Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 21 of 168
Found at i:5468365 original size:44 final size:43
Alignment explanation
Indices: 5468303--5468555 Score: 165
Period size: 44 Copynumber: 5.8 Consensus size: 43
5468293 ATAATTTCAG
5468303 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-TAGTA
* * * * * *
5468347 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAG-G
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAA-GTAGTA
* * * * * *
5468391 ATCTTATCTCTCTGA-AGTTACAACAGAGTAGATCG-CGTCAG--
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGT-AGTA
* * * ** ** * *
5468432 GTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTA-GT-A
5468477 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 -ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-TAGTA
* * * *
5468522 ATCCTATCTCCCTGAGATTAAAGTGGAGCGGATT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
5468556 AAAATGAAGG
Statistics
Matches: 156, Mismatches: 41, Indels: 24
0.71 0.19 0.11
Matches are distributed among these distances:
41 27 0.17
42 4 0.03
43 1 0.01
44 85 0.54
45 5 0.03
46 33 0.21
47 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGTA
Found at i:5468458 original size:85 final size:85
Alignment explanation
Indices: 5468355--5468633 Score: 303
Period size: 85 Copynumber: 3.2 Consensus size: 85
5468345 TAATCCTATC
5468355 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGT
1 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGT
5468420 AGATCGCGTCAGGTCTTATT
66 AGATCGCGTCAGGTCTTATT
*** ** ** * * *
5468440 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA-GATCTTATCTCCCTG-AGATTACAGCG
1 TCCCTGAGATTACAGTGGAGCGGA-TTAA-AA-TGAAGGATCTTATCTCTCTGAAG-TTACAACA
* * * * * *
5468503 GAGCAGATTGAAG-CTAGTAATCCTATC
62 GAGTAGATCG-CGTC-AG--GTCTTATT
* *
5468530 TCCCTGAGATTAAAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAATTTACAACAGAGT
1 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGT
5468595 AGATCGCGTCAGGTCTTATT
66 AGATCGCGTCAGGTCTTATT
5468615 TCCCTGAGATTACAGTGGA
1 TCCCTGAGATTACAGTGGA
5468634 ACAGACCGAA
Statistics
Matches: 148, Mismatches: 35, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
85 44 0.30
86 4 0.03
87 36 0.24
88 36 0.24
89 3 0.02
90 25 0.17
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (85 bp):
TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGT
AGATCGCGTCAGGTCTTATT
Found at i:5468549 original size:175 final size:175
Alignment explanation
Indices: 5468254--5468686 Score: 785
Period size: 175 Copynumber: 2.5 Consensus size: 175
5468244 GTTCATTATA
*
5468254 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAATAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
*
5468319 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAAAGTGGAGCGGATTAAA
5468384 ATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCGT
131 ATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCGT
5468429 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
5468494 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAAAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAAAGTGGAGCGGATTAAA
*
5468559 ATGAAGGATCTTATCTCTCTGAATTTACAACAGAGTAGATCGCGT
131 ATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCGT
* * * *
5468604 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAAATCCTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
* *
5468669 ATTACAGTGGAGCGGATT
66 ATTACAGCGGAGCAGATT
5468687 AAAATGAAGG
Statistics
Matches: 249, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 249 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (175 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAAAGTGGAGCGGATTAAA
ATGAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCGT
Found at i:5468667 original size:46 final size:45
Alignment explanation
Indices: 5468615--5468943 Score: 132
Period size: 46 Copynumber: 7.5 Consensus size: 45
5468605 AGGTCTTATT
5468615 TCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAAATCCTATC
1 TCCCTGAGATTACAGTGGAACAGACCGAAGAA-TGCAAATCCTATC
* * ** *
5468661 TCCCTGAGATTACAGTGGAGCGGA-TTAA-AATG-AAGGATCTTATC
1 TCCCTGAGATTACAGTGGAACAGACCGAAGAATGCAA--ATCCTATC
* *** ** * * ** * *
5468705 TCTCTGA-AGTTACAACAGAGTAGATC-ACG--T-CAGTTCTTATT
1 TCCCTGAGA-TTACAGTGGAACAGACCGAAGAATGCAAATCCTATC
5468746 TCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAAATCCTATC
1 TCCCTGAGATTACAGTGGAACAGACCGAAGAA-TGCAAATCCTATC
* * * ** *
5468792 TCCCTGATATTACAGTGGAGCGGA-TTAA-AATG-AAGGATCTTATC
1 TCCCTGAGATTACAGTGGAACAGACCGAAGAATGCAA--ATCCTATC
* *** ** * * ** * *
5468836 TCTCTGA-AGTTACAACAGAGTAGATC-ACG--T-CAGGTCTTATT
1 TCCCTGAGA-TTACAGTGGAACAGACCGAAGAATGCAAATCCTATC
*
5468877 TCCCTGAGATTATAGTGGAACAGACCGAAGAATTGCAAATCCTATC
1 TCCCTGAGATTACAGTGGAACAGACCGAAGAA-TGCAAATCCTATC
*
5468923 TCCCTGAGATTACAGAGGAAC
1 TCCCTGAGATTACAGTGGAAC
5468944 GGATTAAAAT
Statistics
Matches: 199, Mismatches: 60, Indels: 48
0.65 0.20 0.16
Matches are distributed among these distances:
41 45 0.23
42 10 0.05
43 10 0.05
44 52 0.26
45 6 0.03
46 76 0.38
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
TCCCTGAGATTACAGTGGAACAGACCGAAGAATGCAAATCCTATC
Found at i:5468678 original size:131 final size:131
Alignment explanation
Indices: 5468521--5469079 Score: 974
Period size: 131 Copynumber: 4.3 Consensus size: 131
5468511 TGAAGCTAGT
* *
5468521 AATCCTATCTCCCTGAGATTAAAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAATTTA
1 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
*
5468586 CAACAGAGTAGATCGCGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
66 CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
5468651 A
131 A
5468652 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
*
5468717 CAACAGAGTAGATCACGTCAGTTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
66 CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
5468782 A
131 A
*
5468783 AATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
*
5468848 CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTATAGTGGAACAGACCGAAGAATTGC
66 CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
5468913 A
131 A
* *
5468914 AATCCTATCTCCCTGAGATTACAGAGGAACGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
* * *
5468979 CAACAGAGTAGATCGCGTCAGGTCTTATTTCCCTGAGATTACAGTAGAACAGACCGAAGAATTTC
66 CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
5469044 A
131 A
* * * * *
5469045 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATT
1 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
5469080 GAAGCTAGTA
Statistics
Matches: 408, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 408 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (131 bp):
AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTA
CAACAGAGTAGATCACGTCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
A
Found at i:5469902 original size:16 final size:16
Alignment explanation
Indices: 5469883--5469915 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5469873 TAATTTCTTC
5469883 TATTTTTTATTTATTT
1 TATTTTTTATTTATTT
*
5469899 TATTTTTTGTTTATTT
1 TATTTTTTATTTATTT
5469915 T
1 T
5469916 CTACAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TATTTTTTATTTATTT
Found at i:5473375 original size:9 final size:9
Alignment explanation
Indices: 5473361--5473386 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5473351 TTCAACCAAT
5473361 ATTATAAAA
1 ATTATAAAA
5473370 ATTATAAAA
1 ATTATAAAA
5473379 ATTATAAA
1 ATTATAAA
5473387 TGATGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTATAAAA
Found at i:5474297 original size:21 final size:22
Alignment explanation
Indices: 5474273--5474319 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
5474263 AAACTGTTAC
5474273 AAAACACTAG-AAAACGTCACA
1 AAAACACTAGAAAAACGTCACA
*
5474294 AAAACACTAGAAAAATGTCACA
1 AAAACACTAGAAAAACGTCACA
5474316 AAAA
1 AAAA
5474320 GCATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.62, C:0.19, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAACACTAGAAAAACGTCACA
Found at i:5474660 original size:72 final size:71
Alignment explanation
Indices: 5474520--5474662 Score: 166
Period size: 72 Copynumber: 2.0 Consensus size: 71
5474510 AAACATCATA
* * *
5474520 GATTGATTGCCTCTTTTCTGGCATTTAAAAACGTCACGAAAAATGCTATCCAAAATGTGACACGT
1 GATTGATTGCCTCTTTTCTGGAATTTAAAAACATCACGAAAAATGCTATCCAAAACGT-ACACGT
5474585 TGTTTGT
65 TGTTTGT
* * *
5474592 GATTGATTGCCTCTTTT-T-TAATGTATAAAAACATCACGAAAAATTCTATTCAAAACGT-CACG
1 GATTGATTGCCTCTTTTCTGGAAT-T-TAAAAACATCACGAAAAATGCTATCCAAAACGTACACG
5474654 AATTGTTTG
64 --TTGTTTG
5474663 ATTATTTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
70 6 0.10
71 2 0.03
72 53 0.87
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (71 bp):
GATTGATTGCCTCTTTTCTGGAATTTAAAAACATCACGAAAAATGCTATCCAAAACGTACACGTT
GTTTGT
Found at i:5475631 original size:42 final size:42
Alignment explanation
Indices: 5475572--5475654 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
5475562 TGCTTTAGAA
*
5475572 CCACACGGTCAAGGACATAGACGTGTGCCCAGGCCATGTAAG
1 CCACACGGGCAAGGACATAGACGTGTGCCCAGGCCATGTAAG
* * *
5475614 CCACACGGGCAAGGACATGGGCGTGTGTCCAGGCCATGTAA
1 CCACACGGGCAAGGACATAGACGTGTGCCCAGGCCATGTAA
5475655 CTCACTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.27, C:0.28, G:0.31, T:0.14
Consensus pattern (42 bp):
CCACACGGGCAAGGACATAGACGTGTGCCCAGGCCATGTAAG
Found at i:5475648 original size:104 final size:105
Alignment explanation
Indices: 5475491--5475714 Score: 303
Period size: 104 Copynumber: 2.2 Consensus size: 105
5475481 GACATGGGCT
* * *
5475491 TGTGCCTAGG-CAGTGTGAGCCACACCGACAAGGACATGGGCGTGTGTCCAGGCCGTGTAACTCA
1 TGTGCCCAGGCCAGTGTAAGCCACACCGACAAGGACATGGGCGTGTGTCCAGGCCATGTAACTCA
* *
5475555 CTGTTTATGCTTTAGAACCACACG-GTCAAGGACATAGACG
66 CTGTTTATGATTAAGAACCACACGAG-CAAGGACATAGACG
* *
5475595 TGTGCCCAGGCCA-TGTAAGCCACACGGGCAAGGACATGGGCGTGTGTCCAGGCCATGTAACTCA
1 TGTGCCCAGGCCAGTGTAAGCCACACCGACAAGGACATGGGCGTGTGTCCAGGCCATGTAACTCA
* * * *
5475659 CTTTTTATGATTAAGAACCACATGAGCAAGGACATGGGCG
66 CTGTTTATGATTAAGAACCACACGAGCAAGGACATAGACG
*
5475699 TGTGTCCAGGCC-GTGT
1 TGTGCCCAGGCCAGTGT
5475715 GGCATATGAA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
104 102 0.97
105 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (105 bp):
TGTGCCCAGGCCAGTGTAAGCCACACCGACAAGGACATGGGCGTGTGTCCAGGCCATGTAACTCA
CTGTTTATGATTAAGAACCACACGAGCAAGGACATAGACG
Found at i:5480843 original size:2 final size:2
Alignment explanation
Indices: 5480836--5480860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5480826 TACTTGAAGC
5480836 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5480861 AGTTTAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5481239 original size:24 final size:24
Alignment explanation
Indices: 5481207--5481267 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
5481197 GCTTCTGCTG
5481207 CCACTTGATCTTTCGTTGCTTCTT
1 CCACTTGATCTTTCGTTGCTTCTT
5481231 CCACTTGATCTTTCGTTGCTTCTT
1 CCACTTGATCTTTCGTTGCTTCTT
5481255 CCACTTGATCTTT
1 CCACTTGATCTTT
5481268 TGCTAGACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.10, C:0.30, G:0.11, T:0.49
Consensus pattern (24 bp):
CCACTTGATCTTTCGTTGCTTCTT
Found at i:5486679 original size:22 final size:22
Alignment explanation
Indices: 5486645--5486686 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5486635 ATTTTAAAAT
**
5486645 TAATTTGTTTTTAATAAAATGA
1 TAATTTGACTTTAATAAAATGA
*
5486667 TAATTTGACTTTAGTAAAAT
1 TAATTTGACTTTAATAAAAT
5486687 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
TAATTTGACTTTAATAAAATGA
Found at i:5489111 original size:20 final size:20
Alignment explanation
Indices: 5489088--5489140 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
5489078 CTTACAAAAA
5489088 AAAAATAAAAAA-AATTATTT
1 AAAAATAAAAAAGAATTA-TT
*
5489108 AAAAGTAAAAAAGAATTATT
1 AAAAATAAAAAAGAATTATT
5489128 AAAAATAGAAAAA
1 AAAAATA-AAAAA
5489141 TTGTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAAAGAATTATT
Found at i:5489464 original size:20 final size:20
Alignment explanation
Indices: 5489427--5489473 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5489417 AAGTTACAAA
5489427 AAAAATA-TTAAAAATTA-T
1 AAAAATATTTAAAAATTATT
**
5489445 AGAAAATATTTAAATTTTATT
1 A-AAAATATTTAAAAATTATT
5489466 AAAAATAT
1 AAAAATAT
5489474 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 6 0.25
20 15 0.62
21 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATATTTAAAAATTATT
Found at i:5489509 original size:19 final size:20
Alignment explanation
Indices: 5489456--5489533 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
5489446 GAAAATATTT
*
5489456 AAATTTTATTAAAAATATAAAA
1 AAATTTTA-TAAAAA-ATCAAA
* *
5489478 AAAATTTATAAAAAATC-AC
1 AAATTTTATAAAAAATCAAA
*
5489497 AAATTTTAAAAAAAATCATAA
1 AAATTTTATAAAAAATCA-AA
5489518 AAATTTTATAAAAAAT
1 AAATTTTATAAAAAAT
5489534 GTAAAAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.34
20 2 0.04
21 22 0.47
22 7 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTTTATAAAAAATCAAA
Found at i:5489510 original size:40 final size:41
Alignment explanation
Indices: 5489456--5489533 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
5489446 GAAAATATTT
*
5489456 AAATTTTATTAAAAATAT-AAAAAAAATTTATAAAAAATCAC
1 AAATTTTA-TAAAAAAATCAAAAAAAATTTATAAAAAATCAC
* *
5489497 AAATTTTA-AAAAAAATCATAAAAATTTTATAAAAAAT
1 AAATTTTATAAAAAAATCAAAAAAAATTTATAAAAAAT
5489534 GTAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.21
40 18 0.55
41 8 0.24
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (41 bp):
AAATTTTATAAAAAAATCAAAAAAAATTTATAAAAAATCAC
Found at i:5489539 original size:19 final size:18
Alignment explanation
Indices: 5489427--5489548 Score: 59
Period size: 19 Copynumber: 6.2 Consensus size: 18
5489417 AAGTTACAAA
*
5489427 AAAAATATTAAAA-ATTAT
1 AAAAA-ATTAAAATTTTAT
*
5489445 AGAAAATATTTAAATTTTATT
1 A-AAAA-ATTAAAATTTTA-T
* *
5489466 AAAAATATAAAAAAAATTTAT
1 AAAAA-AT--TAAAATTTTAT
* *
5489487 AAAAAATCACAAATTTTAA
1 AAAAAATTA-AAATTTTAT
5489506 AAAAAATCATAAAAATTTTAT
1 AAAAAAT--T-AAAATTTTAT
*
5489527 AAAAAATGTAAAA-ATTAT
1 AAAAAAT-TAAAATTTTAT
5489545 AAAA
1 AAAA
5489549 TATATAGTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.12
19 29 0.35
20 13 0.16
21 23 0.28
22 8 0.10
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAAATTAAAATTTTAT
Found at i:5489549 original size:28 final size:28
Alignment explanation
Indices: 5489507--5489597 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
5489497 AAATTTTAAA
*
5489507 AAAAATCATAAAAATTTTATAAAAAATGT
1 AAAAATTAT-AAAATTTTATAAAAAATGT
* * * *
5489536 AAAAATTATAAAA-TATATAGTAATATAT
1 AAAAATTATAAAATTTTATA-AAAAATGT
*
5489564 AAAAATTAT--AATTTTTTAATAAAATAGT
1 AAAAATTATAAAATTTTATAA-AAAAT-GT
5489592 AAAAAT
1 AAAAAT
5489598 ATTGTAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
26 2 0.04
27 13 0.27
28 25 0.52
29 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTATAAAATTTTATAAAAAATGT
Found at i:5490113 original size:9 final size:9
Alignment explanation
Indices: 5490052--5490113 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
5490042 AATTTTTTTC
5490052 TATAT-TTT
1 TATATATTT
5490060 TATATATTT
1 TATATATTT
5490069 TATAT-TTT
1 TATATATTT
*
5490077 TCTAT-TTT
1 TATATATTT
5490085 TA-ATAACTTT
1 TATAT-A-TTT
5490095 TATA-ACTTT
1 TATATA-TTT
5490104 TATATATTT
1 TATATATTT
5490113 T
1 T
5490114 TATTAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 2 0.04
8 16 0.35
9 21 0.46
10 6 0.13
11 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (9 bp):
TATATATTT
Found at i:5490145 original size:20 final size:19
Alignment explanation
Indices: 5490082--5490150 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
5490072 ATTTTTCTAT
5490082 TTTTAATAACTTTTAT-AAC
1 TTTTAATAA-TTTTATAAAC
*
5490101 TTTTATATATTTTTATTAAA-
1 TTTTA-ATAATTTTA-TAAAC
*
5490121 ATTTAATAATTCTTATAAAC
1 TTTTAATAATT-TTATAAAC
*
5490141 TTTTATTAAT
1 TTTTAATAAT
5490151 AATTATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 19 0.47
20 19 0.47
21 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATAATTTTATAAAC
Found at i:5496028 original size:2 final size:2
Alignment explanation
Indices: 5496021--5496047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5496011 TCAGAACCAA
5496021 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5496048 AAAGAAAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5498181 original size:4 final size:4
Alignment explanation
Indices: 5498172--5498198 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5498162 TTAAGAGATC
5498172 TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTC
5498199 AATGGCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:5508951 original size:14 final size:14
Alignment explanation
Indices: 5508934--5508977 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5508924 TTCAAACTTT
5508934 AAACCCTGAACTCG
1 AAACCCTGAACTCG
* *
5508948 AAACACTAAACTC-
1 AAACCCTGAACTCG
5508961 AAACCCTGAACCTCG
1 AAACCCTGAA-CTCG
5508976 AA
1 AA
5508978 TCTCAAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.33
14 14 0.58
15 2 0.08
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.14
Consensus pattern (14 bp):
AAACCCTGAACTCG
Found at i:5509005 original size:7 final size:7
Alignment explanation
Indices: 5508995--5509061 Score: 91
Period size: 7 Copynumber: 9.7 Consensus size: 7
5508985 TCCAAACTCA
5508995 AACCTTG
1 AACCTTG
*
5509002 AACCCT-
1 AACCTTG
*
5509008 AAACTTG
1 AACCTTG
*
5509015 AACCTTT
1 AACCTTG
5509022 AACCTTG
1 AACCTTG
5509029 AACCTTG
1 AACCTTG
*
5509036 AACCTCG
1 AACCTTG
5509043 AACCTTG
1 AACCTTG
5509050 AACCTTG
1 AACCTTG
5509057 AACCT
1 AACCT
5509062 CGGGTTTGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
6 4 0.08
7 47 0.92
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.27
Consensus pattern (7 bp):
AACCTTG
Found at i:5509832 original size:2 final size:2
Alignment explanation
Indices: 5509825--5509857 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5509815 ATCCCAAAAT
5509825 TA TA TA 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
5509858 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5512145 original size:2 final size:2
Alignment explanation
Indices: 5512138--5512162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5512128 TCGTGGAGTG
5512138 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5512163 TTAAAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5513436 original size:29 final size:28
Alignment explanation
Indices: 5513387--5513441 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
5513377 TTTTTTGATT
*
5513387 CTTTTAATAATACATGAATTAAATTTACC
1 CTTTTAATAATAAATGAATT-AATTTACC
*
5513416 CTTTTAATAGTAAAATG-ATTAATTTA
1 CTTTTAATAAT-AAATGAATTAATTTA
5513442 ATCTGATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 13 0.57
30 4 0.17
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (28 bp):
CTTTTAATAATAAATGAATTAATTTACC
Found at i:5513662 original size:21 final size:20
Alignment explanation
Indices: 5513638--5513706 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
5513628 ATTAGCAAGC
5513638 CCAAGAGAAAAAACTTGAAAT
1 CCAA-AGAAAAAACTTGAAAT
*
5513659 CCAAAG---AAA-TTAGCAAGT
1 CCAAAGAAAAAACTT-G-AAAT
5513677 CCAAGAGAAAAAACTTGAAAT
1 CCAA-AGAAAAAACTTGAAAT
5513698 CCAAAGAAA
1 CCAAAGAAA
5513707 TTAGCAAGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
16 2 0.05
17 4 0.10
18 7 0.18
19 2 0.05
20 7 0.18
21 11 0.28
22 4 0.10
23 2 0.05
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.13
Consensus pattern (20 bp):
CCAAAGAAAAAACTTGAAAT
Found at i:5513670 original size:39 final size:39
Alignment explanation
Indices: 5513625--5513721 Score: 185
Period size: 39 Copynumber: 2.5 Consensus size: 39
5513615 AATTAATTAT
5513625 GAAATTAGCAAGCCCAAGAGAAAAAACTTGAAATCCAAA
1 GAAATTAGCAAGCCCAAGAGAAAAAACTTGAAATCCAAA
*
5513664 GAAATTAGCAAGTCCAAGAGAAAAAACTTGAAATCCAAA
1 GAAATTAGCAAGCCCAAGAGAAAAAACTTGAAATCCAAA
5513703 GAAATTAGCAAGCCCAAGA
1 GAAATTAGCAAGCCCAAGA
5513722 AGGCAAAGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.53, C:0.18, G:0.16, T:0.13
Consensus pattern (39 bp):
GAAATTAGCAAGCCCAAGAGAAAAAACTTGAAATCCAAA
Found at i:5514819 original size:18 final size:18
Alignment explanation
Indices: 5514777--5514820 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5514767 TATTTCTTTA
*
5514777 AATTAATTAATTAGAAAT
1 AATTAATTAATTAGAAAC
*
5514795 AATTAATTAATT-TAAAC
1 AATTAATTAATTAGAAAC
5514812 AATCTAATT
1 AAT-TAATT
5514821 TCAGTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTAATTAATTAGAAAC
Found at i:5515083 original size:14 final size:15
Alignment explanation
Indices: 5515007--5515083 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5514997 GATTGCCAGT
*
5515007 AAAAT-ATTTTCTGT
1 AAAATGATTTTCTGG
*
5515021 AAAATGA-TTTCGGG
1 AAAATGATTTTCTGG
*
5515035 AAAATGTTCTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
5515055 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
5515070 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
5515084 TGTTTGATTG
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 24 0.49
15 12 0.24
16 1 0.02
18 1 0.02
20 11 0.22
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:5526224 original size:41 final size:41
Alignment explanation
Indices: 5526160--5526259 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
5526150 CCCACAGGGT
* * * ** *
5526160 CTGACACATGACCATGTGGCTCACATGGTCTGGCACACGGA
1 CTGACACATGGCCGTGTGACTCACACAGTCTAGCACACGGA
* * *
5526201 CTGACACATGGCTGTGTGACTCACACAGTCTAGCGCACGGC
1 CTGACACATGGCCGTGTGACTCACACAGTCTAGCACACGGA
*
5526242 CTGACACACGGCCGTGTG
1 CTGACACATGGCCGTGTG
5526260 GCATCGCCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (41 bp):
CTGACACATGGCCGTGTGACTCACACAGTCTAGCACACGGA
Found at i:5527656 original size:3 final size:3
Alignment explanation
Indices: 5527648--5527673 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5527638 TCTATTTTCT
5527648 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5527674 TTCATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5529644 original size:19 final size:18
Alignment explanation
Indices: 5529603--5529645 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
5529593 GTCTCTTTTT
5529603 TGCATTCATTTCATGCATC
1 TGCATTCATTTCATGCA-C
5529622 TGCATTGCATTTCATTGCA-
1 TGCATT-CATTTCA-TGCAC
5529641 TGCAT
1 TGCAT
5529646 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCATTCATTTCATGCAC
Found at i:5531687 original size:9 final size:9
Alignment explanation
Indices: 5531673--5531737 Score: 91
Period size: 8 Copynumber: 7.3 Consensus size: 9
5531663 TCAGACTAAA
5531673 AAAAAAATC
1 AAAAAAATC
5531682 AAAAAAATC
1 AAAAAAATC
5531691 -AAAAAATC
1 AAAAAAATC
5531699 -AAAAAATC
1 AAAAAAATC
5531707 AAAAAAAAAT-
1 --AAAAAAATC
5531717 AAAAAAATC
1 AAAAAAATC
5531726 AAAAAAATC
1 AAAAAAATC
5531735 AAA
1 AAA
5531738 GTCAAAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
8 24 0.46
9 21 0.40
11 7 0.13
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:5531756 original size:44 final size:42
Alignment explanation
Indices: 5531670--5531764 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 42
5531660 AGTTCAGACT
*
5531670 AAAAAAAAAATCAAAAAAATCAAAAAATCAAAAAATCAAAAAA
1 AAAAAAAAAATCAAAAAAATC-AAAAATCAAAAAAGCAAAAAA
* * *
5531713 AAATAAAAAAATCAAAAAAATC-AAAGTCAAAAATAGGAGAAAA
1 AAA-AAAAAAATCAAAAAAATCAAAAATCAAAAA-AGCAAAAAA
*
5531756 AGAAAAAAA
1 AAAAAAAAA
5531765 GAAAAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 16 0.36
43 11 0.24
44 18 0.40
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.09
Consensus pattern (42 bp):
AAAAAAAAAATCAAAAAAATCAAAAATCAAAAAAGCAAAAAA
Found at i:5531769 original size:7 final size:7
Alignment explanation
Indices: 5531752--5531784 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5531742 AAAATAGGAG
5531752 AAAAAGAA
1 AAAAAG-A
5531760 AAAAAGA
1 AAAAAGA
5531767 AAAAAGA
1 AAAAAGA
5531774 AAAAAGA
1 AAAAAGA
5531781 AAAA
1 AAAA
5531785 GGAGAGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:5532628 original size:14 final size:14
Alignment explanation
Indices: 5532591--5532625 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5532581 GAAAAAAATG
*
5532591 AATGAAAATGAGAG
1 AATGAAAATGAGAA
5532605 AATGAAAATGA-AA
1 AATGAAAATGAGAA
5532618 AATGAAAA
1 AATGAAAA
5532626 ATGGAGAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (14 bp):
AATGAAAATGAGAA
Found at i:5532628 original size:20 final size:20
Alignment explanation
Indices: 5532591--5532628 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5532581 GAAAAAAATG
*
5532591 AATGAAAATGAGAGAATGAA
1 AATGAAAATGAGAAAATGAA
5532611 AATGAAAAATGA-AAAATG
1 AATG-AAAATGAGAAAATG
5532629 GAGAGGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (20 bp):
AATGAAAATGAGAAAATGAA
Found at i:5534774 original size:46 final size:46
Alignment explanation
Indices: 5533835--5534759 Score: 1312
Period size: 46 Copynumber: 20.1 Consensus size: 46
5533825 ACAGATCAAT
* *
5533835 GAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCAGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * * *
5533881 GAAGATAGTAGATCTTGTCTTCTTATAATTGGCAGCGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * * *
5533927 GAATATAGCAGATCTTATTTTTCTGTATTTGGCAACGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
*
5533973 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* *
5534019 GAAGATAGCAGATCTTGTCTTCCTGTAATTAGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
*
5534065 GAAGATAGCAGATCTTGTCTTCCGGTATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
*
5534111 GAAGATAGCAGATCTTGTCTTCCGGTATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * *
5534157 GAAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCGAAAGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
**
5534203 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGAAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * * *
5534249 GAAGATAGCAGATCTTATCTTCATGTATTTGGCAGTGTAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* *
5534295 GAGGATAGCAGATCTTGTCTTCCTGTAATTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * *
5534341 GAAGATAGCAGATCTTATTTTCCTATATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
*
5534387 GAAGATAGCAGATCTTGTCTTCCTGTAATTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * *
5534433 GAAGATAGCAGA-CTTATCTTCCTGTAATTGACACCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* *
5534478 GAAGATAGCAGATCTTGTCTTCTTATATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * ** *
5534524 GAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAGCGAAGAAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * * * * *
5534570 AAAGATAACATATCTTATCTTCATGTATTTGGCAGCGAAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * *
5534616 GAGGATAGCAGATCTTGTCTTCCTGTAATTGGCAGCAGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
5534662 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
* * * * *
5534708 GAAGATGGCAGATCTTATCTTCATGTATTTGGCAACGGAGGAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
5534754 GAAGAT
1 GAAGAT
5534760 GGTGAATCTT
Statistics
Matches: 779, Mismatches: 99, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 0.05
46 737 0.95
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (46 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATC
Found at i:5534869 original size:44 final size:44
Alignment explanation
Indices: 5534815--5535451 Score: 225
Period size: 44 Copynumber: 14.5 Consensus size: 44
5534805 ATTAGTCCTA
5534815 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * * * ** * *
5534859 TCACCTTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAATCTTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC-TG
* * * * * * * * * *
5534903 TCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TCCTA
1 TC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAG--ATTGCAGATTCTG
5534947 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * * ** * *
5534991 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAATCTTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC-TG
* * * * * * * * * *
5535035 TCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TCCTA
1 TC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAG--ATTGCAGATTCTG
* *
5535079 TCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTACAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * * * ** * *
5535123 TCACCCTAAGCAATAGTGGACTAGATCGAAGA-TGGTGAATCTTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC-TG
* * * * * * * * * *
5535167 TCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--A-ATCCTA
1 TC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAG--ATTGCAGATTCTG
5535211 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * * ** * *
5535255 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAATCTTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC-TG
* * * * * * * * * *
5535299 TCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TCCTA
1 TC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAG--ATTGCAGATTCTG
* * * *
5535343 TCACGCTAAGCAGTAGTGGAGTAGGTTAAAGATTGTAGATTCTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
** * *
5535387 TCACCCTAAGCAGTAGTGGAGTAGGTCAAAGACTGTAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
*
5535431 TCCCCCTAAGCAGTAGTGGAG
1 TCACCCTAAGCAGTAGTGGAG
5535452 CAGATCAACA
Statistics
Matches: 431, Mismatches: 122, Indels: 80
0.68 0.19 0.13
Matches are distributed among these distances:
41 12 0.03
43 100 0.23
44 231 0.54
45 77 0.18
46 3 0.01
47 4 0.01
48 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
Found at i:5534986 original size:132 final size:132
Alignment explanation
Indices: 5534744--5535407 Score: 1204
Period size: 132 Copynumber: 5.0 Consensus size: 132
5534734 ATTTGGCAAC
* * *
5534744 GGAGGAGATCGAAGATGGTGAATCTTATCTTTCCAATATAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
*
5534809 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCTTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
5534874 GT
131 GT
5534876 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
5534941 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
5535006 GT
131 GT
5535008 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * *
5535073 GTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTACAGATTCTGTCACCCTAAGCAATA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
5535138 GT
131 GT
5535140 GGA-CTAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
1 GGAGC-AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
*
5535204 AATCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
65 AGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
5535269 AGT
130 AGT
5535272 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * * *
5535337 GTCCTATCACGCTAAGCAGTAGTGGAGTAGGTTAAAGATTGTAGATTCTATCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
5535402 GT
131 GT
5535404 GGAG
1 GGAG
5535408 TAGGTCAAAG
Statistics
Matches: 514, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
131 1 0.00
132 512 1.00
133 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTA
GT
Found at i:5536970 original size:21 final size:21
Alignment explanation
Indices: 5536940--5537007 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 21
5536930 TTATAATTTT
*
5536940 TTATCTATTTTC-TTTATTATTA
1 TTAT-TATTTTCATTTATT-TAA
5536962 TTATTATTTTCATTTATTTAA
1 TTATTATTTTCATTTATTTAA
*
5536983 TTATTTATATGTCCATTTATTTAA
1 TTA-TTAT-T-TTCATTTATTTAA
5537007 T
1 T
5537008 GTTTTAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.30
22 14 0.35
23 1 0.03
24 13 0.32
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (21 bp):
TTATTATTTTCATTTATTTAA
Found at i:5538137 original size:21 final size:22
Alignment explanation
Indices: 5538101--5538145 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
5538091 GATTACCACC
*
5538101 AAGGAATAAGGCAAAAAAATGA
1 AAGGAATAAGGAAAAAAAATGA
5538123 AAGGAA-AAGGAAAAAAAATGA
1 AAGGAATAAGGAAAAAAAATGA
5538144 AA
1 AA
5538146 ACAAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.07
Consensus pattern (22 bp):
AAGGAATAAGGAAAAAAAATGA
Found at i:5539848 original size:64 final size:64
Alignment explanation
Indices: 5539744--5539878 Score: 245
Period size: 64 Copynumber: 2.1 Consensus size: 64
5539734 ATCACTAGTG
*
5539744 TTAGAATAAATTAAACAATTATTGATTTAAAAATTCTAATTGACAAGACAAATATTCTAAGCTA
1 TTAGAATAAATTAAACAATTATTGATTTAAAAATTATAATTGACAAGACAAATATTCTAAGCTA
*
5539808 TTAGAATAAATTAAACAATTATTGATTTAAAAATTATAATTGACAAGACAAATATTCTAATCTA
1 TTAGAATAAATTAAACAATTATTGATTTAAAAATTATAATTGACAAGACAAATATTCTAAGCTA
5539872 TT-GAATA
1 TTAGAATA
5539879 CGAATCCAAC
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 5 0.07
64 64 0.93
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (64 bp):
TTAGAATAAATTAAACAATTATTGATTTAAAAATTATAATTGACAAGACAAATATTCTAAGCTA
Found at i:5543620 original size:43 final size:43
Alignment explanation
Indices: 5543574--5543728 Score: 215
Period size: 43 Copynumber: 3.6 Consensus size: 43
5543564 ACTTTTTGCG
* *
5543574 GCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGATT-TTTAGTG
1 GCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATG-TTCTTTAGTA
*
5543617 GCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
1 GCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
* * *
5543660 GCGTTTGTG-AAAAAGTGCAGCTAAAGGTCATGTTCTTTAGCA
1 GCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
* *
5543702 GCGTTTGTGAAAAAAGCACTGCTAAAG
1 GCGTTTGTGAAAAAAGCGCCGCTAAAG
5543729 AACATGACCT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
42 40 0.40
43 60 0.60
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (43 bp):
GCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
Found at i:5543687 original size:42 final size:42
Alignment explanation
Indices: 5543574--5543715 Score: 205
Period size: 42 Copynumber: 3.3 Consensus size: 42
5543564 ACTTTTTGCG
* *
5543574 GCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGATT-TTTAGTG
1 GCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATG-TTCTTTAGTA
5543617 GCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
1 GCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
* * *
5543660 GCGTTTGTGAAAAAGTGCAGCTAAAGGTCATGTTCTTTAGCA
1 GCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
5543702 GCGTTTGTGAAAAA
1 GCGTTTGTGAAAAA
5543716 AGCACTGCTA
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
42 46 0.50
43 46 0.50
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (42 bp):
GCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGTA
Found at i:5543741 original size:85 final size:86
Alignment explanation
Indices: 5543574--5543742 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 86
5543564 ACTTTTTGCG
* ** * *
5543574 GCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGATTTTTAGTGGCGTTTGTGATAAAAGCGCCGC
1 GCGTTTGTAAAAAAAGCGCAGCTAAAGGTCATGATTTTTAGCAGCGTTTGTGAAAAAAGCACCGC
** **
5543639 TAAAGGTCATGTTCTTTAGTA
66 TAAAGAACATGACCTTTAGTA
* * *
5543660 GCGTTTGT-GAAAAAGTGCAGCTAAAGGTCATG-TTCTTTAGCAGCGTTTGTGAAAAAAGCACTG
1 GCGTTTGTAAAAAAAGCGCAGCTAAAGGTCATGATT-TTTAGCAGCGTTTGTGAAAAAAGCACCG
5543723 CTAAAGAACATGACCTTTAG
65 CTAAAGAACATGACCTTTAG
5543743 CTGCGCTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 2 0.03
85 60 0.86
86 8 0.11
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (86 bp):
GCGTTTGTAAAAAAAGCGCAGCTAAAGGTCATGATTTTTAGCAGCGTTTGTGAAAAAAGCACCGC
TAAAGAACATGACCTTTAGTA
Found at i:5544700 original size:24 final size:23
Alignment explanation
Indices: 5544664--5544715 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
5544654 CCCCCCCCAA
*
5544664 AAAAAACTTCACCATGAATCTAC
1 AAAAAACTCCACCATGAATCTAC
*
5544687 AGAAAAACTCCACCGTGAATCTAC
1 A-AAAAACTCCACCATGAATCTAC
5544711 AAAAA
1 AAAAA
5544716 TCAACATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (23 bp):
AAAAAACTCCACCATGAATCTAC
Found at i:5545247 original size:26 final size:25
Alignment explanation
Indices: 5545214--5545267 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
5545204 ACTTTTAAAT
5545214 AAATAGTTAATAGAATCAATTGGTC
1 AAATAGTTAATAGAATCAATTGGTC
**
5545239 AAATCAGTTAATAGAATCGGTTGGTC
1 AAAT-AGTTAATAGAATCAATTGGTC
5545265 AAA
1 AAA
5545268 CCAACCACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (25 bp):
AAATAGTTAATAGAATCAATTGGTC
Found at i:5545441 original size:17 final size:17
Alignment explanation
Indices: 5545419--5545453 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5545409 ATAATTTTTA
5545419 CAAGATAGATTATCAAT
1 CAAGATAGATTATCAAT
5545436 CAAGATAGATTATCAAT
1 CAAGATAGATTATCAAT
5545453 C
1 C
5545454 TTTCAACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (17 bp):
CAAGATAGATTATCAAT
Found at i:5545782 original size:17 final size:17
Alignment explanation
Indices: 5545770--5545802 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5545760 GCTGTGATTT
5545770 TGTGCATCTTGTGTTTG
1 TGTGCATCTTGTGTTTG
*
5545787 TGTTCATCTTGTGTTT
1 TGTGCATCTTGTGTTT
5545803 AACATATTGC
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (17 bp):
TGTGCATCTTGTGTTTG
Found at i:5552736 original size:48 final size:48
Alignment explanation
Indices: 5552658--5552837 Score: 164
Period size: 48 Copynumber: 3.8 Consensus size: 48
5552648 AGGTGAAAGA
* * * *
5552658 AATAGTGTCTGGTTACCTGTTTGGGTTAAACCTACATGAATAA-AAATT
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACATGAATAATAAA-T
* * *
5552706 AATAGTGCCTAGTTACCCGTTAGGGCTAAACCTACACGAATAATGAAT
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACATGAATAATAAAT
* * * * * * *
5552754 AGTAGTACCTAATTACCCATTAGGGTTAAACCTACATGATTAATGAAC
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACATGAATAATAAAT
** * * * *
5552802 AATAGTGTTTGGTTACCCATTAAGGTTAAAACTACA
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACA
5552838 CGACAAATAG
Statistics
Matches: 108, Mismatches: 23, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 106 0.98
49 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (48 bp):
AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACATGAATAATAAAT
Found at i:5558527 original size:160 final size:161
Alignment explanation
Indices: 5558262--5558587 Score: 505
Period size: 160 Copynumber: 2.0 Consensus size: 161
5558252 GTGTGATGGT
* * *
5558262 CACTTGAAAGATTGTAGGAGATATTCCTTAATTTAAAAAAAACACTATTATCTTAACTAACAAGA
1 CACTTGAAAGATTGTAAGAGATATTCCTCAATTTAAAAAAAACACTATTATCTCAACTAACAAGA
* *
5558327 TTTAACCACTAATTCTATCTAACTAATCAAAATTTGAATTTAACCCAATTACCATCAACATAGGC
66 TTTAACCACTAATTCTATCTAACAAATCAAAATTTGAATTTAACCCAATTACCAACAACATAGGC
*
5558392 GGCACAAACAAGGAGTAGGAAAAATAATTCC
131 GACACAAACAAGGAGTAGGAAAAATAATTCC
*
5558423 CACTTGAAAGAATT-TAAGAGCTATTCCTCAA-TTAAAAAAAACACTATTATCTCAACTAACAAG
1 CACTTGAAAG-ATTGTAAGAGATATTCCTCAATTTAAAAAAAACACTATTATCTCAACTAACAAG
* * * *
5558486 ATTTCACCACTAA-TCTTATCTAACAAATTAGAATTTGAATTTAACCCAATTACCAACAACATGG
65 ATTTAACCACTAATTC-TATCTAACAAATCAAAATTTGAATTTAACCCAATTACCAACAACATAG
*
5558550 GCGACACAAACAGGGAGTAGGAAAAATAATTCC
129 GCGACACAAACAAGGAGTAGGAAAAATAATTCC
5558583 CACTT
1 CACTT
5558588 CAGCACAACA
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
159 2 0.01
160 122 0.81
161 24 0.16
162 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.27
Consensus pattern (161 bp):
CACTTGAAAGATTGTAAGAGATATTCCTCAATTTAAAAAAAACACTATTATCTCAACTAACAAGA
TTTAACCACTAATTCTATCTAACAAATCAAAATTTGAATTTAACCCAATTACCAACAACATAGGC
GACACAAACAAGGAGTAGGAAAAATAATTCC
Found at i:5564967 original size:27 final size:27
Alignment explanation
Indices: 5564927--5565149 Score: 200
Period size: 27 Copynumber: 8.3 Consensus size: 27
5564917 GAAATGTTAT
* * *
5564927 AAATGACTGTAATACCCTTGTAGGGTA
1 AAATGACCGAAATACCCTCGTAGGGTA
* * *
5564954 AAATGATCGAAATACCC-CTATAGGGAA
1 AAATGACCGAAATACCCTC-GTAGGGTA
** * *
5564981 AAATGACCGTCATACCCTCATAAGGTA
1 AAATGACCGAAATACCCTCGTAGGGTA
*
5565008 AAATGACCGTAATACCC-CTGTAGGGTA
1 AAATGACCGAAATACCCTC-GTAGGGTA
**
5565035 AAATGACCGAAA-ACCCTTATAGGGTA
1 AAATGACCGAAATACCCTCGTAGGGTA
** * *
5565061 AAATGATTGTAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGTAGGGTA
* * * *
5565088 AAATTTATCGAATTACCCTCGAAGGGTA
1 AAA-TGACCGAAATACCCTCGTAGGGTA
*
5565116 AAATGACCGAAATACCCTCGTAGGATA
1 AAATGACCGAAATACCCTCGTAGGGTA
5565143 AAATGAC
1 AAATGAC
5565150 TGTTATAGCC
Statistics
Matches: 158, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
26 21 0.13
27 113 0.72
28 24 0.15
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGTAGGGTA
Found at i:5565114 original size:81 final size:81
Alignment explanation
Indices: 5564927--5565149 Score: 247
Period size: 81 Copynumber: 2.8 Consensus size: 81
5564917 GAAATGTTAT
* * * * * *
5564927 AAATGACTGTAATACCCTTGTAGGGTAAAATGATCGAAATACCCCTATAGGGAAAAATGACCGTC
1 AAATGACCGTAATACCCTCGTAGGGTAAAATGACCGAAATACCCTTATAGGGTAAAATGACCGTA
5564992 ATACCCTCATAAGGTA
66 ATACCCTCATAAGGTA
**
5565008 AAATGACCGTAATACCC-CTGTAGGGTAAAATGACCGAAA-ACCCTTATAGGGTAAAATGATTGT
1 AAATGACCGTAATACCCTC-GTAGGGTAAAATGACCGAAATACCCTTATAGGGTAAAATGACCGT
*
5565071 AATACCCTCGA-AGGGTA
65 AATACCCTC-ATAAGGTA
* * * ** *
5565088 AAATTTATCG-AATTACCCTCGAAGGGTAAAATGACCGAAATACCCTCGTAGGATAAAATGAC
1 AAA-TGACCGTAA-TACCCTCGTAGGGTAAAATGACCGAAATACCCTTATAGGGTAAAATGAC
5565150 TGTTATAGCC
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
80 38 0.32
81 64 0.53
82 18 0.15
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (81 bp):
AAATGACCGTAATACCCTCGTAGGGTAAAATGACCGAAATACCCTTATAGGGTAAAATGACCGTA
ATACCCTCATAAGGTA
Found at i:5569261 original size:12 final size:13
Alignment explanation
Indices: 5569215--5569264 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
5569205 GTTGATGTCC
5569215 TGAAATAATA-AAT
1 TGAAA-AATACAAT
5569228 TGATTAAAATACAATT
1 TGA--AAAATACAA-T
5569244 TGAAAAATACAA-
1 TGAAAAATACAAT
5569256 TGAAAAATA
1 TGAAAAATA
5569265 ATCTCATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 9 0.27
13 3 0.09
14 13 0.39
15 4 0.12
16 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (13 bp):
TGAAAAATACAAT
Found at i:5577572 original size:33 final size:33
Alignment explanation
Indices: 5577531--5577655 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
5577521 ATCGGTAGAT
5577531 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
* *
5577564 TCAACACTTAGCAACCCCTTTCAGATTCAAAGATAT-GGTGGAA
1 TCAGCACTTAGCAACCAC---CAG--T----GAT-TCGG-GGAA
*
5577607 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
*
5577640 TCAGCACTTACCAACC
1 TCAGCACTTAGCAACC
5577656 CCTTGGGAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
33 36 0.49
34 5 0.07
36 3 0.04
38 2 0.03
40 2 0.03
42 5 0.07
43 21 0.28
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
Found at i:5577745 original size:33 final size:30
Alignment explanation
Indices: 5577703--5577784 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 30
5577693 AAAATACGGT
5577703 GGAATCAACACTTAGCAACCACCAATGAGTAGG
1 GGAATCAACACTTAGCAACC-CCAAT-A-TAGG
*
5577736 GGAATCAACACTTAGCAACCCC--T-TGGG
1 GGAATCAACACTTAGCAACCCCAATATAGG
*
5577763 GGAATCAGCACTTAGCAACCCC
1 GGAATCAACACTTAGCAACCCC
5577785 CTTCAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 24 0.51
30 1 0.02
32 2 0.04
33 20 0.43
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (30 bp):
GGAATCAACACTTAGCAACCCCAATATAGG
Found at i:5577830 original size:102 final size:102
Alignment explanation
Indices: 5577558--5577889 Score: 515
Period size: 102 Copynumber: 3.3 Consensus size: 102
5577548 CCAGTGATTC
* * * *
5577558 GGGGAATCAACACTTAGCAACCCCTTTCAGATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAACACTTAGCAACCCCCTTCAAATTTAAA-ATACGGTGGAATCAGCACTTAGCAACC
* * *
5577623 ACCAATGATTCGGGGAATCAGCACTTACCAACCCCTTG
65 ACCAATGAGTAGGGGAATCAGCACTTAGCAACCCCTTG
* * *
5577661 GGAGAATCAGCACTTA-CAA-CCCCTTCAAATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
5577724 CCAATGAGTAGGGGAATCAACACTTAGCAACCCCTTG
66 CCAATGAGTAGGGGAATCAGCACTTAGCAACCCCTTG
* * *
5577761 GGGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGGTAGAATCAGCACTTAACAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
5577826 CCAATGAGTAGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAGTAGGGGAATCAGCACTTAGCAACCCCTTG
5577863 GGGGAATCAACACTTAGCAACCCCCTT
1 GGGGAATCAACACTTAGCAACCCCCTT
5577890 TATATTCAAT
Statistics
Matches: 210, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
100 74 0.35
101 16 0.08
102 106 0.50
103 14 0.07
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAGTAGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:5586290 original size:9 final size:9
Alignment explanation
Indices: 5586274--5586308 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5586264 TTAATTGAGA
5586274 AATTAATTT
1 AATTAATTT
*
5586283 AGTTAATTT
1 AATTAATTT
*
5586292 AATTAATTA
1 AATTAATTT
5586301 AATTAATT
1 AATTAATT
5586309 GAATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:5588642 original size:3 final size:3
Alignment explanation
Indices: 5588634--5588683 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5588624 ACTAAAATCC
5588634 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5588682 TA
1 TA
5588684 CACAACTCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5591845 original size:3 final size:3
Alignment explanation
Indices: 5591837--5591862 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5591827 CTTTCTTTCT
5591837 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
5591863 GCCTTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5595297 original size:22 final size:23
Alignment explanation
Indices: 5595272--5595315 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5595262 TCAGATTTTC
5595272 CTTTTCCTTT-TTT-TTTTTTTGA
1 CTTTT-CTTTCTTTCTTTTTTTGA
5595294 CTTTTCTTTCTTTCTTTTTTTG
1 CTTTTCTTTCTTTCTTTTTTTG
5595316 CTGATTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (23 bp):
CTTTTCTTTCTTTCTTTTTTTGA
Found at i:5598119 original size:6 final size:6
Alignment explanation
Indices: 5598108--5598142 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5598098 AAAATGTATG
*
5598108 TATTTT TATTTT TATTCT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTT
5598143 AAAATTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:5603830 original size:18 final size:19
Alignment explanation
Indices: 5603795--5603832 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5603785 AACTAAAGGA
**
5603795 AATTTTATTATTCTATTTT
1 AATTTTATTATTAAATTTT
5603814 AATTTTA-TATTAAATTTT
1 AATTTTATTATTAAATTTT
5603832 A
1 A
5603833 TGACGTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTATTATTAAATTTT
Found at i:5604094 original size:18 final size:17
Alignment explanation
Indices: 5604043--5604097 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
5604033 CTTCGTTTAT
* *
5604043 TATTAATTTTATGTAATA
1 TATTAATTAT-TGTAAAA
*
5604061 TATTAATTATTATAAAA
1 TATTAATTATTGTAAAA
*
5604078 TATTACCTTATTGTAAAA
1 TATTA-ATTATTGTAAAA
5604096 TA
1 TA
5604098 AATTTCAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (17 bp):
TATTAATTATTGTAAAA
Found at i:5604527 original size:19 final size:21
Alignment explanation
Indices: 5604465--5604521 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
5604455 ATTTTCAATG
5604465 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
5604486 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
5604507 ATATACAATCTTAGA
1 ATATACAATCTTAGA
5604522 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:5604737 original size:19 final size:21
Alignment explanation
Indices: 5604713--5604751 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5604703 GGCTTACTGT
*
5604713 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
5604732 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
5604752 TTAAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:5608000 original size:15 final size:15
Alignment explanation
Indices: 5607980--5608012 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5607970 ATTTGCATGA
*
5607980 CATGGCATTTCATTT
1 CATGGCATTACATTT
5607995 CATGGCATTACATTT
1 CATGGCATTACATTT
5608010 CAT
1 CAT
5608013 CATAAAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (15 bp):
CATGGCATTACATTT
Found at i:5612753 original size:46 final size:45
Alignment explanation
Indices: 5612700--5612897 Score: 256
Period size: 46 Copynumber: 4.6 Consensus size: 45
5612690 TTTGAGTACT
* *
5612700 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
5612746 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
5612782 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
5612828 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
5612873 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
5612898 ATCATACGTA
Statistics
Matches: 137, Mismatches: 5, Indels: 23
0.83 0.03 0.14
Matches are distributed among these distances:
36 31 0.23
37 2 0.01
40 2 0.01
42 2 0.01
43 12 0.09
44 5 0.04
45 22 0.16
46 61 0.45
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:5612777 original size:36 final size:36
Alignment explanation
Indices: 5612736--5612808 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
5612726 GGTAGCTTTA
5612736 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
5612772 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
5612808 G
1 G
5612809 GTAGCCTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:5612837 original size:82 final size:82
Alignment explanation
Indices: 5612700--5612854 Score: 274
Period size: 82 Copynumber: 1.9 Consensus size: 82
5612690 TTTGAGTACT
* *
5612700 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
5612765 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
5612782 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
5612847 GATAAGTG
66 GATAAGTG
5612855 GTAGCCTAGC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:5617131 original size:44 final size:44
Alignment explanation
Indices: 5617058--5617397 Score: 117
Period size: 44 Copynumber: 7.7 Consensus size: 44
5617048 CCAAGCCTTG
* * * * *
5617058 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATCTTA
** * *
5617102 TCTCCCTAAGCAGTAGTGGAGCAGATTGAA-AGCGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TTGTAGATCTTA
* * * *** * *
5617146 TATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 T-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATTGTAGATCTTA
* * * * *
5617190 TCTCCTTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATCTTA
* * ** ** *
5617234 GCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATCTTA
* * *** * *
5617278 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATTGTAGATCTTA
* * * * * *
5617322 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATTTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATCTTA
*
5617366 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
5617398 CGACAAATCT
Statistics
Matches: 201, Mismatches: 73, Indels: 44
0.63 0.23 0.14
Matches are distributed among these distances:
42 10 0.05
43 16 0.08
44 155 0.77
45 13 0.06
46 6 0.03
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATTGTAGATCTTA
Found at i:5617284 original size:132 final size:132
Alignment explanation
Indices: 5617046--5617448 Score: 691
Period size: 132 Copynumber: 3.1 Consensus size: 132
5617036 ACCGGTGAAA
5617046 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5617111 GCAGTAGTGGAGCAGATTGAAAG-CGGCAAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTA
66 GCAGTAGTGGAGCAGA-TCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
5617175 AGC
130 AGC
* * * *
5617178 CACCAAGCCTTGTCTCCTTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTAGCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5617243 GCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5617308 GC
131 GC
*
5617310 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATTTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5617375 GCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5617440 GC
131 GC
*
5617442 CAGCAAG
1 CACCAAG
5617449 TCTTATCCTC
Statistics
Matches: 254, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 5 0.02
132 249 0.98
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:5618202 original size:21 final size:21
Alignment explanation
Indices: 5618173--5618271 Score: 180
Period size: 21 Copynumber: 4.7 Consensus size: 21
5618163 ATTTTCGAGG
*
5618173 ATATACAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5618194 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5618215 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
5618236 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
5618257 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
5618272 AGATATGATT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:5618489 original size:19 final size:21
Alignment explanation
Indices: 5618465--5618503 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5618455 GCTTACTGTT
*
5618465 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
5618484 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
5618504 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:5618949 original size:4 final size:4
Alignment explanation
Indices: 5618899--5618965 Score: 66
Period size: 4 Copynumber: 17.0 Consensus size: 4
5618889 AATTATTTCT
* * * * *
5618899 TTTA TTT- TTTA ATTA TTT- TTTA TTTA TATA TATA TTTG TTGTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
5618946 TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA
5618966 AAAAAATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 6 0.11
4 44 0.83
5 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:5620643 original size:20 final size:21
Alignment explanation
Indices: 5620603--5620648 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5620593 TTCATATTTA
* *
5620603 ATAATATAATTATTTATTATT
1 ATAATATAATTATTAAATATT
*
5620624 TTAATA-AATTATTAAATATT
1 ATAATATAATTATTAAATATT
5620644 ATAAT
1 ATAAT
5620649 TTTATTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATATAATTATTAAATATT
Found at i:5620643 original size:23 final size:24
Alignment explanation
Indices: 5620599--5620645 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5620589 ATTATTCATA
**
5620599 TTTAATAATATAATTATTTATTAT
1 TTTAATAATATAATTAAATATTAT
*
5620623 TTTAATAA-ATTATTAAATATTAT
1 TTTAATAATATAATTAAATATTAT
5620646 AATTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAATAATATAATTAAATATTAT
Found at i:5625008 original size:28 final size:31
Alignment explanation
Indices: 5624955--5625011 Score: 93
Period size: 28 Copynumber: 1.9 Consensus size: 31
5624945 TAGTTAAAAA
5624955 TTAAAATTTTCATAAGAAATTAATTAATTTT
1 TTAAAATTTTCATAAGAAATTAATTAATTTT
5624986 TTAAAATTTT-A-AA-AAATTAATTAATT
1 TTAAAATTTTCATAAGAAATTAATTAATT
5625012 GTTGATGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.50
29 2 0.08
30 1 0.04
31 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TTAAAATTTTCATAAGAAATTAATTAATTTT
Found at i:5625648 original size:21 final size:21
Alignment explanation
Indices: 5625609--5625648 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5625599 TTTAGCTTTC
* **
5625609 AAAATTCAAAATATTAACAGA
1 AAAATTCAAAAGAAAAACAGA
5625630 AAAATTCAAAAGAAAAACA
1 AAAATTCAAAAGAAAAACA
5625649 ATTTTAGCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATTCAAAAGAAAAACAGA
Found at i:5628463 original size:2 final size:2
Alignment explanation
Indices: 5628451--5628498 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5628441 CACATTGCTA
5628451 AT AT A- 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 AT AT
5628492 AT AT AT A
1 AT AT AT A
5628499 CTTTGAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5640184 original size:24 final size:25
Alignment explanation
Indices: 5640152--5640199 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
5640142 TTAATAGTTA
5640152 TAATGATAAAATATTATATTAATGC
1 TAATGATAAAATATTATATTAATGC
*
5640177 TAAT-ATAATATATTATATTAATG
1 TAATGATAAAATATTATATTAATG
5640200 ATAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
TAATGATAAAATATTATATTAATGC
Found at i:5640203 original size:19 final size:19
Alignment explanation
Indices: 5640152--5640191 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5640142 TTAATAGTTA
*
5640152 TAATGATAAAATATTATAT
1 TAATGATAAAATAATATAT
* *
5640171 TAATGCTAATATAATATAT
1 TAATGATAAAATAATATAT
5640190 TA
1 TA
5640192 TATTAATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (19 bp):
TAATGATAAAATAATATAT
Found at i:5640210 original size:19 final size:19
Alignment explanation
Indices: 5640152--5640211 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 19
5640142 TTAATAGTTA
5640152 TAATGATAAAATATTATAT
1 TAATGATAAAATATTATAT
5640171 TAATGCTAATATAATATATTATAT
1 TAATG---ATA-AA-ATATTATAT
*
5640195 TAATGATAAAAAATTAT
1 TAATGATAAAATATTAT
5640212 CATAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 3 0.09
22 3 0.09
23 2 0.06
24 14 0.40
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (19 bp):
TAATGATAAAATATTATAT
Found at i:5644220 original size:168 final size:168
Alignment explanation
Indices: 5643942--5644275 Score: 614
Period size: 168 Copynumber: 2.0 Consensus size: 168
5643932 CGAAATTACC
*
5643942 GAATCTTTATTCTGAGTAGACAGCAACGCCTCAGCAACGAGTAATCTGATCTACTATCGAACCAA
1 GAATCTTTATTCTGAGTAGACAGCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
* *
5644007 GCAGCAATCTATTGTGACTCTGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
66 GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
5644072 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
131 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
*
5644110 GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
1 GAATCTTTATTCTGAGTAGACAGCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
* *
5644175 GCCGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAATGGAAGGAATC
66 GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
5644240 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACA
131 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACA
5644276 ACTGCTAGAC
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 160 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (168 bp):
GAATCTTTATTCTGAGTAGACAGCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
Found at i:5654440 original size:21 final size:21
Alignment explanation
Indices: 5654416--5654455 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5654406 CTTAATGATT
* *
5654416 TAATTGCAATAAATTAAATAA
1 TAATTGAAAGAAATTAAATAA
*
5654437 TAATTTAAAGAAATTAAAT
1 TAATTGAAAGAAATTAAAT
5654456 TTATTTCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATTGAAAGAAATTAAATAA
Found at i:5659554 original size:30 final size:29
Alignment explanation
Indices: 5659516--5659643 Score: 121
Period size: 29 Copynumber: 4.3 Consensus size: 29
5659506 ACAAAATTAG
* *
5659516 CCACAAAGGCTCACATATAATAGATAACAT
1 CCACAAAGGCTCACATATAACAGAT-ACAA
* * *
5659546 CTACAAAGGCTTCCACATATAACAGATTCAG
1 CCACAAAGGC-T-CACATATAACAGATACAA
* * * * *
5659577 TCACAAAGCCTCGCATATAATAGATTCAA
1 CCACAAAGGCTCACATATAACAGATACAA
*
5659606 CCACAAAGGCTCACATATAACAGAGAACAA
1 CCACAAAGGCTCACATATAACAGA-TACAA
5659636 CCACAAAG
1 CCACAAAG
5659644 ACATCACTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
29 35 0.44
30 21 0.27
31 10 0.13
32 13 0.16
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.18
Consensus pattern (29 bp):
CCACAAAGGCTCACATATAACAGATACAA
Found at i:5659584 original size:61 final size:58
Alignment explanation
Indices: 5659517--5659629 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 58
5659507 CAAAATTAGC
* * *
5659517 CACAAAGGCTCACATATAATAGATAACATCTACAAAGGCTTCCACATATAACAGATTCAGT
1 CACAAAGCCTCACATATAATAGAT-ACAACCACAAAGGC-T-CACATATAACAGATTCAGT
* *
5659578 CACAAAGCCTCGCATATAATAGATTCAACCACAAAGGCTCACATATAACAGA
1 CACAAAGCCTCACATATAATAGATACAACCACAAAGGCTCACATATAACAGA
5659630 GAACAACCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 13 0.28
59 1 0.02
60 11 0.23
61 22 0.47
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (58 bp):
CACAAAGCCTCACATATAATAGATACAACCACAAAGGCTCACATATAACAGATTCAGT
Found at i:5659829 original size:54 final size:54
Alignment explanation
Indices: 5659760--5659913 Score: 200
Period size: 54 Copynumber: 2.9 Consensus size: 54
5659750 CTTTTCCCAC
* * * * *
5659760 ATGACGCCAAAGTCCCAGACTAGGTCTTGCACTACGTGGTCTTCACATCCTTAT
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
* * * * *
5659814 ATGACACCATAGTCCCAAACTAGGTTTTACACAATGTGATTTTCACATCCTCAT
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
* *
5659868 ATGACGCCATAGTCCTAGACTAGGTTTTACACTATATGGTCTTCAC
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCAC
5659914 TTGTCATGGC
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (54 bp):
ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
Found at i:5663907 original size:31 final size:30
Alignment explanation
Indices: 5663872--5664001 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 30
5663862 AGAGAACAAT
5663872 CACAAAGGCTTCAACATATAACAGATTCAGC
1 CACAAAGGCTTC-ACATATAACAGATTCAGC
** * *
5663903 CACAAA-TATTCACATATAATAGATTTAGC
1 CACAAAGGCTTCACATATAACAGATTCAGC
* * * *
5663932 GACAAATGC-TCACATATAACAAAGA-ACAAC
1 CACAAAGGCTTCACATATAAC--AGATTCAGC
* *
5663962 CAAAAAAAGCTTCCACATATAACAGATTCAGC
1 C-ACAAAGGCTT-CACATATAACAGATTCAGC
5663994 CACAAAGG
1 CACAAAGG
5664002 TGTACATATA
Statistics
Matches: 74, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
29 31 0.42
30 5 0.07
31 23 0.31
32 5 0.07
33 10 0.14
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (30 bp):
CACAAAGGCTTCACATATAACAGATTCAGC
Found at i:5663997 original size:91 final size:90
Alignment explanation
Indices: 5663849--5664016 Score: 239
Period size: 91 Copynumber: 1.9 Consensus size: 90
5663839 ACCACAAAAA
* * * * * *
5663849 GCTCACATATAATAGAGAACAATCACAAAGGCTTCAACATATAACAGATTCAGCCACAAATAT-T
1 GCTCACATATAACAAAGAACAACCAAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATGT
5663913 CACATATAATAGATTTAGCGACAAAT
66 -ACATATAATAGATTTAGCGACAAAT
* *
5663939 GCTCACATATAACAAAGAACAACCAAAAAAAGCTTCCACATATAACAGATTCAGCCACAAAGGTG
1 GCTCACATATAACAAAGAACAACC-AAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATG
5664004 TACATATAATAGA
65 TACATATAATAGA
5664017 GAATAATCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
90 21 0.31
91 46 0.68
92 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (90 bp):
GCTCACATATAACAAAGAACAACCAAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATGT
ACATATAATAGATTTAGCGACAAAT
Found at i:5683774 original size:2 final size:2
Alignment explanation
Indices: 5683767--5683802 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5683757 TGTGCGTATG
5683767 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
5683803 CTAGTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5684872 original size:23 final size:24
Alignment explanation
Indices: 5684844--5684888 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5684834 AAATTAAATC
5684844 TCTAAGATTACA-AAATCATATTT
1 TCTAAGATTACATAAATCATATTT
*
5684867 TCTAAGATTACATATATCATAT
1 TCTAAGATTACATAAATCATAT
5684889 CTAAGATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATTT
Found at i:5684893 original size:21 final size:22
Alignment explanation
Indices: 5684844--5684902 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
5684834 AAATTAAATC
*
5684844 TCTAAGATTACA-AAATCATATTT
1 TCTAAGATTACATATATCATA--T
5684867 TCTAAGATTACATATATCATA-
1 TCTAAGATTACATATATCATAT
*
5684888 TCTAAGATTGCATAT
1 TCTAAGATTACATAT
5684903 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
23 12 0.36
24 7 0.21
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTAAGATTACATATATCATAT
Found at i:5686429 original size:29 final size:29
Alignment explanation
Indices: 5686387--5686442 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
5686377 CTTTAGCGGC
5686387 GCTTAGAAAAAAACGCCGCTAAAGAACTT
1 GCTTAGAAAAAAACGCCGCTAAAGAACTT
*
5686416 GCTTTGAAAAAAACGCCGCTAAAGAAC
1 GCTTAGAAAAAAACGCCGCTAAAGAAC
5686443 ATGTTCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (29 bp):
GCTTAGAAAAAAACGCCGCTAAAGAACTT
Found at i:5686480 original size:42 final size:42
Alignment explanation
Indices: 5686416--5686584 Score: 284
Period size: 42 Copynumber: 4.0 Consensus size: 42
5686406 TAAAGAACTT
* *
5686416 GCTTTGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
1 GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
*
5686458 GCTTAGAAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGC
1 GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
5686500 GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
* **
5686542 GCTGAGAAAAAAACGCAACTAAAGACCATGTTCTTTAGCGGC
1 GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
5686584 G
1 G
5686585 TTTATTCTTA
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 120 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
GCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
Found at i:5692076 original size:9 final size:9
Alignment explanation
Indices: 5692048--5692338 Score: 245
Period size: 9 Copynumber: 32.2 Consensus size: 9
5692038 GTTATGTATA
*
5692048 ATGTATGTT
1 ATGTAAGTT
**
5692057 ATGCCAGTT
1 ATGTAAGTT
* *
5692066 ATTTAATTT
1 ATGTAAGTT
5692075 ATGTAAGTT
1 ATGTAAGTT
5692084 ATGTAAGTT
1 ATGTAAGTT
* *
5692093 ATTTAATTT
1 ATGTAAGTT
5692102 ATGTAAGTT
1 ATGTAAGTT
5692111 ATGTAAGTT
1 ATGTAAGTT
* *
5692120 ATTTAATTT
1 ATGTAAGTT
*
5692129 ATGTAAGCT
1 ATGTAAGTT
5692138 ATGTAAGTT
1 ATGTAAGTT
* *
5692147 ATTTAATTT
1 ATGTAAGTT
*
5692156 ACT-TAATTT
1 A-TGTAAGTT
*
5692165 GTGTAAGTT
1 ATGTAAGTT
5692174 ATGTAAAGTT
1 ATGT-AAGTT
5692184 ATGTAAGTT
1 ATGTAAGTT
* *
5692193 ATTTAATTT
1 ATGTAAGTT
5692202 ATGTAAGTT
1 ATGTAAGTT
5692211 ATGTAAGTT
1 ATGTAAGTT
* *
5692220 ATTTAATTT
1 ATGTAAGTT
*
5692229 ACT-TAATTT
1 A-TGTAAGTT
5692238 ATGTAAGTT
1 ATGTAAGTT
5692247 ATGTAAGTT
1 ATGTAAGTT
*
5692256 ACT-TAAATT
1 A-TGTAAGTT
*
5692265 TTGTAAGTT
1 ATGTAAGTT
5692274 ATGTAA-TT
1 ATGTAAGTT
5692282 AATGTAAGTT
1 -ATGTAAGTT
* *
5692292 ATTTAATTT
1 ATGTAAGTT
5692301 ATGTAAG--
1 ATGTAAGTT
*
5692308 ATGTGATAGTC
1 ATGT-A-AGTT
5692319 ATGTAA-TT
1 ATGTAAGTT
5692327 AATGTAAGTT
1 -ATGTAAGTT
5692337 AT
1 AT
5692339 TTAATTTGTG
Statistics
Matches: 227, Mismatches: 40, Indels: 30
0.76 0.13 0.10
Matches are distributed among these distances:
7 4 0.02
8 7 0.03
9 195 0.86
10 17 0.07
11 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.49
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:5692084 original size:27 final size:27
Alignment explanation
Indices: 5692048--5692345 Score: 284
Period size: 27 Copynumber: 11.0 Consensus size: 27
5692038 GTTATGTATA
* **
5692048 ATGTATGTTATGCCAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
5692075 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
5692102 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
5692129 ATGTAAGCTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
* * * *
5692156 ACT-TAATTTGTGTAAGTTATGTAAAGTT
1 A-TGTAAGTTATGTAAGTTAT-TTAATTT
* * * *
5692184 ATGTAAGTTATTTAATTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
* * *
5692211 ATGTAAGTTATTTAATTTACTTAATTT
1 ATGTAAGTTATGTAAGTTATTTAATTT
*
5692238 ATGTAAGTTATGTAAGTTACTTAAATTT
1 ATGTAAGTTATGTAAGTTA-TTTAATTT
* *
5692266 -TGTAAGTTATGTAA-TTAATGTAAGTT
1 ATGTAAGTTATGTAAGTT-ATTTAATTT
* * * * *
5692292 ATTTAATTTATGTAAG--ATGTGATAGTC
1 ATGTAAGTTATGTAAGTTAT-TTA-ATTT
5692319 ATGTAA-TTAATGTAAGTTATTTAATTT
1 ATGTAAGTT-ATGTAAGTTATTTAATTT
5692346 GTGATACCTA
Statistics
Matches: 225, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.01
26 10 0.04
27 183 0.81
28 28 0.12
29 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (27 bp):
ATGTAAGTTATGTAAGTTATTTAATTT
Found at i:5695072 original size:84 final size:83
Alignment explanation
Indices: 5694923--5695192 Score: 246
Period size: 84 Copynumber: 3.3 Consensus size: 83
5694913 ACTGAACAGA
* * * *
5694923 AAACGGTGCCGCATTGACAAACATTAATTCACACTTGCGGCATTTTCTTAAAAACGCCACTATAA
1 AAACGGCGCCGTATTGGCAAACATTAATTCACACTTGCGGCATTTTCTAAAAAACGCCACTATAA
5694988 GATTTCATTCCAGTAGAG
66 GATTTCATTCCAGTAGAG
* ** *
5695006 AAACGAG-GCCGTATTGGCAAAGATTAATTCACTTTTGCGGCGTTTTTCTAAAAAACGCCACTAT
1 AAACG-GCGCCGTATTGGCAAACATTAATTCACACTTGCGGC-ATTTTCTAAAAAACGCCACTAT
* *
5695070 AAGATTTTATTCCAGTAGAT
64 AAGATTTCATTCCAGTAGAG
** * * * *
5695090 AAACGGCGCCGCT-TTGGCAAATTTTAATACATC-CTTGTGGCGTTTTCATCAAAAACGCCAC-A
1 AAACGGCGCCG-TATTGGCAAACATTAATTCA-CACTTGCGGCATTTTC-TAAAAAACGCCACTA
* * * *
5695152 AAATATTTCTTTCC-TTA-AG
63 TAAGATTTCATTCCAGTAGAG
* *
5695171 AAAACGGCGCCGTTTTGTCAAA
1 -AAACGGCGCCGTATTGGCAAA
5695193 TTTTAAAACA
Statistics
Matches: 156, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
81 2 0.01
82 20 0.13
83 51 0.33
84 81 0.52
85 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (83 bp):
AAACGGCGCCGTATTGGCAAACATTAATTCACACTTGCGGCATTTTCTAAAAAACGCCACTATAA
GATTTCATTCCAGTAGAG
Found at i:5695545 original size:84 final size:84
Alignment explanation
Indices: 5695457--5695612 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
5695447 CACATTGCCA
* * * *
5695457 AACATTAATTCAC-TCTTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGTACA
1 AACATTAATTCACGT-TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAA
5695521 GAAACGGCACCGTATTGGCC
65 GAAACGGCACCGTATTGGCC
* * *
5695541 AACATTAATTCACGTTTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGTAAAG
1 AACATTAATTCACGTTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAG
5695606 AAACGGC
66 AAACGGC
5695613 GCCACTTTGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 63 0.98
85 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (84 bp):
AACATTAATTCACGTTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAG
AAACGGCACCGTATTGGCC
Found at i:5695633 original size:84 final size:84
Alignment explanation
Indices: 5695453--5695629 Score: 216
Period size: 84 Copynumber: 2.1 Consensus size: 84
5695443 GTGTCACATT
* * *
5695453 GCCAAACATTAATTCACTCTTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGT
1 GCCAAA-ATTAATTCACTCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGT
* *
5695518 ACAGAAACGGCACCGTATTG
65 AAAGAAACGGCACCCTATTG
* * * *
5695538 GCCAACATTAATTCACGT-TTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGT
1 GCCAAAATTAATTCAC-TCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGT
*
5695602 AAAGAAACGGCGCCACT-TTG
65 AAAGAAACGGCACC-CTATTG
5695622 G-CAAAATT
1 GCCAAAATT
5695630 TAATGAATCA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
83 6 0.08
84 66 0.84
85 7 0.09
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (84 bp):
GCCAAAATTAATTCACTCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTA
AAGAAACGGCACCCTATTG
Found at i:5695644 original size:84 final size:84
Alignment explanation
Indices: 5695472--5695666 Score: 189
Period size: 84 Copynumber: 2.3 Consensus size: 84
5695462 TAATTCACTC
* * * * *
5695472 TTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGTACAGAAACGGCACCGTATT
1 TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACCCTATT
* ** *
5695537 GGCCAACATTAATTCACGT
66 GGCCAAAATTAATGAACGA
* * * *
5695556 TTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGTAAAGAAACGGCGCCACT-T
1 TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACC-CTAT
5695620 TGG-CAAAATTTAATGAATC-A
65 TGGCCAAAA-TTAATGAA-CGA
* * * *
5695640 TTGCGGCGTTTTTATTAAAATCGCCAC
1 TTGCGGCATTTTCATAAAAAACGCCAC
5695667 AAATTATTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
83 4 0.04
84 84 0.93
85 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (84 bp):
TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACCCTATT
GGCCAAAATTAATGAACGA
Found at i:5695914 original size:82 final size:81
Alignment explanation
Indices: 5695809--5696062 Score: 278
Period size: 90 Copynumber: 3.0 Consensus size: 81
5695799 ACTAATTAAT
* * * *
5695809 CTAAATCTTGTTTAATATATAAATTAA-AAAGTACTAATTAATCTAAATCTTAAACCCTAACCCG
1 CTAAATTTTATTTAATATATAAATTAACAAA-TACTAATTAATCTAAACCCTAAACCCTAACCCG
5695873 ACTCCAAATCCCTAACCC
65 A-TCCAAATCCCTAACCC
*
5695891 CTAAATTTTATTTAATATGTAAATTAACAAACT-CTAATTAATCTAAACCCTAAACCCTAAACCT
1 CTAAATTTTATTTAATATATAAATTAACAAA-TACTAATTAATCTAAACCCTAAA--C----CCT
*
5695955 AACCCCAAATCCCAAATCCCTAACCC
59 AA-CCC-GAT-CCAAATCCCTAACCC
* * * **
5695981 CTAAACTTAATTTAATATATAAATTAACAAACACTAATTAATCTAAACCCTAAACCAAAACCCGA
1 CTAAATTTTATTTAATATATAAATTAACAAATACTAATTAATCTAAACCCTAAACCCTAACCCGA
5696046 TCCTAAATCCCTAACCC
66 TCC-AAATCCCTAACCC
5696063 TTAACCCTTA
Statistics
Matches: 146, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
81 2 0.01
82 58 0.40
83 7 0.05
84 4 0.03
88 6 0.04
89 4 0.03
90 65 0.45
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (81 bp):
CTAAATTTTATTTAATATATAAATTAACAAATACTAATTAATCTAAACCCTAAACCCTAACCCGA
TCCAAATCCCTAACCC
Found at i:5695945 original size:7 final size:7
Alignment explanation
Indices: 5695933--5695986 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
5695923 TCTAATTAAT
5695933 CTAAACC
1 CTAAACC
5695940 CTAAACC
1 CTAAACC
5695947 CTAAA-C
1 CTAAACC
5695953 CT-AACC
1 CTAAACC
*
5695959 CCAAATCC
1 CTAAA-CC
5695967 C-AAATCC
1 CTAAA-CC
*
5695974 CTAACCC
1 CTAAACC
5695981 CTAAAC
1 CTAAAC
5695987 TTAATTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 2 0.05
6 5 0.12
7 28 0.70
8 5 0.12
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:5696076 original size:14 final size:14
Alignment explanation
Indices: 5696054--5696093 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5696044 GATCCTAAAT
5696054 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
5696068 CCTTAACCCATAAC
1 CCCTAACCCTTAAC
*
5696082 CCCTAAACCTTA
1 CCCTAACCCTTA
5696094 TTTAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:5697233 original size:229 final size:229
Alignment explanation
Indices: 5696818--5697252 Score: 631
Period size: 229 Copynumber: 1.9 Consensus size: 229
5696808 TAAATCCTTG
* *
5696818 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGAGCCGTT
1 AGCATTAGCGACGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGAGCCGTC
* *
5696883 GGGCTTAGGTCCCTTTGCGGCACTTCTCCCAAAACGCATCTAAAGCCCTCAGCATTAGCGACGCC
66 GGGCTTAGGTCCCTTTGCGGCACTTCTCCCAAAACGCAGCTAAAGCCCTAAGCATTAGCGACGCC
* ** *
5696948 TAACCAAAAACGCCACTAAATACTTAAAGGCTAAGAAAACGACGTCGTTGGGCTTAGG-TCCGTT
131 TAACCAAAAACGCCACTAAAGACCGAAAGGCTAAGAAAACGACATCGTTGGGCTTAGGTTCC-TT
5697012 TGCGGCGCTTTTCCCAAAACGCTGCTAAAGCCCTA
195 TGCGGCGCTTTTCCCAAAACGCTGCTAAAGCCCTA
* * * *
5697047 AGCATTAGTGGCGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGCGTCGTC
1 AGCATTAGCGACGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGAGCCGTC
* * *
5697112 GGGCTTAGGTCCCTTTGCGGCGCTT-TACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGC
66 GGGCTTAGGTCCCTTTGCGGCACTTCT-CCCAAAACGCAGCTAAAGCCCTAAGCATTAGCGACGC
* * * * * * *
5697176 TTTACTAAAAACGCCACTAAAGACCGAAAGGCTTAGAAAACGGCATCGTTTGGCTTAGGTTTTCT
130 CTAACCAAAAACGCCACTAAAGACCGAAAGGCTAAGAAAACGACATCGTTGGGCTTAGG-TTCCT
5697241 TTGCGGCGCTTT
194 TTGCGGCGCTTT
5697253 ACTGAAAACG
Statistics
Matches: 181, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
228 1 0.01
229 165 0.91
230 13 0.07
231 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (229 bp):
AGCATTAGCGACGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGAGCCGTC
GGGCTTAGGTCCCTTTGCGGCACTTCTCCCAAAACGCAGCTAAAGCCCTAAGCATTAGCGACGCC
TAACCAAAAACGCCACTAAAGACCGAAAGGCTAAGAAAACGACATCGTTGGGCTTAGGTTCCTTT
GCGGCGCTTTTCCCAAAACGCTGCTAAAGCCCTA
Found at i:5697243 original size:115 final size:115
Alignment explanation
Indices: 5696818--5697274 Score: 535
Period size: 115 Copynumber: 4.0 Consensus size: 115
5696808 TAAATCCTTG
* * *
5696818 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGG-AGCCGT
1 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCACCAAAAAGCTAAGAAAACGGCA-TCGT
* ** *
5696882 TGGGCTTAGGTCCCTTTGCGGCACTTCT-CCCAAAACGCATCTAAAGCCCTC
65 TGGGCTTAGGTCCCTTTGCGGCGCTT-TACCCAAAACGCCGCTAAAGCCCTA
* * * ** * * *
5696933 AGCATTAGCGACGCCTAACCAAAAACGCCACTAAAT-ACTTAAAGGCTAAGAAAACGACGTCGTT
1 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCACCAAAAAGCTAAGAAAACGGCATCGTT
* * *
5696997 GGGCTTAGGTCCGTTTGCGGCGCTTTTCCCAAAACGCTGCTAAAGCCCTA
66 GGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTA
* * * * * * *
5697047 AGCATTAGTGGCGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGCGTCGTC
1 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCACCAAAAAGCTAAGAAAACGGCATCGTT
5697112 GGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTA
66 GGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTA
* * * * *
5697162 AGCATTAGCGGCGCTTTACTAAAAACGCCACTAAA-GACCGAAAGGCTTAGAAAACGGCATCGTT
1 AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCACCAAAAAGCTAAGAAAACGGCATCGTT
* ** ** *
5697226 TGGCTTAGGTTTTCTTTGCGGCGCTTTACTGAAAACGCCGCAAAAGCCC
66 GGGCTTAGG-TCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCC
5697275 GGAACATCAG
Statistics
Matches: 291, Mismatches: 47, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
113 1 0.00
114 122 0.42
115 168 0.58
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (115 bp):
AGCATTAGCGACGCTTTACTAAAAACGCCACTAAATCACCAAAAAGCTAAGAAAACGGCATCGTT
GGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTA
Found at i:5697398 original size:111 final size:113
Alignment explanation
Indices: 5696913--5697403 Score: 302
Period size: 115 Copynumber: 4.3 Consensus size: 113
5696903 CACTTCTCCC
** * * * * * **
5696913 AAAACGCATCTAAAGCCCTCAGCATTAGCGACGC-CTAACCAAAAACGCCACTAAATACTTAAAG
1 AAAACGCCGCTAAAGCCCT-AACATTAGCG--GCACTTACTAAAAACGCCACGAAAGACCGAAAG
* * * * * * * **
5696977 GCTAAGAAAACGACGTCGTTGGGCTTAGG--TCCGTTTGCGGCGCTTTTCCC
63 GCTTAGAAAACGGCATCGTTGGGATTAGGTTTTC-TTTGCGGCGATTTACTG
* * * * ** * *
5697027 AAAACGCTGCTAAAGCCCTAAGCATTAGTGGCGCTTCACTAAAAACGCCACTAAATCCCCAAAAA
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCACTT-ACTAAAAACGCCACGAAA-GACCGAAAG
* * * * * ** * **
5697092 GCTAATAAAACGGCGTCGTCGGGCTTAGG-TCCCTTTGCGGCGCTTTACCC
63 GCTTAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
* *
5697142 AAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTACTAAAAACGCCACTAAAGACCGAAAGG
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCAC-TTACTAAAAACGCCACGAAAGACCGAAAGG
* * *
5697207 CTTAGAAAACGGCATCGTTTGGCTTAGGTTTTCTTTGCGGCGCTTTACTG
64 CTTAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
* * * * * *
5697257 AAAACGCCGCAAAAGCCCGGAACATCAGCGGCACTTACTTACAAACGCCGCGAAAGCCCCG-AA-
1 AAAACGCCGCTAAAGCCC-TAACATTAGCGGCACTTAC-TAAAAACGCCACGAAAG-ACCGAAAG
* * * * *
5697320 GC-TCGTTAAACGGCGTCGTTGGGATTA-G-TTT-TTTGTGGC-ATTTTCGTG
63 GCTTAG-AAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTAC-TG
5697368 AAAACGCCGCTAAAGCCCTAATCATTAGCGGCACTT
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCACTT
5697404 TATTAAAATC
Statistics
Matches: 314, Mismatches: 50, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
110 6 0.02
111 39 0.12
112 5 0.02
113 6 0.02
114 93 0.30
115 156 0.50
116 9 0.03
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (113 bp):
AAAACGCCGCTAAAGCCCTAACATTAGCGGCACTTACTAAAAACGCCACGAAAGACCGAAAGGCT
TAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
Found at i:5699334 original size:7 final size:7
Alignment explanation
Indices: 5699308--5699397 Score: 71
Period size: 7 Copynumber: 12.7 Consensus size: 7
5699298 ATACACGACC
*
5699308 CTTTTTC
1 CTTTTTT
5699315 CTTTTTT
1 CTTTTTT
5699322 C-TTTTT
1 CTTTTTT
5699328 CTTTTTTT
1 C-TTTTTT
5699336 CTTCTTTT
1 CTT-TTTT
*
5699344 CTCTTTT
1 CTTTTTT
*
5699351 -TTCTTT
1 CTTTTTT
5699357 CTTTTTCT
1 CTTTTT-T
5699365 CTTTTTCTT
1 C-TTTT-TT
*
5699374 CTCTTTT
1 CTTTTTT
5699381 C-TTTTT
1 CTTTTTT
5699387 CTTTTTT
1 CTTTTTT
5699394 -TTTT
1 CTTTT
5699398 CTGCTGGGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
6 19 0.28
7 25 0.37
8 17 0.25
9 6 0.09
10 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:5699340 original size:11 final size:11
Alignment explanation
Indices: 5699316--5699399 Score: 56
Period size: 11 Copynumber: 8.0 Consensus size: 11
5699306 CCCTTTTTCC
5699316 TTTTTTCTT-T
1 TTTTTTCTTCT
*
5699326 TTCTTTTTTTCT
1 TT-TTTTCTTCT
*
5699338 TCTTTTC-TC-
1 TTTTTTCTTCT
5699347 TTTTTTCTT-T
1 TTTTTTCTTCT
*
5699357 CTTTTTC-TCT
1 TTTTTTCTTCT
5699367 TTTTCTTC-TCT
1 TTTT-TTCTTCT
5699378 TTTCTTT-TTCT
1 TTT-TTTCTTCT
*
5699389 TTTTTTTTTCT
1 TTTTTTCTTCT
5699400 GCTGGGCTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
9 7 0.12
10 18 0.31
11 31 0.53
12 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:5699342 original size:17 final size:17
Alignment explanation
Indices: 5699316--5699399 Score: 93
Period size: 18 Copynumber: 4.9 Consensus size: 17
5699306 CCCTTTTTCC
5699316 TTTT-TTCTTTTTCTTT
1 TTTTCTTCTTTTTCTTT
5699332 TTTTCTTC-TTTTCTCTT
1 TTTTCTTCTTTTTCT-TT
*
5699349 TTTTCTTTCTTTTTCTCT
1 TTTTC-TTCTTTTTCTTT
5699367 TTTTCTTCTCTTTTCTTT
1 TTTTCTTCT-TTTTCTTT
*
5699385 TTCTT-TTTTTTTTCT
1 TT-TTCTTCTTTTTCT
5699400 GCTGGGCTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.17
17 20 0.34
18 21 0.36
19 8 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTCTTTTTCTTT
Found at i:5699348 original size:24 final size:22
Alignment explanation
Indices: 5699317--5699399 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 22
5699307 CCTTTTTCCT
5699317 TTTTTCTTTTTCTTTTTTTCTTC
1 TTTTTCTTTTTCTTTTTTT-TTC
5699340 TTTTCTCTTTTTTCTTTCTTTTTCTC
1 TTTT-TC-TTTTTCTTT-TTTTT-TC
*
5699366 TTTTTC-TTCTCTTTTCTTTTTC
1 TTTTTCTTTTTCTTTT-TTTTTC
5699388 TTTTT-TTTTTCT
1 TTTTTCTTTTTCT
5699400 GCTGGGCTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
22 13 0.25
23 15 0.29
24 2 0.04
25 12 0.23
26 10 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTTTTTC
Found at i:5699370 original size:35 final size:34
Alignment explanation
Indices: 5699319--5699396 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 34
5699309 TTTTTCCTTT
*
5699319 TTTCTTTTTCTTTTTTTCTTCT-TTTCTCTTTTTTC
1 TTTCTTTTTCTCTTTTTCTTCTCTTT-TC-TTTTTC
5699354 TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
1 TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
*
5699388 TTTTTTTTT
1 TTTCTTTTT
5699397 TCTGCTGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 14 0.35
35 23 0.57
36 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
Found at i:5699397 original size:35 final size:35
Alignment explanation
Indices: 5699308--5699399 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 35
5699298 ATACACGACC
5699308 CTTTTTCCTTTTTTCTTTT-TCTTTTTTTCTTCTTTT
1 CTTTTT-CTTTTTT-TTTTCTCTTTTTTTCTTCTTTT
5699344 CTCTTTT-TTCTTTCTTTTTCTCTTTTTCTTC-TCTTTT
1 CT-TTTTCTT-TTT-TTTTTCTCTTTTT-TTCTTCTTTT
5699381 CTTTTTCTTTTTTTTTTCT
1 CTTTTTCTTTTTTTTTTCT
5699400 GCTGGGCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
35 9 0.18
36 16 0.32
37 22 0.44
38 3 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (35 bp):
CTTTTTCTTTTTTTTTTCTCTTTTTTTCTTCTTTT
Found at i:5699439 original size:26 final size:23
Alignment explanation
Indices: 5699398--5699452 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
5699388 TTTTTTTTTT
5699398 CTGCTGGGCTAATGGGCGAACTGGG
1 CTGCTGGGCTAATGGG-G-ACTGGG
**
5699423 CCTGCTGGGCTGCTGGGGACTGGG
1 -CTGCTGGGCTAATGGGGACTGGG
5699447 CTGCTG
1 CTGCTG
5699453 TAGGTTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 6 0.22
25 1 0.04
26 14 0.52
ACGTcount: A:0.09, C:0.24, G:0.45, T:0.22
Consensus pattern (23 bp):
CTGCTGGGCTAATGGGGACTGGG
Found at i:5699672 original size:14 final size:16
Alignment explanation
Indices: 5699655--5699687 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
5699645 ATTTTAAAAG
5699655 TTTTCTTT-T-TTCTT
1 TTTTCTTTCTCTTCTT
5699669 TTTTCTTTCTCTTCTT
1 TTTTCTTTCTCTTCTT
5699685 TTT
1 TTT
5699688 CTTCCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCTCTTCTT
Done.