Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 12 of 19
Found at i:4768679 original size:30 final size:30
Alignment explanation
Indices: 4768638--4768703 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
4768628 TAGTATATTT
* * * * *
4768638 AATATATTTTTATATTTTTATTTTTAATTA
1 AATAAATTTTTATATATTTATATTAAATCA
4768668 AATAAATTTTTATATATTTATATTAAATCA
1 AATAAATTTTTATATATTTATATTAAATCA
4768698 AATAAA
1 AATAAA
4768704 CTCTTATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
AATAAATTTTTATATATTTATATTAAATCA
Found at i:4768700 original size:26 final size:22
Alignment explanation
Indices: 4768651--4768700 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
4768641 ATATTTTTAT
4768651 ATTTTTATTTTTAATTAAATAA
1 ATTTTTATTTTTAATTAAATAA
4768673 ATTTTTATATATTTATATTAAATCAA
1 ATTTTTAT-T-TTTA-ATTAAAT-AA
4768699 AT
1 AT
4768701 AAACTCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
23 1 0.04
24 4 0.17
25 7 0.29
26 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTATTTTTAATTAAATAA
Found at i:4768711 original size:30 final size:30
Alignment explanation
Indices: 4768647--4768711 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
4768637 TAATATATTT
* * * * * *
4768647 TTATATTTTTATTTTTAATTAAATAAATTT
1 TTATATATTTATATTAAATCAAATAAACTC
4768677 TTATATATTTATATTAAATCAAATAAACTC
1 TTATATATTTATATTAAATCAAATAAACTC
4768707 TTATA
1 TTATA
4768712 ATTAATGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (30 bp):
TTATATATTTATATTAAATCAAATAAACTC
Found at i:4774165 original size:21 final size:21
Alignment explanation
Indices: 4774114--4774153 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4774104 CCGCCACCAT
4774114 CAAATTAATTATAATTAAAAA
1 CAAATTAATTATAATTAAAAA
4774135 CAAATTAATTATAATTAAA
1 CAAATTAATTATAATTAAA
4774154 TGGTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
CAAATTAATTATAATTAAAAA
Found at i:4778800 original size:84 final size:84
Alignment explanation
Indices: 4778659--4778817 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 84
4778649 CGACATTTTA
* * * * *
4778659 TAGGCAATAATTAAAAGATTTCCTAATTGGAGGGTGAAATTGAAACGGAAGGAGAGTTCTGAACA
1 TAGGCAATAATTAAAAGATTTCCTAATAGGAGAGTCAAACTGAAACGAAAGGAGAGTTCTGAACA
4778724 AATTCAATTTATTTGGAAG
66 AATTCAATTTATTTGGAAG
* *
4778743 TAGGCAATAATTAAAAGATTTCCTAGTAGGAGAGTCAAGCTGAAACGAAAGGAGAGTTCTGAACA
1 TAGGCAATAATTAAAAGATTTCCTAATAGGAGAGTCAAACTGAAACGAAAGGAGAGTTCTGAACA
*
4778808 AATTTAATTT
66 AATTCAATTT
4778818 CTTTATTTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (84 bp):
TAGGCAATAATTAAAAGATTTCCTAATAGGAGAGTCAAACTGAAACGAAAGGAGAGTTCTGAACA
AATTCAATTTATTTGGAAG
Found at i:4799023 original size:45 final size:45
Alignment explanation
Indices: 4798939--4799025 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
4798929 TTGCCAATAA
* * * * *
4798939 TTGCATCAATGTGTATCCTGCCACTGATGTACCGGGCAATAAGAC
1 TTGCATCAATGCGTATCCTGCCACAGATATACAGAGCAATAAGAC
* *
4798984 TTGCATCAATGCGTTTCCTGCGACAGATATACAGAGCAATAA
1 TTGCATCAATGCGTATCCTGCCACAGATATACAGAGCAATAA
4799026 AACACTGCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (45 bp):
TTGCATCAATGCGTATCCTGCCACAGATATACAGAGCAATAAGAC
Found at i:4808731 original size:13 final size:13
Alignment explanation
Indices: 4808715--4808739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4808705 AAAGAGTTTT
4808715 TAAAATAAAAAAA
1 TAAAATAAAAAAA
4808728 TAAAATAAAAAA
1 TAAAATAAAAAA
4808740 TAGAAAAATT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:4812376 original size:14 final size:14
Alignment explanation
Indices: 4812359--4812418 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
4812349 AATAAATATT
4812359 AAATAAATAATAAA
1 AAATAAATAATAAA
4812373 AAATTTAAA-AATAAA
1 AAA--TAAATAATAAA
* *
4812388 AATATATATAATTAA
1 AA-ATAAATAATAAA
* *
4812403 AATTTAATAATAAA
1 AAATAAATAATAAA
4812417 AA
1 AA
4812419 TCATTACTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 16 0.44
15 15 0.42
16 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAATAATAAA
Found at i:4818357 original size:2 final size:2
Alignment explanation
Indices: 4818352--4818377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4818342 ATACACACTC
4818352 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4818378 TGAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4821530 original size:4 final size:4
Alignment explanation
Indices: 4821514--4821580 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
4821504 GTTAAATTTG
* * * * * *
4821514 ATAT ATAT GTAT ATAT ATAT ACAT ACAT ACAT ATAT ATAT ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
4821562 ATAT ACAT ACAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATA
4821581 GGTAACTTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:4821547 original size:14 final size:14
Alignment explanation
Indices: 4821516--4821580 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
4821506 TAAATTTGAT
* * *
4821516 ATATATGTATATAT
1 ATATATATACATAC
*
4821530 ATATACATACATAC
1 ATATATATACATAC
*
4821544 ATATATATATATAC
1 ATATATATACATAC
*
4821558 ATACATATACATAC
1 ATATATATACATAC
4821572 ATATATATA
1 ATATATATA
4821581 GGTAACTTCG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:4821549 original size:18 final size:18
Alignment explanation
Indices: 4821526--4821574 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
4821516 ATATATGTAT
4821526 ATATATATACATACATAC
1 ATATATATACATACATAC
*
4821544 ATATATATATATACATAC
1 ATATATATACATACATAC
*
4821562 ATATACATACATA
1 ATATATATACATA
4821575 TATATAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATATATACATACATAC
Found at i:4821551 original size:22 final size:23
Alignment explanation
Indices: 4821523--4821580 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 23
4821513 GATATATATG
4821523 TATATATATATACATAC-ATACA
1 TATATATATATACATACAATACA
4821545 TATATATATATACATACATATACA
1 TATATATATATACATACA-ATACA
*
4821569 TACATATATATA
1 TATATATATATA
4821581 GGTAACTTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 17 0.52
24 16 0.48
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATATATATACATACAATACA
Found at i:4821567 original size:10 final size:10
Alignment explanation
Indices: 4821536--4821576 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
4821526 ATATATATAC
4821536 ATACATACAT
1 ATACATACAT
*
4821546 AT--ATATAT
1 ATACATACAT
4821554 ATACATACAT
1 ATACATACAT
4821564 ATACATACAT
1 ATACATACAT
4821574 ATA
1 ATA
4821577 TATAGGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.26
10 20 0.74
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (10 bp):
ATACATACAT
Found at i:4827305 original size:1 final size:1
Alignment explanation
Indices: 4827301--4827357 Score: 96
Period size: 1 Copynumber: 57.0 Consensus size: 1
4827291 GGTTTTTGCT
* *
4827301 GGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4827358 AAACAGTCCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.02, G:0.96, T:0.02
Consensus pattern (1 bp):
G
Found at i:4827412 original size:1 final size:1
Alignment explanation
Indices: 4827401--4827440 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
4827391 ATGATCTGAC
*
4827401 GGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4827441 ACACAATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:4836113 original size:22 final size:22
Alignment explanation
Indices: 4836088--4836161 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
4836078 ATTGTAAAAC
*
4836088 TAGTTTTTAGGCATTACGTGAT
1 TAGTTTTTAGGTATTACGTGAT
* * *
4836110 TAG-TTATAAGTATTGCGTGAT
1 TAGTTTTTAGGTATTACGTGAT
*
4836131 TGGTTTTTAGGTATTACGTGAT
1 TAGTTTTTAGGTATTACGTGAT
4836153 T-GATTTTTA
1 TAG-TTTTTA
4836162 AGCAATGCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
22 25 0.60
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (22 bp):
TAGTTTTTAGGTATTACGTGAT
Found at i:4836199 original size:23 final size:23
Alignment explanation
Indices: 4836173--4836251 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
4836163 GCAATGCCTA
*
4836173 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* *
4836196 AGTCACGCAATGGCTTACTAACA
1 AGTCACGCAATGCCTTACTAACT
*
4836219 AGTCACGCAATGCC-TACCAACT
1 AGTCACGCAATGCCTTACTAACT
4836241 AGTCACGCAAT
1 AGTCACGCAAT
4836252 ACTTAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 17 0.34
23 33 0.66
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:4836322 original size:21 final size:21
Alignment explanation
Indices: 4836241--4836322 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
4836231 CCTACCAACT
*
4836241 AGTCACGCAATACTTAAAAATA
1 AGTCACGCAATACTT-AAAGTA
* * *
4836263 AGTTACGCAATACTCAAAGTC
1 AGTCACGCAATACTTAAAGTA
* *
4836284 AGTCACGTAAT-GTATAAAGTA
1 AGTCACGCAATACT-TAAAGTA
*
4836305 AATCACGCAATACTTAAA
1 AGTCACGCAATACTTAAA
4836323 AATTAGTCAC
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.02
21 31 0.67
22 14 0.30
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (21 bp):
AGTCACGCAATACTTAAAGTA
Found at i:4836332 original size:22 final size:22
Alignment explanation
Indices: 4836241--4836346 Score: 83
Period size: 22 Copynumber: 4.9 Consensus size: 22
4836231 CCTACCAACT
4836241 AGTCACGCAATACTTAAAAATA
1 AGTCACGCAATACTTAAAAATA
* * * *
4836263 AGTTACGCAATAC-TCAAAGTC
1 AGTCACGCAATACTTAAAAATA
* * *
4836284 AGTCACGTAAT--GTATAAAGTA
1 AGTCACGCAATACTTA-AAAATA
* *
4836305 AATCACGCAATACTTAAAAATT
1 AGTCACGCAATACTTAAAAATA
* *
4836327 AGTCACGCCATACCTAAAAA
1 AGTCACGCAATACTTAAAAA
4836347 ACACCAAAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.02
21 28 0.44
22 33 0.52
23 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (22 bp):
AGTCACGCAATACTTAAAAATA
Found at i:4841378 original size:36 final size:36
Alignment explanation
Indices: 4841325--4841393 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
4841315 TGATTAACAC
4841325 AAACGTTGTTCAATTTTTTATTTTTTTTAAAAAGAT
1 AAACGTTGTTCAATTTTTTATTTTTTTTAAAAAGAT
** * *
4841361 AAACGTTGTTCTTTTTTTTTTTTTTTTTGAAAA
1 AAACGTTGTTCAATTTTTTATTTTTTTTAAAAA
4841394 TTGAGTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.58
Consensus pattern (36 bp):
AAACGTTGTTCAATTTTTTATTTTTTTTAAAAAGAT
Found at i:4851537 original size:181 final size:180
Alignment explanation
Indices: 4851309--4851743 Score: 590
Period size: 181 Copynumber: 2.4 Consensus size: 180
4851299 TTTGTAAAAA
* *
4851309 AAAAAAAAGAAATCATAACAGTCTCCTTAATTTATGAATATCCATGAACATAATCCAATTT-CT-
1 AAAAAAAAGAGATCATAACAGTCTCCTTAATTTATGAAT-TCCATGAACACAATCC-ATTTACTA
* * *
4851372 GAAAATCTAAAACCATTGATGAATCACTCCTCAACACCATCGCTTTTATCACATCCAAGTGTTAA
64 G-AAATCTAAAACCATTAATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAA
* * * ** *
4851437 GCTTGTATTAACATGAACAACTTGCAAAAAGATCGTTGTTCATGGCAATTCAC
128 ACTTGTAATAACATGAACAACCTGCAAAAAGATCACTGTTCATGACAATTCAC
* * *
4851490 AAAATAAAGAGATCATAACAATCTCCTTAATTTATGAATTGCCATGAACACGATCCATTTACTAG
1 AAAAAAAAGAGATCATAACAGTCTCCTTAATTTATGAATT-CCATGAACACAATCCATTTACTAG
* *
4851555 AAATTTAAAACCATTAATGAATCACTCCTCAACACCATCGCTTTGATCACATCCATGTATTAAAC
65 AAATCTAAAACCATTAATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAAC
**
4851620 TTGTAATAACATGAACAACCTGCAAAGGGATCACTGTTCATGACAATTCAC
130 TTGTAATAACATGAACAACCTGCAAAAAGATCACTGTTCATGACAATTCAC
* * *
4851671 AAAACAAAA-AGATCATAACAGTCTTCTTACTTTAT-AAGTCACCATGAACACAATCCATTTACT
1 AAAA-AAAAGAGATCATAACAGTCTCCTTAATTTATGAA-T-TCCATGAACACAATCCATTTACT
4851734 AGAAATCTAA
63 AGAAATCTAA
4851744 GATATATATA
Statistics
Matches: 223, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
180 7 0.03
181 212 0.95
182 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (180 bp):
AAAAAAAAGAGATCATAACAGTCTCCTTAATTTATGAATTCCATGAACACAATCCATTTACTAGA
AATCTAAAACCATTAATGAATCACTCCTCAACACCATCGCTTTGATCACATCCAAGTATTAAACT
TGTAATAACATGAACAACCTGCAAAAAGATCACTGTTCATGACAATTCAC
Found at i:4852351 original size:23 final size:23
Alignment explanation
Indices: 4852324--4852374 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
4852314 GAATAGGTAG
4852324 AGAAAGTGATGGAGCACAACGAA
1 AGAAAGTGATGGAGCACAACGAA
4852347 AGAAAGTGATGGAGCACAACGAA
1 AGAAAGTGATGGAGCACAACGAA
*
4852370 TGAAA
1 AGAAA
4852375 AAGTTGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.49, C:0.12, G:0.29, T:0.10
Consensus pattern (23 bp):
AGAAAGTGATGGAGCACAACGAA
Found at i:4852779 original size:53 final size:53
Alignment explanation
Indices: 4852708--4852816 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
4852698 ACAAATGATC
* *
4852708 TTTGCAACTTATTATGAATTACCTTCATTTCCTTGTATGACATAATTATTCCA
1 TTTGCAACTCATTATGAATTACCTTCATTTCCTTCTATGACATAATTATTCCA
* *
4852761 TTTGCAACTCATTCTGAATTACCTTCATTTCCTTCTATGACATAGTTATTCCA
1 TTTGCAACTCATTATGAATTACCTTCATTTCCTTCTATGACATAATTATTCCA
4852814 TTT
1 TTT
4852817 TTATTTTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (53 bp):
TTTGCAACTCATTATGAATTACCTTCATTTCCTTCTATGACATAATTATTCCA
Found at i:4870259 original size:32 final size:31
Alignment explanation
Indices: 4870179--4870261 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
4870169 TTGAAAAAAT
*
4870179 AAAATTT-TAAAATTTTT-AAAAAATTAA-AA
1 AAAATTTAT-AAATTTTTAAAAAAAATAATAA
* * *
4870208 GAAAAATTATAACTATTTAAAATAAAATAATAA
1 -AAAATTTATAAATTTTTAAAA-AAAATAATAA
4870241 AAAATTTATAAATTTTTAAAA
1 AAAATTTATAAATTTTTAAAA
4870262 CTTTGAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
30 12 0.29
31 4 0.10
32 24 0.57
33 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (31 bp):
AAAATTTATAAATTTTTAAAAAAAATAATAA
Found at i:4872531 original size:17 final size:18
Alignment explanation
Indices: 4872509--4872552 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4872499 TAGATGTTAT
4872509 TATTCAAATTAAG-TGAC
1 TATTCAAATTAAGATGAC
*
4872526 TATTCAGATTAAGACATGAC
1 TATTCAAATTAAG--ATGAC
4872546 TATTCAA
1 TATTCAA
4872553 TAAAAAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 12 0.55
20 10 0.45
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
TATTCAAATTAAGATGAC
Found at i:4877761 original size:17 final size:17
Alignment explanation
Indices: 4877736--4877781 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
4877726 TAGATGTAAT
*
4877736 TATTTAAATTAAGTGAC
1 TATTCAAATTAAGTGAC
4877753 TATTCAAATTAAGTGAC
1 TATTCAAATTAAGTGAC
4877770 TATTCAAATTAA
1 TATTCAAATTAA
4877782 AACATAACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (17 bp):
TATTCAAATTAAGTGAC
Found at i:4891648 original size:2 final size:2
Alignment explanation
Indices: 4891643--4891669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4891633 TATGTGTGCA
4891643 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4891670 ATAATTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4891916 original size:96 final size:96
Alignment explanation
Indices: 4891784--4891974 Score: 292
Period size: 96 Copynumber: 2.0 Consensus size: 96
4891774 ATCACTCACT
* *
4891784 AGACAATGCAAGAAGAAACTGCACTTCTCTTCTTCCAATATTTTTTGAGTAAAATTTTCTCAAAC
1 AGACAATGCAACAAGAAACTGCACTTCTCTTCTTCCAATATTTTTTGAGTAAAAGTTTCTCAAAC
** * *
4891849 ATTTCTAGATTTTAATAAATTTGGTGATGGC
66 ATTTCTAGACATTAAGAAATGTGGTGATGGC
* * * *
4891880 AGACAATGCGACAAGAAACTGTACTTCTTTTCTTCCAATATTTTTTGAGTGAAAGTTTCTCAAAC
1 AGACAATGCAACAAGAAACTGCACTTCTCTTCTTCCAATATTTTTTGAGTAAAAGTTTCTCAAAC
4891945 ATTTCTAGACATTAAGAAATGTGGTGATGG
66 ATTTCTAGACATTAAGAAATGTGGTGATGG
4891975 GTACTATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (96 bp):
AGACAATGCAACAAGAAACTGCACTTCTCTTCTTCCAATATTTTTTGAGTAAAAGTTTCTCAAAC
ATTTCTAGACATTAAGAAATGTGGTGATGGC
Found at i:4895287 original size:32 final size:32
Alignment explanation
Indices: 4895250--4895313 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
4895240 TCACAATAAT
* *
4895250 TTTTTTTATTTTTTATTTTTGCTTG-TTTTTCTA
1 TTTTTTT-TTCTTTATTTCT-CTTGCTTTTTCTA
*
4895283 TTTTTTTTTCTTTCTTTCTCTTGCTTTTTCT
1 TTTTTTTTTCTTTATTTCTCTTGCTTTTTCT
4895314 CACATGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 4 0.15
32 16 0.59
33 7 0.26
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (32 bp):
TTTTTTTTTCTTTATTTCTCTTGCTTTTTCTA
Found at i:4917746 original size:26 final size:26
Alignment explanation
Indices: 4917707--4917757 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
4917697 ATTAGTTAAC
*
4917707 TTTTGAGACGTTACTGGTTGTTATTT
1 TTTTGAGACCTTACTGGTTGTTATTT
*
4917733 TTTTGTGACCTTACTGGTTGTTATT
1 TTTTGAGACCTTACTGGTTGTTATT
4917758 GGAATGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.10, G:0.22, T:0.55
Consensus pattern (26 bp):
TTTTGAGACCTTACTGGTTGTTATTT
Found at i:4918791 original size:20 final size:20
Alignment explanation
Indices: 4918766--4918805 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4918756 ATCATTTATG
4918766 AATTTATTATTATTTTTTCA
1 AATTTATTATTATTTTTTCA
4918786 AATTTATTATTATTTTTTCA
1 AATTTATTATTATTTTTTCA
4918806 TTCTCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTTATTATTATTTTTTCA
Found at i:4931118 original size:21 final size:21
Alignment explanation
Indices: 4931094--4931140 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4931084 GATTAAGGAT
4931094 TATTGGGGCTGAGATTTGCCA
1 TATTGGGGCTGAGATTTGCCA
4931115 TATTGGGGCTGAGATTTGCCA
1 TATTGGGGCTGAGATTTGCCA
*
4931136 CATTG
1 TATTG
4931141 TGGAGTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.34
Consensus pattern (21 bp):
TATTGGGGCTGAGATTTGCCA
Found at i:4933272 original size:2 final size:2
Alignment explanation
Indices: 4933265--4933300 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4933255 GGAACCCAGG
* *
4933265 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4933301 TTTCAATTTC
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:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4938844 original size:32 final size:31
Alignment explanation
Indices: 4938774--4938845 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 31
4938764 TATATGTCTT
* * *
4938774 ATTTTCTTTATTTTTTTTAGTTAGAATTTTAA
1 ATTTTCTTTACTATTTTAAGTTAG-ATTTTAA
4938806 ATTTTTCTTTACTATTTTAAGTTAG-TTTATGAA
1 A-TTTTCTTTACTATTTTAAGTTAGATTT-T-AA
4938839 ATTTTCT
1 ATTTTCT
4938846 ATGTTGTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 3 0.09
32 8 0.24
33 23 0.68
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.62
Consensus pattern (31 bp):
ATTTTCTTTACTATTTTAAGTTAGATTTTAA
Found at i:4938912 original size:2 final size:2
Alignment explanation
Indices: 4938899--4938942 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4938889 CAACATAATC
*
4938899 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4938941 TA
1 TA
4938943 GCTAAACAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4945932 original size:3 final size:3
Alignment explanation
Indices: 4945920--4945949 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4945910 TCTCAATATG
4945920 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4945950 CAAATAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:4951837 original size:62 final size:62
Alignment explanation
Indices: 4951740--4951864 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
4951730 GTTTTAGACA
4951740 AGAATTATTCAGGCTTGCTGATTGACAACAGAGGGGTTCTATTAGGGAATGTAGTACATAGG
1 AGAATTATTCAGGCTTGCTGATTGACAACAGAGGGGTTCTATTAGGGAATGTAGTACATAGG
4951802 AGAATTATTCAGGCTTGCTGATTGACAACAGAGGGGTTCTATTAGGGAATGTAGTACATAGG
1 AGAATTATTCAGGCTTGCTGATTGACAACAGAGGGGTTCTATTAGGGAATGTAGTACATAGG
4951864 A
1 A
4951865 TTTGGTAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (62 bp):
AGAATTATTCAGGCTTGCTGATTGACAACAGAGGGGTTCTATTAGGGAATGTAGTACATAGG
Found at i:4967664 original size:6 final size:6
Alignment explanation
Indices: 4967653--4967685 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4967643 CCAACCATTC
*
4967653 CGGGTG CGGGTG CGGGTG CGGGTG CCGGTG CGG
1 CGGGTG CGGGTG CGGGTG CGGGTG CGGGTG CGG
4967686 CCGAATGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.21, G:0.64, T:0.15
Consensus pattern (6 bp):
CGGGTG
Found at i:4968775 original size:2 final size:2
Alignment explanation
Indices: 4968768--4968794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4968758 TAACTAGGAT
4968768 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4968795 TGCTTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4970522 original size:16 final size:17
Alignment explanation
Indices: 4970501--4970542 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4970491 AAAATGAACT
4970501 ATTTTCTAGAAA-ATG-C
1 ATTTTCT-GAAAGATGAC
4970517 ATTTTCTGAAAGGATGAC
1 ATTTTCTGAAA-GATGAC
4970535 ATTTTCTG
1 ATTTTCTG
4970543 TTGTTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 7 0.30
17 3 0.13
18 9 0.39
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (17 bp):
ATTTTCTGAAAGATGAC
Found at i:4985339 original size:19 final size:21
Alignment explanation
Indices: 4985326--4985375 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4985316 CCGCCGCGGC
4985326 GCCCCCCCCCCGCCCCGGCCG
1 GCCCCCCCCCCGCCCCGGCCG
**
4985347 GCCCCCCCCCC-CCCCCCCCG
1 GCCCCCCCCCCGCCCCGGCCG
*
4985367 GCGCCCCCC
1 GCCCCCCCC
4985376 GACTTCGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.00, C:0.82, G:0.18, T:0.00
Consensus pattern (21 bp):
GCCCCCCCCCCGCCCCGGCCG
Found at i:4985348 original size:23 final size:21
Alignment explanation
Indices: 4985322--4985375 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
4985312 CCGCCCGCCG
*
4985322 CGGCGCCCCCCCCCCGCCCCGGC
1 CGGCGCCCCCCCCCC-CCCC-CC
4985345 CGGC-CCCCCCCCCCCCCCCC
1 CGGCGCCCCCCCCCCCCCCCC
4985365 CGGCGCCCCCC
1 CGGCGCCCCCC
4985376 GACTTCGCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.17
21 10 0.34
22 10 0.34
23 4 0.14
ACGTcount: A:0.00, C:0.80, G:0.20, T:0.00
Consensus pattern (21 bp):
CGGCGCCCCCCCCCCCCCCCC
Found at i:4985354 original size:24 final size:22
Alignment explanation
Indices: 4985327--4985375 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
4985317 CGCCGCGGCG
*
4985327 CCCCCCCCCCGCCCCGGCCGGCCC
1 CCCCCCCCCCCCCCCGG-C-GCCC
4985351 CCCCCCCCCCCCCCCGGCGCCC
1 CCCCCCCCCCCCCCCGGCGCCC
4985373 CCC
1 CCC
4985376 GACTTCGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
23 1 0.04
24 16 0.67
ACGTcount: A:0.00, C:0.84, G:0.16, T:0.00
Consensus pattern (22 bp):
CCCCCCCCCCCCCCCGGCGCCC
Found at i:4985387 original size:14 final size:13
Alignment explanation
Indices: 4985368--4985397 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4985358 CCCCCCCCGG
*
4985368 CGCCCCCCGACTT
1 CGCCCCCCGACCT
4985381 CGCCCCCCGACCT
1 CGCCCCCCGACCT
4985394 CGCC
1 CGCC
4985398 GCGGCGCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.67, G:0.17, T:0.10
Consensus pattern (13 bp):
CGCCCCCCGACCT
Found at i:4985526 original size:2 final size:2
Alignment explanation
Indices: 4985519--4985553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4985509 GTATGCATGT
4985519 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4985554 TAACTCCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4987308 original size:18 final size:18
Alignment explanation
Indices: 4987274--4987308 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4987264 CAACAACTAC
**
4987274 CATTAAAACATGGAAAAG
1 CATTAAAACATCCAAAAG
4987292 CATTAAAACATCCAAAA
1 CATTAAAACATCCAAAA
4987309 TTCAGCAGTT
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:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (18 bp):
CATTAAAACATCCAAAAG
Found at i:5003169 original size:2 final size:2
Alignment explanation
Indices: 5003162--5003191 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5003152 ATCAGTATGC
*
5003162 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5003192 TTTCAGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5023143 original size:10 final size:9
Alignment explanation
Indices: 5023123--5023147 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5023113 TTCCAGATAT
5023123 AAAAGAAAA
1 AAAAGAAAA
5023132 AAAAGAAAA
1 AAAAGAAAA
5023141 AAAAGAA
1 AAAAGAA
5023148 GAAGATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:5023988 original size:14 final size:15
Alignment explanation
Indices: 5023956--5023993 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5023946 ATCCTGAGAA
*
5023956 TTTACATTGGAGCTG
1 TTTAGATTGGAGCTG
5023971 TTTAGATTGGAG-TG
1 TTTAGATTGGAGCTG
5023985 TTTATGATT
1 TTTA-GATT
5023994 TGCTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (15 bp):
TTTAGATTGGAGCTG
Found at i:5027496 original size:19 final size:20
Alignment explanation
Indices: 5027472--5027511 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5027462 CCCTCGAGTC
5027472 CTCGACCTAATTTC-CCCCT
1 CTCGACCTAATTTCTCCCCT
5027491 CTCGACCTAATTTCTCCCCT
1 CTCGACCTAATTTCTCCCCT
5027511 C
1 C
5027512 CTCCTTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.15, C:0.47, G:0.05, T:0.33
Consensus pattern (20 bp):
CTCGACCTAATTTCTCCCCT
Found at i:5030975 original size:2 final size:2
Alignment explanation
Indices: 5030968--5030993 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5030958 ATACAACACG
5030968 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
5030994 ATATTCTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5033209 original size:27 final size:28
Alignment explanation
Indices: 5033177--5033230 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5033167 ACAATTTCTC
* *
5033177 TTTAAAT-ATATATATATATATTATACG
1 TTTAAATAATAAAGATATATATTATACG
5033204 TTTAAATAAATAAAGATATATATTATA
1 TTTAAAT-AATAAAGATATATATTATA
5033231 ATTAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTAAATAATAAAGATATATATTATACG
Found at i:5035910 original size:15 final size:15
Alignment explanation
Indices: 5035890--5035920 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5035880 ATGATTATAA
*
5035890 ACAGGACAGACCTAT
1 ACAGGACAAACCTAT
5035905 ACAGGACAAACCTAT
1 ACAGGACAAACCTAT
5035920 A
1 A
5035921 GATGCATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (15 bp):
ACAGGACAAACCTAT
Found at i:5041616 original size:22 final size:21
Alignment explanation
Indices: 5041565--5041618 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
5041555 TTTTTTTTAA
5041565 TAATTAA-AAAAAATTAAAAT
1 TAATTAATAAAAAATTAAAAT
** *
5041585 TTTTTAAATAAAAAATTATATAT
1 TAATT-AATAAAAAATTA-AAAT
5041608 TAATTAATAAA
1 TAATTAATAAA
5041619 TTAAGTGTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 15 0.58
23 6 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAATAAAAAATTAAAAT
Found at i:5047197 original size:10 final size:10
Alignment explanation
Indices: 5047178--5047243 Score: 66
Period size: 10 Copynumber: 6.7 Consensus size: 10
5047168 TAAAATAAAA
5047178 TATTTAAATAT
1 TATTT-AATAT
5047189 TATTTAATA-
1 TATTTAATAT
5047198 TA-TTAATAT
1 TATTTAATAT
*
5047207 GATTTAACTA-
1 TATTTAA-TAT
* *
5047217 TAATAAATAT
1 TATTTAATAT
5047227 TATTTAATAT
1 TATTTAATAT
5047237 TATTTAA
1 TATTTAA
5047244 ATTTAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
9 5 0.11
10 27 0.60
11 7 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (10 bp):
TATTTAATAT
Found at i:5047202 original size:12 final size:11
Alignment explanation
Indices: 5047178--5047290 Score: 62
Period size: 10 Copynumber: 10.6 Consensus size: 11
5047168 TAAAATAAAA
5047178 TATTTAAATAT
1 TATTTAAATAT
5047189 TATTT-AATA-
1 TATTTAAATAT
5047198 TA-TT-AATAT
1 TATTTAAATAT
* *
5047207 GATTTAACTA-
1 TATTTAAATAT
*
5047217 TA-ATAAATAT
1 TATTTAAATAT
5047227 TATTT-AATAT
1 TATTTAAATAT
5047237 TATTTAAAT-T
1 TATTTAAATAT
* * *
5047247 TAATAAAAAAT
1 TATTTAAATAT
* *
5047258 ATATTTTATATTT
1 -TA-TTTAAATAT
5047271 TAATATTAAATAT
1 T-AT-TTAAATAT
5047284 TATTTAA
1 TATTTAA
5047291 TTATAATAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 22
0.66 0.14 0.19
Matches are distributed among these distances:
8 6 0.08
9 8 0.11
10 26 0.35
11 17 0.23
12 6 0.08
13 12 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (11 bp):
TATTTAAATAT
Found at i:5047231 original size:20 final size:18
Alignment explanation
Indices: 5047176--5047236 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
5047166 AATAAAATAA
*
5047176 AATATTTAAATATTATTT
1 AATATATAAATATTATTT
* *
5047194 AATATATTAATATGATTT
1 AATATATAAATATTATTT
5047212 AACTATAATAAATATTATTT
1 AA-TAT-ATAAATATTATTT
5047232 AATAT
1 AATAT
5047237 TATTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.47
19 6 0.17
20 13 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
AATATATAAATATTATTT
Found at i:5047236 original size:30 final size:28
Alignment explanation
Indices: 5047200--5047291 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
5047190 ATTTAATATA
5047200 TTAATATGATTTAACTATAATAAATATTAT
1 TTAATAT-ATTTAA-TATAATAAATATTAT
* *
5047230 TTAATATTATTTAAATTTAATAAAAAATATAT
1 TTAATA-TATTT-AATATAAT-AAATAT-TAT
*
5047262 TTTATAT-TTTAATAT--TAAATATTAT
1 TTAATATATTTAATATAATAAATATTAT
5047287 TTAAT
1 TTAAT
5047292 TATAATAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
25 7 0.13
26 5 0.10
27 1 0.02
29 4 0.08
30 18 0.35
31 9 0.17
32 8 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TTAATATATTTAATATAATAAATATTAT
Found at i:5047259 original size:23 final size:23
Alignment explanation
Indices: 5047232--5047353 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
5047222 AATATTATTT
*
5047232 AATATTATTTAAATTTAATAAAA
1 AATATTATTTAATTTTAATAAAA
**
5047255 AATA-TATTTTATATTTTAATATTA
1 AATATTA-TTTA-ATTTTAATAAAA
*
5047279 AATATTATTTAATTATAATAAAA
1 AATATTATTTAATTTTAATAAAA
* * *
5047302 AGTA-TACTTATCTTTTAATAAAA
1 AATATTATTTA-ATTTTAATAAAA
*
5047325 TAA-ATTCTTTAATTTTAATAAAA
1 -AATATTATTTAATTTTAATAAAA
5047348 AATATT
1 AATATT
5047354 TTTTTCTCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
22 9 0.12
23 45 0.58
24 22 0.28
25 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATTATTTAATTTTAATAAAA
Found at i:5047290 original size:47 final size:47
Alignment explanation
Indices: 5047227--5047357 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 47
5047217 TAATAAATAT
*
5047227 TATTTAATATTATTTAAATTTAATAAAAAATATATTTTATATTTTAA
1 TATTAAATATTATTTAAATTTAATAAAAAATATATTTTATATTTTAA
* * *
5047274 TATTAAATATTATTT-AATTATAATAAAAAGTATA-CTTATCTTTTAA
1 TATTAAATATTATTTAAATT-TAATAAAAAATATATTTTATATTTTAA
* * *
5047320 TA--AAATAAATTCTTTAATTTTAATAAAAAATATTTTTT
1 TATTAAAT--ATTATTTAAATTTAATAAAAAATATATTTT
5047358 TCTCATCATA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
44 4 0.06
46 34 0.49
47 32 0.46
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (47 bp):
TATTAAATATTATTTAAATTTAATAAAAAATATATTTTATATTTTAA
Found at i:5047421 original size:23 final size:22
Alignment explanation
Indices: 5047232--5047421 Score: 88
Period size: 23 Copynumber: 8.5 Consensus size: 22
5047222 AATATTATTT
5047232 AATATTATTTAAA-TTTAATAAAA
1 AATATT-TTTAAATTTTAAT-AAA
* *
5047255 AATATATTTTATATTTTAATATTA
1 AATAT-TTTTAAATTTTAATA-AA
*
5047279 AATATTATTT-AATTATAATAAA
1 AATATT-TTTAAATTTTAATAAA
** **
5047301 AAGTATACTTATCTTTTAATAAA
1 AA-TATTTTTAAATTTTAATAAA
*
5047324 ATAAATTCTTT-AATTTTAATAAAA
1 A-ATATT-TTTAAATTTTAAT-AAA
* * * *
5047348 AATATTTTT---TTCTCATCAT
1 AATATTTTTAAATTTTAATAAA
* **
5047367 AGTATTTTTATTTTTTAAATAAA
1 AATATTTTTAAATTTT-AATAAA
*
5047390 AA-ATCTTTAAATTTTAATAAA
1 AATATTTTTAAATTTTAATAAA
5047411 AGATATTTTTA
1 A-ATATTTTTA
5047422 TCATTTAACC
Statistics
Matches: 122, Mismatches: 30, Indels: 30
0.67 0.16 0.16
Matches are distributed among these distances:
19 9 0.07
20 5 0.04
21 7 0.06
22 22 0.18
23 56 0.46
24 23 0.19
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATTTTTAAATTTTAATAAA
Found at i:5048026 original size:16 final size:16
Alignment explanation
Indices: 5047994--5048032 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5047984 ATTTTTTTTC
5047994 AAATAAAAATAATAAT
1 AAATAAAAATAATAAT
*
5048010 ATATAATAAATAA-AAT
1 AAATAA-AAATAATAAT
5048026 AAATAAA
1 AAATAAA
5048033 TCAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAAATAATAAT
Found at i:5049678 original size:24 final size:24
Alignment explanation
Indices: 5049640--5049696 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5049630 AAAATAAAAT
* * *
5049640 GATATGGTCCCTAGATC-ATGGATC
1 GATATGATCCATAGA-CGATGGACC
5049664 GATATGATCCATAGACGATGGACC
1 GATATGATCCATAGACGATGGACC
*
5049688 TATATGATC
1 GATATGATC
5049697 GAAAAAGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (24 bp):
GATATGATCCATAGACGATGGACC
Found at i:5068918 original size:17 final size:16
Alignment explanation
Indices: 5068884--5068925 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5068874 ATTCACATTT
* *
5068884 ATAAGTTTTTTTATAA
1 ATAAATTTTTTAATAA
5068900 ATAAATTTTTTAATAA
1 ATAAATTTTTTAATAA
5068916 A-ATAATTTTT
1 ATA-AATTTTT
5068926 AGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATAAATTTTTTAATAA
Found at i:5069185 original size:17 final size:18
Alignment explanation
Indices: 5069165--5069211 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
5069155 AATCTTTTAC
5069165 TTTTTTTAAAAA-AATT-
1 TTTTTTTAAAAAGAATTA
*
5069181 GTTTTTTAAAAAGAATTA
1 TTTTTTTAAAAAGAATTA
5069199 TTTTTTTCAAAAA
1 TTTTTTT-AAAAA
5069212 CTTTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 11 0.42
17 4 0.15
18 6 0.23
19 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTTTTTAAAAAGAATTA
Found at i:5077101 original size:13 final size:13
Alignment explanation
Indices: 5077085--5077129 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5077075 AAAAATAAAA
5077085 ATATTAA-ATAATT
1 ATATTAATAT-ATT
*
5077098 ATATTATTATATT
1 ATATTAATATATT
5077111 ATATTAATATATT
1 ATATTAATATATT
5077124 ATATTA
1 ATATTA
5077130 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 27 0.93
14 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTAATATATT
Found at i:5077109 original size:21 final size:21
Alignment explanation
Indices: 5077085--5077125 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5077075 AAAAATAAAA
5077085 ATATTA-AATAATTATATTATT
1 ATATTATAATAA-TATATTATT
*
5077106 ATATTATATTAATATATTAT
1 ATATTATAATAATATATTAT
5077126 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTATAATAATATATTATT
Found at i:5106187 original size:28 final size:30
Alignment explanation
Indices: 5106150--5106205 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5106140 TAAAAATAAA
5106150 TAAAATTTAAAATATAA-AACAAAATTCTG
1 TAAAATTTAAAATATAATAACAAAATTCTG
* *
5106179 TAAAA-TTAAATTATAATAGCAAAATTC
1 TAAAATTTAAAATATAATAACAAAATTC
5106206 AACTTTATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (30 bp):
TAAAATTTAAAATATAATAACAAAATTCTG
Found at i:5107696 original size:2 final size:2
Alignment explanation
Indices: 5107689--5107716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5107679 CTGTTTTTGG
5107689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5107717 GTAAACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5108691 original size:2 final size:2
Alignment explanation
Indices: 5108684--5108714 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5108674 AATTTAATGA
*
5108684 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5108715 GCTGCACTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5116672 original size:2 final size:2
Alignment explanation
Indices: 5116665--5116692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5116655 AAACGGAATA
5116665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5116693 GAAAACGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5121066 original size:12 final size:12
Alignment explanation
Indices: 5121049--5121073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5121039 TTAAGCCAAA
5121049 ACTTCCTTAAGC
1 ACTTCCTTAAGC
5121061 ACTTCCTTAAGC
1 ACTTCCTTAAGC
5121073 A
1 A
5121074 TTGACCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
ACTTCCTTAAGC
Found at i:5130628 original size:18 final size:18
Alignment explanation
Indices: 5130602--5130636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5130592 ACTACCGATT
*
5130602 ACTCGGATGGCTCTGGTA
1 ACTCAGATGGCTCTGGTA
*
5130620 ACTCAGATGGCTTTGGT
1 ACTCAGATGGCTCTGGT
5130637 GGCTCTGATG
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:0.17, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
ACTCAGATGGCTCTGGTA
Found at i:5130930 original size:15 final size:15
Alignment explanation
Indices: 5130906--5130940 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5130896 AAAAAAATTA
*
5130906 AAAATTATAATTTAT
1 AAAATAATAATTTAT
*
5130921 AAAATAATAATTTTT
1 AAAATAATAATTTAT
5130936 AAAAT
1 AAAAT
5130941 TAATGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATAATAATTTAT
Found at i:5131712 original size:22 final size:20
Alignment explanation
Indices: 5131687--5131736 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
5131677 TTTGTTATAA
*
5131687 TTATTAATAAAATTTATTTAAT
1 TTATTAATAAAA-ATA-TTAAT
*
5131709 TTATAAATAAAAATATTAAT
1 TTATTAATAAAAATATTAAT
5131729 TATATTAA
1 T-TATTAA
5131737 ATGATTTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTAATAAAAATATTAAT
Found at i:5138089 original size:33 final size:33
Alignment explanation
Indices: 5138052--5138117 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5138042 CTTTTGTTCT
*
5138052 TATATTAAAGCTTTTCTTCTCATTGCTTCTTGA
1 TATATTAAAGCTGTTCTTCTCATTGCTTCTTGA
* *
5138085 TATATTGAAGCTGTTGTTCTCATTGCTTCTTGA
1 TATATTAAAGCTGTTCTTCTCATTGCTTCTTGA
5138118 CATACTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.50
Consensus pattern (33 bp):
TATATTAAAGCTGTTCTTCTCATTGCTTCTTGA
Found at i:5139093 original size:58 final size:58
Alignment explanation
Indices: 5139014--5139125 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
5139004 TTTTTTTGGG
* *
5139014 GTTACTCCCTTCCCTCCCTTTCTTTACAGTCAATATAGAAGTTTATCATGTTTTCATA
1 GTTACTCCCTTCCCTCACTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTCATA
5139072 GTTACTTCCC-TCCCTCACTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTT
1 GTTAC-TCCCTTCCCTCACTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTT
5139126 TGTAGCTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
58 47 0.92
59 4 0.08
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.43
Consensus pattern (58 bp):
GTTACTCCCTTCCCTCACTTTCTTTACAGTCAACATAGAAGTTTATCATGTTTTCATA
Found at i:5153984 original size:16 final size:16
Alignment explanation
Indices: 5153963--5153994 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5153953 CTATTATCTG
5153963 TTAAATATTTATATTT
1 TTAAATATTTATATTT
5153979 TTAAATATTTATATTT
1 TTAAATATTTATATTT
5153995 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAAATATTTATATTT
Found at i:5154001 original size:21 final size:22
Alignment explanation
Indices: 5153967--5154047 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 22
5153957 TATCTGTTAA
5153967 ATATTTATATTTTTAAATATTT
1 ATATTTATATTTTTAAATATTT
*
5153989 ATATTTA-ATTTTTTAATATTT
1 ATATTTATATTTTTAAATATTT
*
5154010 -TAATTT-TATTAATTT-AATTTTT
1 AT-ATTTATATT--TTTAAATATTT
*
5154032 ATATGATATATTTTTA
1 ATAT-TTATATTTTTA
5154048 TGTAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
20 1 0.02
21 20 0.42
22 18 0.38
23 5 0.10
24 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (22 bp):
ATATTTATATTTTTAAATATTT
Found at i:5154009 original size:15 final size:14
Alignment explanation
Indices: 5153986--5154035 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 14
5153976 TTTTTAAATA
5153986 TTTATATTTAATTT
1 TTTATATTTAATTT
5154000 TTTAATATTTTAATTT
1 TTT-ATA-TTTAATTT
5154016 TATTA-ATTTAA-TT
1 T-TTATATTTAATTT
5154029 TTTATAT
1 TTTATAT
5154036 GATATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.09
13 5 0.16
14 8 0.25
15 4 0.12
16 10 0.31
17 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATTTAATTT
Found at i:5154578 original size:5 final size:5
Alignment explanation
Indices: 5154564--5154618 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
5154554 TTGAAATCCA
* * * *
5154564 AAAAG AAAAG GAAAG AAAAG AATAG AAAAG AACAG ATAAG AAAAG AAAATG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G
5154615 AAAA
1 AAAA
5154619 TGGAAGAGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
5 36 0.88
6 5 0.12
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:5169778 original size:1 final size:1
Alignment explanation
Indices: 5169774--5169811 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
5169764 GGGAAGAGGT
* *
5169774 GGGGGTGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
5169812 AGTAAAGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (1 bp):
G
Found at i:5174547 original size:16 final size:17
Alignment explanation
Indices: 5174523--5174555 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5174513 GTCAAGCATA
*
5174523 CATATTCCAC-ATCTTT
1 CATACTCCACAATCTTT
5174539 CATACTCCACAATCTTT
1 CATACTCCACAATCTTT
5174556 GATTCTCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (17 bp):
CATACTCCACAATCTTT
Found at i:5180759 original size:54 final size:54
Alignment explanation
Indices: 5180700--5180805 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
5180690 TATCTTTCCT
* * * *
5180700 ATTCAGGTGTATGAAGTGTTCAATAATATAACTTACTATGTGAAAGTTCCTCCC
1 ATTCAGGTGTATGAACTGTGCAATAATATAACTTACCATATGAAAGTTCCTCCC
*
5180754 ATTCAGGTGTATGAACTGTGCAATAATATAACTTACCATATGAAATTTCCTC
1 ATTCAGGTGTATGAACTGTGCAATAATATAACTTACCATATGAAAGTTCCTC
5180806 TACTATCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (54 bp):
ATTCAGGTGTATGAACTGTGCAATAATATAACTTACCATATGAAAGTTCCTCCC
Found at i:5186548 original size:7 final size:7
Alignment explanation
Indices: 5186536--5186574 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
5186526 AAGACTCTGA
5186536 AGAGACG
1 AGAGACG
5186543 AGAGACG
1 AGAGACG
5186550 AGAGACG
1 AGAGACG
*
5186557 AGTGACG
1 AGAGACG
5186564 AGAGACG
1 AGAGACG
5186571 AGAG
1 AGAG
5186575 GTATATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.44, T:0.03
Consensus pattern (7 bp):
AGAGACG
Found at i:5191397 original size:2 final size:2
Alignment explanation
Indices: 5191392--5191417 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5191382 AAAAGAGCAG
5191392 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5191418 CTAATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5192397 original size:24 final size:22
Alignment explanation
Indices: 5192369--5192413 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
5192359 TTATATTAAA
5192369 AAAAAGATTATTACTCGTTATATTG
1 AAAAA-ATT-TTA-TCGTTATATTG
*
5192394 AAAAAATTTTATTGTTATAT
1 AAAAAATTTTATCGTTATAT
5192414 GTTATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 3 0.16
25 5 0.26
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (22 bp):
AAAAAATTTTATCGTTATATTG
Found at i:5192440 original size:33 final size:33
Alignment explanation
Indices: 5192394--5192462 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5192384 CGTTATATTG
** * *
5192394 AAAAAATTTTATTGTTATATGTTAT-TTTGAAAA
1 AAAAAATCATATTGTTACATGTCATATTT-AAAA
5192427 AAAAAATCATATTGTTACATGTCATATTTAAAA
1 AAAAAATCATATTGTTACATGTCATATTTAAAA
5192460 AAA
1 AAA
5192463 TTTTGCTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (33 bp):
AAAAAATCATATTGTTACATGTCATATTTAAAA
Found at i:5200517 original size:17 final size:17
Alignment explanation
Indices: 5200495--5200527 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5200485 TGGTGCAAAG
5200495 AGGGTTGGAAGATTTTT
1 AGGGTTGGAAGATTTTT
*
5200512 AGGGTTTGAAGATTTT
1 AGGGTTGGAAGATTTT
5200528 CATTCAACAC
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:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (17 bp):
AGGGTTGGAAGATTTTT
Found at i:5203452 original size:14 final size:15
Alignment explanation
Indices: 5203435--5203480 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
5203425 ATTATAATAA
5203435 TTTAATT-TTTTAAT
1 TTTAATTATTTTAAT
5203449 TTTAAAAATTATTTTAA-
1 TTT---AATTATTTTAAT
5203466 TTTAATTATTTTAAT
1 TTTAATTATTTTAAT
5203481 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 14 0.52
17 7 0.26
18 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATTATTTTAAT
Found at i:5203460 original size:31 final size:30
Alignment explanation
Indices: 5203406--5203480 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
5203396 TTTTCTTTGT
* *
5203406 TTTAGTTTTTCAA-TTTAAAATTATAATAA
1 TTTAATTTTTTAATTTTAAAATTATAATAA
**
5203435 TTTAATTTTTTAATTTTAAAAATTATTTTAA
1 TTTAATTTTTTAATTTT-AAAATTATAATAA
5203466 TTTAATTATTTTAAT
1 TTTAATT-TTTTAAT
5203481 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 11 0.28
30 3 0.08
31 18 0.46
32 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAATTTTTTAATTTTAAAATTATAATAA
Found at i:5203501 original size:12 final size:12
Alignment explanation
Indices: 5203447--5203501 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
5203437 TAATTTTTTA
*
5203447 ATTTTAAAAATT
1 ATTTTAATAATT
5203459 ATTTTAATTTAATT
1 ATTTTAA--TAATT
5203473 ATTTTAATAATT
1 ATTTTAATAATT
*
5203485 TTTTTAA-AATT
1 ATTTTAATAATT
5203496 ACTTTT
1 A-TTTT
5203502 CACAGAGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.11
12 22 0.59
14 11 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTAATAATT
Found at i:5203902 original size:12 final size:13
Alignment explanation
Indices: 5203880--5203912 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5203870 ATTGTTTTTG
5203880 TTTCTTTTCTTC-T
1 TTTC-TTTCTTCTT
5203893 TTTCTTTCTTCTT
1 TTTCTTTCTTCTT
5203906 TTTCTTT
1 TTTCTTT
5203913 TTTTCTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTCTT
Found at i:5204288 original size:27 final size:27
Alignment explanation
Indices: 5204258--5204313 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5204248 TTAAAAAAAA
*
5204258 AAACACGTATCAT-TCCTTTGTCATGCC
1 AAACACGTATC-TCTCCCTTGTCATGCC
*
5204285 AAACACGTGTCTCTCCCTTGTCATGCC
1 AAACACGTATCTCTCCCTTGTCATGCC
5204312 AA
1 AA
5204314 TGTCAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.30
Consensus pattern (27 bp):
AAACACGTATCTCTCCCTTGTCATGCC
Found at i:5204581 original size:170 final size:170
Alignment explanation
Indices: 5204285--5204591 Score: 418
Period size: 170 Copynumber: 1.8 Consensus size: 170
5204275 TTGTCATGCC
* * * *
5204285 AAACACGTGTCTCTCCCTTGTCATGCCAATGTCAAATTGATATAGCATTGTCACATCAGCATCTC
1 AAACACGTGTCACTCCCTTATCATGCCAATATCAAATTGATATAGCATTGCCACATCAGCATCTC
* * *
5204350 CAATCCACCTCACATACTACGTTAGCAAGCGATATCATGTCAACATCCTATCAACAATGACATCA
66 CAATCCACCTCACATACTACGTGAGCAAGCGATACCATGTCAACATCATATCAACAATGACATCA
*
5204415 GCTCTATGAAGCACATAATATTTTTAAAGAAATAAGGAAG
131 ACTCTATGAAGCACATAATATTTTTAAAGAAATAAGGAAG
* * *
5204455 AAACACGTGTCACTCTCTTATCATGCCAATATCAAATTGATATAGCATTGCCACATCAGCATTTT
1 AAACACGTGTCACTCCCTTATCATGCCAATATCAAATTGATATAGCATTGCCACATCAGCATCTC
* * * * * ** * *
5204520 CAATCCACTTCACAT-GTCATGTGAGCAAGCGGTACCATGTTAATGTCATGTCAATAATGACATC
66 CAATCCACCTCACATACT-ACGTGAGCAAGCGATACCATGTCAACATCATATCAACAATGACATC
5204584 AACTCTAT
130 AACTCTAT
5204592 AAAAAATAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
169 1 0.01
170 115 0.99
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (170 bp):
AAACACGTGTCACTCCCTTATCATGCCAATATCAAATTGATATAGCATTGCCACATCAGCATCTC
CAATCCACCTCACATACTACGTGAGCAAGCGATACCATGTCAACATCATATCAACAATGACATCA
ACTCTATGAAGCACATAATATTTTTAAAGAAATAAGGAAG
Found at i:5205966 original size:29 final size:29
Alignment explanation
Indices: 5205925--5205992 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
5205915 AGGATGATCG
* *
5205925 ATTACCTTATTTACATATTCATT-ATTATT
1 ATTATCTTTTTTA-ATATTCATTAATTATT
* **
5205954 ATTATCTTTTTTATTATTTTTTAATTATT
1 ATTATCTTTTTTAATATTCATTAATTATT
5205983 ATTAT-TTTTT
1 ATTATCTTTTT
5205993 ATTATATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.66
Consensus pattern (29 bp):
ATTATCTTTTTTAATATTCATTAATTATT
Found at i:5205986 original size:17 final size:16
Alignment explanation
Indices: 5205946--5205997 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5205936 TACATATTCA
*
5205946 TTATTATTATTATCTT
1 TTATTATTATTATTTT
5205962 TT-TTATTA-T-TTTT
1 TTATTATTATTATTTT
*
5205975 TAATTATTATTATTTT
1 TTATTATTATTATTTT
5205991 TTATTAT
1 TTATTAT
5205998 ATACATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 7 0.23
16 12 0.40
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTATTTT
Found at i:5208801 original size:4 final size:4
Alignment explanation
Indices: 5208794--5208835 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
5208784 TATATATATA
* *
5208794 TATG TATG CATG TATG TATG TATG TATA TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
5208836 CTTCATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:5213425 original size:17 final size:16
Alignment explanation
Indices: 5213405--5213439 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5213395 TTTAACTTTC
*
5213405 TTTTAGTTTTTACTAGT
1 TTTTAGATTTT-CTAGT
5213422 TTTTAGATTTTCTAGT
1 TTTTAGATTTTCTAGT
5213438 TT
1 TT
5213440 GGAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTAGATTTTCTAGT
Found at i:5218745 original size:24 final size:24
Alignment explanation
Indices: 5218696--5218746 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5218686 ATTCAAATTG
** *
5218696 AAACAAAGTCATAACTACCGCCAA
1 AAACAAAGTCATAACTACAACAAA
*
5218720 AAACAAAGTCATAACTACAATAAA
1 AAACAAAGTCATAACTACAACAAA
5218744 AAA
1 AAA
5218747 AATAACGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.22, G:0.06, T:0.14
Consensus pattern (24 bp):
AAACAAAGTCATAACTACAACAAA
Found at i:5220671 original size:136 final size:136
Alignment explanation
Indices: 5220425--5220682 Score: 354
Period size: 136 Copynumber: 1.9 Consensus size: 136
5220415 AATTACAATT
* * * * * *
5220425 AAAAAGTCAAAATTACTACAAAAGAATTTTTTAAATTAGGAAATATCGATAGGGCTATTCATCAA
1 AAAAAGTCAAAATCACTACAAAAGAATATTTCAAATTAGAAAATATCAATAGGGCTATTCAACAA
* * ** * * * *
5220490 GAGTTTGTAATGCTTGACTTGATAGTTTAGAAATGCATTAGTGCCTATCTGGTTCACTAAAATTG
66 GAATTTGCAATGCTTGACTTGATAGTCCAAAAATACATTAATGCCTATCTAGTTCACTAAAATTG
5220555 TAACTA
131 TAACTA
* * *
5220561 AAAAAGTCAAAATCACTGCAAAAGAATATTTCAAGTTAGAAAATATCAATAGTGCTATTCAACAA
1 AAAAAGTCAAAATCACTACAAAAGAATATTTCAAATTAGAAAATATCAATAGGGCTATTCAACAA
*
5220626 GAATTTGCAATGCTTGACTTGATAGTCCAAAAATATATTAATGCCTATCTAGTTCAC
66 GAATTTGCAATGCTTGACTTGATAGTCCAAAAATACATTAATGCCTATCTAGTTCAC
5220683 AAGTTTGTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
136 104 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (136 bp):
AAAAAGTCAAAATCACTACAAAAGAATATTTCAAATTAGAAAATATCAATAGGGCTATTCAACAA
GAATTTGCAATGCTTGACTTGATAGTCCAAAAATACATTAATGCCTATCTAGTTCACTAAAATTG
TAACTA
Found at i:5231197 original size:24 final size:26
Alignment explanation
Indices: 5231170--5231221 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
5231160 TTATTTTATT
5231170 TAATTT-TT-AAATATTAATAACTTA
1 TAATTTATTAAAATATTAATAACTTA
*
5231194 TAATTTAATTAAAATATTAATATCTTA
1 TAATTT-ATTAAAATATTAATAACTTA
5231221 T
1 T
5231222 TTATAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
26 2 0.08
27 16 0.67
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATTTATTAAAATATTAATAACTTA
Found at i:5231339 original size:26 final size:25
Alignment explanation
Indices: 5231304--5231367 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
5231294 TTTCATTTGA
*
5231304 TTTTTAAATATTATTAATTGATAAT
1 TTTTTAAATATTAATAATTGATAAT
5231329 TTTTTAAAATATTAATAATTGATAA-
1 TTTTT-AAATATTAATAATTGATAAT
5231354 --TTTAAATATTAATA
1 TTTTTAAATATTAATA
5231368 TTTTATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 11 0.30
23 3 0.08
25 5 0.14
26 18 0.49
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTTTAAATATTAATAATTGATAAT
Found at i:5231379 original size:26 final size:26
Alignment explanation
Indices: 5231350--5231504 Score: 115
Period size: 26 Copynumber: 5.9 Consensus size: 26
5231340 TTAATAATTG
5231350 ATAATTTAAATATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
* *
5231376 ATAATATAATTATTAATA-TTTA-TT
1 ATAATTTAAATATTAATATTTTATTT
5231400 -TAATTTAAATATTATGATTATTTTCATTT
1 ATAATTTAAATATTA--A-TATTTT-ATTT
* * * * *
5231429 -T-ATTTTATTTTTAAATATTAATAATTG
1 ATAATTTAAATATT-AATATT--TTATTT
*
5231456 ATCATTTAAATATTAATATTTTATTT
1 ATAATTTAAATATTAATATTTTATTT
*
5231482 ATGATTT-AATCATTAATATTTTA
1 ATAATTTAAAT-ATTAATATTTTA
5231505 AAATATTAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
23 12 0.12
24 2 0.02
25 8 0.08
26 44 0.43
27 7 0.07
28 17 0.17
29 12 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATAATTTAAATATTAATATTTTATTT
Found at i:5231389 original size:20 final size:19
Alignment explanation
Indices: 5231353--5231525 Score: 72
Period size: 22 Copynumber: 9.3 Consensus size: 19
5231343 ATAATTGATA
5231353 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
5231372 ATTTATAATA-T-A-A--TT
1 ATTTA-AATATTAATATTTT
*
5231387 A-TT-AATATT--TATTTA
1 ATTTAAATATTAATATTTT
5231402 ATTTAAATATT-ATGA--TT
1 ATTTAAATATTAAT-ATTTT
**
5231419 ATTTTCAT-TT--TATTTT
1 ATTTAAATATTAATATTTT
*
5231435 ATTTTTAAATATTAATAATTGATC
1 A--TTTAAATATTAAT-ATT--TT
5231459 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
* *
5231478 ATTTATGAT-TTAATCATTAAT
1 ATTTA-AATATTAAT-ATT-TT
5231499 ATTTTAAAATATTAATATTTT
1 A-TTT-AAATATTAATATTTT
5231520 ATTTAA
1 ATTTAA
5231526 TTTAAATAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 50
0.65 0.07 0.28
Matches are distributed among these distances:
12 4 0.03
13 2 0.02
14 3 0.03
15 6 0.05
16 7 0.06
17 14 0.12
18 7 0.06
19 22 0.19
20 12 0.10
21 8 0.07
22 24 0.21
23 6 0.05
24 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTAAATATTAATATTTT
Found at i:5231390 original size:48 final size:48
Alignment explanation
Indices: 5231338--5231499 Score: 155
Period size: 48 Copynumber: 3.2 Consensus size: 48
5231328 TTTTTTAAAA
*
5231338 TATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATATAAT
1 TATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAT
* * *
5231386 TATTAAT-ATTTATTTAATTTAAATATTATGATTATTTTCATTTTATTTTATTTTTAAA
1 TATTAATAATTGA--TAATTTAAATATTA--A-TATTTT-A-TTTA---TA-ATTTAAT
* *
5231444 TATTAATAATTGATCATTTAAATATTAATATTTTATTTATGATTTAAT
1 TATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAT
*
5231492 CATTAATA
1 TATTAATA
5231500 TTTTAAAATA
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
47 4 0.04
48 19 0.21
49 15 0.16
51 1 0.01
52 10 0.11
53 2 0.02
54 10 0.11
55 1 0.01
57 15 0.16
58 11 0.12
59 4 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (48 bp):
TATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAAT
Found at i:5231515 original size:42 final size:42
Alignment explanation
Indices: 5231429--5231653 Score: 165
Period size: 42 Copynumber: 5.3 Consensus size: 42
5231419 ATTTTCATTT
* *
5231429 TATTTTATTTTTAAATATTAATAATTGATCA-TTT-AAATATTAA
1 TATTTTATTTAT-AAT-TTAATAATTAAT-ATTTTAAAATATTAA
* *
5231472 TATTTTATTTATGATTTAATCATTAATATTTTAAAATATTAA
1 TATTTTATTTATAATTTAATAATTAATATTTTAAAATATTAA
* ** ** *
5231514 TATTTTA-TT-TAATTTAAATAA-TATTATGATAAGTTATT-T
1 TATTTTATTTATAATTT-AATAATTAATATTTTAAAATATTAA
* * * * *
5231553 TATTTTATTTTTAAATATTAATAAATGATTATTTATTTAAAATATGAT
1 TATTTTATTTAT-AAT-TTAAT-AAT--TAATAT-TTTAAAATATTAA
* *
5231601 TATTTTATTTATAACTTAATAATTAATATTTTAAAATATGAA
1 TATTTTATTTATAATTTAATAATTAATATTTTAAAATATTAA
5231643 TATTTTATTTA
1 TATTTTATTTA
5231654 ATTGAAATAT
Statistics
Matches: 144, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
39 7 0.05
40 20 0.14
41 20 0.14
42 47 0.33
43 19 0.13
45 3 0.02
46 8 0.06
47 8 0.06
48 12 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (42 bp):
TATTTTATTTATAATTTAATAATTAATATTTTAAAATATTAA
Found at i:5231609 original size:20 final size:20
Alignment explanation
Indices: 5231577--5231654 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
5231567 ATATTAATAA
5231577 ATGATTA-TTTATTTAAAAT
1 ATGATTATTTTATTTAAAAT
*
5231596 ATGATTATTTTATTTATAACT
1 ATGATTATTTTATTTA-AAAT
* * *
5231617 -TAATAATTAATATTTTAAAAT
1 ATGATTATT-TTA-TTTAAAAT
*
5231638 ATGAATATTTTATTTAA
1 ATGATTATTTTATTTAA
5231655 TTGAAATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
19 7 0.16
20 19 0.42
21 10 0.22
22 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (20 bp):
ATGATTATTTTATTTAAAAT
Found at i:5231627 original size:129 final size:129
Alignment explanation
Indices: 5231158--5231717 Score: 605
Period size: 129 Copynumber: 4.4 Consensus size: 129
5231148 ATATATGGTT
* * * * *
5231158 ATTTATTTTATTTAATTTTTAAATATTAATAACTTATAATTTAATTAAAATATTAATATCTTATT
1 ATTTATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTTAAAATATTAATATTTTATT
* * *
5231223 TATAATTAATCATTAATATTTTCAAATGTTAATATTTTATTTAATTTAAAT-TTATTATGATTA
66 TATAATTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAATATTATGATTA
* * * *
5231286 ATTTTTTATTTCATTTGATTTTTAAATATTATTAATTGATAATTT-TTTAAAATATTAATAATTG
1 A---TTTATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTTAAAATATTAAT-ATT-
* * *
5231350 ATAATTTAAATATTAAT-ATT-TTATTTATAATATAATTATTAATA-TTTATTTAATTT--A-AA
61 -TTATTTATA-ATTAATCATTAATATTT-T-A-A-AA-TATTAATATTTTATTTAATTTAAATAA
5231409 TATTATGATTA
119 TATTATGATTA
* * *
5231420 TTTTCATTTTATTTTATTTTTAAATATTAAT-AAT--TGA-TCATTT-AAATATTAATATTTTAT
1 ATTT-ATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTTAAAATATTAATATTTTAT
*
5231480 TTATGATTTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAATATTATGA-T
65 TTAT-AATTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAATATTATGATT
5231544 A
129 A
* * * *
5231545 AGTTATTTTATTTTATTTTTAAATATTAATAAATGATTATTTATTTAAAATATGATTATTTTATT
1 ATTTATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTTAAAATATTAATATTTTATT
* * * *
5231610 TATAACTTAATAATTAATATTTTAAAATATGAATATTTTATTTAATTGAAATATTATTATGATT-
66 TATAA-TTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAATATTATGATTA
* *
5231674 -TTTATTTTA-TTTATTTTTAAATATTAATAATTGTTAATTTATTT
1 ATTTATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTT
5231718 TACATATAAT
Statistics
Matches: 364, Mismatches: 39, Indels: 59
0.79 0.08 0.13
Matches are distributed among these distances:
122 8 0.02
123 14 0.04
124 27 0.07
125 20 0.05
126 15 0.04
127 42 0.12
128 26 0.07
129 76 0.21
130 14 0.04
131 43 0.12
132 28 0.08
133 11 0.03
134 18 0.05
135 1 0.00
136 14 0.04
137 7 0.02
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (129 bp):
ATTTATTTTATTTTATTTTTAAATATTAATAAATGATAATTTATTTAAAATATTAATATTTTATT
TATAATTAATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAATATTATGATTA
Found at i:5231756 original size:18 final size:18
Alignment explanation
Indices: 5231730--5231766 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5231720 CATATAATTT
*
5231730 AAATGTTAATAATTGATA
1 AAATATTAATAATTGATA
5231748 AAATATTAATAATTGATA
1 AAATATTAATAATTGATA
5231766 A
1 A
5231767 TTTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
AAATATTAATAATTGATA
Found at i:5231868 original size:27 final size:28
Alignment explanation
Indices: 5231829--5231887 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
5231819 TTTAATCTAT
*
5231829 TTTATTTTTAAATAGTAATAATTTATAA
1 TTTATTTTTAAATAGTAATAATTGATAA
* *
5231857 TTTA-TTTTAAATATTAATAATTGATAT
1 TTTATTTTTAAATAGTAATAATTGATAA
5231884 TTTA
1 TTTA
5231888 AATATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTATTTTTAAATAGTAATAATTGATAA
Found at i:5231912 original size:27 final size:25
Alignment explanation
Indices: 5231826--5231929 Score: 99
Period size: 22 Copynumber: 4.2 Consensus size: 25
5231816 ATTTTTAATC
*
5231826 TATTTTATTTTTAAATAGTAATAATTT
1 TATTTTA-TTTTAAATATTAAT-ATTT
* *
5231853 ATAATTTATTTTAAATATTAATAATT
1 -TATTTTATTTTAAATATTAATATTT
*
5231879 GA---TATTTTAAATATTAATATTT
1 TATTTTATTTTAAATATTAATATTT
*
5231901 TATTTATAATTT-AATATTAATATTT
1 TATTT-TATTTTAAATATTAATATTT
5231926 TATT
1 TATT
5231930 AGAAGTTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
22 20 0.31
25 18 0.28
26 8 0.12
27 13 0.20
28 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTTTATTTTAAATATTAATATTT
Found at i:5236079 original size:18 final size:17
Alignment explanation
Indices: 5236029--5236079 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
5236019 TTTATACGTG
*
5236029 ATATTTTGATTAAAATA
1 ATATTTTGATTAAAAAA
* *
5236046 AT-TATTAATTATAAAAA
1 ATATTTTGATTA-AAAAA
*
5236063 ATATTTTGATTTAAAAA
1 ATATTTTGATTAAAAAA
5236080 TAAAAATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.27
17 13 0.50
18 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
ATATTTTGATTAAAAAA
Found at i:5236110 original size:30 final size:30
Alignment explanation
Indices: 5236029--5236122 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 30
5236019 TTTATACGTG
5236029 ATATTTTGA-TTAAAATAATTATTAATTATAAAAA
1 ATATTTTGATTTAAAATAA--A--AA-TATAAAAA
5236063 ATATTTTGATTTAAAAATAAAAATATAAAAA
1 ATATTTTGATTT-AAAATAAAAATATAAAAA
5236094 ATATTTTGATTTAAAATAAAAATATAAAA
1 ATATTTTGATTTAAAATAAAAATATAAAA
5236123 TTTTAATTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
30 17 0.29
31 20 0.34
32 2 0.03
34 10 0.17
35 2 0.03
36 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
ATATTTTGATTTAAAATAAAAATATAAAAA
Found at i:5248436 original size:254 final size:254
Alignment explanation
Indices: 5247987--5248494 Score: 989
Period size: 254 Copynumber: 2.0 Consensus size: 254
5247977 ATAAGCTATT
*
5247987 TTGGAACCTCTGATGTGGAGGTTGAGTTGTCCAAAGCAGATATACCTTTTTCTGATTGACATAAA
1 TTGGAACCTCTGATGTGGAGGTTGAGTTGTCCAAAGCAGACATACCTTTTTCTGATTGACATAAA
5248052 TTTTTCATGAATGTACTATGGGATTCATATCCGTCTCTCCCCTTGGGGGTTCATGGTTTATCCTA
66 TTTTTCATGAATGTACTATGGGATTCATATCCGTCTCTCCCCTTGGGGGTTCATGGTTTATCCTA
5248117 TCGTGGACCTTCTAACCATTGTGTCAATATTGAACGTTGCATATTCTGTGATAAAACTGCTATGC
131 TCGTGGACCTTCTAACCATTGTGTCAATATTGAACGTTGCATATTCTGTGATAAAACTGCTATGC
*
5248182 TTCAGTTTTAAGTTGGTGTTTGAAATTTGTGACTTTAGTTTTGAGAAGTCCCCGAGACA
196 TTCAGTTTTAAGTTGGTGTCTGAAATTTGTGACTTTAGTTTTGAGAAGTCCCCGAGACA
*
5248241 TTGGAACCTCTGATGTGGAGGTTGAGTTGTCCAAAGCAGACATTCCTTTTTCTGATTGACATAAA
1 TTGGAACCTCTGATGTGGAGGTTGAGTTGTCCAAAGCAGACATACCTTTTTCTGATTGACATAAA
5248306 TTTTTCATGAATGTACTATGGGATTCATATCCGTCTCTCCCCTTGGGGGTTCATGGTTTATCCTA
66 TTTTTCATGAATGTACTATGGGATTCATATCCGTCTCTCCCCTTGGGGGTTCATGGTTTATCCTA
5248371 TCGTGGACCTTCTAACCATTGTGTCAATATTGAACGTTGCATATTCTGTGATAAAACTGCTATGC
131 TCGTGGACCTTCTAACCATTGTGTCAATATTGAACGTTGCATATTCTGTGATAAAACTGCTATGC
5248436 TTCAGTTTTAAGTTGGTGTCTGAAATTTGTGACTTTAGTTTTGAGAAGTCCCCGAGACA
196 TTCAGTTTTAAGTTGGTGTCTGAAATTTGTGACTTTAGTTTTGAGAAGTCCCCGAGACA
5248495 CGATGCTTAT
Statistics
Matches: 251, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
254 251 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (254 bp):
TTGGAACCTCTGATGTGGAGGTTGAGTTGTCCAAAGCAGACATACCTTTTTCTGATTGACATAAA
TTTTTCATGAATGTACTATGGGATTCATATCCGTCTCTCCCCTTGGGGGTTCATGGTTTATCCTA
TCGTGGACCTTCTAACCATTGTGTCAATATTGAACGTTGCATATTCTGTGATAAAACTGCTATGC
TTCAGTTTTAAGTTGGTGTCTGAAATTTGTGACTTTAGTTTTGAGAAGTCCCCGAGACA
Found at i:5261084 original size:11 final size:12
Alignment explanation
Indices: 5261062--5261103 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5261052 AATAATTCTA
*
5261062 AATATAAACATG
1 AATATTAACATG
5261074 AAT-TTAACATG
1 AATATTAACATG
*
5261085 AATATTATCATG
1 AATATTAACATG
*
5261097 AAAATTA
1 AATATTA
5261104 TTATATCCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (12 bp):
AATATTAACATG
Found at i:5263697 original size:2 final size:2
Alignment explanation
Indices: 5263690--5263719 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5263680 AGTTCAGGAA
5263690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5263720 GAAAAAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5271910 original size:2 final size:2
Alignment explanation
Indices: 5271898--5271940 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
5271888 GAACATATCA
5271898 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5271940 A
1 A
5271941 AGAAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5278015 original size:15 final size:14
Alignment explanation
Indices: 5277992--5278040 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
5277982 GCTGAATATT
*
5277992 AATATTTAATTTTAA
1 AATAATTAATTTT-A
5278007 AATAATTAA-TTTA
1 AATAATTAATTTTA
*
5278020 AATTATTAATATTTA
1 AATAATTAAT-TTTA
5278035 AATAAT
1 AATAAT
5278041 ATAACACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 17 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATAATTAATTTTA
Done.