTTAATAA-ATTAAATATAATTAT
1 TTTAATAATATTAAA-ATAATTAT
4761695 GAAAATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAATAATATTAAAATAATTAT
Found at i:4764437 original size:19 final size:20
Alignment explanation
Indices: 4764402--4764443 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
4764392 GGACCAACAT
4764402 AAAGTTATAAAACATTA-TA
1 AAAGTTATAAAACATTATTA
4764421 AAAGTTATAAATA-ATTATTA
1 AAAGTTATAAA-ACATTATTA
4764441 AAA
1 AAA
4764444 AATTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAGTTATAAAACATTATTA
Found at i:4768534 original size:28 final size:27
Alignment explanation
Indices: 4768481--4768535 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4768471 GGTTATATAT
*
4768481 ATAATATTTTAAAAGTAAATATAATAA
1 ATAATATTTAAAAAGTAAATATAATAA
* *
4768508 ATAATATTTAAATAATTTAATATAATAA
1 ATAATATTTAAA-AAGTAAATATAATAA
4768536 TTTTACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATAATATTTAAAAAGTAAATATAATAA
Found at i:4769022 original size:6 final size:6
Alignment explanation
Indices: 4768969--4769003 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4768959 TATATTATTT
4768969 AATATA AATATA AATATA AATATA AATATA AATAT
1 AATATA AATATA AATATA AATATA AATATA AATAT
4769004 TTATTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:4769163 original size:21 final size:21
Alignment explanation
Indices: 4769113--4769164 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4769103 TCGTTATTTT
* * *
4769113 TAATCTAACCGCTACAGTATC
1 TAATCTCACCACTACAGTAAC
* *
4769134 CAATTTCACCACTACAGTAAC
1 TAATCTCACCACTACAGTAAC
4769155 TAATCTCACC
1 TAATCTCACC
4769165 GCCACCGCTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.33, G:0.06, T:0.27
Consensus pattern (21 bp):
TAATCTCACCACTACAGTAAC
Found at i:4772488 original size:22 final size:21
Alignment explanation
Indices: 4772450--4772493 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
4772440 TTTCTTAAAT
** *
4772450 AATATATATATTTTTATTATA
1 AATATATATATAATTATAATA
4772471 AATATTATATATAATTATAATA
1 AATA-TATATATAATTATAATA
4772493 A
1 A
4772494 TAATCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATATATAATTATAATA
Found at i:4772913 original size:210 final size:210
Alignment explanation
Indices: 4772551--4772966 Score: 832
Period size: 210 Copynumber: 2.0 Consensus size: 210
4772541 TTATTTGAGG
4772551 GAGACTCTCACTCTATTTTTTAGACGAGAAGATCATTCTTTCCATCTTGATCTCTATTGATATCA
1 GAGACTCTCACTCTATTTTTTAGACGAGAAGATCATTCTTTCCATCTTGATCTCTATTGATATCA
4772616 TGTATCAATAAATATCAATTTTATTATTTGTATGTGAAATTAATCCATTGACTGCATCTCAATTT
66 TGTATCAATAAATATCAATTTTATTATTTGTATGTGAAATTAATCCATTGACTGCATCTCAATTT
4772681 CCAACAAGTCTTCGACTACGGCTTCAACTTTTCCAATAATCCATCCGCGTCTTCAAAATGATTGG
131 CCAACAAGTCTTCGACTACGGCTTCAACTTTTCCAATAATCCATCCGCGTCTTCAAAATGATTGG
4772746 CTTTTTGTTTTGGTT
196 CTTTTTGTTTTGGTT
4772761 GAGACTCTCACTCTATTTTTTAGACGAGAAGATCATTCTTTCCATCTTGATCTCTATTGATATCA
1 GAGACTCTCACTCTATTTTTTAGACGAGAAGATCATTCTTTCCATCTTGATCTCTATTGATATCA
4772826 TGTATCAATAAATATCAATTTTATTATTTGTATGTGAAATTAATCCATTGACTGCATCTCAATTT
66 TGTATCAATAAATATCAATTTTATTATTTGTATGTGAAATTAATCCATTGACTGCATCTCAATTT
4772891 CCAACAAGTCTTCGACTACGGCTTCAACTTTTCCAATAATCCATCCGCGTCTTCAAAATGATTGG
131 CCAACAAGTCTTCGACTACGGCTTCAACTTTTCCAATAATCCATCCGCGTCTTCAAAATGATTGG
4772956 CTTTTTGTTTT
196 CTTTTTGTTTT
4772967 TGTTTTTGTT
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 206 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (210 bp):
GAGACTCTCACTCTATTTTTTAGACGAGAAGATCATTCTTTCCATCTTGATCTCTATTGATATCA
TGTATCAATAAATATCAATTTTATTATTTGTATGTGAAATTAATCCATTGACTGCATCTCAATTT
CCAACAAGTCTTCGACTACGGCTTCAACTTTTCCAATAATCCATCCGCGTCTTCAAAATGATTGG
CTTTTTGTTTTGGTT
Found at i:4774805 original size:11 final size:13
Alignment explanation
Indices: 4774779--4774812 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4774769 ATATATTTTT
4774779 TAAAAATTATATA
1 TAAAAATTATATA
*
4774792 TAAAAATAATATA
1 TAAAAATTATATA
*
4774805 AAAAAATT
1 TAAAAATT
4774813 TAATACAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATTATATA
Found at i:4782182 original size:51 final size:51
Alignment explanation
Indices: 4782106--4782222 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
4782096 TGGATCACAT
* *
4782106 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCAACCAC
* * *
4782157 TTATCACTTGTCACTTGTCGCTGATCAGATAAGTATAGCTGAGGCAACGAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCAACCAC
4782208 TTATCACTTGTCACT
1 TTATCACTTGTCACT
4782223 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCAACCAC
Found at i:4784998 original size:24 final size:24
Alignment explanation
Indices: 4784970--4785021 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4784960 TTAGTAGGTC
*
4784970 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
4784994 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4785018 AAAT
1 AAAT
4785022 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4786111 original size:4 final size:4
Alignment explanation
Indices: 4786102--4786147 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
4786092 ATCTACTTCA
4786102 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
4786148 ATCTAGCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4816759 original size:13 final size:14
Alignment explanation
Indices: 4816743--4816776 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4816733 CGAAATTTTT
4816743 TAAATTAAAAAA-A
1 TAAATTAAAAAATA
*
4816756 TAAAATAAAAAATA
1 TAAATTAAAAAATA
4816770 TAAATTA
1 TAAATTA
4816777 TTTAAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATTAAAAAATA
Found at i:4818697 original size:12 final size:12
Alignment explanation
Indices: 4818671--4818709 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4818661 AGTGCCGCCC
* *
4818671 TCTCCTTCTCCT
1 TCTCCTTTTCTT
4818683 TCTCCTTTTCTT
1 TCTCCTTTTCTT
*
4818695 TCTCTTTTTCTT
1 TCTCCTTTTCTT
4818707 TCT
1 TCT
4818710 TTTTCTCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (12 bp):
TCTCCTTTTCTT
Found at i:4833762 original size:71 final size:71
Alignment explanation
Indices: 4833677--4833819 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
4833667 GGGATTAGAA
* *
4833677 AGGTTTCTAGTTAAGCTTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAGAACTAGGAGGTA
1 AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
4833742 GGTTCT
66 GGTTCT
* * * *
4833748 AGGTTTTTATTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGTCATAAAAACTAGGAGTTA
1 AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
4833813 GGTTCT
66 GGTTCT
4833819 A
1 A
4833820 TCTTAACCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.37
Consensus pattern (71 bp):
AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
GGTTCT
Found at i:4837208 original size:26 final size:28
Alignment explanation
Indices: 4837179--4837230 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
4837169 TATTGTCATC
*
4837179 TCATTTTATTTTAT-T-TTATTTTATTT
1 TCATTTCATTTTATGTGTTATTTTATTT
4837205 TCATTTCATTTTATGTGTTATTTTAT
1 TCATTTCATTTTATGTGTTATTTTAT
4837231 GGTTCCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 1 0.04
28 9 0.39
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (28 bp):
TCATTTCATTTTATGTGTTATTTTATTT
Found at i:4837214 original size:31 final size:33
Alignment explanation
Indices: 4837163--4837230 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
4837153 TTTGTACATA
4837163 TTATTATATTGTCATCTCATTTTAT-T-TTATT
1 TTATTATATTGTCATCTCATTTTATGTGTTATT
* * *
4837194 TTATTTTATTTTCATTTCATTTTATGTGTTATT
1 TTATTATATTGTCATCTCATTTTATGTGTTATT
4837227 TTAT
1 TTAT
4837231 GGTTCCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 22 0.69
32 1 0.03
33 9 0.28
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (33 bp):
TTATTATATTGTCATCTCATTTTATGTGTTATT
Found at i:4837247 original size:5 final size:5
Alignment explanation
Indices: 4837181--4837230 Score: 64
Period size: 5 Copynumber: 9.4 Consensus size: 5
4837171 TTGTCATCTC
*
4837181 ATTTT ATTTT ATTTT ATTTT ATTTT CATTTC ATTTT ATGTGTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT AT-T-TT ATTTT
4837229 AT
1 AT
4837231 GGTTCCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 30 0.75
6 6 0.15
7 4 0.10
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:4838383 original size:2 final size:2
Alignment explanation
Indices: 4838376--4838400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4838366 CCAAATAGTT
4838376 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4838401 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4838658 original size:16 final size:15
Alignment explanation
Indices: 4838637--4838701 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
4838627 CCATGCTCTC
4838637 TTTTATTTTTTGAATT
1 TTTTATTTTTT-AATT
*
4838653 TTTTATTTTTTAAAAT
1 TTTTATTTTTT-AATT
*
4838669 TTTAATTTGCTTT-ATT
1 TTTTATTT--TTTAATT
4838685 TTTTATTTTTATAATT
1 TTTTATTTTT-TAATT
4838701 T
1 T
4838702 ATAAATTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 34 0.85
18 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTATTTTTTAATT
Found at i:4838714 original size:31 final size:32
Alignment explanation
Indices: 4838650--4838715 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
4838640 TATTTTTTGA
* *
4838650 ATTTTTTATTTTTTAAAATTTTAATTTGCTTT
1 ATTTTTTATTTTTTAAAATTTTAAATTGATTT
*
4838682 ATTTTTTA-TTTTTATAATTTATAAATT-ATTT
1 ATTTTTTATTTTTTAAAATTT-TAAATTGATTT
4838713 ATT
1 ATT
4838716 GACGTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (32 bp):
ATTTTTTATTTTTTAAAATTTTAAATTGATTT
Found at i:4841065 original size:21 final size:20
Alignment explanation
Indices: 4841037--4841076 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
4841027 ATCTTTAACA
4841037 TTTATATTTATTTT-GTTAAT
1 TTTATA-TTATTTTAGTTAAT
4841057 TTTATTATTATTTTAGTTAA
1 TTTA-TATTATTTTAGTTAA
4841077 ATTTGACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTATATTATTTTAGTTAAT
Found at i:4847291 original size:6 final size:6
Alignment explanation
Indices: 4847280--4847304 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4847270 TAATATTATA
4847280 TAAAAG TAAAAG TAAAAG TAAAAG T
1 TAAAAG TAAAAG TAAAAG TAAAAG T
4847305 GAAATGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (6 bp):
TAAAAG
Found at i:4849453 original size:36 final size:36
Alignment explanation
Indices: 4849385--4849454 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
4849375 GTACTAAAAT
* * *
4849385 TAACAATAAAATAAGAGTTATAAAATATCAAAATAA
1 TAACAACAAAATAAGAGTAATAAAATAGCAAAATAA
*
4849421 TAACAACAAAAT-AGTAGTAATATAATAGCAAAAT
1 TAACAACAAAATAAG-AGTAATAAAATAGCAAAAT
4849455 GTCATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (36 bp):
TAACAACAAAATAAGAGTAATAAAATAGCAAAATAA
Found at i:4860611 original size:12 final size:12
Alignment explanation
Indices: 4860596--4860624 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4860586 ATATATTTAA
4860596 AAATATTAAAAT
1 AAATATTAAAAT
4860608 AAATATTAAAAT
1 AAATATTAAAAT
4860620 AAATA
1 AAATA
4860625 AAAATAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:4860611 original size:24 final size:24
Alignment explanation
Indices: 4860550--4860613 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
4860540 TTTCTTATTT
* *
4860550 TATT-AAATAAAAAAATTTAAAAA
1 TATTAAAATAAATATATTTAAAAA
*
4860573 TATAATAAATCAAATATATTTAAAAA
1 TATTA-AAAT-AAATATATTTAAAAA
4860599 TATTAAAATAAATAT
1 TATTAAAATAAATAT
4860614 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 8 0.24
26 17 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TATTAAAATAAATATATTTAAAAA
Found at i:4860633 original size:21 final size:20
Alignment explanation
Indices: 4860553--4860639 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 20
4860543 CTTATTTTAT
4860553 TAAATAAAAAAAT-TTAAAAA
1 TAAATAAAAAAATATT-AAAA
4860573 TATAATAAATCAAATATATTTAAAA
1 TA-AATAAA--AAA-ATA-TTAAAA
*
4860598 -ATATTAAAATAAATATTAAAA
1 TA-AATAAAA-AAATATTAAAA
*
4860619 TAAATAAAAATAATACTAAAA
1 TAAATAAAAA-AATATTAAAA
4860640 CAATTCTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.05
21 27 0.49
22 5 0.09
23 5 0.09
24 9 0.16
25 4 0.07
26 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATAAAAAAATATTAAAA
Found at i:4861275 original size:13 final size:12
Alignment explanation
Indices: 4861246--4861277 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
4861236 ACCAAAACAG
4861246 GTTTTTAGCGGC
1 GTTTTTAGCGGC
4861258 GTTTTTAGCGGC
1 GTTTTTAGCGGC
4861270 GCTTTTTA
1 G-TTTTTA
4861278 AAAAAACGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (12 bp):
GTTTTTAGCGGC
Found at i:4861367 original size:74 final size:75
Alignment explanation
Indices: 4861262--4861402 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 75
4861252 AGCGGCGTTT
* * *
4861262 TTAGCGGCGCTTTTTAAAAAAACGCCGC-AAAAAGTTATGCTAAACACTGTCATTTTATATTGAG
1 TTAGCGGCGCTTTTTAAAAAAACGCCACAAAAAACTT-TGCAAAACACTGTCATTTTATATTGAG
4861326 CTTAAGCAGTG
65 CTTAAGCAGTG
* * **
4861337 TTAGTGGCGC-TTTTCAAAAAACGCCACAAAAAACTTTGCAAAATGCTGTCATTTTATATTGAGC
1 TTAGCGGCGCTTTTTAAAAAAACGCCACAAAAAACTTTGCAAAACACTGTCATTTTATATTGAGC
4861401 TT
66 TT
4861403 CTAGTGGCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
74 42 0.72
75 16 0.28
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (75 bp):
TTAGCGGCGCTTTTTAAAAAAACGCCACAAAAAACTTTGCAAAACACTGTCATTTTATATTGAGC
TTAAGCAGTG
Found at i:4861903 original size:15 final size:14
Alignment explanation
Indices: 4861883--4861920 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
4861873 TACTATTTAA
4861883 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
4861897 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
4861912 GGTTTATGG
1 GGTTTATGG
4861921 TTCAGGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Done.