Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 279 of 325
Found at i:89444054 original size:41 final size:41
Alignment explanation
Indices: 89443975--89444107 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 41
89443965 ACCAGTTTGG
* * * *
89443975 CACCCAGTGCCTCATTGTAT-AATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAAATCCGAAGTAGTAAATTGA
*
89444015 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATAAATCCGAAGTAGTAAATTGA
* * * ** *
89444056 CACCTAATGTCTCATCGGTTAAA-CC-AA--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAAATCCGAAGTAGTAAATTGA
89444093 CACCCAGTGCCTCAT
1 CACCCAGTGCCTCAT
89444108 TGACTCGAAG
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
37 21 0.27
39 2 0.03
40 19 0.24
41 37 0.47
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATAAATCCGAAGTAGTAAATTGA
Found at i:89450639 original size:13 final size:13
Alignment explanation
Indices: 89450610--89450664 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
89450600 ATAACCAAAC
*
89450610 TTTTTAAAAGT-AA
1 TTTTTAAAA-TCAT
89450623 TTTTTAAAATCAT
1 TTTTTAAAATCAT
89450636 TTTTCTAAAA-CACT
1 TTTT-TAAAATCA-T
89450650 TTTTTAAAATCAT
1 TTTTTAAAATCAT
89450663 TT
1 TT
89450665 CTCAAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 1 0.03
13 24 0.65
14 12 0.32
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTTTAAAATCAT
Found at i:89450671 original size:13 final size:13
Alignment explanation
Indices: 89450622--89450671 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
89450612 TTTAAAAGTA
89450622 ATTTTT-AAAATC
1 ATTTTTCAAAATC
89450634 ATTTTTCTAAAA-C
1 ATTTTTC-AAAATC
*
89450647 ACTTTTTTAAAATC
1 A-TTTTTCAAAATC
*
89450661 ATTTCTCAAAA
1 ATTTTTCAAAA
89450672 ACTTGCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.19
13 14 0.45
14 11 0.35
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTTCAAAATC
Found at i:89451495 original size:24 final size:24
Alignment explanation
Indices: 89451468--89451513 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
89451458 TATTTTTAAT
*
89451468 TTAA-AATTTAACAAGTAATTTATA
1 TTAATAATTTAAAAAGT-ATTTATA
*
89451492 TTAATTATTTAAAAAGTATTTA
1 TTAATAATTTAAAAAGTATTTA
89451514 ACTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TTAATAATTTAAAAAGTATTTATA
Found at i:89457693 original size:9 final size:8
Alignment explanation
Indices: 89457681--89457737 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 8
89457671 AATCAGGAAA
89457681 AAAATTAT
1 AAAATTAT
*
89457689 CAAAAATAT
1 -AAAATTAT
89457698 AAAATTAT
1 AAAATTAT
89457706 GAAAATTGAT
1 -AAAATT-AT
89457716 ATAAACTTAT
1 A-AAA-TTAT
89457726 GAAAATTAT
1 -AAAATTAT
89457735 AAA
1 AAA
89457738 CAAAATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 10 0.24
9 18 0.44
10 10 0.24
11 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (8 bp):
AAAATTAT
Found at i:89457717 original size:20 final size:20
Alignment explanation
Indices: 89457694--89457732 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
89457684 ATTATCAAAA
89457694 ATATAAAATTATGAAAATTG
1 ATATAAAATTATGAAAATTG
*
89457714 ATATAAACTTATGAAAATT
1 ATATAAAATTATGAAAATT
89457733 ATAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
ATATAAAATTATGAAAATTG
Found at i:89465052 original size:3 final size:3
Alignment explanation
Indices: 89465044--89465072 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
89465034 TTTATAAAAC
89465044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
89465073 AATTGCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:89469614 original size:48 final size:48
Alignment explanation
Indices: 89469532--89469625 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
89469522 TTTCTTGGCT
* * *
89469532 TAAAAATGCCTAAGTCAGCCTAATTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
*
89469580 TAAAAACGCCTAAGTTAG-CTCAA-TTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AATTTC-CAACAATAAAGGATTCAAC
89469626 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
Found at i:89472131 original size:48 final size:48
Alignment explanation
Indices: 89472049--89472142 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
89472039 TTTCTTGGCT
* * *
89472049 TAAAAATGCCTAAGTCAGCCTAATTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
*
89472097 TAAAAACGCCTAAGTTAG-CTCAA-TTCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AATTTC-CAACAATAAAGGATTCAAC
89472143 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAATTTCCAACAATAAAGGATTCAACCG
Found at i:89473003 original size:27 final size:27
Alignment explanation
Indices: 89472970--89473026 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
89472960 AAATTTTAAG
89472970 TTTAATTCTTGATGTATTTGCTAAGTT
1 TTTAATTCTTGATGTATTTGCTAAGTT
89472997 TTTAATTCTTGATGTATTTGCTAAGTT
1 TTTAATTCTTGATGTATTTGCTAAGTT
89473024 TTT
1 TTT
89473027 GTAAGCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.58
Consensus pattern (27 bp):
TTTAATTCTTGATGTATTTGCTAAGTT
Found at i:89473800 original size:6 final size:6
Alignment explanation
Indices: 89473769--89473794 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
89473759 AGTATTAATT
89473769 AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
89473795 ACAAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:89474324 original size:40 final size:40
Alignment explanation
Indices: 89474277--89474918 Score: 838
Period size: 40 Copynumber: 16.1 Consensus size: 40
89474267 CATGTTTTGA
* *
89474277 TTGGATCAGCTCTTATGAGCTTCTGTTTAGCGTGTTTCAG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * * *
89474317 TTAGATCAACTCTTATGAGCTTTTGTTTGGTGTGTTT-GAG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCG-G
* *
89474357 TTGGATAAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCAG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* *
89474397 TTGGATTAGCTCTTATGAGCTTCTGTTTGGCATGTTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * *
89474437 TTGGATCAGCTCTTATGAGCTTCTGTTTGGTGTGCTTCGA
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* *
89474477 TTGGATCAACTCTTATGAGCTTCTATTTGGCGTGTTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * *
89474517 TTGGCTCAGCTCTTATGAGCCTCTGTTTGGTGTGTTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * * * *
89474557 TTGGATAAACTCTTATGAGCCTCTGTTTGGCATGTTTCGA
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
*
89474597 TTGGATCAGCTCTTATGAGCCTCTGTTTGGCGTGTTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
*
89474637 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCAG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * * *
89474677 TTGGATCAGATTTTATGAGCTTCTGTTTGGTGTGTTTCGA
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * *
89474717 TTGGATCAACTCTTATGATCTTCTGTTTGGCGTGCTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * * *
89474757 TTGGATAAACTCTTATGAGCTTCTGTTTGACGTGTTTCTG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * **
89474797 TTGGATCAACTCTTATGAGCCTCTGTTTGGCGTGTTTCTA
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * *
89474837 TTGGATCAGCTATTATGAGCTTTTGTTTAGCGTGTTTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
* * * *
89474877 TTGGATTAGCTCTTATGAGCTTCTATCTGGTGTG-TTCGG
1 TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
89474916 TTG
1 TTG
89474919 ATCTGACGAT
Statistics
Matches: 523, Mismatches: 77, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
39 8 0.02
40 515 0.98
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.43
Consensus pattern (40 bp):
TTGGATCAGCTCTTATGAGCTTCTGTTTGGCGTGTTTCGG
Found at i:89476814 original size:19 final size:18
Alignment explanation
Indices: 89476792--89476837 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
89476782 TTTTAGTCTC
89476792 ATTTTTTTATTTGTTTTTT
1 ATTTTTTTATTTG-TTTTT
**
89476811 ATTTTAATATTTGTTTTT
1 ATTTTTTTATTTGTTTTT
*
89476829 ATGTTTTTA
1 ATTTTTTTA
89476838 AATTCTTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (18 bp):
ATTTTTTTATTTGTTTTT
Found at i:89477834 original size:21 final size:20
Alignment explanation
Indices: 89477776--89477839 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
89477766 CCTGATCAAT
89477776 ATACGACACATAAGTGCCTG
1 ATACGACACATAAGTGCCTG
* * * *
89477796 AAATGACACACGAGGTGCCTG
1 ATACGACACA-TAAGTGCCTG
89477817 ATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTG
89477838 AT
1 AT
89477840 TGGCAAAGCC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:89479015 original size:21 final size:20
Alignment explanation
Indices: 89478991--89479029 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
89478981 TCAAATTTCC
89478991 CTTTTCTTCATTCCGTTCTTT
1 CTTTTCTTCATTCC-TTCTTT
* *
89479012 CTTTTTTTCCTTCCTTCT
1 CTTTTCTTCATTCCTTCT
89479030 CTATTTCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.64
Consensus pattern (20 bp):
CTTTTCTTCATTCCTTCTTT
Found at i:89479073 original size:14 final size:15
Alignment explanation
Indices: 89479056--89479088 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
89479046 ATTCTGTTTC
89479056 TTTCCTTTCCTTT-T
1 TTTCCTTTCCTTTAT
*
89479070 TTTCCTTTCTTTTAT
1 TTTCCTTTCCTTTAT
89479085 TTTC
1 TTTC
89479089 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCCTTTCCTTTAT
Found at i:89479257 original size:31 final size:32
Alignment explanation
Indices: 89479201--89479263 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
89479191 TACATTTGTC
*
89479201 ATAATTTAATTTATTTGTTACATAAAAATCTT
1 ATAATATAATTTATTTGTTACATAAAAATCTT
*
89479233 ATAATATAA-TTATTTGATTA-ATAAATATCTT
1 ATAATATAATTTATTTG-TTACATAAAAATCTT
89479264 TTACTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATATAATTTATTTGTTACATAAAAATCTT
Found at i:89479273 original size:18 final size:19
Alignment explanation
Indices: 89479250--89479285 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
89479240 AATTATTTGA
89479250 TTAATAAATATCT-TTTAC
1 TTAATAAATATCTATTTAC
*
89479268 TTAATAATTATCTATTTA
1 TTAATAAATATCTATTTA
89479286 ATAACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATAAATATCTATTTAC
Found at i:89481847 original size:2 final size:2
Alignment explanation
Indices: 89481840--89481874 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
89481830 CATGAGACCT
*
89481840 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
89481875 TTAGATTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:89490238 original size:21 final size:21
Alignment explanation
Indices: 89490213--89490255 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
89490203 AAGAATGATT
89490213 TTTAACTCTTTTCTTAA-TTAA
1 TTTAA-TCTTTTCTTAACTTAA
* *
89490234 TTTAATGTTTTGTTAACTTAA
1 TTTAATCTTTTCTTAACTTAA
89490255 T
1 T
89490256 CAAAAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTAATCTTTTCTTAACTTAA
Found at i:89494359 original size:23 final size:24
Alignment explanation
Indices: 89494333--89494386 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
89494323 TACCAACATC
*
89494333 AATAATCGAAAA-AAAATGAAATA
1 AATAATAGAAAACAAAATGAAATA
* **
89494356 AATAATATAAAACAATTTGAAATA
1 AATAATAGAAAACAAAATGAAATA
89494380 AATAATA
1 AATAATA
89494387 AGATAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24
Consensus pattern (24 bp):
AATAATAGAAAACAAAATGAAATA
Found at i:89494381 original size:24 final size:23
Alignment explanation
Indices: 89494351--89494477 Score: 87
Period size: 24 Copynumber: 5.1 Consensus size: 23
89494341 AAAAAAAATG
89494351 AAATAAATAATATAAAACAATTT
1 AAATAAATAATATAAAACAATTT
* *
89494374 GAAATAAATAATA-AGATA-ATTTT
1 -AAATAAATAATATA-AAACAATTT
*
89494397 AAATAAATAATATATATCAAAAAGGGTTT
1 AAATAAATAATATA-A--AACAA---TTT
* *
89494426 AAATAGATACTATAAAAAGCAATTT
1 AAATAAATAATAT-AAAA-CAATTT
*
89494451 AAAGTAAATAATATAAAATAATTT
1 AAA-TAAATAATATAAAACAATTT
89494475 AAA
1 AAA
89494478 ATCATTAATA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
22 12 0.15
23 7 0.09
24 22 0.27
25 11 0.14
26 9 0.11
27 2 0.02
28 2 0.02
29 15 0.19
30 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (23 bp):
AAATAAATAATATAAAACAATTT
Found at i:89494387 original size:22 final size:22
Alignment explanation
Indices: 89494349--89494408 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
89494339 CGAAAAAAAA
89494349 TGAAATAAATAATATAAAACAATT
1 TGAAATAAAT-A-ATAAAACAATT
* *
89494373 TGAAATAAATAATAAGATAATT
1 TGAAATAAATAATAAAACAATT
*
89494395 TTAAATAAATAATA
1 TGAAATAAATAATA
89494409 TATATCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 22 0.67
23 1 0.03
24 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (22 bp):
TGAAATAAATAATAAAACAATT
Found at i:89494598 original size:29 final size:27
Alignment explanation
Indices: 89494559--89494627 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 27
89494549 GCTAACATAT
* * *
89494559 AAAAAGTTTAAAATAAATAATATGTGAA
1 AAAAAATTTAAAATAAAGAATATAT-AA
*
89494587 AAATAAATTTAAAATAGAGAATATATAA
1 AAA-AAATTTAAAATAAAGAATATATAA
*
89494615 AAAAAATATAAAA
1 AAAAAATTTAAAA
89494628 CGGTTCTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 9 0.26
28 8 0.23
29 18 0.51
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAAAATTTAAAATAAAGAATATATAA
Found at i:89494796 original size:21 final size:18
Alignment explanation
Indices: 89494765--89494803 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
89494755 TAAAATAGAT
89494765 AATATATAAAATAGTTTAA
1 AATATATAAAATA-TTTAA
89494784 AATATATGAAAAATATTTAA
1 AATATAT--AAAATATTTAA
89494804 TAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AATATATAAAATATTTAA
Found at i:89501351 original size:3 final size:3
Alignment explanation
Indices: 89501343--89501374 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
89501333 TACTAAACAT
89501343 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
89501375 TTCAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:89506440 original size:38 final size:38
Alignment explanation
Indices: 89506398--89506474 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
89506388 GAATCTTGAA
89506398 TGTTGTTTTGCTAATACTACCCATTATTGCTACCAATT
1 TGTTGTTTTGCTAATACTACCCATTATTGCTACCAATT
89506436 TGTTGTTTTGCTAATACTACCCATTATTGCTACCAATT
1 TGTTGTTTTGCTAATACTACCCATTATTGCTACCAATT
89506474 T
1 T
89506475 CTTGCTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.45
Consensus pattern (38 bp):
TGTTGTTTTGCTAATACTACCCATTATTGCTACCAATT
Found at i:89506694 original size:26 final size:27
Alignment explanation
Indices: 89506649--89506699 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
89506639 TTTCCCTTTG
*
89506649 GGTTAGATATAATTTGATTAGTATTTA
1 GGTTAGATATAATTTGATTAATATTTA
*
89506676 GGTTAGATGT-ATTTGATTAATATT
1 GGTTAGATATAATTTGATTAATATT
89506700 AATTAGGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (27 bp):
GGTTAGATATAATTTGATTAATATTTA
Found at i:89507432 original size:72 final size:72
Alignment explanation
Indices: 89507286--89507542 Score: 284
Period size: 72 Copynumber: 3.6 Consensus size: 72
89507276 ATCCAAGCCC
* * * * * *
89507286 AAACTTTTCAACCAAGTGAGGACCTCTCTTATAGACATAGCCTCTACCAGCCGTGGTTCCATTAA
1 AAACCTTTCAGCCAGGTGAGGGCCTCTCTTATAGACATAGCATCTGCCAGCCGTGGTTCCATTAA
*
89507351 TGGGAAG
66 TGGGGAG
* * * * * *
89507358 AAACCTTTTAGCTAGGTGCGGGCCTCTCTAATAGACATAGCTTCTGCCAGCCGTGGTTCCGTTAA
1 AAACCTTTCAGCCAGGTGAGGGCCTCTCTTATAGACATAGCATCTGCCAGCCGTGGTTCCATTAA
*
89507423 CGGGGAG
66 TGGGGAG
* * * ***
89507430 AAACCTTTCATCCAGGTGAGGGCCTAT-TTGATAGACATAGCCATC-GCAAATTGTGGTTCCATT
1 AAACCTTTCAGCCAGGTGAGGGCCTCTCTT-ATAGACATAG-CATCTGCCAGCCGTGGTTCCATT
*
89507493 AATGAGGAG
64 AATGGGGAG
*
89507502 AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGC
1 AAACCTTTCAGCCAGGTGAGGGCCTCTCTTATAGACATAGC
89507543 CACCACCGAT
Statistics
Matches: 152, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
71 2 0.01
72 145 0.95
73 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (72 bp):
AAACCTTTCAGCCAGGTGAGGGCCTCTCTTATAGACATAGCATCTGCCAGCCGTGGTTCCATTAA
TGGGGAG
Found at i:89507565 original size:72 final size:72
Alignment explanation
Indices: 89507286--89507577 Score: 257
Period size: 72 Copynumber: 4.1 Consensus size: 72
89507276 ATCCAAGCCC
* * * * *
89507286 AAACTTTTCAACCAAGTGAGGACCTCTCTTATAGACATAGCCTCTACCAGCCGTGGTTCCATTAA
1 AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGCCACCACCAGCCGTGGTTCCATTAA
*
89507351 TG-GGAAG
66 CGAGG-AG
* * * * * ** ** *
89507358 AAACCTTTTAGCTAGGTGCGGGCCTCTCTAATAGACATAGCTTCTGCCAGCCGTGGTTCCGTTAA
1 AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGCCACCACCAGCCGTGGTTCCATTAA
*
89507423 CGGGGAG
66 CGAGGAG
* * * * * * ***
89507430 AAACCTTTCATCCAGGTGAGGGCCTAT-TTGATAGACATAGCCATCGCAAATTGTGGTTCCATTA
1 AAACCTTTCAGCCAAGTGAGGGCCTCTCTT-ATAGACATAGCCACCACCAGCCGTGGTTCCATTA
*
89507494 ATGAGGAG
65 ACGAGGAG
* * *
89507502 AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGCCACCACC-GATCGTGATTTCATTA
1 AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGCCACCACCAG-CCGTGGTTCCATTA
*
89507566 ACGAGGAT
65 ACGAGGAG
89507574 AAAC
1 AAAC
89507578 AATGTGTGAA
Statistics
Matches: 175, Mismatches: 41, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
71 1 0.01
72 170 0.97
73 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (72 bp):
AAACCTTTCAGCCAAGTGAGGGCCTCTCTTATAGACATAGCCACCACCAGCCGTGGTTCCATTAA
CGAGGAG
Found at i:89508123 original size:16 final size:16
Alignment explanation
Indices: 89508074--89508124 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
89508064 TTTAATTTTG
89508074 TAGATAATAGAGTAAATT
1 TAGATAATA-A-TAAATT
* *
89508092 TAAGAAAATTATAAATT
1 T-AGATAATAATAAATT
89508109 TAGATAATAATAAATT
1 TAGATAATAATAAATT
89508125 AAACCCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.46
17 7 0.25
18 2 0.07
19 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
TAGATAATAATAAATT
Found at i:89515005 original size:50 final size:50
Alignment explanation
Indices: 89514881--89515129 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
89514871 GATAATAACA
* * ** * *
89514881 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
89514932 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
89514982 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
89515032 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
89515087 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
89515130 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:89515059 original size:100 final size:104
Alignment explanation
Indices: 89514880--89515129 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
89514870 TGATAATAAC
**
89514880 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
89514945 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
89514982 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
89515045 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
89515087 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
89515130 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:89515245 original size:13 final size:13
Alignment explanation
Indices: 89515224--89515255 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
89515214 GCTTGGATCA
*
89515224 TCATCAAATAAAT
1 TCATAAAATAAAT
89515237 TCATAAAATAAAT
1 TCATAAAATAAAT
89515250 TCATAA
1 TCATAA
89515256 TTGCTGGAAA
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:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:89515502 original size:30 final size:30
Alignment explanation
Indices: 89515467--89515524 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
89515457 CCTCGACTCT
*
89515467 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
89515497 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
89515525 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:89516215 original size:13 final size:13
Alignment explanation
Indices: 89516197--89516222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89516187 GCCCAAACGT
89516197 CGAAATTTTCAAA
1 CGAAATTTTCAAA
89516210 CGAAATTTTCAAA
1 CGAAATTTTCAAA
89516223 AAATCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CGAAATTTTCAAA
Found at i:89517089 original size:21 final size:21
Alignment explanation
Indices: 89517063--89517107 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
89517053 TTTTCTCTTA
89517063 GGGTAGCTTCTT-AGTGAGTTG
1 GGGTAGCTTCTTGA-TGAGTTG
89517084 GGGTAGCTTCTTGATGAGTTG
1 GGGTAGCTTCTTGATGAGTTG
89517105 GGG
1 GGG
89517108 CAACCACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.13, C:0.09, G:0.42, T:0.36
Consensus pattern (21 bp):
GGGTAGCTTCTTGATGAGTTG
Found at i:89522483 original size:44 final size:44
Alignment explanation
Indices: 89522420--89522503 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
89522410 TAATAAGCAA
* **
89522420 ACACTTTAAAACAAACAAATCTATTTCTGTCATGCACATGTCAT
1 ACACTTTAAAACAAACAAATCCATTTCTACCATGCACATGTCAT
* *
89522464 ACACTTTAATACAATCAAATCCATTTCTACCATGCACATG
1 ACACTTTAAAACAAACAAATCCATTTCTACCATGCACATG
89522504 GCAAACAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (44 bp):
ACACTTTAAAACAAACAAATCCATTTCTACCATGCACATGTCAT
Found at i:89522852 original size:199 final size:199
Alignment explanation
Indices: 89522505--89522898 Score: 490
Period size: 199 Copynumber: 2.0 Consensus size: 199
89522495 ATGCACATGG
* * *
89522505 CAAACAATAATCATATTTGAATTAGCATTTAAAAAATATGTTCCACAACTAGGAACTGATTTGTC
1 CAAACAATAATCATATTTGAATCAACATTTAAAAAATATGTTCCACAACTAGGAACTGATTTATC
* ** * *
89522570 ATATTTAAATCCAAATAAGCTTAATATTGTTGGTCATACAAATAGGAACTGATTTATCTCTTTCC
66 ATATTTAAATCCAAAGAAGCTTAATATTAATAGTCATAAAAATAGGAACTGATTTATCTCTTTCC
* * * * * *
89522635 TAAAGATATCTATATGCACATGGCAAACAATATCTTTATAAA-AATCCAAATCTGTCATACACTT
131 TAAAGATATATATATGCACATAGCAAACAATAACTTTA-AAAGAATCCAAACCCGCCATACACTT
89522699 TGATA
195 TGATA
* * * *
89522704 CAAATAATAATCATATTTGAATCAACATTT-AAAAA-ATGTTCTTGACAATTAGGAACTTATTTA
1 CAAACAATAATCATATTTGAATCAACATTTAAAAAATATGTTC--CACAACTAGGAACTGATTTA
* * * * *
89522767 TCATATTTGAA-CCTAAAGAAGCTTGATATTAATAGTCATAAAAATATGAATTGATTTGTCTCTT
64 TCATATTTAAATCC-AAAGAAGCTTAATATTAATAGTCATAAAAATAGGAACTGATTTATCTCTT
* * *
89522831 TCTTAAAGCTATATGTATGCACATAGCAAACAATAACTTTAAAAGAATCCAAACCCGCCATACAC
128 TCCTAAAGATATATATATGCACATAGCAAACAATAACTTTAAAAGAATCCAAACCCGCCATACAC
89522896 TTT
193 TTT
89522899 AATAACCAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
197 6 0.04
198 10 0.06
199 149 0.90
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (199 bp):
CAAACAATAATCATATTTGAATCAACATTTAAAAAATATGTTCCACAACTAGGAACTGATTTATC
ATATTTAAATCCAAAGAAGCTTAATATTAATAGTCATAAAAATAGGAACTGATTTATCTCTTTCC
TAAAGATATATATATGCACATAGCAAACAATAACTTTAAAAGAATCCAAACCCGCCATACACTTT
GATA
Found at i:89522911 original size:34 final size:35
Alignment explanation
Indices: 89522872--89522937 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
89522862 AATAACTTTA
*
89522872 AAAG-AATCCAAACCCGCCATACACTTTAATAACC
1 AAAGAAATCAAAACCCGCCATACACTTTAATAACC
*
89522906 AAAGAAATCAAAATCCGCCATACACTTTAATA
1 AAAGAAATCAAAACCCGCCATACACTTTAATA
89522938 CAAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.47, C:0.27, G:0.06, T:0.20
Consensus pattern (35 bp):
AAAGAAATCAAAACCCGCCATACACTTTAATAACC
Found at i:89523051 original size:25 final size:24
Alignment explanation
Indices: 89523001--89523050 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
89522991 ACAAAGAAAT
89523001 CCAAAAAACCCTAAACTCAAATCC
1 CCAAAAAACCCTAAACTCAAATCC
89523025 CCAAAAAACCCTAAACTCAAATCC
1 CCAAAAAACCCTAAACTCAAATCC
89523049 CC
1 CC
89523051 CTAAGTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (24 bp):
CCAAAAAACCCTAAACTCAAATCC
Found at i:89523324 original size:30 final size:30
Alignment explanation
Indices: 89523288--89523376 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
89523278 CCCTAAAATA
*
89523288 TTAATCCTAATCAATTTTCTTTTCTTCTCC
1 TTAATCCCAATCAATTTTCTTTTCTTCTCC
** *
89523318 TTAATCCCAATTGATCCTTTCTTTT-TTTTCC
1 TTAATCCCAATCAAT--TTTCTTTTCTTCTCC
*
89523349 TTAATCCCAATCCATCTTTTCTTTTCTT
1 TTAATCCCAAT-CA-ATTTTCTTTTCTT
89523377 TTCCCTAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
30 12 0.26
31 24 0.51
32 10 0.21
33 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.01, T:0.54
Consensus pattern (30 bp):
TTAATCCCAATCAATTTTCTTTTCTTCTCC
Found at i:89523353 original size:31 final size:32
Alignment explanation
Indices: 89523303--89523380 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 32
89523293 CCTAATCAAT
* **
89523303 TTTCTTTTCTTCTCCTTAATCCCAATTGATCC
1 TTTCTTTTCTTTTCCTTAATCCCAATCCATCC
*
89523335 TTTCTTTT-TTTTCCTTAATCCCAATCCATCT
1 TTTCTTTTCTTTTCCTTAATCCCAATCCATCC
89523366 TTTCTTTTCTTTTCC
1 TTTCTTTTCTTTTCC
89523381 CTAAACTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 27 0.66
32 14 0.34
ACGTcount: A:0.13, C:0.29, G:0.01, T:0.56
Consensus pattern (32 bp):
TTTCTTTTCTTTTCCTTAATCCCAATCCATCC
Found at i:89523984 original size:27 final size:27
Alignment explanation
Indices: 89523954--89524009 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
89523944 CTATGCTTGA
*
89523954 ATTATTTATTCACATCAAAATTTATAT
1 ATTATTTATTCACAACAAAATTTATAT
89523981 ATTATTTATTCACAACAAAATTTATAT
1 ATTATTTATTCACAACAAAATTTATAT
89524008 AT
1 AT
89524010 AGCCAAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTATTTATTCACAACAAAATTTATAT
Found at i:89525087 original size:2 final size:2
Alignment explanation
Indices: 89525082--89525118 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
89525072 CATATGCTAA
*
89525082 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
89525119 TTATTTCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:89529310 original size:12 final size:12
Alignment explanation
Indices: 89529293--89529325 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
89529283 AAATTCACCC
89529293 ATATTAATTTTT
1 ATATTAATTTTT
89529305 ATATT-ATTTTT
1 ATATTAATTTTT
89529316 ATA-TAATTTT
1 ATATTAATTTT
89529326 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:89529557 original size:22 final size:22
Alignment explanation
Indices: 89529510--89529559 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
89529500 TAATAACAAC
* * *
89529510 AAAATAGTAGTAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
89529532 AAAATAGTAGCAAAATAAGGAG-
1 AAAATAGTAGCAAAATAA-GAGT
89529554 AAAATA
1 AAAATA
89529560 ATAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.16, T:0.20
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:89529877 original size:31 final size:33
Alignment explanation
Indices: 89529842--89529902 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
89529832 TTCTAAAAAA
89529842 TTCAAACAAAT-TATAA-A-TATACATAAATATT
1 TTCAAA-AAATATATAATACTATACATAAATATT
*
89529873 TTCAAAAAATATATAATACTATATATAAAT
1 TTCAAAAAATATATAATACTATACATAAAT
89529903 TACATCGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 11 0.42
32 1 0.04
33 10 0.38
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (33 bp):
TTCAAAAAATATATAATACTATACATAAATATT
Found at i:89529947 original size:16 final size:17
Alignment explanation
Indices: 89529922--89529955 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
89529912 TTTTATATAA
*
89529922 AATAATAAATTA-ATAT
1 AATAAAAAATTACATAT
89529938 AATAAAAAATTACATAT
1 AATAAAAAATTACATAT
89529955 A
1 A
89529956 CCTAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAAAATTACATAT
Found at i:89530730 original size:25 final size:26
Alignment explanation
Indices: 89530682--89530736 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
89530672 CTACACTAAT
* **
89530682 CAAAGTTTAAGTGGGAAACTAAAA-A
1 CAAAGTTTAAGTGGAAAAAAAAAAGA
*
89530707 CAAAGTTTAATTGGAAAAAAAAAAGA
1 CAAAGTTTAAGTGGAAAAAAAAAAGA
89530733 CAAA
1 CAAA
89530737 AAAATGTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.18
Consensus pattern (26 bp):
CAAAGTTTAAGTGGAAAAAAAAAAGA
Found at i:89532612 original size:25 final size:25
Alignment explanation
Indices: 89532565--89532612 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
89532555 TACACTAATC
* * *
89532565 AGAGTTTAAGTGGAAAACTAAAAAT
1 AGAGTTTAACTAGAAAACAAAAAAT
*
89532590 AGAGTTTAACTAGAAAAGAAAAA
1 AGAGTTTAACTAGAAAACAAAAA
89532613 GCTAAAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAGTTTAACTAGAAAACAAAAAAT
Found at i:89534413 original size:21 final size:21
Alignment explanation
Indices: 89534389--89534458 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
89534379 TTGCTAGTAC
89534389 GGTGTGGATAAATCACTCATT
1 GGTGTGGATAAATCACTCATT
* **
89534410 GGTGTAGATAAAAGTTGCT-AGTAT
1 GGTGTGGAT-AAA-TCACTCA-T-T
*
89534434 GGTGTGGATAAACCACTCATT
1 GGTGTGGATAAATCACTCATT
89534455 GGTG
1 GGTG
89534459 CAGATAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
21 13 0.35
22 7 0.19
23 8 0.22
24 9 0.24
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (21 bp):
GGTGTGGATAAATCACTCATT
Found at i:89534431 original size:45 final size:45
Alignment explanation
Indices: 89534379--89534542 Score: 204
Period size: 45 Copynumber: 3.6 Consensus size: 45
89534369 TGTAGACAAA
* *
89534379 TTGCTAGTACGGTGTGGATAAATCACTCATTGGTGTAGATAAAAG
1 TTGCTAGTATGGTGTGGATAAACCACTCATTGGTGTAGATAAAAG
*
89534424 TTGCTAGTATGGTGTGGATAAACCACTCATTGGTGCAGATAAAAG
1 TTGCTAGTATGGTGTGGATAAACCACTCATTGGTGTAGATAAAAG
* * * * * **
89534469 TTGTTAATATGGTATGGATAAACTACTTATCAGTGTAGATAAAAG
1 TTGCTAGTATGGTGTGGATAAACCACTCATTGGTGTAGATAAAAG
* *
89534514 ATGCT-GATATGATGTGGATAAACCACTCA
1 TTGCTAG-TATGGTGTGGATAAACCACTCA
89534543 ACAGTGCAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (45 bp):
TTGCTAGTATGGTGTGGATAAACCACTCATTGGTGTAGATAAAAG
Found at i:89534658 original size:34 final size:34
Alignment explanation
Indices: 89534607--89534751 Score: 145
Period size: 34 Copynumber: 4.3 Consensus size: 34
89534597 AATGGAAAAT
* *
89534607 GTCATGCTTATAGCAGATCAATATGATAGCAATA
1 GTCATGCTTATAACAGATCAATATAATAGCAATA
* * * *
89534641 TTCATGCTTACAACAGATCAATACAGTAGCAATA
1 GTCATGCTTATAACAGATCAATATAATAGCAATA
* * *
89534675 GGCATGCTTATAACATATCAATATAATAACAATA
1 GTCATGCTTATAACAGATCAATATAATAGCAATA
*
89534709 GACATGCTTATAACA-A--AATAGTACAGTAGCAA-A
1 GTCATGCTTATAACAGATCAATA-TA-A-TAGCAATA
89534742 GTCATGCTTA
1 GTCATGCTTA
89534752 ACATGTATTC
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
31 4 0.04
32 2 0.02
33 12 0.13
34 74 0.80
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (34 bp):
GTCATGCTTATAACAGATCAATATAATAGCAATA
Found at i:89534718 original size:68 final size:67
Alignment explanation
Indices: 89534609--89534751 Score: 171
Period size: 68 Copynumber: 2.1 Consensus size: 67
89534599 TGGAAAATGT
* * * ** *
89534609 CATGCTTATAGCAGATCAATATGATAGCAATATTCATGCTTACAAC-AGATCAATACAGTAGCAA
1 CATGCTTATAACAGATCAATATAATAACAATAGACATGCTTACAACAAAAT-AATACAGTAGCAA
89534673 TAGG
65 -AGG
* * *
89534677 CATGCTTATAACATATCAATATAATAACAATAGACATGCTTATAACAAAATAGTACAGTAGCAAA
1 CATGCTTATAACAGATCAATATAATAACAATAGACATGCTTACAACAAAATAATACAGTAGCAAA
*
89534742 GT
66 GG
89534744 CATGCTTA
1 CATGCTTA
89534752 ACATGTATTC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
67 10 0.16
68 51 0.80
69 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (67 bp):
CATGCTTATAACAGATCAATATAATAACAATAGACATGCTTACAACAAAATAATACAGTAGCAAA
GG
Found at i:89537374 original size:19 final size:20
Alignment explanation
Indices: 89537352--89537391 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
89537342 TAAATTAACC
89537352 AATAT-TTTATAAAAATTAA
1 AATATATTTATAAAAATTAA
* *
89537371 AATATATTTGTAATAATTAA
1 AATATATTTATAAAAATTAA
89537391 A
1 A
89537392 TTTTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AATATATTTATAAAAATTAA
Found at i:89548735 original size:25 final size:27
Alignment explanation
Indices: 89548707--89548756 Score: 86
Period size: 25 Copynumber: 1.9 Consensus size: 27
89548697 AGATCAATAA
89548707 ACAAATAATTAAA-TAAAA-TCTAACC
1 ACAAATAATTAAATTAAAAGTCTAACC
89548732 ACAAATAATTAAATTAAAAGTCTAA
1 ACAAATAATTAAATTAAAAGTCTAA
89548757 TTATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 13 0.57
26 5 0.22
27 5 0.22
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (27 bp):
ACAAATAATTAAATTAAAAGTCTAACC
Found at i:89549651 original size:22 final size:22
Alignment explanation
Indices: 89549626--89549667 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
89549616 TTAAAAGATA
89549626 TTTTA-ATAATTAAATTTAATGT
1 TTTTACAT-ATTAAATTTAATGT
*
89549648 TTTTACATTTTAAATTTAAT
1 TTTTACATATTAAATTTAAT
89549668 CTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTACATATTAAATTTAATGT
Found at i:89551250 original size:240 final size:240
Alignment explanation
Indices: 89550827--89551306 Score: 960
Period size: 240 Copynumber: 2.0 Consensus size: 240
89550817 CTCTTTGGAA
89550827 TAATATTCATTCTCCCAATATGATCCTATTTTATCTCATAGTAACCTTTACATATTTTTTCATGA
1 TAATATTCATTCTCCCAATATGATCCTATTTTATCTCATAGTAACCTTTACATATTTTTTCATGA
89550892 AAAGTCAATTACTATCAATTAGTGATCAAGTCATCCATCATAAAGACGGACGACCTGTGGCTACA
66 AAAGTCAATTACTATCAATTAGTGATCAAGTCATCCATCATAAAGACGGACGACCTGTGGCTACA
89550957 TTTACTTTTCATCAACCATGTAATGCCAATGAGAGGATATTATTTACCCATGTTTTAGGCTATGA
131 TTTACTTTTCATCAACCATGTAATGCCAATGAGAGGATATTATTTACCCATGTTTTAGGCTATGA
89551022 ATTCCACTGTTGTGAATAACGTTACATGCTACAAAACTCATACAC
196 ATTCCACTGTTGTGAATAACGTTACATGCTACAAAACTCATACAC
89551067 TAATATTCATTCTCCCAATATGATCCTATTTTATCTCATAGTAACCTTTACATATTTTTTCATGA
1 TAATATTCATTCTCCCAATATGATCCTATTTTATCTCATAGTAACCTTTACATATTTTTTCATGA
89551132 AAAGTCAATTACTATCAATTAGTGATCAAGTCATCCATCATAAAGACGGACGACCTGTGGCTACA
66 AAAGTCAATTACTATCAATTAGTGATCAAGTCATCCATCATAAAGACGGACGACCTGTGGCTACA
89551197 TTTACTTTTCATCAACCATGTAATGCCAATGAGAGGATATTATTTACCCATGTTTTAGGCTATGA
131 TTTACTTTTCATCAACCATGTAATGCCAATGAGAGGATATTATTTACCCATGTTTTAGGCTATGA
89551262 ATTCCACTGTTGTGAATAACGTTACATGCTACAAAACTCATACAC
196 ATTCCACTGTTGTGAATAACGTTACATGCTACAAAACTCATACAC
89551307 CCAATGCACT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 240 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (240 bp):
TAATATTCATTCTCCCAATATGATCCTATTTTATCTCATAGTAACCTTTACATATTTTTTCATGA
AAAGTCAATTACTATCAATTAGTGATCAAGTCATCCATCATAAAGACGGACGACCTGTGGCTACA
TTTACTTTTCATCAACCATGTAATGCCAATGAGAGGATATTATTTACCCATGTTTTAGGCTATGA
ATTCCACTGTTGTGAATAACGTTACATGCTACAAAACTCATACAC
Found at i:89552037 original size:31 final size:32
Alignment explanation
Indices: 89551975--89552037 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
89551965 AACTTAATTA
* ** *
89551975 CCATATGGCACATTAGTGATTGGTTTGATGTG
1 CCATATGGCACAATAGTGATTGGCGTCATGTG
*
89552007 CCATGTGGCACAATA-TGATTGGCGTCATGTG
1 CCATATGGCACAATAGTGATTGGCGTCATGTG
89552038 ACAACTGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (32 bp):
CCATATGGCACAATAGTGATTGGCGTCATGTG
Found at i:89552478 original size:55 final size:56
Alignment explanation
Indices: 89552409--89552544 Score: 152
Period size: 59 Copynumber: 2.4 Consensus size: 56
89552399 TATATTAGTA
* * * * * *
89552409 GTCACCTAATTATTAGTAATTTTTTTGGTCACTCAATTATAAAAA-TTATAAAATT
1 GTCACTTAACTATTAGTAATTTTTTTGGTCACCCAACTATAAAAAGTTACAAAATG
89552464 GTCACTTAACTATTAGTAAATTTTTTTTTTGGTCACCCAACTATAAAAAGTTACAAAATG
1 GTCACTTAACTATTAGT-AA---TTTTTTTGGTCACCCAACTATAAAAAGTTACAAAATG
*
89552524 GTCATTTAACTATT--TAATTTT
1 GTCACTTAACTATTAGTAATTTT
89552545 GTCTTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
54 4 0.06
55 15 0.22
56 2 0.03
57 2 0.03
58 1 0.01
59 24 0.35
60 21 0.30
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (56 bp):
GTCACTTAACTATTAGTAATTTTTTTGGTCACCCAACTATAAAAAGTTACAAAATG
Found at i:89552553 original size:60 final size:58
Alignment explanation
Indices: 89552428--89552544 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 58
89552418 TTATTAGTAA
* * * *
89552428 TTTTTTTGGTCACTCAATTATAAAAATTATAAAATTGTCACTTAACTATTAGTAAATTT
1 TTTTTTTGGTCACCCAACTATAAAAATTACAAAATGGTCACTTAACTATTA-TAAATTT
*
89552487 TTTTTTTGGTCACCCAACTATAAAAAGTTACAAAATGGTCATTTAACTATT-T-AATTT
1 TTTTTTTGGTCACCCAACTATAAAAA-TTACAAAATGGTCACTTAACTATTATAAATTT
89552544 T
1 T
89552545 GTCTTTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 6 0.12
58 1 0.02
59 24 0.46
60 21 0.40
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (58 bp):
TTTTTTTGGTCACCCAACTATAAAAATTACAAAATGGTCACTTAACTATTATAAATTT
Found at i:89557451 original size:17 final size:17
Alignment explanation
Indices: 89557426--89557458 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
89557416 GTGAGAAATT
89557426 TAAGCCAACAAGGGGAC
1 TAAGCCAACAAGGGGAC
*
89557443 TAAGGCAACAAGGGGA
1 TAAGCCAACAAGGGGA
89557459 TCCTTTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.18, G:0.33, T:0.06
Consensus pattern (17 bp):
TAAGCCAACAAGGGGAC
Found at i:89560016 original size:22 final size:23
Alignment explanation
Indices: 89559991--89560042 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
89559981 TGTAGAACTC
89559991 AATAGAA-GTGGTTAAATGTA-AA
1 AATAGAATGTGGTT-AATGTACAA
*
89560013 AATA-AATGTTGTTAATGTACAA
1 AATAGAATGTGGTTAATGTACAA
89560035 AATTAGAA
1 AA-TAGAA
89560043 CTGAGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 8 0.32
22 13 0.52
23 2 0.08
24 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (23 bp):
AATAGAATGTGGTTAATGTACAA
Found at i:89561022 original size:30 final size:30
Alignment explanation
Indices: 89560988--89561048 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
89560978 AAGAAGAGTG
89560988 TGTATTTGCTATTAAGCGGTATAGCATGAA
1 TGTATTTGCTATTAAGCGGTATAGCATGAA
89561018 TGTATTTGCTATTAAGCGGTATAGCATGAA
1 TGTATTTGCTATTAAGCGGTATAGCATGAA
89561048 T
1 T
89561049 ATATCAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (30 bp):
TGTATTTGCTATTAAGCGGTATAGCATGAA
Found at i:89561264 original size:35 final size:35
Alignment explanation
Indices: 89561218--89561287 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
89561208 TCAATACGTA
*
89561218 TGACTGAAGACCATGGAAACCTTGATTCTAAAACT
1 TGACTGAAGACCATGAAAACCTTGATTCTAAAACT
89561253 TGACTGAAGACCATGAAAACCTTGATTCTAAAACT
1 TGACTGAAGACCATGAAAACCTTGATTCTAAAACT
89561288 ATCTGTATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (35 bp):
TGACTGAAGACCATGAAAACCTTGATTCTAAAACT
Found at i:89566133 original size:144 final size:143
Alignment explanation
Indices: 89565525--89566829 Score: 1761
Period size: 144 Copynumber: 9.1 Consensus size: 143
89565515 TATTTTGGTA
*
89565525 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTA-TTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
* *
89565589 TTTAGTACATAATGTTTCAAATGTATTATTTTTGTATTTTTTATATTAATTTAATAAAAAT-T-T
66 TTTAGTACATAATGTTTC-AATGTATTATTTTAGT-TTTTTTATATTAATTTAGTAAAAATCTCT
*
89565652 GATTTTGACCGTTTGTTT
129 GATTTTGGCC--TT-TTT
* * * *
89565670 TTTATTTTATTCTCGGATTTTACTTTTTAAAATAAACTATTTTCATATTTTATTTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
* *
89565735 TTTAGTACATAATGTTCCAAATGTATTATTTTAG-TTTTTTATATTAATTTAATAAAAA-CTCTG
66 TTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTCTG
*
89565798 ATTTTTGCCGTTTATTT
130 ATTTTGGCC--TT-TTT
*
89565815 TTTATTTTATTTTTGGATTTTAGTTTTTTAAAATATACTATTTTCGTATTTTATGTTTTTTATAT
1 TTTATTTTATTTTCGGATTTTA-TTTTTTAAAATATACTATTTTCGTATTTTA--TTTTTTATAT
* * * * * * *
89565880 TATTTTAGTATATAATATTTAAAATGTATTATTTTAGTTTTTTTATATGAATATAGAAAAAAAAC
63 TATTTTAGTACATAATGTTT-CAATGTATTATTTTAGTTTTTTTATATTAATTTAG-TAAAAATC
*
89565945 TCTGATTTTGGCCCTTCTT
126 TCTGATTTTGG-CCTTTTT
* *
89565964 ATT-TTTTATTTTCGAATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
* * *
89566027 TATAGTACATAATGTTTC-ATTTATTATTTTAGTTTTTTTTATATTAATTTAGTAAAAATCTGTG
66 TTTAGTACATAATGTTTCAATGTATTATTTTAG-TTTTTTTATATTAATTTAGTAAAAATCTCTG
*
89566091 ATTTTGGCCGTTTTA
130 ATTTTGGCC-TTTTT
*
89566106 TTTATTTTGTTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
* * * *
89566171 TTTAGTATATAATGTTTCAAATGTATTATTTTAATTTTTTTATATTAATTTAG-AAAAAACTTTG
66 TTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTCTG
89566235 ATTTTGGCC--TTT
130 ATTTTGGCCTTTTT
* * *
89566247 TTTATTTTTTTTTCAGG-TTTTATTTTTTAAGATATATTATTTTCGTATTTTATTTTTTTATATT
1 TTTATTTTATTTTC-GGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTTATATT
*
89566311 ATTTTAGTACATAATGTTTC-ATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTGT
64 ATTTTAGTACATAATGTTTCAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTCT
*
89566375 GGTTTTGGCC-TTTT
129 GATTTTGGCCTTTTT
* *
89566389 TTTATTTTGTTTTCGGATTTT-TTATTTT-AAA-ATACTATTTTTGTATTTTATTTTTTATATTA
1 TTTATTTTATTTTCGGATTTTATT-TTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
*
89566451 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTGT
65 TTTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTCT
*
89566516 GGTTTTGGCC-TTTT
129 GATTTTGGCCTTTTT
* *
89566530 TTTATTTTGTTTTCGGATTTT-TTATTTTAAAATATACTATTTTTGTATTTTATTTTTTTATATT
1 TTTATTTTATTTTCGGATTTTATT-TTTTAAAATATACTATTTTCGTATTTTA-TTTTTTATATT
89566594 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAAAT-T
64 ATTTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTTATATTAATTTAGT-AAAAATCT
89566658 CTGATTTTGGCCGTTTATTT
127 CTGATTTTGGCC--TT-TTT
*
89566678 TTTATTTTATTTTCGGATTTTATTTTTCAAAATATACTATTTTCGTATTTTATTTTTT-TATTAT
1 TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
* * *
89566742 TTTAGTACATAATGTTTCATATGTATTATTTTAGTATATTTATATTAATTTAGTAAAAAAACTCT
66 TTTAGTACATAATGTTTCA-ATGTATTATTTTAGTTTTTTTATATTAATTTAGT-AAAAATCTCT
*
89566807 GATTTTGACCTTTTT
129 GATTTTGGCCTTTTT
89566822 TTTATTTT
1 TTTATTTT
89566830 CGAATTTCTT
Statistics
Matches: 1053, Mismatches: 71, Indels: 73
0.88 0.06 0.06
Matches are distributed among these distances:
139 31 0.03
140 49 0.05
141 159 0.15
142 93 0.09
143 82 0.08
144 186 0.18
145 111 0.11
146 145 0.14
147 49 0.05
148 107 0.10
149 21 0.02
150 7 0.01
151 11 0.01
152 2 0.00
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (143 bp):
TTTATTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTAT
TTTAGTACATAATGTTTCAATGTATTATTTTAGTTTTTTTATATTAATTTAGTAAAAATCTCTGA
TTTTGGCCTTTTT
Found at i:89567333 original size:12 final size:12
Alignment explanation
Indices: 89567318--89567351 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
89567308 CTTCTTCTCC
89567318 TTCTCTTTTTCT
1 TTCTCTTTTTCT
89567330 TTCTCTTTTTCT
1 TTCTCTTTTTCT
*
89567342 TTTTCTTTTT
1 TTCTCTTTTT
89567352 TCTTCCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTCTTTTTCT
Found at i:89567333 original size:18 final size:18
Alignment explanation
Indices: 89567303--89567349 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
89567293 TCCCTCCCTC
*
89567303 CTCTTCTTC-TTCTCCTT
1 CTCTTTTTCTTTCTCCTT
*
89567320 CTCTTTTTCTTTCTCTTT
1 CTCTTTTTCTTTCTCCTT
*
89567338 TTCTTTTTCTTT
1 CTCTTTTTCTTT
89567350 TTTCTTCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
CTCTTTTTCTTTCTCCTT
Found at i:89567531 original size:27 final size:27
Alignment explanation
Indices: 89567493--89567545 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
89567483 AGGAGTCAGC
89567493 GGTGCCGCCTGTGGGGTACCCTCCACT
1 GGTGCCGCCTGTGGGGTACCCTCCACT
89567520 GGTGCCGCCTGTGGGGTACCCTCCAC
1 GGTGCCGCCTGTGGGGTACCCTCCAC
89567546 CCATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.08, C:0.38, G:0.34, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTGTGGGGTACCCTCCACT
Found at i:89567881 original size:40 final size:38
Alignment explanation
Indices: 89567817--89567899 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 38
89567807 TTAAAATATC
* *
89567817 AAAAAATATAAAAACTATTTTAATAATTATAATTTATT
1 AAAAAATAAAAAAAATATTTTAATAATTATAATTTATT
* *
89567855 AAAAATATAAAAAAAATATTTTTAATATTTTTAATTTA--
1 AAAAA-ATAAAAAAAATA-TTTTAATAATTATAATTTATT
89567893 AAAAAAT
1 AAAAAAT
89567900 TAATTAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 2 0.05
38 10 0.26
39 10 0.26
40 17 0.44
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (38 bp):
AAAAAATAAAAAAAATATTTTAATAATTATAATTTATT
Found at i:89568820 original size:44 final size:44
Alignment explanation
Indices: 89568751--89568834 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
89568741 TATCTCCCAG
* * * * * *
89568751 CAATGTAATATCTTTATATCTGATTCGATCCTCTGAACTCAATA
1 CAATGCAACATCTTTATACCCGATTCAATCCTCTAAACTCAATA
89568795 CAATGCAACATCTTTATACCCGATTCAATCCTCTAAACTC
1 CAATGCAACATCTTTATACCCGATTCAATCCTCTAAACTC
89568835 GATATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (44 bp):
CAATGCAACATCTTTATACCCGATTCAATCCTCTAAACTCAATA
Found at i:89571068 original size:25 final size:25
Alignment explanation
Indices: 89570990--89571087 Score: 94
Period size: 25 Copynumber: 3.9 Consensus size: 25
89570980 CAGCTCGTAT
*
89570990 GAGCTTCCCGATAT-ATAGCTTGTGA
1 GAGCTTACCGAT-TCATAGCTTGTGA
** * *
89571015 GAGCTTATTGATTC-TAAACTCGT-A
1 GAGCTTACCGATTCAT-AGCTTGTGA
89571039 TGAGCTTACCGATTCATAGCTTGTGA
1 -GAGCTTACCGATTCATAGCTTGTGA
*
89571065 GAGCATACCGATTCATAGCTTGT
1 GAGCTTACCGATTCATAGCTTGT
89571088 ATGAACATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
24 3 0.05
25 53 0.91
26 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTACCGATTCATAGCTTGTGA
Found at i:89571078 original size:50 final size:50
Alignment explanation
Indices: 89570983--89571078 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
89570973 CAGACCACAG
* * **
89570983 CTCGTATGAGCTTCCCGATATATAGCTTGTGAGAGCTTATTGATTCTAAA
1 CTCGTATGAGCTTACCGATATATAGCTTGTGAGAGCATACCGATTCTAAA
89571033 CTCGTATGAGCTTACCGAT-TCATAGCTTGTGAGAGCATACCGATTC
1 CTCGTATGAGCTTACCGATAT-ATAGCTTGTGAGAGCATACCGATTC
89571079 ATAGCTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.02
50 40 0.98
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
CTCGTATGAGCTTACCGATATATAGCTTGTGAGAGCATACCGATTCTAAA
Found at i:89571090 original size:50 final size:50
Alignment explanation
Indices: 89570981--89571091 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 50
89570971 GACAGACCAC
* * **
89570981 AGCTCGTATGAGCTTCCCGATATATAGCTTGTGAGAGCTTATTGATTCTA
1 AGCTCGTATGAGCTTACCGATATATAGCTTGTGAGAGCATACCGATTCTA
*
89571031 AACTCGTATGAGCTTACCGAT-TCATAGCTTGTGAGAGCATACCGATTC-A
1 AGCTCGTATGAGCTTACCGATAT-ATAGCTTGTGAGAGCATACCGATTCTA
*
89571080 TAGCTTGTATGA
1 -AGCTCGTATGA
89571092 ACATATATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.04
50 50 0.96
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (50 bp):
AGCTCGTATGAGCTTACCGATATATAGCTTGTGAGAGCATACCGATTCTA
Found at i:89571096 original size:25 final size:25
Alignment explanation
Indices: 89571036--89571096 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
89571026 TTCTAAACTC
*
89571036 GTATGAGCTTACCGATTCATAGCTT
1 GTATGAGCATACCGATTCATAGCTT
89571061 GTGA-GAGCATACCGATTCATAGCTT
1 GT-ATGAGCATACCGATTCATAGCTT
*
89571086 GTATGAACATA
1 GTATGAGCATA
89571097 TATGTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (25 bp):
GTATGAGCATACCGATTCATAGCTT
Found at i:89574636 original size:24 final size:22
Alignment explanation
Indices: 89574609--89574652 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
89574599 AAAAAGCAAA
89574609 AAGAAGAACACAAGAAAAAAAACC
1 AAGAAGAA-AC-AGAAAAAAAACC
*
89574633 AAGAAGAAACAGAACAAAAA
1 AAGAAGAAACAGAAAAAAAA
89574653 TAACGTGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.73, C:0.14, G:0.14, T:0.00
Consensus pattern (22 bp):
AAGAAGAAACAGAAAAAAAACC
Found at i:89579594 original size:14 final size:16
Alignment explanation
Indices: 89579563--89579596 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
89579553 TTTCACCTAT
89579563 TCATTCAACACATCTC
1 TCATTCAACACATCTC
* *
89579579 TCATTCCACACTTCTC
1 TCATTCAACACATCTC
89579595 TC
1 TC
89579597 TTTCTTGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (16 bp):
TCATTCAACACATCTC
Found at i:89581511 original size:6 final size:6
Alignment explanation
Indices: 89581500--89581565 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
89581490 TTCTGTTTTA
* * * * *
89581500 TTTATT TTTATT TTTATT TTAAGT TGTACT TTTATT TTTATT GTTGATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT
*
89581549 GTTTTTAT TTTATT TTT
1 -TTTAT-T TTTATT TTT
89581566 GAGACTTATA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 33 0.70
7 13 0.28
8 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:89581533 original size:24 final size:21
Alignment explanation
Indices: 89581495--89581564 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 21
89581485 TAGTTTTCTG
* *
89581495 TTTTATTTATTTTTATTTTTA
1 TTTTAATTGTTTTTATTTTTA
89581516 TTTTAAGTTGTACTTTTATTTTTA
1 TTTTAA-TTGT--TTTTATTTTTA
*
89581540 TTGTTGATTGTTTTTA-TTTTA
1 TT-TTAATTGTTTTTATTTTTA
89581561 TTTT
1 TTTT
89581565 TGAGACTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 2 0.05
21 12 0.29
22 8 0.19
24 17 0.40
25 3 0.07
ACGTcount: A:0.17, C:0.01, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTTAATTGTTTTTATTTTTA
Found at i:89583247 original size:27 final size:28
Alignment explanation
Indices: 89583217--89583273 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
89583207 AAATGAATGG
*
89583217 AATAATTAGATCTAGTTATTA-AATATA
1 AATAATTAGATCTAGCTATTATAATATA
* *
89583244 AATAATTAGTTCTAGCTATTATACTATA
1 AATAATTAGATCTAGCTATTATAATATA
89583272 AA
1 AA
89583274 AAAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (28 bp):
AATAATTAGATCTAGCTATTATAATATA
Found at i:89583793 original size:18 final size:18
Alignment explanation
Indices: 89583772--89583806 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
89583762 AAAGAAAGCA
*
89583772 AATAAATAAATGAAAGAG
1 AATAAACAAATGAAAGAG
*
89583790 AATAAACAATTGAAAGA
1 AATAAACAAATGAAAGA
89583807 AGTGGGATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.14, T:0.17
Consensus pattern (18 bp):
AATAAACAAATGAAAGAG
Found at i:89584717 original size:10 final size:10
Alignment explanation
Indices: 89584702--89584741 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
89584692 TCACAAGTCT
89584702 TGTGATATAG
1 TGTGATATAG
*
89584712 TGTGATATAT
1 TGTGATATAG
89584722 TGTGATATATG
1 TGTGATATA-G
*
89584733 TATGATATA
1 TGTGATATA
89584742 TGTAGGGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (10 bp):
TGTGATATAG
Found at i:89584726 original size:20 final size:21
Alignment explanation
Indices: 89584701--89584742 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
89584691 ATCACAAGTC
*
89584701 TTGTGATATA-GTGTGATATA
1 TTGTGATATATGTATGATATA
89584721 TTGTGATATATGTATGATATA
1 TTGTGATATATGTATGATATA
89584742 T
1 T
89584743 GTAGGGGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (21 bp):
TTGTGATATATGTATGATATA
Found at i:89589038 original size:15 final size:17
Alignment explanation
Indices: 89589004--89589036 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
89588994 ATAATTAATA
89589004 TATTATATTATAAAATT
1 TATTATATTATAAAATT
89589021 TATTAT-TTATAAAATT
1 TATTATATTATAAAATT
89589037 ATACATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATATTATAAAATT
Found at i:89590259 original size:20 final size:19
Alignment explanation
Indices: 89590234--89590322 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
89590224 TCAGGAAAAT
*
89590234 TATAAATATATTAAAATTA
1 TATAAATATATAAAAATTA
*
89590253 GTATAAACATATAAAAATTA
1 -TATAAATATATAAAAATTA
*
89590273 TA-AAATATATAAATAATAA
1 TATAAATATATAAA-AATTA
* *
89590292 TAAAAACT-TATAAATATTA
1 TATAAA-TATATAAAAATTA
*
89590311 TAAAAATATATA
1 TATAAATATATA
89590323 TTTTTATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.19
19 21 0.36
20 26 0.44
21 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (19 bp):
TATAAATATATAAAAATTA
Found at i:89590276 original size:9 final size:9
Alignment explanation
Indices: 89590229--89590322 Score: 68
Period size: 9 Copynumber: 10.0 Consensus size: 9
89590219 AAAAATCAGG
89590229 AAAATTATA
1 AAAATTATA
* *
89590238 AATA-TATT
1 AAAATTATA
89590246 AAAATTAGTA
1 AAAATTA-TA
89590256 TAAACA-TATA
1 -AAA-ATTATA
89590266 AAAATTAT-
1 AAAATTATA
89590274 AAAATATATA
1 AAAAT-TATA
*
89590284 AATAATAATA
1 AA-AATTATA
89590294 AAAACTTATA
1 AAAA-TTATA
*
89590304 AATATTATA
1 AAAATTATA
89590313 AAAATATATA
1 AAAAT-TATA
89590323 TTTTTATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
8 12 0.18
9 25 0.37
10 21 0.31
11 8 0.12
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:89590276 original size:28 final size:30
Alignment explanation
Indices: 89590245--89590318 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 30
89590235 ATAAATATAT
*
89590245 TAAAATTAGTATAAA-CAT-ATAAAAA-TTA
1 TAAAATTA-TATAAATAATAATAAAAACTTA
89590273 TAAAA-TATATAAATAATAATAAAAACTTA
1 TAAAATTATATAAATAATAATAAAAACTTA
*
89590302 TAAATATTATAAAAATA
1 TAAA-ATTATATAAATA
89590319 TATATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.15
27 4 0.10
28 12 0.31
29 7 0.18
30 1 0.03
31 9 0.23
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (30 bp):
TAAAATTATATAAATAATAATAAAAACTTA
Found at i:89590279 original size:38 final size:39
Alignment explanation
Indices: 89590229--89590321 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 39
89590219 AAAAATCAGG
* * *
89590229 AAAATTAT-AAATATATTAAA-ATTAGTATAAACATATA
1 AAAATTATAAAATATATTAAATAATAATAAAAACATATA
*
89590266 AAAATTATAAAATATA-TAAATAATAATAAAAACTTATA
1 AAAATTATAAAATATATTAAATAATAATAAAAACATATA
*
89590304 AATATTATAAAAATATAT
1 AAAATTAT-AAAATATAT
89590322 ATTTTTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 12 0.26
38 27 0.57
39 8 0.17
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (39 bp):
AAAATTATAAAATATATTAAATAATAATAAAAACATATA
Found at i:89590378 original size:29 final size:28
Alignment explanation
Indices: 89590346--89590412 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
89590336 AAAAAACATA
*
89590346 TTTAAAATTTTATAAAAAAT-TAAAATTCT
1 TTTAAAATTATA-AAAAAATATAAAATT-T
*
89590375 TTTAAACTTATAAAAAAATCATAAAATTT
1 TTTAAAATTATAAAAAAAT-ATAAAATTT
*
89590404 ATTAAAATT
1 TTTAAAATT
89590413 GATATAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.22
29 18 0.56
30 7 0.22
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTAAAATTATAAAAAAATATAAAATTT
Found at i:89590980 original size:9 final size:9
Alignment explanation
Indices: 89590968--89591060 Score: 57
Period size: 10 Copynumber: 10.1 Consensus size: 9
89590958 TATCTTTTTT
89590968 AATTTTTAA
1 AATTTTTAA
89590977 AATTTTTAA
1 AATTTTTAA
*
89590986 TATGTTTT--
1 AAT-TTTTAA
*
89590994 TATTTTTAA
1 AATTTTTAA
*
89591003 AATTTATTAT
1 AATTT-TTAA
89591013 AATTTTT-A
1 AATTTTTAA
* *
89591021 CATTATTTAT
1 AATT-TTTAA
*
89591031 AATTTTTATG
1 AATTTTTA-A
89591041 AATTTTTATA
1 AATTTTTA-A
*
89591051 AAATTTTAA
1 AATTTTTAA
89591060 A
1 A
89591061 TATATTTTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
7 4 0.06
8 6 0.09
9 26 0.39
10 31 0.46
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (9 bp):
AATTTTTAA
Found at i:89590982 original size:17 final size:18
Alignment explanation
Indices: 89590968--89591076 Score: 80
Period size: 18 Copynumber: 5.8 Consensus size: 18
89590958 TATCTTTTTT
*
89590968 AATTTTTAAAATTTTTAA
1 AATTTTTATAATTTTTAA
*
89590986 TATGTTTT-T-ATTTTTAA
1 AAT-TTTTATAATTTTTAA
89591003 AATTTATTATAATTTTT-A
1 AATTT-TTATAATTTTTAA
* *
89591021 CATTATTTATAATTTTTATG
1 AATT-TTTATAATTTTTA-A
*
89591041 AATTTTTATAAAATTTTAA
1 AATTTTTAT-AATTTTTAA
89591060 ATATATTTTATTAATTT
1 A-AT-TTTTA-TAATTT
89591077 CATATATGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.03
17 12 0.17
18 18 0.25
19 17 0.24
20 12 0.17
21 9 0.13
22 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (18 bp):
AATTTTTATAATTTTTAA
Found at i:89590984 original size:27 final size:26
Alignment explanation
Indices: 89590953--89591048 Score: 90
Period size: 26 Copynumber: 3.6 Consensus size: 26
89590943 TAAATAGTTC
*
89590953 TTTTATATCTTTTTTAATTTTTAAAAT
1 TTTTATAT-ATTTTTAATTTTTAAAAT
*
89590980 TTTTA-ATATGTTTTTATTTTTAAAAT
1 TTTTATATAT-TTTTAATTTTTAAAAT
*
89591006 TTATTATA-ATTTTTACATTATTTATAAT
1 TT-TTATATATTTTTA-ATT-TTTAAAAT
89591034 TTTTATGA-ATTTTTA
1 TTTTAT-ATATTTTTA
89591049 TAAAATTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.02
26 23 0.39
27 17 0.29
28 18 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTATATATTTTTAATTTTTAAAAT
Found at i:89591055 original size:11 final size:10
Alignment explanation
Indices: 89590968--89591076 Score: 51
Period size: 10 Copynumber: 11.5 Consensus size: 10
89590958 TATCTTTTTT
89590968 AATTTTTA-A
1 AATTTTTATA
89590977 AATTTTTA-A
1 AATTTTTATA
*
89590986 TATGTTTT-T-
1 AAT-TTTTATA
89590995 -ATTTTTA-A
1 AATTTTTATA
89591003 AATTTATTAT-
1 AATTT-TTATA
89591013 AA-TTTT-TA
1 AATTTTTATA
*
89591021 CATTATTTAT-
1 AATT-TTTATA
*
89591031 AATTTTTATG
1 AATTTTTATA
89591041 AATTTTTATA
1 AATTTTTATA
*
89591051 AAATTTTA-A
1 AATTTTTATA
*
89591060 ATATATTTTATT
1 A-AT-TTTTATA
89591072 AATTT
1 AATTT
89591077 CATATATGTT
Statistics
Matches: 78, Mismatches: 7, Indels: 29
0.68 0.06 0.25
Matches are distributed among these distances:
7 5 0.06
8 5 0.06
9 25 0.32
10 34 0.44
11 8 0.10
12 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (10 bp):
AATTTTTATA
Found at i:89591338 original size:10 final size:9
Alignment explanation
Indices: 89591323--89591425 Score: 65
Period size: 9 Copynumber: 11.6 Consensus size: 9
89591313 TCAATATTAA
89591323 TTTTATAATT
1 TTTTATAA-T
*
89591333 TTTTATAGT
1 TTTTATAAT
*
89591342 TTATTA-GAT
1 TT-TTATAAT
89591351 TTTTAT-AT
1 TTTTATAAT
89591359 TTTTATAAT
1 TTTTATAAT
*
89591368 ATTTATAAT
1 TTTTATAAT
89591377 GTTTTATAAGT
1 -TTTTATAA-T
* *
89591388 TTATATAAA
1 TTTTATAAT
89591397 TTTTA-ATAT
1 TTTTATA-AT
*
89591406 TTTGA-AAT
1 TTTTATAAT
89591414 TTTT-T-AT
1 TTTTATAAT
89591421 TTTTA
1 TTTTA
89591426 AAATATTCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
7 6 0.08
8 17 0.23
9 26 0.35
10 24 0.32
11 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:89591371 original size:19 final size:19
Alignment explanation
Indices: 89591323--89591385 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
89591313 TCAATATTAA
89591323 TTTTATAAT-TTTTTATA-
1 TTTTATAATATTTTTATAT
* * *
89591340 GTTTATTAGATTTTTATAT
1 TTTTATAATATTTTTATAT
*
89591359 TTTTATAATATTTATA-AT
1 TTTTATAATATTTTTATAT
89591377 GTTTTATAA
1 -TTTTATAA
89591386 GTTTATATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 6 0.17
18 10 0.28
19 20 0.56
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTATAATATTTTTATAT
Found at i:89593430 original size:17 final size:17
Alignment explanation
Indices: 89593408--89593444 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
89593398 TTAAGTTAAT
89593408 ATTAGATACGTACCCTG
1 ATTAGATACGTACCCTG
89593425 ATTAGATACGTACCCTG
1 ATTAGATACGTACCCTG
89593442 ATT
1 ATT
89593445 TTCTATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (17 bp):
ATTAGATACGTACCCTG
Found at i:89598716 original size:17 final size:19
Alignment explanation
Indices: 89598680--89598723 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
89598670 ATATAATTTT
*
89598680 TAAAAATATATATAATACA
1 TAAAAATATATATAAGACA
89598699 TAAAAATAT-TA-AAGACA
1 TAAAAATATATATAAGACA
*
89598716 TTAAAATA
1 TAAAAATA
89598724 AATTAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
19 9 0.39
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAATATATATAAGACA
Found at i:89599451 original size:15 final size:15
Alignment explanation
Indices: 89599433--89599461 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
89599423 GAAAAATCAT
89599433 AAAAATAAAAAATTG
1 AAAAATAAAAAATTG
89599448 AAAAATAAAAAATT
1 AAAAATAAAAAATT
89599462 AGTTCAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAAATTG
Found at i:89600030 original size:18 final size:16
Alignment explanation
Indices: 89599953--89600030 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 16
89599943 ATTTTTTTTC
*
89599953 ATAATTTTTAATTAAT
1 ATAATTTTTAAATAAT
* *
89599969 AACAAGTTATTTAAA-ATT
1 -ATAA-TT-TTTAAATAAT
*
89599987 AAAATTTATTAAATAAT
1 ATAATTT-TTAAATAAT
*
89600004 ATAAATTTTAAATATAT
1 ATAATTTTTAAATA-AT
89600021 GATAATTTTT
1 -ATAATTTTT
89600031 TATTTATATG
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.02
16 14 0.30
17 15 0.32
18 12 0.26
19 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATTTTTAAATAAT
Found at i:89601356 original size:56 final size:56
Alignment explanation
Indices: 89601295--89601406 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
89601285 TAGGAAATCA
89601295 ATAATGCATACTTAGAGTAAAAAAAAATATAAGTTATGTATATACATGTATAATGG
1 ATAATGCATACTTAGAGTAAAAAAAAATATAAGTTATGTATATACATGTATAATGG
89601351 ATAATGCATACTTAGAGTAAAAAAAAATATAAGTTATGTATATACATGTATAATGG
1 ATAATGCATACTTAGAGTAAAAAAAAATATAAGTTATGTATATACATGTATAATGG
89601407 TATTGAATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.32
Consensus pattern (56 bp):
ATAATGCATACTTAGAGTAAAAAAAAATATAAGTTATGTATATACATGTATAATGG
Found at i:89603235 original size:177 final size:177
Alignment explanation
Indices: 89602936--89603310 Score: 570
Period size: 177 Copynumber: 2.1 Consensus size: 177
89602926 CTACTGCTTA
* *
89602936 GGAGATAAGATCTGCAATTTTTAGCCTGTTACCCTACAGCTTAGGGGGTTAAGGCTCGTATCTTC
1 GGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACAGCTTAAGGGGTTAAGGCTCGTATCTTC
* * * *
89603001 AACCTGCTCTCTTGCTACCTCAGAAAGATAAAGCTGGTGGCTAAAATCTGCTCCATAGTCAATAC
66 AACCTGCTCTCTTGCCACCTCAGAAAGATAAAGCCGGTGGCTAAAACCTGCTCCATAGCCAATAC
* * * * * *
89603066 ATAGAGATAGGACTCTCCATTTTTGATCTGCTTCATAGCCGATACAT
131 ATAGAGATAAGACTCGCAATTTCTGATCTACTCCATAGCCGATACAT
*
89603113 GGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCGTATCTTC
1 GGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACAGCTTAAGGGGTTAAGGCTCGTATCTTC
* * * * * *
89603178 AACCTGCTCTCTTGCCATCTTAGAGAGATAAGGCCGGTGGCTAAAACCTGTTCCATAGCCGATAC
66 AACCTGCTCTCTTGCCACCTCAGAAAGATAAAGCCGGTGGCTAAAACCTGCTCCATAGCCAATAC
*
89603243 ATGGAGATAAGACTCGCAATTTCTGATCTACTCCATAGCCGATACAT
131 ATAGAGATAAGACTCGCAATTTCTGATCTACTCCATAGCCGATACAT
89603290 GGAGATAAGATCTGTAATTTT
1 GGAGATAAGATCTGTAATTTT
89603311 CAGTCTGCTT
Statistics
Matches: 178, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (177 bp):
GGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACAGCTTAAGGGGTTAAGGCTCGTATCTTC
AACCTGCTCTCTTGCCACCTCAGAAAGATAAAGCCGGTGGCTAAAACCTGCTCCATAGCCAATAC
ATAGAGATAAGACTCGCAATTTCTGATCTACTCCATAGCCGATACAT
Found at i:89603452 original size:45 final size:45
Alignment explanation
Indices: 89603229--89603432 Score: 116
Period size: 45 Copynumber: 4.6 Consensus size: 45
89603219 TAAAACCTGT
* * *
89603229 TCCATAGCCGATACATGGAGATAAGACTCGCAATTTCTGATCTAC
1 TCCATAACCGATACATGGAGATAAGACTCGCAATTTCAGATCTGC
* *
89603274 TCCATAGCCGATACATGGAGATAAGA-TCTGTAATTTTCAG-TCTGC
1 TCCATAACCGATACATGGAGATAAGACTC-GCAA-TTTCAGATCTGC
* * * * * * **** * *
89603319 TTCC-TGCAA-C--TTCAAGAACATAATACTTG-TGGCTAAAATCTGC
1 -TCCAT--AACCGATACATGGAGATAAGACTCGCAATTTCAGATCTGC
* * *
89603362 TCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTGATCTGC
1 TCCATAACCGATACATGGAGATAAGACTCGCAATTTCAGATCTGC
* *
89603407 TCTATAACCGATGCATGGAGATAAGA
1 TCCATAACCGATACATGGAGATAAGA
89603433 TCTGTAATTT
Statistics
Matches: 114, Mismatches: 33, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
41 1 0.01
42 6 0.05
43 6 0.05
44 26 0.23
45 65 0.57
46 9 0.08
47 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
TCCATAACCGATACATGGAGATAAGACTCGCAATTTCAGATCTGC
Found at i:89603651 original size:133 final size:133
Alignment explanation
Indices: 89603214--89603610 Score: 634
Period size: 133 Copynumber: 3.0 Consensus size: 133
89603204 GATAAGGCCG
* * * *
89603214 GTGGCTAAAACCTGTTCCATAGCCGATACATGGAGATAAGACTCGCAATTTCTGATCTACTCCAT
1 GTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTGATCTGCTCCAT
* * *
89603279 AGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAACATAATA
66 AGCCGATGCATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGA
89603344 CTT
131 CTT
*
89603347 GTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTGATCTGCTCTAT
1 GTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTGATCTGCTCCAT
* *
89603412 AACCGATGCATGGAGATAAGATCTGTAATTTACAGTCTGCTTCCTGCAACTTCAAGAAGATAAGA
66 AGCCGATGCATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGA
89603477 CTT
131 CTT
* * * * *
89603480 GTGGCTAAAATCTACTCCATAGCCGATACATGGAGATAATACTTGCCA-TTCTTTATTTGCTCCA
1 GTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTC-TGATCTGCTCCA
*
89603544 TAGCCGATGCATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAG
65 TAGCCGATGCATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAG
89603609 AC
130 AC
89603611 CTGTATCTTC
Statistics
Matches: 244, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 3 0.01
133 241 0.99
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (133 bp):
GTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTGATCTGCTCCAT
AGCCGATGCATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGA
CTT
Found at i:89616098 original size:2 final size:2
Alignment explanation
Indices: 89616091--89616126 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
89616081 GTACAAAATT
* *
89616091 CA CA CA CA CA CA CA CA TA CA CA CA TA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
89616127 TAATATGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (2 bp):
CA
Found at i:89617255 original size:23 final size:24
Alignment explanation
Indices: 89617215--89617276 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
89617205 AACCAGAATG
*
89617215 AAGAAAAATAAAA-AGAAT-TGAAA
1 AAGAAAAA-AAAAGAGAATGGGAAA
*
89617238 AAGAAAAAAAAAGGGAATGGGAAA
1 AAGAAAAAAAAAGAGAATGGGAAA
89617262 AATGAAAAAAAAAGA
1 AA-GAAAAAAAAAGA
89617277 ATGAGATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 4 0.12
23 12 0.36
24 6 0.18
25 11 0.33
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (24 bp):
AAGAAAAAAAAAGAGAATGGGAAA
Found at i:89617278 original size:23 final size:22
Alignment explanation
Indices: 89617219--89617279 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 22
89617209 AGAATGAAGA
*
89617219 AAAATAAAAAGAAT-TGAAAAAG
1 AAAA-AAAAAGAATGGGAAAAAG
89617241 AAAAAAAAAGGGAATGGGAAAAATG
1 AAAAAAAAA--GAATGGGAAAAA-G
89617266 AAAAAAAAAGAATG
1 AAAAAAAAAGAATG
89617280 AGATGATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 5 0.15
22 4 0.12
23 9 0.26
24 6 0.18
25 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAGAATGGGAAAAAG
Found at i:89617771 original size:57 final size:58
Alignment explanation
Indices: 89617708--89617825 Score: 193
Period size: 57 Copynumber: 2.1 Consensus size: 58
89617698 CATTTCCAGA
* *
89617708 TCATTTTTATTTTGAAGAAAACCACATTCATTTCCAAATG-TTTCCATTTCTCCATTT
1 TCATTTTCATTTTGAAAAAAACCACATTCATTTCCAAATGTTTTCCATTTCTCCATTT
* *
89617765 TCATTTTCATTTTGAAAAAAACCACATTCATTTCTAAATGTTTTCCATTTCTCCTTTT
1 TCATTTTCATTTTGAAAAAAACCACATTCATTTCCAAATGTTTTCCATTTCTCCATTT
89617823 TCA
1 TCA
89617826 CAATTTCTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
57 37 0.66
58 19 0.34
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (58 bp):
TCATTTTCATTTTGAAAAAAACCACATTCATTTCCAAATGTTTTCCATTTCTCCATTT
Found at i:89620508 original size:21 final size:21
Alignment explanation
Indices: 89620482--89620521 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89620472 AAATCTGTTG
89620482 TTTTCTTCTTCTTTTTTTCTA
1 TTTTCTTCTTCTTTTTTTCTA
* *
89620503 TTTTCTTGTTGTTTTTTTC
1 TTTTCTTCTTCTTTTTTTC
89620522 ATTATTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTCTTCTTCTTTTTTTCTA
Found at i:89620773 original size:13 final size:14
Alignment explanation
Indices: 89620741--89620782 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
89620731 ATTGTATTTT
* *
89620741 TAAAAAAAATTATA
1 TAAAAAAAGTAATA
*
89620755 TAAAAATAGTAATA
1 TAAAAAAAGTAATA
89620769 T-AAAAAAGTAATA
1 TAAAAAAAGTAATA
89620782 T
1 T
89620783 GGTCGGGCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (14 bp):
TAAAAAAAGTAATA
Found at i:89631188 original size:26 final size:27
Alignment explanation
Indices: 89631159--89631212 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
89631149 TTTAGTGATG
*
89631159 ATGGGTTA-TTCCAAGTGTTTAAGCAA
1 ATGGGTTAGTTCAAAGTGTTTAAGCAA
* *
89631185 ATGGGTTAGTTGAAAGTTTTTAAGCAA
1 ATGGGTTAGTTCAAAGTGTTTAAGCAA
89631212 A
1 A
89631213 CGTTTCTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (27 bp):
ATGGGTTAGTTCAAAGTGTTTAAGCAA
Found at i:89633485 original size:15 final size:15
Alignment explanation
Indices: 89633465--89633494 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89633455 AATGTTCATG
89633465 AATAATAAAAAAACA
1 AATAATAAAAAAACA
*
89633480 AATAATAAATAAACA
1 AATAATAAAAAAACA
89633495 TATATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AATAATAAAAAAACA
Found at i:89636586 original size:38 final size:39
Alignment explanation
Indices: 89636536--89636785 Score: 243
Period size: 46 Copynumber: 5.9 Consensus size: 39
89636526 CTGATATGAA
89636536 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
89636575 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-C---T-TG
* * *
89636618 AAATGTATAAGATCATGGTTGAAAGATACCATGGCAACCTG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
89636659 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-C---T-T--G
* *
89636704 ATGTGTAAGACCATAGTTGAAAGATACCATGGCAACGTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
*
89636743 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
89636786 ATGACAGAAA
Statistics
Matches: 178, Mismatches: 10, Indels: 39
0.78 0.04 0.17
Matches are distributed among these distances:
38 66 0.37
39 3 0.02
41 6 0.03
42 1 0.01
43 3 0.02
44 1 0.01
45 3 0.02
46 95 0.53
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTG
Found at i:89636646 original size:46 final size:45
Alignment explanation
Indices: 89636579--89636829 Score: 293
Period size: 46 Copynumber: 5.6 Consensus size: 45
89636569 AACTTGTGTG
*
89636579 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATG-A
*
89636625 TAAGATCATGGTTGAAAGATACCATGGCAACCTG---TG---TG-
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
* * *
89636663 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATG-A
* * *
89636709 TAAGACCATAGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATG-A
*
89636755 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAATGA
* * *
89636800 GTAAGACCATAGTTGAAAGACACTATGGCA
1 -TAAGACCATGGTTGAAAGATACCATGGCA
89636830 TCACGTCAAA
Statistics
Matches: 180, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
38 33 0.18
40 2 0.01
41 2 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 137 0.76
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (45 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
Found at i:89636661 original size:84 final size:84
Alignment explanation
Indices: 89636526--89636829 Score: 387
Period size: 84 Copynumber: 3.5 Consensus size: 84
89636516 AGTGTGCTCT
* * *
89636526 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTATAAGACCATAGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
89636591 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
* *
89636610 CTGATATGAAATGTATAAGATCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTATAAGACCATAGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
89636675 TGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAAC
* * * *
89636694 CTGATATGAGATGTGTAAGACCATAGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
1 CTGATATGAAATGTATAAGACCATAGTTGAAAGATACCATGGCAACCTG---TG---TG--TAAG
89636759 ACCATGGTTGAAAGATACCATGGCAAC
58 ACCATGGTTGAAAGATACCATGGCAAC
* * * *
89636786 ATGACA-GAAAATG-AGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTA-TAAGACCATAGTTGAAAGATACCATGGCA
89636830 TCACGTCAAA
Statistics
Matches: 195, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
84 125 0.64
87 2 0.01
90 1 0.01
91 1 0.01
92 66 0.34
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (84 bp):
CTGATATGAAATGTATAAGACCATAGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
TGAAAGATACCATGGCAAC
Found at i:89637135 original size:23 final size:25
Alignment explanation
Indices: 89637090--89637136 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
89637080 AATAAATATA
*
89637090 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
89637115 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
89637137 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:89638809 original size:22 final size:22
Alignment explanation
Indices: 89638781--89638824 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
89638771 TTTGTGTATC
89638781 CATTTGAGTCCAAATCAAGTTA
1 CATTTGAGTCCAAATCAAGTTA
89638803 CATTTGAGTCCAAATCAAGTTA
1 CATTTGAGTCCAAATCAAGTTA
89638825 ACAGGGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
CATTTGAGTCCAAATCAAGTTA
Found at i:89639737 original size:12 final size:12
Alignment explanation
Indices: 89639720--89639755 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
89639710 TAATAGCTGA
89639720 ATATATATATAC
1 ATATATATATAC
89639732 ATATATATATAC
1 ATATATATATAC
89639744 ATATATAATATA
1 ATATAT-ATATA
89639756 GATGAGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:89646042 original size:11 final size:12
Alignment explanation
Indices: 89646018--89646048 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
89646008 AAAATTTAAA
89646018 ATAAATAATAAT
1 ATAAATAATAAT
89646030 ATAAATAAT-AT
1 ATAAATAATAAT
89646041 ATAAATAA
1 ATAAATAA
89646049 ATAAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:89646044 original size:19 final size:19
Alignment explanation
Indices: 89646017--89646054 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
89646007 TAAAATTTAA
89646017 AATAAAT-AATAATATAAAT
1 AATAAATAAATAA-ATAAAT
*
89646036 AATATATAAATAAATAAAT
1 AATAAATAAATAAATAAAT
89646055 CAAATGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAATAAATAAATAAAT
Done.