Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, 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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 26
Found at i:5360653 original size:25 final size:25
Alignment explanation
Indices: 5360610--5360658 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5360600 AAAAAAGAGA
*
5360610 AAATAAATAAAAGGAAAAATAAAAT
1 AAATAAATAAAAGAAAAAATAAAAT
5360635 AAATAAATAAAA-AATAAAATAAAA
1 AAATAAATAAAAGAA-AAAATAAAA
5360659 CAGAATGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (25 bp):
AAATAAATAAAAGAAAAAATAAAAT
Found at i:5364304 original size:85 final size:85
Alignment explanation
Indices: 5364187--5364978 Score: 1016
Period size: 85 Copynumber: 9.3 Consensus size: 85
5364177 AATGGAGTCA
* * *
5364187 AACTCGAAGATTTTTTTTGCCAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
5364252 CCTTGAGCTGAATGAAATCG
66 CCTTGAGCTGAATGTAATCG
* * *
5364272 ATCTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTCAGCTATGCTGTAAATTTGATATGC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* *
5364337 CCTTGAGTTGAATTTAATCG
66 CCTTGAGCTGAATGTAATCG
* * * * *
5364357 ATCTCAAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
5364422 CCTTGAGCTGAATGTAATCG
66 CCTTGAGCTGAATGTAATCG
* * * ** *
5364442 AACTCGAAGGTTTTTGTTGATAGATAGCCCTTCTCTCCTTGAGATATATTGTAAATTTGATATAC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
5364507 CCTTGAGCTGAATGTAATCG
66 CCTTGAGCTGAATGTAATCG
* * * * *
5364527 AACTCGAAGGTTTTAGTTGACAGAT-GTCATTCTCACCTCGAGCTATGCTGTAAATTTGATATGC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
5364591 CTTTGAGCTGAATGTAATCG
66 CCTTGAGCTGAATGTAATCG
* * * * *
5364611 AACTCGAAGATTTTTGTTGAAAGATAGCTCTTCTCGCCTTAAGCTATGTTGTAAATTTGATATGT
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-
* *
5364676 CAC-TGAGCTGAATGTAATCA
65 CCCTTGAGCTGAATGTAATCG
* ** * * * *
5364696 AACTCGAAGGTTTTTATTGACAGATAGCTTTTCTCGACTTAAACTATGCTGTAAATTTGATATGT
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
* ** *
5364761 CCTTAAATTGAATGCAATCG
66 CCTTGAGCTGAATGTAATCG
* * * *
5364781 AACTCGAAGGTTTTAGTTGAAAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGC
1 AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
5364846 CTTTGAGCTGAATGTAATCG
66 CCTTGAGCTGAATGTAATCG
* * * *
5364866 -ACTTTGAAGGTTTTTGTTGACAGATAGCTCTTCTCGCCTTAAGCTATGCTATAAATTTGATAT-
1 AAC-TCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
*
5364929 TCCTCTGAGCTGAATGTAATCG
65 CCCT-TGAGCTGAATGTAATCG
* * *
5364951 AACACGATGGTTTTTGTTGGCAGATAGC
1 AACTCGAAGGTTTTTGTTGACAGATAGC
5364979 TTTTCTCGAC
Statistics
Matches: 608, Mismatches: 93, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
84 77 0.13
85 528 0.87
86 3 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (85 bp):
AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
CCTTGAGCTGAATGTAATCG
Found at i:5364854 original size:339 final size:340
Alignment explanation
Indices: 5364207--5365008 Score: 1072
Period size: 339 Copynumber: 2.4 Consensus size: 340
5364197 TTTTTTTTGC
* * *
5364207 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGAAATCG
1 CAGATAGCTCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCG
* * * *
5364272 ATCTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTCAGCTATGCTGTAAATTTGATATGC
66 AACTCGAAGGTTTTTGTTGACAGATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGC
* * * * * * * *
5364337 CCTTGAGTTGAATTTAATCGATCTCAAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGCT
131 ACTTGAGCTGAATGTAATCAAACTCAAAGGTTTTTATTGACAGATAACCCTTCTCGACTTAAACT
* * * * *
5364402 ATGATGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGATAGAT
196 ATGATGTAAATTTGATATGCCCTTAAACTGAATGCAATCGAACTCGAAGGTTTTAGTTGAAAGAT
* * *
5364467 AGCCCTTCTCTCCTTGAGATATATTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGAAC-T
261 AACCCTTCTCACCTTGAGATATACTGTAAATTTGATATACCCTTGAGCTGAATGTAATCG-ACTT
5364531 CGAAGGTTTTAGTTGA
325 CGAAGGTTTTAGTTGA
* *
5364547 CAGAT-G-TCATTCTCACCTCGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATC
1 CAGATAGCTC-TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATC
* * *
5364610 GAACTCGAAGATTTTTGTTGAAAGATAGCTCTTCTCGCCTTAAGCTATGTTGTAAATTTGATATG
65 GAACTCGAAGGTTTTTGTTGACAGATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATG
* * **
5364675 TCAC-TGAGCTGAATGTAATCAAACTCGAAGGTTTTTATTGACAGATAGCTTTTCTCGACTTAAA
130 -CACTTGAGCTGAATGTAATCAAACTCAAAGGTTTTTATTGACAGATAACCCTTCTCGACTTAAA
* * *
5364739 CTATGCTGTAAATTTGATATGTCCTTAAATTGAATGCAATCGAACTCGAAGGTTTTAGTTGAAAG
194 CTATGATGTAAATTTGATATGCCCTTAAACTGAATGCAATCGAACTCGAAGGTTTTAGTTGAAAG
* * * *
5364804 ATAACCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGACT
259 ATAACCCTTCTCACCTTGAGATATACTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGACT
* *
5364869 TTGAAGGTTTTTGTTGA
324 TCGAAGGTTTTAGTTGA
* * * *
5364886 CAGATAGCTCTTCTCGCCTTAAGCTATGCTATAAATTTGATATTCCTCTGAGCTGAATGTAATCG
1 CAGATAGCTCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCG
* * * * * * * *
5364951 AACACGATGGTTTTTGTTGGCAGATAGCTTTTCTCGACTTAAGTTGTGCTTTAAATTT
66 AACTCGAAGGTTTTTGTTGACAGATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTT
5365009 CCTCTAAATT
Statistics
Matches: 399, Mismatches: 58, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
338 3 0.01
339 290 0.73
340 104 0.26
341 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (340 bp):
CAGATAGCTCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCG
AACTCGAAGGTTTTTGTTGACAGATAGCTCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGC
ACTTGAGCTGAATGTAATCAAACTCAAAGGTTTTTATTGACAGATAACCCTTCTCGACTTAAACT
ATGATGTAAATTTGATATGCCCTTAAACTGAATGCAATCGAACTCGAAGGTTTTAGTTGAAAGAT
AACCCTTCTCACCTTGAGATATACTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGACTTC
GAAGGTTTTAGTTGA
Found at i:5366498 original size:99 final size:99
Alignment explanation
Indices: 5366327--5366528 Score: 323
Period size: 99 Copynumber: 2.0 Consensus size: 99
5366317 GGACAACTCA
* **
5366327 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGTGTTTAACCAATT
1 ATATTATAATAACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATT
* * * *
5366392 GCTCTAGAGGGACAGCTCAAGCTTTATTGTATAT
66 GCTCTAGAGGGACAACTCAAGCATTATCGTATAG
**
5366426 ATATTATAATAACCTTTATCAGGCTTTCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATT
1 ATATTATAATAACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATT
5366491 GCTCTAGAGGGACAACTCAAGCATTATCGTATAG
66 GCTCTAGAGGGACAACTCAAGCATTATCGTATAG
5366525 ATAT
1 ATAT
5366529 AATATTATAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATTATAATAACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAGCATTATCGTATAG
Found at i:5367069 original size:36 final size:37
Alignment explanation
Indices: 5367019--5367095 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
5367009 AAATATCCTA
*
5367019 ACAAAAATAAATATGAGAAAGTTC-AAAAAACAAGTT
1 ACAAAAAGAAATATGAGAAAGTTCAAAAAAACAAGTT
* *
5367055 ACAAAAAGATATATGATAAAGTTCAAAAAAACAAGTT
1 ACAAAAAGAAATATGAGAAAGTTCAAAAAAACAAGTT
5367092 -CAAA
1 ACAAA
5367096 CAGGATGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.19
Consensus pattern (37 bp):
ACAAAAAGAAATATGAGAAAGTTCAAAAAAACAAGTT
Found at i:5369672 original size:25 final size:24
Alignment explanation
Indices: 5369624--5369698 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
5369614 TCGAATTGTG
* *
5369624 AAAAGAAAAA-GAAAAAA-AATAA
1 AAAAGAAAAATAAAAAAATAACAA
*
5369646 AAAAGTATAAATAAATAAAATAA-AA
1 AAAAG-AAAAATAAA-AAAATAACAA
* *
5369671 AAGAGAAAAATAAAATAATAACAA
1 AAAAGAAAAATAAAAAAATAACAA
5369695 AAAA
1 AAAA
5369699 TTAAAACAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.12
23 10 0.24
24 15 0.36
25 10 0.24
26 2 0.05
ACGTcount: A:0.80, C:0.01, G:0.07, T:0.12
Consensus pattern (24 bp):
AAAAGAAAAATAAAAAAATAACAA
Found at i:5369690 original size:23 final size:22
Alignment explanation
Indices: 5369624--5369696 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
5369614 TCGAATTGTG
5369624 AAAAGAAAAAGA-AAAAAAATAA
1 AAAAGAAAAA-ATAAAAAAATAA
* *
5369646 AAAAGTATAAATAAATAAAATAA
1 AAAAGAAAAAATAAA-AAAATAA
*
5369669 AAAAGAGAAAAATAAAATAATAA
1 AAAAGA-AAAAATAAAAAAATAA
5369692 CAAAA
1 -AAAA
5369697 AATTAAAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 1 0.02
22 11 0.26
23 18 0.43
24 12 0.29
ACGTcount: A:0.79, C:0.01, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAAATAAAAAAATAA
Found at i:5381527 original size:17 final size:16
Alignment explanation
Indices: 5381499--5381532 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5381489 AGGTTGAGAG
*
5381499 ATAAATTTATTATTAT
1 ATAAATTTATTAATAT
5381515 ATAAATCTTATTAATAT
1 ATAAAT-TTATTAATAT
5381532 A
1 A
5381533 ATATCATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAAATTTATTAATAT
Found at i:5383308 original size:4 final size:4
Alignment explanation
Indices: 5383299--5383368 Score: 68
Period size: 4 Copynumber: 17.5 Consensus size: 4
5383289 ATCATAACGC
* * * * *
5383299 ACAT ACAT ACAT GCAT GCAT ACAT ACAT GCAT GCAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
5383347 GCAT ACAT ACAT GCAT GCAT AC
1 ACAT ACAT ACAT ACAT ACAT AC
5383369 TACCATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:5383319 original size:12 final size:12
Alignment explanation
Indices: 5383304--5383368 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
5383294 AACGCACATA
5383304 CATACATGCATG
1 CATACATGCATG
*
5383316 CATACATACATG
1 CATACATGCATG
* * *
5383328 CATGCATACATA
1 CATACATGCATG
* *
5383340 CATGCATGCATA
1 CATACATGCATG
5383352 CATACATGCATG
1 CATACATGCATG
5383364 CATAC
1 CATAC
5383369 TACCATTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (12 bp):
CATACATGCATG
Found at i:5383319 original size:16 final size:16
Alignment explanation
Indices: 5383300--5383368 Score: 138
Period size: 16 Copynumber: 4.3 Consensus size: 16
5383290 TCATAACGCA
5383300 CATACATACATGCATG
1 CATACATACATGCATG
5383316 CATACATACATGCATG
1 CATACATACATGCATG
5383332 CATACATACATGCATG
1 CATACATACATGCATG
5383348 CATACATACATGCATG
1 CATACATACATGCATG
5383364 CATAC
1 CATAC
5383369 TACCATTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.25
Consensus pattern (16 bp):
CATACATACATGCATG
Found at i:5386610 original size:17 final size:17
Alignment explanation
Indices: 5386556--5386612 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
5386546 CCGATACTAG
5386556 CCTTATGGTATCGATA-C
1 CCTTA-GGTATCGATACC
*
5386573 CCTT-GGTATTGATACTACC
1 CCTTAGGTATCG--A-TACC
5386592 CCTTAGGTATCGATACC
1 CCTTAGGTATCGATACC
5386609 CCTT
1 CCTT
5386613 GAATAACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 6 0.18
17 13 0.39
18 3 0.09
19 5 0.15
20 6 0.18
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (17 bp):
CCTTAGGTATCGATACC
Found at i:5388003 original size:15 final size:15
Alignment explanation
Indices: 5387983--5388013 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5387973 TAAGTGTGTG
*
5387983 TTATTTTATATATTT
1 TTATTTTATAAATTT
5387998 TTATTTTATAAATTT
1 TTATTTTATAAATTT
5388013 T
1 T
5388014 AAAAGATAAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTATAAATTT
Found at i:5390446 original size:21 final size:20
Alignment explanation
Indices: 5390399--5390447 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
5390389 GATGGGTTAC
5390399 ATAGTTTCTTTCGAACACTA
1 ATAGTTTCTTTCGAACACTA
5390419 ATAGTTTCTTTCGAACACTA
1 ATAGTTTCTTTCGAACACTA
5390439 AGTAGTTTC
1 A-TAGTTTC
5390448 CTAAGGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
ATAGTTTCTTTCGAACACTA
Found at i:5398232 original size:17 final size:17
Alignment explanation
Indices: 5398210--5398245 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5398200 TGATTTTCTC
5398210 TTGATTCTTGATTCTTG
1 TTGATTCTTGATTCTTG
* *
5398227 TTGATTGTTGTTTCTTG
1 TTGATTCTTGATTCTTG
5398244 TT
1 TT
5398246 ATTGATCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.19, T:0.64
Consensus pattern (17 bp):
TTGATTCTTGATTCTTG
Found at i:5418848 original size:23 final size:23
Alignment explanation
Indices: 5418822--5418872 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
5418812 TCCATTTTTA
5418822 CCATT-TTACCCCAAATAAACCAC
1 CCATTATTACCCCAAA-AAACCAC
* *
5418845 CCATTACTTTCCCTAAAAAACCAC
1 CCATTA-TTACCCCAAAAAACCAC
5418869 CCAT
1 CCAT
5418873 CCCTCATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 11 0.46
25 8 0.33
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (23 bp):
CCATTATTACCCCAAAAAACCAC
Found at i:5421587 original size:35 final size:35
Alignment explanation
Indices: 5421541--5421614 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
5421531 TATGTCTAAA
5421541 CATTGTTGTCGTAGCATATTAACTGCATTTAGTTG
1 CATTGTTGTCGTAGCATATTAACTGCATTTAGTTG
5421576 CATTGTTGTCGTAGCATATTAACTGCATTTAGTTG
1 CATTGTTGTCGTAGCATATTAACTGCATTTAGTTG
5421611 CATT
1 CATT
5421615 TAGGTCATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (35 bp):
CATTGTTGTCGTAGCATATTAACTGCATTTAGTTG
Found at i:5435014 original size:20 final size:20
Alignment explanation
Indices: 5434989--5435026 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5434979 ACTATAATTC
5434989 TAATGAACTTGTATTATATA
1 TAATGAACTTGTATTATATA
*
5435009 TAATGAATTTGTATTATA
1 TAATGAACTTGTATTATA
5435027 CACATATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (20 bp):
TAATGAACTTGTATTATATA
Found at i:5435745 original size:2 final size:2
Alignment explanation
Indices: 5435738--5435775 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5435728 TTAGATTATC
5435738 AT AT AT AT 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 AT AT AT AT
5435776 TGTGTGGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5437887 original size:24 final size:24
Alignment explanation
Indices: 5437860--5437908 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5437850 CGTTCGTATT
* * *
5437860 CCTGTCATTCTTGGTGCTCGTACC
1 CCTGACATTCCTGGTGCTCGAACC
5437884 CCTGACATTCCTGGTGCTCGAACC
1 CCTGACATTCCTGGTGCTCGAACC
5437908 C
1 C
5437909 GAAATCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.37, G:0.20, T:0.31
Consensus pattern (24 bp):
CCTGACATTCCTGGTGCTCGAACC
Found at i:5438530 original size:60 final size:60
Alignment explanation
Indices: 5438419--5438579 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
5438409 TCGGGTAATC
* * * *
5438419 ATTTTCTAACTTTTAATAGTCG-GGGACTTAACAAAGCAACATCATATAGTCAGAGAATT
1 ATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACATCATATAGTCAGAGAATT
* * * * *
5438478 ATTTTGTAATTTTTAATAGTCGAGAGACTCAACAAAATAACGTCATATAGTCAGAGGATT
1 ATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACATCATATAGTCAGAGAATT
* *
5438538 ATTTTATAACCTTTAATAGTCGAGAGACTCAACAAAGCAACA
1 ATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACA
5438580 CTTATAACCG
Statistics
Matches: 87, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 20 0.23
60 67 0.77
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACATCATATAGTCAGAGAATT
Found at i:5439251 original size:18 final size:18
Alignment explanation
Indices: 5439228--5439262 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5439218 AAAAAAATAC
5439228 TTAAAAAATTTATTTTAT
1 TTAAAAAATTTATTTTAT
*
5439246 TTAAAAAATTTTTTTTA
1 TTAAAAAATTTATTTTA
5439263 AAAAAATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAAAAATTTATTTTAT
Found at i:5439520 original size:30 final size:29
Alignment explanation
Indices: 5439481--5439543 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
5439471 AATAATAATA
* *
5439481 TTTATGCACATGAATTAACAAAAAAAT-TAG
1 TTTAGGCACAT-AAATAA-AAAAAAATATAG
*
5439511 TTTAGGCACATAAATGAAAAAAAATATAG
1 TTTAGGCACATAAATAAAAAAAAATATAG
5439540 TTTA
1 TTTA
5439544 AATATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 11 0.38
30 10 0.34
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (29 bp):
TTTAGGCACATAAATAAAAAAAAATATAG
Found at i:5440732 original size:6 final size:5
Alignment explanation
Indices: 5440715--5440769 Score: 74
Period size: 5 Copynumber: 10.8 Consensus size: 5
5440705 AACGAAATAA
* **
5440715 AAAAT AAAAT AAACAT AAAAT TAAAT ATTAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
5440766 AAAA
1 AAAA
5440770 AGTTATTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 38 0.88
6 5 0.12
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:5441833 original size:24 final size:24
Alignment explanation
Indices: 5441806--5441884 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
5441796 ACCATGTTCG
5441806 GTATCGATACTACTATACATAGTA
1 GTATCGATACTACTATACATAGTA
* * ** *
5441830 GTATCAATACTCCT-TGGA-CG--
1 GTATCGATACTACTATACATAGTA
5441850 GTATCGATACTACTATACATAGTA
1 GTATCGATACTACTATACATAGTA
5441874 GTATCGATACT
1 GTATCGATACT
5441885 CCTTGGAAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 12 0.29
21 2 0.05
22 2 0.05
23 2 0.05
24 23 0.56
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (24 bp):
GTATCGATACTACTATACATAGTA
Found at i:5441859 original size:20 final size:20
Alignment explanation
Indices: 5441830--5441904 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
5441820 ATACATAGTA
* *
5441830 GTATCAATACTCCTTGGACG
1 GTATCGATACTCCTTGGAAG
* **
5441850 GTATCGATACTACTATACATAG
1 GTATCGATACTCCT-TGGA-AG
5441872 TAGTATCGATACTCCTTGGAAG
1 --GTATCGATACTCCTTGGAAG
5441894 GTATCGATACT
1 GTATCGATACT
5441905 GTTGGGTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
20 23 0.53
21 2 0.05
22 3 0.07
23 2 0.05
24 13 0.30
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCCTTGGAAG
Found at i:5441867 original size:44 final size:44
Alignment explanation
Indices: 5441804--5441904 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
5441794 ATACCATGTT
5441804 CGGTATCGATACTACTATACATAGTAGTATCAATACTCCTTGGA
1 CGGTATCGATACTACTATACATAGTAGTATCAATACTCCTTGGA
*
5441848 CGGTATCGATACTACTATACATAGTAGTATCGATACTCCTTGGA
1 CGGTATCGATACTACTATACATAGTAGTATCAATACTCCTTGGA
*
5441892 AGGTATCGATACT
1 CGGTATCGATACT
5441905 GTTGGGTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
CGGTATCGATACTACTATACATAGTAGTATCAATACTCCTTGGA
Found at i:5443908 original size:21 final size:21
Alignment explanation
Indices: 5443884--5443932 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5443874 CAACAATTAA
*
5443884 TGATTATTATCAAAAGAAAAT
1 TGATGATTATCAAAAGAAAAT
5443905 TGATGATTATCAAAAGAAAAT
1 TGATGATTATCAAAAGAAAAT
5443926 TGATGAT
1 TGATGAT
5443933 CTTAAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (21 bp):
TGATGATTATCAAAAGAAAAT
Found at i:5443910 original size:24 final size:23
Alignment explanation
Indices: 5443878--5443932 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 23
5443868 TACTTTCAAC
*
5443878 AATTAATGATTATTATCAAAAGAA
1 AATTGATGA-TATTATCAAAAGAA
5443902 AATTGATG--ATTATCAAAAGAA
1 AATTGATGATATTATCAAAAGAA
5443923 AATTGATGAT
1 AATTGATGAT
5443933 CTTAAAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 21 0.75
24 7 0.25
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.33
Consensus pattern (23 bp):
AATTGATGATATTATCAAAAGAA
Found at i:5447627 original size:22 final size:20
Alignment explanation
Indices: 5447573--5447634 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
5447563 CTATTTTGTG
*
5447573 TATTTGGTATCGATACTACT
1 TATTAGGTATCGATACTACT
*
5447593 CACTTA-GTATCGATACTAATCT
1 TA-TTAGGTATCGATACT-A-CT
*
5447615 TATTAGGTATCGATATTACT
1 TATTAGGTATCGATACTACT
5447635 AGCCTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.41
21 7 0.21
22 13 0.38
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
TATTAGGTATCGATACTACT
Found at i:5447658 original size:42 final size:42
Alignment explanation
Indices: 5447573--5447673 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
5447563 CTATTTTGTG
* * *
5447573 TATTTGGTATCGATACTACTCACTTAGTATCGATACTAATCT
1 TATTAGGTATCGATACTACTCACCTAATATCGATACTAATCT
* **
5447615 TATTAGGTATCGATATTACT-AGCCTAATATCGATACTGCTCT
1 TATTAGGTATCGATACTACTCA-CCTAATATCGATACTAATCT
*
5447657 TA-TCGAGTATCGATACT
1 TATTAG-GTATCGATACT
5447674 GTTCATGCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (42 bp):
TATTAGGTATCGATACTACTCACCTAATATCGATACTAATCT
Found at i:5449004 original size:23 final size:24
Alignment explanation
Indices: 5448954--5449005 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
5448944 TAACCACATG
* *
5448954 CCAAAACGGCGTCGTCGCGTTTAGGT
1 CCAAAACGGCGTCGT--CGTTGACGT
5448980 CCAAAACGGCGTCGT-GTTGACGT
1 CCAAAACGGCGTCGTCGTTGACGT
5449003 CCA
1 CCA
5449006 TGAGGGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
26 15 0.62
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (24 bp):
CCAAAACGGCGTCGTCGTTGACGT
Found at i:5451628 original size:21 final size:21
Alignment explanation
Indices: 5451607--5451720 Score: 135
Period size: 21 Copynumber: 5.5 Consensus size: 21
5451597 TACCAAGGAT
* *
5451607 GAGAAGAACATTCATCAAGAT
1 GAGAAGACCATTCATCAAGAC
5451628 GAGAATG-CCATTCATCAAGAC
1 GAGAA-GACCATTCATCAAGAC
5451649 GAGAATG-CCATTCATCAAGAC
1 GAGAA-GACCATTCATCAAGAC
* *
5451670 GAGAAGACCCTTCATAAAGAC
1 GAGAAGACCATTCATCAAGAC
* *
5451691 GAGAAGACC-TTCGTAAAGAC
1 GAGAAGACCATTCATCAAGAC
5451711 GAGAAGACCA
1 GAGAAGACCA
5451721 CATCGCATGG
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
20 20 0.24
21 64 0.75
22 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (21 bp):
GAGAAGACCATTCATCAAGAC
Found at i:5454318 original size:17 final size:17
Alignment explanation
Indices: 5454298--5454337 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5454288 AGAGAAATGT
*
5454298 AGAAAGAGAA-AAGGAAA
1 AGAAA-AGAAGAAAGAAA
5454315 AGAAAAGAAGAAAGAAA
1 AGAAAAGAAGAAAGAAA
5454332 AGAAAA
1 AGAAAA
5454338 AATTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAGAAAGAAA
Found at i:5454328 original size:12 final size:11
Alignment explanation
Indices: 5454298--5454338 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5454288 AGAGAAATGT
*
5454298 AGAAAGAGAAA
1 AGAAAAAGAAA
*
5454309 AGGAAAAGAAA
1 AGAAAAAGAAA
5454320 AGAAGAAAGAAA
1 AGAA-AAAGAAA
5454332 AGAAAAA
1 AGAAAAA
5454339 ATTGAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:5459198 original size:8 final size:9
Alignment explanation
Indices: 5459167--5459209 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
5459157 AAATGAATGG
*
5459167 AAAAAAATG
1 AAAAAAATA
*
5459176 AAAAGAATA
1 AAAAAAATA
5459185 ATAAAAAAT-
1 A-AAAAAATA
5459194 AAAAAAATA
1 AAAAAAATA
5459203 AAAAAAA
1 AAAAAAA
5459210 AAGAGAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.24
9 16 0.55
10 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5459211 original size:19 final size:19
Alignment explanation
Indices: 5459167--5459210 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
5459157 AAATGAATGG
*
5459167 AAAAAAATGAAAAGAATAA
1 AAAAAAATGAAAAAAATAA
*
5459186 TAAAAAAT-AAAAAAATAA
1 AAAAAAATGAAAAAAATAA
5459204 AAAAAAA
1 AAAAAAA
5459211 AGAGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAAATGAAAAAAATAA
Found at i:5460278 original size:53 final size:52
Alignment explanation
Indices: 5460213--5460326 Score: 185
Period size: 53 Copynumber: 2.2 Consensus size: 52
5460203 AGGTTCCCTA
*
5460213 CGATCG-TGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGGGCGGACG
1 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGGG-AGACG
*
5460265 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTGAAGAAATAGGGGGAGACG
1 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGGGAGACG
*
5460317 CGATAGTTGA
1 CGATCGTTGA
5460327 CTCTGACGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 19 0.33
53 39 0.67
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (52 bp):
CGATCGTTGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGGGAGACG
Found at i:5460385 original size:86 final size:86
Alignment explanation
Indices: 5460240--5460402 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 86
5460230 CAAGTCTCAT
* *
5460240 ACTCTGAAGAAATAGGGGGCGGACGCGATCGTTGAAGATTGTTCAAGTCTTATACTCTGAAGAAA
1 ACTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTTCAAGTCTTATACTCTGAAGAAA
5460305 TAGGGGG-AGACGCGATAGTTG
66 T-GGGGGCAGACGCGATAGTTG
* * *
5460326 ACTCTGACGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GAGTCTTATACTCTCTGAAGA
1 ACTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTTCAAGTCTTATA--CTCTGAAGA
5460389 AATGGGGGCAGACG
64 AATGGGGGCAGACG
5460403 TGATCATTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
84 9 0.13
85 6 0.09
86 54 0.78
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.23
Consensus pattern (86 bp):
ACTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTTCAAGTCTTATACTCTGAAGAAA
TGGGGGCAGACGCGATAGTTG
Found at i:5460476 original size:55 final size:55
Alignment explanation
Indices: 5460327--5460496 Score: 256
Period size: 55 Copynumber: 3.1 Consensus size: 55
5460317 CGATAGTTGA
* *
5460327 CTCTGACGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GAGTCTTATACT
1 CTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACT
* **
5460380 CTCTGAAGAAAT-GGGGGCAGACGTGATCATTGAAGATTGTTCGAGTCTTATACT
1 CTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACT
* *
5460434 CTCTGAAGAAATAGGGGGCAGGCGCGATTGTTAAAGATTGTTCGAGTCTTATACT
1 CTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACT
5460489 CTCTGAAG
1 CTCTGAAG
5460497 GACTATGGAG
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
52 23 0.22
53 12 0.12
54 24 0.23
55 45 0.43
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
CTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACT
Found at i:5463968 original size:2 final size:2
Alignment explanation
Indices: 5463963--5464002 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5463953 CGTTTTAGTC
5463963 TA TA 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
5464003 ATTTTGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5469334 original size:6 final size:6
Alignment explanation
Indices: 5469295--5469323 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5469285 TTTCCATTTT
5469295 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
5469324 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (6 bp):
TTCTTG
Found at i:5471867 original size:22 final size:22
Alignment explanation
Indices: 5471839--5471900 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
5471829 GTAAAATTTA
*
5471839 TCCCGAAGTACATATGTATATG
1 TCCCGAAGGACATATGTATATG
* *
5471861 TCCCGAAGGACCTCTGTATATG
1 TCCCGAAGGACATATGTATATG
5471883 TCCCGAAGGATC-TATGTA
1 TCCCGAAGGA-CATATGTA
5471901 ACCCTCAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (22 bp):
TCCCGAAGGACATATGTATATG
Found at i:5479464 original size:171 final size:171
Alignment explanation
Indices: 5479179--5479512 Score: 668
Period size: 171 Copynumber: 2.0 Consensus size: 171
5479169 AGCAGTGTGT
5479179 TTCAGGATGACATCAGGGAAGGGTGACAAGTCTTCATTGGTGATTGGGAGTAGCTACTTGAAAAA
1 TTCAGGATGACATCAGGGAAGGGTGACAAGTCTTCATTGGTGATTGGGAGTAGCTACTTGAAAAA
5479244 GGCATTGAGTTGTGCATCCCTTACCTTGACATAGCCAAAGAAGATCTCTATGTGATTTTCCAGAT
66 GGCATTGAGTTGTGCATCCCTTACCTTGACATAGCCAAAGAAGATCTCTATGTGATTTTCCAGAT
5479309 GCTAGATCTTCTCACGGGTTTCTTGTGTGTATACCACACTG
131 GCTAGATCTTCTCACGGGTTTCTTGTGTGTATACCACACTG
5479350 TTCAGGATGACATCAGGGAAGGGTGACAAGTCTTCATTGGTGATTGGGAGTAGCTACTTGAAAAA
1 TTCAGGATGACATCAGGGAAGGGTGACAAGTCTTCATTGGTGATTGGGAGTAGCTACTTGAAAAA
5479415 GGCATTGAGTTGTGCATCCCTTACCTTGACATAGCCAAAGAAGATCTCTATGTGATTTTCCAGAT
66 GGCATTGAGTTGTGCATCCCTTACCTTGACATAGCCAAAGAAGATCTCTATGTGATTTTCCAGAT
5479480 GCTAGATCTTCTCACGGGTTTCTTGTGTGTATA
131 GCTAGATCTTCTCACGGGTTTCTTGTGTGTATA
5479513 TGACCACTAC
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 163 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (171 bp):
TTCAGGATGACATCAGGGAAGGGTGACAAGTCTTCATTGGTGATTGGGAGTAGCTACTTGAAAAA
GGCATTGAGTTGTGCATCCCTTACCTTGACATAGCCAAAGAAGATCTCTATGTGATTTTCCAGAT
GCTAGATCTTCTCACGGGTTTCTTGTGTGTATACCACACTG
Found at i:5491052 original size:19 final size:21
Alignment explanation
Indices: 5491025--5491067 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
5491015 CAATTATCTA
5491025 TCATCCTTTAG-AAAAC-TAG
1 TCATCCTTTAGCAAAACATAG
* *
5491044 TCATTCTTTGGCAAAACATAG
1 TCATCCTTTAGCAAAACATAG
5491065 TCA
1 TCA
5491068 AATGTGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 5 0.25
21 6 0.30
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
TCATCCTTTAGCAAAACATAG
Found at i:5494734 original size:42 final size:42
Alignment explanation
Indices: 5494688--5494767 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
5494678 ATTTTTATAT
* * *
5494688 AACCACACACAAACTAACCACTTAAGATCACACAATGACAAC
1 AACCAAACAAAAACTAACCACTCAAGATCACACAATGACAAC
* **
5494730 AACCAAACAAAAATTAGTCACTCAAGATCACACAATGA
1 AACCAAACAAAAACTAACCACTCAAGATCACACAATGA
5494768 ATTAAGATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.51, C:0.29, G:0.06, T:0.14
Consensus pattern (42 bp):
AACCAAACAAAAACTAACCACTCAAGATCACACAATGACAAC
Found at i:5496138 original size:30 final size:30
Alignment explanation
Indices: 5496104--5496160 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5496094 TCATACAATT
5496104 TCTAAATTTGACA-CCCCAAAATAAATTTTA
1 TCTAAATTTGACATCCCC-AAATAAATTTTA
5496134 TCTAAATTTGACATCCCCAAATAAATT
1 TCTAAATTTGACATCCCCAAATAAATT
5496161 ATCTAGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (30 bp):
TCTAAATTTGACATCCCCAAATAAATTTTA
Found at i:5496794 original size:2 final size:2
Alignment explanation
Indices: 5496717--5496774 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
5496707 TTTAAGTTAC
5496717 TA TA -A TA TA TA TA TA TA TA TA TA -A 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
5496757 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
5496775 CTAAAAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5501499 original size:2 final size:2
Alignment explanation
Indices: 5501492--5501523 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5501482 GGCTTCTGTG
5501492 AT 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 AT
5501524 CTTGTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5503461 original size:2 final size:2
Alignment explanation
Indices: 5503449--5503481 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5503439 TTAATTAAAT
*
5503449 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5503482 TTCAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5504286 original size:15 final size:14
Alignment explanation
Indices: 5504260--5504295 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
5504250 GTAAAAAAAT
5504260 AGAAAAAAATGTTA
1 AGAAAAAAATGTTA
5504274 AGAAAATAAATGTTA
1 AGAAAA-AAATGTTA
*
5504289 ATAAAAA
1 AGAAAAA
5504296 TACAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
AGAAAAAAATGTTA
Found at i:5504297 original size:16 final size:16
Alignment explanation
Indices: 5504257--5504297 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
5504247 AAAGTAAAAA
5504257 AATAGAAAA-AAATGTT
1 AATA-AAAATAAATGTT
*
5504273 AA-GAAAATAAATGTT
1 AATAAAAATAAATGTT
5504288 AATAAAAATA
1 AATAAAAATA
5504298 CAAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (16 bp):
AATAAAAATAAATGTT
Found at i:5505005 original size:17 final size:17
Alignment explanation
Indices: 5504983--5505016 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5504973 AAGTCTTTCC
5504983 TTTTATACTTTTGGTTT
1 TTTTATACTTTTGGTTT
**
5505000 TTTTATGTTTTTGGTTT
1 TTTTATACTTTTGGTTT
5505017 GATCGTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.74
Consensus pattern (17 bp):
TTTTATACTTTTGGTTT
Found at i:5507042 original size:65 final size:64
Alignment explanation
Indices: 5506930--5507052 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 64
5506920 ACATAAATCT
* * * *
5506930 CATTCGATGTTTGTATTTTAAGCGGGTGTATCGATGCACTACTTGTGCATCGATACACTGATGA
1 CATTCGATGTTTGTATTTTAAGCGAGTGCATCGATACACTACATGTGCATCGATACACTGATGA
* *
5506994 CATTCGATGTTTTTTATTTTAAAG-GAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCGATG-TTTGTATTTT-AAGCGAGTGCATCGATACACTACATGTGCATCGATACAC
5507053 CTTGAATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 9 0.18
65 39 0.76
66 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAGCGAGTGCATCGATACACTACATGTGCATCGATACACTGATGA
Found at i:5508369 original size:200 final size:200
Alignment explanation
Indices: 5508026--5508426 Score: 766
Period size: 200 Copynumber: 2.0 Consensus size: 200
5508016 AGAAACATTC
**
5508026 TTTCAATTATACTTTAACTTCTTTAATACATATAACTAAGTCTTTATCTTCTTATCTATAACATT
1 TTTCAATTATACTTTAACTTCCATAATACATATAACTAAGTCTTTATCTTCTTATCTATAACATT
5508091 TACTCCTCATCATAATTGCTGAAAACATATATTTCTAAAACCAAACCATCTTTCCACAACACCAT
66 TACTCCTCATCATAATTGCTGAAAACATATATTTCTAAAACCAAACCATCTTTCCACAACACCAT
5508156 ATATCATTTCCTTACTTCCTTATCAAACCTATAATTCACACTTTACACTCATTTCTAATTAATTT
131 ATATCATTTCCTTACTTCCTTATCAAACCTATAATTCACACTTTACACTCATTTCTAATTAATTT
5508221 CTTTA
196 CTTTA
5508226 TTTCAATTATACTTTAACTTCCATAATACATATAACTAAGTCTTTATCTTCTTATCTATAACATT
1 TTTCAATTATACTTTAACTTCCATAATACATATAACTAAGTCTTTATCTTCTTATCTATAACATT
*
5508291 TACTCCTCATCATAATTGGTGAAAACATATATTTCTAAAACCAAACCATCTTTCCACAACACCAT
66 TACTCCTCATCATAATTGCTGAAAACATATATTTCTAAAACCAAACCATCTTTCCACAACACCAT
*
5508356 CTATCATTTCCTTACTTCCTTATCAAACCTATAATTCACACTTTACACTCATTTCTAATTAATTT
131 ATATCATTTCCTTACTTCCTTATCAAACCTATAATTCACACTTTACACTCATTTCTAATTAATTT
5508421 CTTTA
196 CTTTA
5508426 T
1 T
5508427 ATCTATTTAA
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (200 bp):
TTTCAATTATACTTTAACTTCCATAATACATATAACTAAGTCTTTATCTTCTTATCTATAACATT
TACTCCTCATCATAATTGCTGAAAACATATATTTCTAAAACCAAACCATCTTTCCACAACACCAT
ATATCATTTCCTTACTTCCTTATCAAACCTATAATTCACACTTTACACTCATTTCTAATTAATTT
CTTTA
Found at i:5510486 original size:53 final size:53
Alignment explanation
Indices: 5510406--5510507 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
5510396 CCCAGATACA
5510406 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAATAAG
1 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAATAAG
* *
5510459 AGTCTGAAGTGTTACATTGACTTTTCAAACTTTGACACTTAAAGAAAAA
1 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAA
5510508 CATGGGAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (53 bp):
AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAATAAG
Found at i:5515248 original size:53 final size:53
Alignment explanation
Indices: 5515168--5515271 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
5515158 CCCGGATACA
5515168 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAACATG
1 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAACATG
* *
5515221 AGTCTGAAGTGTTACATTGACTTTTCAAACTTTGACACTTAAAGAAAAACA
1 AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAACA
5515272 GGGAATTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (53 bp):
AGTCTGAAGTGTCACATTGACTTTTCAAACTTTAACACTTAAAGAAAAACATG
Found at i:5516669 original size:20 final size:20
Alignment explanation
Indices: 5516644--5516712 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
5516634 GAAGGTATGC
*
5516644 ATCGATGCACTATACCATGT
1 ATCGATGCACTACACCATGT
*
5516664 ATCGATACACTACACCATGT
1 ATCGATGCACTACACCATGT
*
5516684 ATCGATGCAGTACACCATGT
1 ATCGATGCACTACACCATGT
5516704 ATCGATGCA
1 ATCGATGCA
5516713 TCCCTTGACG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
ATCGATGCACTACACCATGT
Found at i:5516875 original size:65 final size:64
Alignment explanation
Indices: 5516763--5516885 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 64
5516753 ACATAAATCC
* * *
5516763 CATTCAATGTTTGTATTTTAAGCGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGA
1 CATTCAATGTTTGTATTTTAAGCGAGTGCATCGATACACTACATGTGCATCGATACACTGATGA
* * *
5516827 CATTCGATGTTTTTTATTTTAAAG-GAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCAATG-TTTGTATTTT-AAGCGAGTGCATCGATACACTACATGTGCATCGATACAC
5516886 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 8 0.16
65 40 0.78
66 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (64 bp):
CATTCAATGTTTGTATTTTAAGCGAGTGCATCGATACACTACATGTGCATCGATACACTGATGA
Found at i:5517411 original size:26 final size:26
Alignment explanation
Indices: 5517372--5517424 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5517362 AACAACTAAT
5517372 AAGAATTCTGACCTTTACCTTGGTTC
1 AAGAATTCTGACCTTTACCTTGGTTC
*
5517398 AAGAATTCTTACCTTTACCTTGGTTC
1 AAGAATTCTGACCTTTACCTTGGTTC
5517424 A
1 A
5517425 TACGCACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (26 bp):
AAGAATTCTGACCTTTACCTTGGTTC
Found at i:5517953 original size:41 final size:40
Alignment explanation
Indices: 5517891--5518025 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 40
5517881 TAATGATATA
* * *
5517891 TATAACTATATA-ATATGTTTTCAAAAAACATTTTTAAAAC
1 TATAAATATATATAT-TATTTTCAAAAAATATTTTTAAAAC
* * *
5517931 TATAAAATATATATATTTTTTTCAAAAATTATTTTCAAAAC
1 TAT-AAATATATATATTATTTTCAAAAAATATTTTTAAAAC
*
5517972 TAT--ATA-ATATA-TATTTTCAAAAAATTTGTTTTCAAAAC
1 TATAAATATATATATTATTTTCAAAAAATAT-TTTT-AAAAC
5518010 TATATAATATATATAT
1 TATA-AATATATATAT
5518026 ATTCAAAATC
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
36 13 0.17
37 8 0.10
38 11 0.14
40 3 0.04
41 35 0.45
42 7 0.09
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (40 bp):
TATAAATATATATATTATTTTCAAAAAATATTTTTAAAAC
Found at i:5517989 original size:36 final size:36
Alignment explanation
Indices: 5517894--5518145 Score: 164
Period size: 38 Copynumber: 6.9 Consensus size: 36
5517884 TGATATATAT
* ** *
5517894 AACTATAT-A-ATATGTTTTCAAAAAACATTTTTAA
1 AACTATATAATATATATTTTCAAAAATTATTTTCAA
*
5517928 AACTATAAAATATATATATTTTTTTCAAAAATTATTTTCAA
1 AACTAT---ATA-ATATA-TATTTTCAAAAATTATTTTCAA
*
5517969 AACTATATAATATATATTTTCAAAAAATTTGTTTTCAA
1 AACTATATAATATATATTTTC-AAAAA-TTATTTTCAA
**
5518007 AACTATATAATATATATATATTC-AAAATCGTTTTCAA
1 AACTATATAATATATAT-T-TTCAAAAATTATTTTCAA
*** *
5518044 AACTATAT-ATAT-T-TTCAAAAGCAAATT-TTTTAAA
1 AACTATATAATATATATTTTCAA--AAATTATTTTCAA
* * * *
5518078 AAGTATATATTATATGTTTTCAAAAATCATTTTCTAAA
1 AACTATATAATATATATTTTCAAAAATTATTTTC--AA
*
5518116 AACTATAT-AT-TTTATTTTCAAAAA-TATTTT
1 AACTATATAATATATATTTTCAAAAATTATTTT
5518146 TGACAACTAT
Statistics
Matches: 174, Mismatches: 24, Indels: 39
0.73 0.10 0.16
Matches are distributed among these distances:
33 2 0.01
34 20 0.11
35 17 0.10
36 27 0.16
37 34 0.20
38 42 0.24
39 2 0.01
40 6 0.03
41 24 0.14
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (36 bp):
AACTATATAATATATATTTTCAAAAATTATTTTCAA
Found at i:5518104 original size:70 final size:71
Alignment explanation
Indices: 5517903--5518139 Score: 182
Period size: 70 Copynumber: 3.2 Consensus size: 71
5517893 TAACTATATA
* * * *
5517903 ATATGTTTTCAAAAAACA-T-TTTT-AAAACTATAAAATATATATATTTTTTTCAAAAATTATTT
1 ATATATTTTCAAAAAA-ATTGTTTTAAAAACTATATAATATATATA---TATTC-AAAATCATTT
*
5517965 TCAAAACTATATAAT
61 TCAAAA--A-CT-AT
* * *
5517980 ATATATTTTCAAAAAATTTGTTTTCAAAACTATATAATATATATATATTCAAAATCGTTTTC-AA
1 ATATATTTTCAAAAAAATTGTTTTAAAAACTATATAATATATATATATTCAAAATCATTTTCAAA
5518044 AACTAT
66 AACTAT
* * *
5518050 ATATATTTTCAAAAGCAAATT-TTTTAAAAAGTATAT-AT-TATATGTTTTCAAAAATCATTTTC
1 ATATATTTTCAAAA--AAATTGTTTTAAAAACTATATAATATATATATATTC-AAAATCATTTTC
5518112 TAAAAACTAT
63 -AAAAACTAT
5518122 ATATTTTATTTTCAAAAA
1 ATA---TATTTTCAAAAA
5518140 TATTTTTGAC
Statistics
Matches: 136, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
69 9 0.07
70 29 0.21
71 14 0.10
72 16 0.12
73 1 0.01
74 3 0.02
75 21 0.15
76 4 0.03
77 16 0.12
78 4 0.03
79 19 0.14
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (71 bp):
ATATATTTTCAAAAAAATTGTTTTAAAAACTATATAATATATATATATTCAAAATCATTTTCAAA
AACTAT
Found at i:5518268 original size:20 final size:20
Alignment explanation
Indices: 5518240--5518280 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5518230 ATAGACTCAT
5518240 ATTAAAAAAATTATAGAATG
1 ATTAAAAAAATTATAGAATG
* *
5518260 ATTAGAAAATTTATAGAATG
1 ATTAAAAAAATTATAGAATG
5518280 A
1 A
5518281 ACCGCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (20 bp):
ATTAAAAAAATTATAGAATG
Found at i:5521463 original size:3 final size:3
Alignment explanation
Indices: 5521442--5521483 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
5521432 GTAGTGGTAT
* *
5521442 ATA ATA ATTA ACA AAA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5521484 TTTTATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5522079 original size:124 final size:124
Alignment explanation
Indices: 5521924--5523337 Score: 1792
Period size: 124 Copynumber: 11.5 Consensus size: 124
5521914 GTTGACAGAC
* * * *
5521924 GCTCGTTCGCTGTGAAGTTGAGCTTTGAATTGGATATCTTTCATCGTGAAGTTGAAATCCAATCT
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* * * * * * *
5521989 AGAGATAAATGTTGTTTGTGGGCATGATATCCTCCGTCGTGAAATTAAAATCGTGGATG
66 AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * * *
5522048 GCCCCGTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCT
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
5522113 AAAGATGAATGTTG-TTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGCTT-GTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * *
5522172 GCTCATTCGTTGTGAAGTTGAGCTTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATTCAATCT
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* *
5522237 AAAGATGAATGTTG-TTGGTAGGCACGGTATCCTTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGCTT-GTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * **
5522296 GC-CCATTCGTTGTGAAGTTGAGCCTTGCATTGGATATCCTTCACCGTGAAGTTGAAATCCAATC
1 GCTCC-TTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC
* *
5522360 TAAAGATGAATGTTGCTTGTGGGCACGATATCCTTCATCATGAAGTTGAAATCGTGGATG
65 TAAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * * * *
5522420 GC-CGCTTCGTTGTGAAGTTGAGCCTAGAATTAGATATCTTTCGCCGTGAAGTTGAAATCCAATC
1 GCTC-CTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC
* *
5522484 TAAAGATGAATGTTG-TAGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATG
65 TAAAGATGAATGTTGCT-TGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * * *
5522544 GCCCCTTCGTTGTGAAGATGAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATCT
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* *
5522609 AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCATCGTGAAGTTGAAATCGCGGATG
66 AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
** * *
5522668 GCTCCTTTTTTGTGAAGTTGAGCTTTGAATTGGATATCATTCGTCGTGAAGTTGAAATTCAATCT
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
5522733 AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* *
5522792 GCTCTTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAT-T
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* * *
5522856 ---GTTGCATTGCTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATG-AATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * * * * *
5522913 GCTCTTTCATTGTGAAGTTGAGCTTTAAACTAGATATCCTTCGTTGTGAAGTTGAAATCC-A---
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
** * * * *
5522974 AGGGTTGTATTGTTGCTTATGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATG-AATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* * * * * * *
5523034 ACTTCTTCATTATGAAGTTGAGCTTTGAATTAGATATCCTTCGCCGTGAAGTTAAAATCC-A---
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
** * * * * * *
5523095 AGGGTTTTATTGCTGCTTGTGGGCACAATATCCTTCGTCGTGAAGTTGAAACCGTGGATG
66 AAAG-ATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
* *
5523155 GCTCCTTCATTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTGGAAATCC-A---
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
** * * * * * * *
5523216 AGGGTTGTATTGCTACTTGTGGGTACGATATCCTTCATCGTGTAA-TTGAAATCGTTGATG
66 AAAGATG-AATGTTGCTTGTGGGCACGATATCCTTCGTCGTG-AAGTTGAAATCGTGGATG
* *
5523276 GCTCATTCGTTGTGAAGTTGAGCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
1 GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
5523338 ATTGGTTTTG
Statistics
Matches: 1162, Mismatches: 113, Indels: 32
0.89 0.09 0.02
Matches are distributed among these distances:
120 6 0.01
121 417 0.36
122 5 0.00
123 5 0.00
124 724 0.62
125 5 0.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (124 bp):
GCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
AAAGATGAATGTTGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
Found at i:5522955 original size:66 final size:65
Alignment explanation
Indices: 5522879--5523213 Score: 221
Period size: 66 Copynumber: 5.4 Consensus size: 65
5522869 TTGTGGGCAC
*
5522879 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCTTTCATTGTGAAGTTGAGCTTTAAACT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCT-TTTCATTGTGAAGTTGAGCTTTGAACT
5522944 A
65 A
* * * * * **
5522945 GATATCCTTCGTTGTGAAGTTGAAATC---CAAGGGTTGT-A-T-T---GTT--GCTTATGGGC-
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTTTTCATTGTGAAGTTGAGCTT-TGAACT
5522998 A
65 A
* * * *
5522999 CGATATCATTCGTCGTGAAGTTGAAATCGTGGATGACTTCTTCATTATGAAGTTGAGCTTTGAAT
1 -GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTT-TTCATTGTGAAGTTGAGCTTTGAAC
5523064 TA
64 TA
* * * * * * ** *
5523066 GATATCCTTCGCCGTGAAGTTAAAATC---CAAGGGTTTT-ATTGCTG--CTT--G-TGGGCAC-
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTTTTCATTG-TGAAGTTGAGCTTTGAACT
5523121 A
65 A
* * *
5523122 -ATATCCTTCGTCGTGAAGTTGAAACCGTGGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCT-TTTCATTGTGAAGTTGAGCTTTGAACT
*
5523186 G
65 A
*
5523187 GATATCCTTCGTCGTGAAGTGGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
5523214 CAAGGGTTGT
Statistics
Matches: 195, Mismatches: 46, Indels: 56
0.66 0.15 0.19
Matches are distributed among these distances:
54 5 0.03
55 50 0.26
56 4 0.02
57 3 0.02
58 9 0.05
59 6 0.03
60 8 0.04
61 7 0.04
62 7 0.04
63 9 0.05
64 3 0.02
65 3 0.02
66 76 0.39
67 5 0.03
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (65 bp):
GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTTTTCATTGTGAAGTTGAGCTTTGAACTA
Found at i:5524543 original size:95 final size:95
Alignment explanation
Indices: 5524415--5524600 Score: 284
Period size: 95 Copynumber: 2.0 Consensus size: 95
5524405 CTGCTCAATA
* *
5524415 TATAGACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGC-C
1 TATAGACACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCTC
* *
5524479 TTAGAGGGACAGCTCGAGCTTTATTGTATAG
66 -TAGAGGGACAACTCAAGCTTTATTGTATAG
* * *
5524510 TATAGTCACCTTTATCAAGCTAGTTGAATCTTATCCATAAATTCGGGGCGTTTAACCAATTGCTC
1 TATAGACACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCTC
*
5524575 TAGAGGGACAATTCAAGCTTTATTGT
66 TAGAGGGACAACTCAAGCTTTATTGT
5524601 GTATATATAA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 81 0.99
96 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (95 bp):
TATAGACACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCTC
TAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:5526082 original size:18 final size:19
Alignment explanation
Indices: 5526038--5526082 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5526028 TGAATGATGC
*
5526038 AAATGATACAAATAAAATG
1 AAATGAAACAAATAAAATG
* *
5526057 AAAGGAAACAAA-AAATTG
1 AAATGAAACAAATAAAATG
5526075 AAATGAAA
1 AAATGAAA
5526083 AAGTTAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.16
Consensus pattern (19 bp):
AAATGAAACAAATAAAATG
Found at i:5527035 original size:13 final size:13
Alignment explanation
Indices: 5527019--5527060 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
5527009 CTTAATGGTG
5527019 AAAATTAAAAATT
1 AAAATTAAAAATT
5527032 AAAATT-AAAATT
1 AAAATTAAAAATT
** *
5527044 TTAATTAAAAATC
1 AAAATTAAAAATT
5527057 AAAA
1 AAAA
5527061 ATGTTAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:5528723 original size:11 final size:11
Alignment explanation
Indices: 5528707--5528731 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5528697 AGGAAAGGCG
5528707 GGTTAATATAC
1 GGTTAATATAC
5528718 GGTTAATATAC
1 GGTTAATATAC
5528729 GGT
1 GGT
5528732 AGTATCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:5529554 original size:227 final size:228
Alignment explanation
Indices: 5528978--5529693 Score: 1328
Period size: 227 Copynumber: 3.1 Consensus size: 228
5528968 GTTATATTGT
* * * *
5528978 AAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
* *
5529042 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
*
5529107 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
5529172 AAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAATTGAAACATAAATTACATAACTTTAAAA
5529205 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
5529270 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
5529335 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
5529400 AAAAATTGAAACATAAATTACATAACTTT-AAA
196 AAAAATTGAAACATAAATTACATAACTTTAAAA
5529432 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
5529497 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
5529562 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
* *
5529627 AAAAATTGAAACGTGAATTACATAACTTTAAAA
196 AAAAATTGAAACATAAATTACATAACTTTAAAA
*
5529660 AAAGTATATATCATTTTTATAAAAGTGTACATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
5529694 GTATAAAAGT
Statistics
Matches: 477, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
227 268 0.56
228 209 0.44
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.40
Consensus pattern (228 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATAAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:5529765 original size:20 final size:19
Alignment explanation
Indices: 5529742--5529788 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
5529732 CGATATACCA
5529742 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
5529762 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
5529782 GGTAAAA
1 GGTAAAA
5529789 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5529945 original size:20 final size:19
Alignment explanation
Indices: 5529922--5529968 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5529912 CGATATAACA
5529922 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
5529942 GGTATCAAAATGATAAAACT
1 GGTA-AAAAATGATAAAACC
5529962 GGTAAAA
1 GGTAAAA
5529969 TGATATCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5532214 original size:21 final size:21
Alignment explanation
Indices: 5532190--5532233 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5532180 AAGACAATCA
5532190 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
5532211 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
5532232 AG
1 AG
5532234 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:5532310 original size:33 final size:33
Alignment explanation
Indices: 5532268--5532333 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
5532258 AAATAGATGG
*
5532268 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
5532301 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
5532334 TATTAAGATG
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:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:5534143 original size:19 final size:19
Alignment explanation
Indices: 5534119--5534167 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5534109 AATGTAGGGT
5534119 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
5534138 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
5534157 TATTTTTGTAT
1 TAATTTTGTAT
5534168 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5534891 original size:199 final size:200
Alignment explanation
Indices: 5534286--5535458 Score: 2167
Period size: 199 Copynumber: 5.9 Consensus size: 200
5534276 CAATATGGCC
*
5534286 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
5534351 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5534416 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
5534481 TGGAA
196 TGGAA
*
5534486 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTTGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
5534551 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5534616 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
5534681 TGGAA
196 TGGAA
* *
5534686 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
5534750 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGATTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5534815 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
5534880 TGGAA
196 TGGAA
*
5534885 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
* *
5534950 CCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTTTACCAGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5535015 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
5535080 TGGAA
196 TGGAA
* * *
5535085 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
*
5535149 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCAGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
*
5535214 GAATATGTCTAAATAATGTGTCGGCACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
5535279 TGGAA
196 TGGAA
* *
5535284 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
5535348 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5535413 GAATATGTCTAAATAATGTGTCGACACGT--TTTAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACAC-TAATTTAGTTTGTGTCGATA
5535459 CTAATTTAAA
Statistics
Matches: 948, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
198 17 0.02
199 481 0.51
200 450 0.47
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
TGGAA
Found at i:5535025 original size:399 final size:399
Alignment explanation
Indices: 5534286--5535458 Score: 2190
Period size: 399 Copynumber: 2.9 Consensus size: 399
5534276 CAATATGGCC
* * *
5534286 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
5534351 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
5534416 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
*
5534481 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTTGATCCCAAAAACATC
195 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
5534546 GAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTA
260 GAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTA
5534611 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGA
325 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGA
5534676 ATGAATGGAA
390 ATGAATGGAA
5534686 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
5534751 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
5534816 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
5534881 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
* *
5534946 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTTTACCAGTTTTAT
261 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
5535011 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
326 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
5535076 TGAATGGAA
391 TGAATGGAA
*
5535085 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
5535150 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCAGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
*
5535215 AATATGTCTAAATAATGTGTCGGCACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
5535280 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
*
5535345 -AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
261 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
5535409 GAGAGAATATGTCTAAATAATGTGTCGACACGT--TTTAGTTTGTGTCGATA
326 GAGAGAATATGTCTAAATAATGTGTCGACAC-TAATTTAGTTTGTGTCGATA
5535459 CTAATTTAAA
Statistics
Matches: 755, Mismatches: 17, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
397 17 0.02
398 92 0.12
399 587 0.78
400 59 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (399 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG
AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
TGAATGGAA
Found at i:5537053 original size:18 final size:18
Alignment explanation
Indices: 5537032--5537068 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5537022 GTAATTGGAG
5537032 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5537050 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5537068 T
1 T
5537069 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5537076 original size:24 final size:24
Alignment explanation
Indices: 5537024--5537070 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5537014 TTTCATATGT
* *
5537024 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
5537048 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
5537071 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:5537370 original size:39 final size:39
Alignment explanation
Indices: 5537327--5537413 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
5537317 TCCGATGCTC
*
5537327 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
5537366 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
5537405 ATCAAAATC
1 ATCAAAATC
5537414 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:5537861 original size:23 final size:23
Alignment explanation
Indices: 5537830--5537902 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
5537820 ATAGGTAAAA
*
5537830 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5537853 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
5537876 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
5537899 ATAT
1 ATAT
5537903 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5538331 original size:21 final size:23
Alignment explanation
Indices: 5538260--5538332 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
5538250 ATAGGTAAAA
* *
5538260 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5538283 ATATAATGTAATAGGTA-TAGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5538306 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5538329 ATAT
1 ATAT
5538333 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5538439 original size:430 final size:429
Alignment explanation
Indices: 5537628--5538680 Score: 2004
Period size: 430 Copynumber: 2.5 Consensus size: 429
5537618 GTTAATGTTG
*
5537628 TTAAATTAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATATTTTTTTGTGCAAAT
1 TTAAATTAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAAT
5537693 GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAA
66 GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAA
5537758 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACA-TTTTCAATATAAT
131 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTT-AATATAAT
*
5537822 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATAGTTTATATAATGTAA
5537887 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
5537952 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTCTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTCTTAAGATATTAATTTAGTAATTATAGGC
*
5538017 GTCTAATGATTTATTTTTTTCGTTACGATATATATTATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
*
5538057 TTAAATTAAAATTTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAA-TTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAA
5538122 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
65 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
5538187 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTTAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTTAATATAAT
5538252 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATAGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATAGTTTATATAATGTAA
5538317 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
*
5538382 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTCTTAAGATATTAATTTAGTAATTATAGGC
5538447 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
5538487 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAA-TTTTTGTGCAAA
1 TTAAATT-AAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAA
5538551 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATA
65 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
*
5538615 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTTAATATAAT
5538680 A
195 A
5538681 TAATGTAATA
Statistics
Matches: 614, Mismatches: 7, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
428 82 0.13
429 70 0.11
430 454 0.74
431 8 0.01
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (429 bp):
TTAAATTAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAAT
GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTTAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATAGTTTATATAATGTAAT
AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTCTTAAGATATTAATTTAGTAATTATAGGCG
TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:5538521 original size:29 final size:30
Alignment explanation
Indices: 5538478--5538543 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
5538468 GTTACGATAT
* *
5538478 ATATTATTATTAAAT-T-AAAAATTCTAAATA
1 ATATT-TTATAAAATATCAAAAAATC-AAATA
5538508 ATATTTTATAAAATATCAAAAAATCAAATA
1 ATATTTTATAAAATATCAAAAAATCAAATA
5538538 AT-TTTT
1 ATATTTT
5538544 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.38
30 13 0.41
31 7 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATTTTATAAAATATCAAAAAATCAAATA
Found at i:5539769 original size:3 final size:3
Alignment explanation
Indices: 5539761--5539788 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5539751 GAATATGGTT
5539761 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
5539789 AATAGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:5541681 original size:2 final size:2
Alignment explanation
Indices: 5541676--5541707 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5541666 CCCTTTTTTG
5541676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5541708 ACGTTGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5543066 original size:3 final size:3
Alignment explanation
Indices: 5543045--5543117 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
5543035 ATTAAATATG
* * * *
5543045 ATT ATG ATT ATT ATG ATT ATT ATG ATT ATT ATG ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5543093 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5543118 AAGTTTTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5543368 original size:16 final size:17
Alignment explanation
Indices: 5543344--5543377 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5543334 TGTCAGTATT
5543344 TTTTATTATATT-TATA
1 TTTTATTATATTATATA
*
5543360 TTTTCTTATATTATATA
1 TTTTATTATATTATATA
5543377 T
1 T
5543378 ATATTTTTAA
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:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTATATTATATA
Found at i:5546243 original size:32 final size:31
Alignment explanation
Indices: 5546197--5546333 Score: 179
Period size: 32 Copynumber: 4.3 Consensus size: 31
5546187 GAGTCGAGGG
*
5546197 TTACCTATGACTTTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
*
5546229 TTACCTATGTCTTTCGGGACATATGAACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAG-A
*
5546261 TTACCTATGTCTTTTGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAG-A
*
5546293 TTACCTATGT-TCTTCGGGACATATAGACA-A
1 TTACCTATGTCT-TTCGGGACATATGGACAGA
5546323 TTTACCTATGT
1 -TTACCTATGT
5546334 TCTTAGGAAC
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.01
31 12 0.13
32 82 0.86
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:5546282 original size:64 final size:63
Alignment explanation
Indices: 5546197--5546333 Score: 197
Period size: 64 Copynumber: 2.2 Consensus size: 63
5546187 GAGTCGAGGG
* * *
5546197 TTACCTATGACTTTCGGGACATATGGACAGGATTACCTATG-TCTTTCGGGACATAT-GAACAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTTC-TTCGGGACATATAG-ACAAT
*
5546260 ATTACCTATGTCTTTTGGGACATATGGACAGAATTACCTATGTTCTTCGGGACATATAGACAAT
1 -TTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTTCTTCGGGACATATAGACAAT
5546324 TTACCTATGT
1 TTACCTATGT
5546334 TCTTAGGAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
63 10 0.15
64 54 0.81
65 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTTCTTCGGGACATATAGACAAT
Found at i:5546346 original size:31 final size:32
Alignment explanation
Indices: 5546212--5546347 Score: 136
Period size: 32 Copynumber: 4.3 Consensus size: 32
5546202 TATGACTTTC
* * *
5546212 GGGACATATGGACAGGATTACCTATG-TCTTTC
1 GGGACATATAGACAGAATTACCTATGTTC-TTA
* *
5546244 GGGACATAT-GAACAGTATTACCTATG-TCTTTT
1 GGGACATATAG-ACAGAATTACCTATGTTC-TTA
* *
5546276 GGGACATATGGACAGAATTACCTATGTTCTTC
1 GGGACATATAGACAGAATTACCTATGTTCTTA
*
5546308 GGGACATATAGACA-ATTTACCTATGTTCTTA
1 GGGACATATAGACAGAATTACCTATGTTCTTA
*
5546339 GGAACATAT
1 GGGACATAT
5546348 GGTGTAACAC
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
31 24 0.26
32 66 0.71
33 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (32 bp):
GGGACATATAGACAGAATTACCTATGTTCTTA
Found at i:5547165 original size:22 final size:22
Alignment explanation
Indices: 5547138--5547203 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
5547128 ATGTGAAATT
5547138 TATCCCGAAGGACCACTATATA
1 TATCCCGAAGGACCACTATATA
* * *
5547160 TGTCCCGAAAGACCACTGTATA
1 TATCCCGAAGGACCACTATATA
5547182 TATCCCGAAGGACCACTATATA
1 TATCCCGAAGGACCACTATATA
5547204 ACTCTAAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (22 bp):
TATCCCGAAGGACCACTATATA
Found at i:5554510 original size:45 final size:46
Alignment explanation
Indices: 5554461--5554548 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
5554451 GAACATTGAA
* *
5554461 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACTAGACCATGCATCGATGCACTTAG
5554506 TGCATTTGATGCATCGATGCACTAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACTAGACCATGCATCGATGCACT
5554549 CAGGCTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACTAGACCATGCATCGATGCACTTAG
Found at i:5562721 original size:31 final size:31
Alignment explanation
Indices: 5562661--5562721 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5562651 TAACGACTAA
* **
5562661 TGGTTAATAAATTAGCAAAGTTAGTGGTTAG
1 TGGTTAATAAATTAACAAAGTTAACGGTTAG
5562692 TGGTTAATAAATTAACAAAGTTAACGGTTA
1 TGGTTAATAAATTAACAAAGTTAACGGTTA
5562722 AATTAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (31 bp):
TGGTTAATAAATTAACAAAGTTAACGGTTAG
Found at i:5563223 original size:23 final size:23
Alignment explanation
Indices: 5563188--5563259 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
5563178 CAGTACTAAC
* *
5563188 TGATTAAGCAAAATAATGTTGAA
1 TGATTAAGCAAAACAATGCTGAA
* *
5563211 TGATTCAGTAAAACAATGCTGAA
1 TGATTAAGCAAAACAATGCTGAA
* *
5563234 TGATTTAGCAAAACAGTGCTGAA
1 TGATTAAGCAAAACAATGCTGAA
5563257 TGA
1 TGA
5563260 CAGAAGTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (23 bp):
TGATTAAGCAAAACAATGCTGAA
Found at i:5565496 original size:43 final size:43
Alignment explanation
Indices: 5565435--5565518 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
5565425 TGTGATTCTG
* *
5565435 AGCACATCAGTGACGTCTGTGTGACGGTGGTGCGTAA-GTACTT
1 AGCACATCAGTGACGTCTGAGTGAAGGTGGTGC-TAATGTACTT
5565478 AGCACATCAGTGACGTCTGAGTGAAGGTGGTGCTAATGTAC
1 AGCACATCAGTGACGTCTGAGTGAAGGTGGTGCTAATGTAC
5565519 CGGGAATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 3 0.08
43 35 0.92
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (43 bp):
AGCACATCAGTGACGTCTGAGTGAAGGTGGTGCTAATGTACTT
Found at i:5565590 original size:20 final size:20
Alignment explanation
Indices: 5565565--5565606 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5565555 GTGATGGTGG
5565565 TGCCTACACATAAATGATGA
1 TGCCTACACATAAATGATGA
5565585 TGCCTACACATAAATGATGA
1 TGCCTACACATAAATGATGA
5565605 TG
1 TG
5565607 GTGCGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCCTACACATAAATGATGA
Found at i:5565604 original size:23 final size:22
Alignment explanation
Indices: 5565556--5565606 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
5565546 GACATCCAAG
* *
5565556 TGATGGTGGTGCCTACACATAA
1 TGATGATGATGCCTACACATAA
5565578 --ATGATGATGCCTACACATAAA
1 TGATGATGATGCCTACACAT-AA
5565599 TGATGATG
1 TGATGATG
5565607 GTGCGATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 16 0.67
21 2 0.08
23 6 0.25
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (22 bp):
TGATGATGATGCCTACACATAA
Found at i:5568838 original size:13 final size:15
Alignment explanation
Indices: 5568807--5568839 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5568797 TTTATTGTTT
5568807 AAAATATAATAATTA
1 AAAATATAATAATTA
5568822 AAAATATAA-AA-TA
1 AAAATATAATAATTA
5568835 AAAAT
1 AAAAT
5568840 CGAAGGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATAATAATTA
Found at i:5581332 original size:36 final size:36
Alignment explanation
Indices: 5581289--5581371 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
5581279 ACCAAATTAA
* *
5581289 ACGGGGACGGGGAAAAATCGTTTATGCTAAACGGGG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGAGG
* *
5581325 ACGGGGACAGGGAAAAACCGTTTATGTTAAACGAGG
1 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGAGG
* *
5581361 ATGGCGACGGG
1 ACGGGGACGGG
5581372 ACGAGTTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.31, C:0.14, G:0.39, T:0.16
Consensus pattern (36 bp):
ACGGGGACGGGGAAAAACCGTTTATGCTAAACGAGG
Done.