Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 130 of 175
Found at i:40568479 original size:104 final size:104
Alignment explanation
Indices: 40568341--40568781 Score: 483
Period size: 104 Copynumber: 4.3 Consensus size: 104
40568331 GGCCAATAGT
* * * *** * *
40568341 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGATAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* *
40568406 TAGCGGACCTACGCTTCCAGCTGATTATTTAAGGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* * * *** *
40568445 AGAGTTAAGCTTGTAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTTGTAACTCCTAGACAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* *
40568510 TAGCGGACCTACAC-TCCAACTGATTATT-AAGGTTAGT
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* * ** *
40568547 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAATTAAGCTCACAACTCCTGGACAGC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
** * * *
40568612 TAGCGGACCTATGCTCCCAGCTGAGTATTAAAAGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* * * * * * *
40568651 AGAGTTAAGCTCGCAACCTCTGGTCTTTTGAGTTAGCAGAGTTAAGCTCACAGCTCTCATACAGC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
* * *
40568716 TCGTGGACCTACACTTCCATCTGATTATTAAAGGTTAGC
66 TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
* *
40568755 ATG-GTTAAGCTCGCAACCCCCAATCTT
1 A-GAGTTAAGCTCGCAACCTCCGATCTT
40568782 ATTTACAAAC
Statistics
Matches: 283, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
102 75 0.27
103 24 0.08
104 183 0.65
105 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (104 bp):
AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAGCTCACAACTCCCAGACAAC
TAGCGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
Found at i:40568726 original size:206 final size:208
Alignment explanation
Indices: 40568337--40568781 Score: 547
Period size: 206 Copynumber: 2.1 Consensus size: 208
40568327 ACCAGGCCAA
* * *** *
40568337 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGA
1 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAATTAAGCTCACAACTCCCAGA
* * * * * * *
40568402 TAACTAGCGGACCTACGCTTCCAGCTGATTATTTAAGGTTAGCAGAGTTAAGCTTGTAACCTCCG
66 CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
***
40568467 ATCTTTTGAGTTAGCAAAGTTAAACTTGTAACTCCTAGACAACTAGCGGACCTACAC-TCCAACT
131 ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCTAGACAACTAGCGGACCTACACTTCCAACT
40568531 GATTATT-AAGGT
196 GATTATTAAAGGT
**
40568543 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAATTAAGCTCACAACTCCTGGA
1 TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAATTAAGCTCACAACTCCCAGA
* * *
40568608 CAGCTAGCGGACCTATGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCTG
66 CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
* * * * * * * * *
40568673 GTCTTTTGAGTTAGCAGAGTTAAGCTCACAGCT-CTCATACAGCTCGTGGACCTACACTTCCATC
131 ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCT-AGACAACTAGCGGACCTACACTTCCAAC
40568737 TGATTATTAAAGGT
195 TGATTATTAAAGGT
* * *
40568751 TAGCATG-GTTAAGCTCGCAACCCCCAATCTT
1 TAGTA-GAGTTAAGCTCGCAACCTCCTATCTT
40568782 ATTTACAAAC
Statistics
Matches: 202, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
205 2 0.01
206 155 0.77
207 13 0.06
208 31 0.15
209 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (208 bp):
TAGTAGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAATTAAGCTCACAACTCCCAGA
CAACTAGCGGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCG
ATCTTTTGAGTTAGCAAAGTTAAACTCACAACTCCTAGACAACTAGCGGACCTACACTTCCAACT
GATTATTAAAGGT
Found at i:40582549 original size:42 final size:42
Alignment explanation
Indices: 40582490--40582571 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
40582480 GGAAGTTGAA
**
40582490 AATTCTTTAATTAAAATCTTTGGACTTCAAATAATGCTAGAC
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
*
40582532 AATTCTTTAAACAAAATCTTTGGACTTCGAATAATGCTAG
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAG
40582572 TACTATGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (42 bp):
AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
Found at i:40582605 original size:14 final size:14
Alignment explanation
Indices: 40582586--40582612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40582576 ATGGAAGTAT
40582586 GAAAGCTCATCTAC
1 GAAAGCTCATCTAC
40582600 GAAAGCTCATCTA
1 GAAAGCTCATCTA
40582613 TAAAGATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (14 bp):
GAAAGCTCATCTAC
Found at i:40582772 original size:20 final size:17
Alignment explanation
Indices: 40582733--40582776 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
40582723 TCAAATGATC
*
40582733 TATTTTATATTGATCTT
1 TATTTTATATTGATATT
40582750 TATTATTATATTGTATATGT
1 TATT-TTATATTG-ATAT-T
40582770 TATTTTA
1 TATTTTA
40582777 GATGGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 6 0.26
20 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (17 bp):
TATTTTATATTGATATT
Found at i:40585330 original size:2 final size:2
Alignment explanation
Indices: 40585323--40585348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40585313 CACTTACGTT
40585323 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
40585349 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40585353 original size:2 final size:2
Alignment explanation
Indices: 40585348--40585373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40585338 ATATATATAT
40585348 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
40585374 CGGTAGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40588155 original size:6 final size:6
Alignment explanation
Indices: 40588136--40588174 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
40588126 TCTAAATAAA
*
40588136 TTCATT TCTCATT TTCATT TTCATT TTCATT TCCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
40588175 GAGAAAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:40595634 original size:7 final size:7
Alignment explanation
Indices: 40595622--40595657 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
40595612 ATATAATAAT
40595622 TTTTTTA
1 TTTTTTA
40595629 TTTTTTA
1 TTTTTTA
40595636 TTTTTTTTA
1 --TTTTTTA
40595645 TTTTTTA
1 TTTTTTA
40595652 TTTTTT
1 TTTTTT
40595658 TTAAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 20 0.74
9 7 0.26
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:40595642 original size:16 final size:16
Alignment explanation
Indices: 40595621--40595660 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
40595611 AATATAATAA
40595621 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
40595637 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
40595653 TTTTTTTA
1 TTTTTTTA
40595661 AAATTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTTTTTAT
Found at i:40595660 original size:9 final size:8
Alignment explanation
Indices: 40595620--40595658 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
40595610 GAATATAATA
40595620 ATTTTTTT
1 ATTTTTTT
40595628 A-TTTTTT
1 ATTTTTTT
40595635 ATTTTTTT
1 ATTTTTTT
40595643 -TATTTTTT
1 AT-TTTTTT
40595651 ATTTTTTT
1 ATTTTTTT
40595659 TAAAATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 8 0.29
8 19 0.68
9 1 0.04
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
ATTTTTTT
Found at i:40595730 original size:30 final size:31
Alignment explanation
Indices: 40595661--40595730 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
40595651 ATTTTTTTTA
40595661 AAATTTGTTTAATTTTAAAATATTTTTAAAAT
1 AAATTT-TTTAATTTTAAAATATTTTTAAAAT
** **
40595693 ACTTTTTTTAATTTTTTAA-ATTTTTAAAAT
1 AAATTTTTTAATTTTAAAATATTTTTAAAAT
40595723 AAATTTTT
1 AAATTTTT
40595731 GGTATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 17 0.53
31 11 0.34
32 4 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
AAATTTTTTAATTTTAAAATATTTTTAAAAT
Found at i:40595730 original size:31 final size:32
Alignment explanation
Indices: 40595661--40595730 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
40595651 ATTTTTTTTA
*
40595661 AAATTTGTTTAATTTTAAAATATTTTTAAAAT
1 AAATTTTTTTAATTTTAAAATATTTTTAAAAT
* **
40595693 -ACTTTTTTTAATTTTTTAA-ATTTTTAAAAT
1 AAATTTTTTTAATTTTAAAATATTTTTAAAAT
40595723 AAATTTTT
1 AAATTTTT
40595731 GGTATTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (32 bp):
AAATTTTTTTAATTTTAAAATATTTTTAAAAT
Found at i:40595743 original size:31 final size:30
Alignment explanation
Indices: 40595682--40595743 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
40595672 ATTTTAAAAT
* * *
40595682 ATTTTTAAAATACTTTTTTTAATTTTTTAA
1 ATTTTTAAAATAATTTTTGTAATTTATTAA
40595712 ATTTTTAAAATAAATTTTTGGT-ATTTATTAA
1 ATTTTTAAAAT-AATTTTT-GTAATTTATTAA
40595743 A
1 A
40595744 AAAATAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 15 0.56
32 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
ATTTTTAAAATAATTTTTGTAATTTATTAA
Found at i:40601784 original size:18 final size:18
Alignment explanation
Indices: 40601761--40601797 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40601751 TGGTTTTCTC
* *
40601761 AAAATAGAAATGAAAATG
1 AAAATAAAAATAAAAATG
40601779 AAAATAAAAATAAAAATG
1 AAAATAAAAATAAAAATG
40601797 A
1 A
40601798 GGAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAATAAAAATAAAAATG
Found at i:40610545 original size:15 final size:16
Alignment explanation
Indices: 40610516--40610553 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
40610506 GCCATGCGTA
40610516 TTCTCTTCTTCTTTCT
1 TTCTCTTCTTCTTTCT
*
40610532 TTCT-TTCTTTTTTCT
1 TTCTCTTCTTCTTTCT
40610547 TTCTCTT
1 TTCTCTT
40610554 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTCTTCTTCTTTCT
Found at i:40613608 original size:9 final size:9
Alignment explanation
Indices: 40613594--40613657 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 9
40613584 GTGATTTCTA
40613594 TTTATTATT
1 TTTATTATT
40613603 TTTATTATT
1 TTTATTATT
40613612 TTT-TATATT
1 TTTAT-TATT
40613621 TTTATTTATT
1 TTTA-TTATT
**
40613631 TTTAAAATTT
1 TTTATTA-TT
40613641 TTTAATCTATT
1 TTT-AT-TATT
40613652 TTTATT
1 TTTATT
40613658 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 1 0.02
9 21 0.47
10 15 0.33
11 7 0.16
12 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTATT
Found at i:40616713 original size:13 final size:13
Alignment explanation
Indices: 40616671--40616713 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40616661 GGCTGAAAGA
40616671 TTATGAAAATATT
1 TTATGAAAATATT
* *
40616684 TTGTAGAAACTTATT
1 TTAT-GAAA-ATATT
40616699 TTATGAAAATATT
1 TTATGAAAATATT
40616712 TT
1 TT
40616714 TAGCTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 9 0.38
14 8 0.33
15 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (13 bp):
TTATGAAAATATT
Found at i:40622153 original size:22 final size:22
Alignment explanation
Indices: 40622110--40622153 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40622100 GGCTCGGCCT
**
40622110 ATTTTTTTAATAAATACCAAAA
1 ATTTTTTTAATAAATAAAAAAA
40622132 ATTTATTTTAA-AAATAAAAAAA
1 ATTT-TTTTAATAAATAAAAAAA
40622154 TAAAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTTTTTAATAAATAAAAAAA
Found at i:40622667 original size:24 final size:24
Alignment explanation
Indices: 40622598--40622821 Score: 192
Period size: 24 Copynumber: 9.5 Consensus size: 24
40622588 TGAACAACTC
*
40622598 TTATACATCAGAAATT-GAGCAGCAT
1 TTATACACCA-AAATTGGA-CAGCAT
*
40622623 ATATATATA-CAAAATTGGACAGCAT
1 -T-TATACACCAAAATTGGACAGCAT
*
40622648 TTATACACCAAAATTTGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
*
40622672 TTATATA-CAAAATTGGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
* *
40622695 TTATTCACCAAAATTGGGCAGCAT
1 TTATACACCAAAATTGGACAGCAT
* * * *
40622719 ATATATACC-AATTTGGACAGCAC
1 TTATACACCAAAATTGGACAGCAT
*
40622742 TTATACA-CAAAATTTGACA-CAT
1 TTATACACCAAAATTGGACAGCAT
* * *
40622764 GTATATA-CAAAATTGGACAACAT
1 TTATACACCAAAATTGGACAGCAT
* * *
40622787 TTATTCACCAAAATTGGGCAACAT
1 TTATACACCAAAATTGGACAGCAT
* *
40622811 ATATATACCAA
1 TTATACACCAA
40622822 TTTGAGCAGC
Statistics
Matches: 162, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
22 19 0.12
23 56 0.35
24 66 0.41
25 11 0.07
26 5 0.03
27 5 0.03
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (24 bp):
TTATACACCAAAATTGGACAGCAT
Found at i:40622689 original size:47 final size:47
Alignment explanation
Indices: 40622598--40622801 Score: 252
Period size: 47 Copynumber: 4.3 Consensus size: 47
40622588 TGAACAACTC
*
40622598 TTATACATCAGAAA-TTGAGCAGCATATATATATACAAAATTGGACAGCAT
1 TTATACACCA-AAATTTGA-CAGCAT-T-TATATACAAAATTGGACAGCAT
40622648 TTATACACCAAAATTTGACAGCATTTATATACAAAATTGGACAGCAT
1 TTATACACCAAAATTTGACAGCATTTATATACAAAATTGGACAGCAT
* * * * * * *
40622695 TTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCAC
1 TTATACACCAAAATTTGACAGCATTTATATACAAAATTGGACAGCAT
* *
40622742 TTATACA-CAAAATTTGACA-CATGTATATACAAAATTGGACAACAT
1 TTATACACCAAAATTTGACAGCATTTATATACAAAATTGGACAGCAT
*
40622787 TTATTCACCAAAATT
1 TTATACACCAAAATT
40622802 GGGCAACATA
Statistics
Matches: 135, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
45 27 0.20
46 17 0.13
47 68 0.50
48 1 0.01
49 9 0.07
50 13 0.10
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.29
Consensus pattern (47 bp):
TTATACACCAAAATTTGACAGCATTTATATACAAAATTGGACAGCAT
Found at i:40622788 original size:92 final size:94
Alignment explanation
Indices: 40622609--40622825 Score: 339
Period size: 92 Copynumber: 2.3 Consensus size: 94
40622599 TATACATCAG
* * * * *
40622609 AAATTGAGCAGCATATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATTT
1 AAATTGGGCAGC--ATATATATACCAATTTGGACAGCACTTATACACCAAAATTTGACAGCATGT
*
40622674 ATATACAAAATTGGACAGCATTTATTCACCA
64 ATATACAAAATTGGACAACATTTATTCACCA
40622705 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACA-CATGTAT
1 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACCAAAATTTGACAGCATGTAT
40622768 ATACAAAATTGGACAACATTTATTCACCA
66 ATACAAAATTGGACAACATTTATTCACCA
*
40622797 AAATTGGGCAACATATATATACCAATTTG
1 AAATTGGGCAGCATATATATACCAATTTG
40622826 AGCAGCATTT
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
92 62 0.54
93 12 0.11
94 29 0.25
96 11 0.10
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (94 bp):
AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACCAAAATTTGACAGCATGTAT
ATACAAAATTGGACAACATTTATTCACCA
Found at i:40622835 original size:47 final size:47
Alignment explanation
Indices: 40622623--40622835 Score: 252
Period size: 47 Copynumber: 4.6 Consensus size: 47
40622613 TGAGCAGCAT
* *
40622623 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAAC
* * * *
40622670 ATTTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAAC
* * * *
40622717 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGAC-AC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAAC
* * * *
40622762 ATGTATATACAAAATTGGACAACATTTATTCACCAAAATTGGGCAAC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAAC
* *
40622809 ATATATATAC-CAATTTGAGCAGCATTT
1 ATATATATACAAAATTGGA-CAGCATTT
40622836 TAGCATAAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
45 27 0.19
46 24 0.17
47 88 0.63
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (47 bp):
ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAAC
Found at i:40623803 original size:30 final size:32
Alignment explanation
Indices: 40623762--40623844 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 32
40623752 TAATAAATAT
*
40623762 ATATTTTTTTTATTTTTAAAAATA-TTTTAAA
1 ATATATTTTTTATTTTTAAAAATATTTTTAAA
* *
40623793 ATA-CTTTTTTATTTTT-GAAATATTTTTAAA
1 ATATATTTTTTATTTTTAAAAATATTTTTAAA
40623823 ATATATTTTTTAATTTTCTAAA
1 ATATATTTTTT-ATTTT-TAAA
40623845 TTTTTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 5 0.12
30 22 0.51
31 9 0.21
32 5 0.12
33 1 0.02
34 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (32 bp):
ATATATTTTTTATTTTTAAAAATATTTTTAAA
Found at i:40623850 original size:31 final size:30
Alignment explanation
Indices: 40623755--40623850 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 30
40623745 CCGAATATAA
* *
40623755 TAAATATATATTTTTTTTATTTTTAAAAATATTT
1 TAAA-ATATA-TTTTTTAATTTTT--AAATTTTT
*
40623789 TAAAATA-CTTTTTT-ATTTTTGAAATATTTT
1 TAAAATATATTTTTTAATTTTT-AAAT-TTTT
40623819 TAAAATATATTTTTTAATTTTCTAAATTTTT
1 TAAAATATATTTTTTAATTTT-TAAATTTTT
40623850 T
1 T
40623851 TTTGGTGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
29 4 0.07
30 16 0.30
31 17 0.31
32 9 0.17
33 4 0.07
34 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (30 bp):
TAAAATATATTTTTTAATTTTTAAATTTTT
Found at i:40628715 original size:20 final size:21
Alignment explanation
Indices: 40628688--40628742 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
40628678 AACAGCGGTG
**
40628688 GCGGTGAGATTAGTTACT-TA
1 GCGGTGAGATTAGACACTATA
* *
40628708 GTGGTGAGATTGGACACTATA
1 GCGGTGAGATTAGACACTATA
40628729 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
40628743 AATAATGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.27, C:0.09, G:0.35, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGACACTATA
Found at i:40629075 original size:12 final size:12
Alignment explanation
Indices: 40629060--40629086 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40629050 TTAAATTTTC
40629060 TATTAATATACA
1 TATTAATATACA
40629072 TATTAATATACA
1 TATTAATATACA
40629084 TAT
1 TAT
40629087 ATGATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTAATATACA
Found at i:40635107 original size:26 final size:26
Alignment explanation
Indices: 40635078--40635128 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
40635068 TTTGACAATA
40635078 CTTTTGAAAAGTGCTCTGGAAAAATG
1 CTTTTGAAAAGTGCTCTGGAAAAATG
** * *
40635104 CTTTTGGGAAGTGCTTTTGAAAAAT
1 CTTTTGAAAAGTGCTCTGGAAAAAT
40635129 TTAGTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAGTGCTCTGGAAAAATG
Found at i:40635405 original size:33 final size:35
Alignment explanation
Indices: 40635310--40635406 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
40635300 TTAATATTTT
*
40635310 AATATATAAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
40635345 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
40635378 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
40635407 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:40635567 original size:20 final size:20
Alignment explanation
Indices: 40635539--40635582 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
40635529 ATTAAACACT
*
40635539 AAAAGTGCTTTTGGGAGAGA
1 AAAAATGCTTTTGGGAGAGA
*
40635559 AAAAATGCTTTTGGGAGATA
1 AAAAATGCTTTTGGGAGAGA
40635579 AAAA
1 AAAA
40635583 GTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (20 bp):
AAAAATGCTTTTGGGAGAGA
Found at i:40644230 original size:35 final size:35
Alignment explanation
Indices: 40644184--40644268 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
40644174 GTATTTTATT
*
40644184 AATAAAAAATCAAGCTCTGTCAAAAAATAAAATAA
1 AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
*
40644219 AATAAAAAATCAAGCTCTATCAACAAATAAAATAA
1 AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
*
40644254 AATAAAAAGTCAAGC
1 AATAAAAAATCAAGC
40644269 AAATTACATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (35 bp):
AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
Found at i:40653397 original size:27 final size:28
Alignment explanation
Indices: 40653365--40653432 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 28
40653355 TATGGTTTCT
40653365 TTTCTTGTTTTAATCTTCCTTTCT-TCC
1 TTTCTTGTTTTAATCTTCCTTTCTCTCC
*
40653392 TTTCTTGTTTCAATCTTCCTTTCTCTCC
1 TTTCTTGTTTTAATCTTCCTTTCTCTCC
*
40653420 TTGTCTTATTTTA
1 TT-TCTTGTTTTA
40653433 CTCTCATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.64
28 5 0.14
29 8 0.22
ACGTcount: A:0.09, C:0.25, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTCTTGTTTTAATCTTCCTTTCTCTCC
Found at i:40655682 original size:13 final size:13
Alignment explanation
Indices: 40655664--40655724 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
40655654 CTCAAATTTT
40655664 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
40655677 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
40655690 TCCACAA-CACTTC
1 T-CAAAAGCACTTC
* * *
40655703 TCAATAGTACTTT
1 TCAAAAGCACTTC
40655716 TCAAAAGCA
1 TCAAAAGCA
40655725 ATAAAGAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
12 3 0.08
13 30 0.81
14 4 0.11
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:40659060 original size:29 final size:29
Alignment explanation
Indices: 40658988--40659069 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
40658978 AGATGCACCA
* * *
40658988 AAGTGCAATAAC-TAAACAGAATGACATTG
1 AAGTGCAATAGCAT-AATAGAATGACACTG
*
40659017 AAGTGCAATATCATAATAGAATGACACTG
1 AAGTGCAATAGCATAATAGAATGACACTG
***
40659046 AAGTGTTTTAGCATAATAGAATGA
1 AAGTGCAATAGCATAATAGAATGA
40659070 TACCAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 44 0.98
30 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (29 bp):
AAGTGCAATAGCATAATAGAATGACACTG
Found at i:40661638 original size:19 final size:19
Alignment explanation
Indices: 40661559--40661638 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 19
40661549 GCCTATTTTT
*
40661559 TTTTATATAAATTTTTGAGTA
1 TTTTATATGAATTTTTGA--A
* *
40661580 TTTTATAT-AGTTTTATAAA
1 TTTTATATGAATTTT-TGAA
*
40661599 TTTTA-AT-AATTTTTTAA
1 TTTTATATGAATTTTTGAA
*
40661616 -TTTATATGTATTTTTGAA
1 TTTTATATGAATTTTTGAA
40661634 TTTTA
1 TTTTA
40661639 ATTTAGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 15 0.31
19 10 0.20
20 5 0.10
21 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTATATGAATTTTTGAA
Found at i:40662745 original size:21 final size:20
Alignment explanation
Indices: 40662720--40662758 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40662710 TGCCGGAAAA
40662720 AGAAAAAAAAAGAGAGAAAGG
1 AGAAAAAAAAAGA-AGAAAGG
* *
40662741 AGAAAGAAAGAGAAGAAA
1 AGAAAAAAAAAGAAGAAA
40662759 AAAAATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAAAGAAGAAAGG
Found at i:40663149 original size:76 final size:77
Alignment explanation
Indices: 40662947--40663151 Score: 213
Period size: 76 Copynumber: 2.6 Consensus size: 77
40662937 TAGTTATTAA
* * * *
40662947 TAATTATTGTTACTTAGTATTATTGTTAGTCAAAAACTAATATTATTATTATGGTTAGTTATTAG
1 TAATTATTATTAGTTAGTATTATTGTTAGT-AAAAA--ACTATTATTATTATTGTTAGTTATTAG
40663012 GATTAGTAAAAACCC
63 GATTAGTAAAAACCC
* **** **
40663027 TAATTATTATTTTAGTTAGTATGATTGTTAGT-TTTTAC-ATTA-TATTATTGTTAGTTATTATT
1 TAATTATTA--TTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATTGTTAGTTATTAGG
*
40663089 TTTAGT-AAAACCC
64 ATTAGTAAAAACCC
40663102 TAATTATTATTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTATT
1 TAATTATTATTAGTTAGTATTATTGTT-AGTAAAAAACTATTATTATTATT
40663152 ATTATTGTGT
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
72 2 0.02
73 17 0.17
74 2 0.02
75 20 0.20
76 29 0.28
77 4 0.04
78 1 0.01
80 8 0.08
82 19 0.19
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (77 bp):
TAATTATTATTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATTGTTAGTTATTAGGAT
TAGTAAAAACCC
Found at i:40668622 original size:153 final size:152
Alignment explanation
Indices: 40668343--40668876 Score: 735
Period size: 153 Copynumber: 3.5 Consensus size: 152
40668333 CAAAACAAAG
* * *
40668343 TTAGTAAAAAACCCTTATTTCGACCCTTTGTTCATATTTTTTCCCCAGATTTTATTACTTTCAAA
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTT-CTCAGATTTTATTACTTTCAAA
* *
40668408 AAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATGA
65 AAATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
* * *
40668473 ATTAATTTTATTTTTTAAATAAAT
130 ATTTAGTGT-TTTTTTAAATAAAT
40668497 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
* *
40668562 AATATACTATTTTCTAATTTTCTAATTTTATATTATTTTAGTACATTATGTTTGAAATGTATTAA
66 AATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
40668627 TTTAGTGTGTTTTTTAAATAAAT
131 TTTAGTGT-TTTTTTAAATAAAT
*
40668650 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTC-CCGTATTTTATTACTTTC--A
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAG-ATTTTATTACTTTCAAA
*
40668712 AAA-A-AC-A-TAT-T-ATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
65 AAATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
* *
40668771 ATTTAGTGTGTTTTTATATAAAT
130 ATTTAGTGTTTTTTTAAATAAAT
* * * *
40668794 TTAGTAAAAAAACCTTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTT
1 TTAGT-AAAAAACCCTTATTTCGGCCCTTTGTTCGTA---TT-TT-TTCTCAGATTTTATTACTT
**
40668859 TCAATGAATATACTATTT
60 TCAAAAAATATACTATTT
40668877 CCATTTTTTT
Statistics
Matches: 341, Mismatches: 25, Indels: 26
0.87 0.06 0.07
Matches are distributed among these distances:
144 17 0.05
145 83 0.24
146 1 0.00
147 2 0.01
148 3 0.01
149 4 0.01
150 17 0.05
151 6 0.02
152 4 0.01
153 160 0.47
154 42 0.12
155 1 0.00
156 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (152 bp):
TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
AATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
TTTAGTGTTTTTTTAAATAAAT
Found at i:40669146 original size:19 final size:20
Alignment explanation
Indices: 40669122--40669161 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
40669112 TTTTTTACAC
40669122 AAATAATA-CAAAAAAATTA
1 AAATAATACCAAAAAAATTA
40669141 AAATAATACCCAAAAAAATTA
1 AAATAATA-CCAAAAAAATTA
40669162 CCTTTCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAATACCAAAAAAATTA
Found at i:40669242 original size:13 final size:13
Alignment explanation
Indices: 40669206--40669260 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
40669196 CTCCCTCTTC
40669206 TTCTTCTCTTTTCCTT
1 TTCTTCTC-TTT-C-T
*
40669222 TTCTTTCTTTTTCT
1 TTC-TTCTCTTTCT
*
40669236 TTCTTCTCCTTCT
1 TTCTTCTCTTTCT
40669249 TTCTTCTCTTTC
1 TTCTTCTCTTTC
40669261 AGCCGAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 19 0.56
14 4 0.12
15 1 0.03
16 6 0.18
17 4 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCTTCTCTTTCT
Found at i:40669339 original size:27 final size:27
Alignment explanation
Indices: 40669290--40669355 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
40669280 ATATAAGAGG
* *
40669290 CTGGTGTCGCCTGTCGCAGTGGCACCT
1 CTGGTGTCGCCTCTCGCACTGGCACCT
*
40669317 TTGGTGTCGCCTCT-GCCACTGGCACCT
1 CTGGTGTCGCCTCTCG-CACTGGCACCT
*
40669344 CTGGTGCCGCCT
1 CTGGTGTCGCCT
40669356 TTGGCAGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.06, C:0.36, G:0.30, T:0.27
Consensus pattern (27 bp):
CTGGTGTCGCCTCTCGCACTGGCACCT
Found at i:40669896 original size:22 final size:20
Alignment explanation
Indices: 40669860--40669918 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
40669850 GGCCCGACCC
40669860 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
40669882 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
40669903 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
40669919 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:40669920 original size:11 final size:11
Alignment explanation
Indices: 40669900--40669966 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
40669890 TAAAAATTAA
40669900 AAAAAGTATTTT
1 AAAAA-TATTTT
40669912 AAAAATATTTT
1 AAAAATATTTT
40669923 --AAA-A--TT
1 AAAAATATTTT
* *
40669929 AAAAAAAATTT
1 AAAAATATTTT
40669940 AAAAAGTATTTT
1 AAAAA-TATTTT
*
40669952 AAAAGTATTTT
1 AAAAATATTTT
40669963 AAAA
1 AAAA
40669967 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 4 0.09
11 23 0.50
12 13 0.28
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40669946 original size:40 final size:40
Alignment explanation
Indices: 40669891--40669984 Score: 152
Period size: 40 Copynumber: 2.3 Consensus size: 40
40669881 AATTTATTTT
*
40669891 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATT-TAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
40669932 AAAAATTTAAAAAGTATTTTAAAAGTATTTTAAAATTAAA
1 AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTAAA
*
40669972 AAAATTTTAAAAA
1 AAAAATTTAAAAA
40669985 TAAATATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
40 43 0.86
41 7 0.14
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:40671482 original size:29 final size:31
Alignment explanation
Indices: 40671450--40671509 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
40671440 TTCAATTTTC
* *
40671450 AAAAACAAT-AAAAA-ATATTTTTAAAAATG
1 AAAAAAAATGAAAAATATATTTTCAAAAATG
40671479 AAAAAAAATGAAAAATATATTTTCAAAAATG
1 AAAAAAAATGAAAAATATATTTTCAAAAATG
40671510 GGGAGCCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAAAAAATGAAAAATATATTTTCAAAAATG
Found at i:40673056 original size:125 final size:122
Alignment explanation
Indices: 40672833--40673083 Score: 394
Period size: 125 Copynumber: 2.0 Consensus size: 122
40672823 AACCCCCAAT
*
40672833 AGTAAAGACATACCTTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
1 AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
* * *
40672898 CAATGACTCCATCTCTAGTTCTTCCAAGCTGTAAGAAAATATCAGTAGTACATTGTA
66 CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
* * *
40672955 AGTAAAGACATACCCTGTGAGAGATCTTATTTTATCAAGGTCTCTAACAAAATCAGAATCAACAT
1 AGTAAAGACATACCCTGTGAGAGATC---TTTTATCAAGGTCTCCAAAAAAATCAAAATCAACAT
* *
40673020 ACTCAATGACTCCATCTCTAGTTCTTCCAAATTGTAAGAAAATATCAATAGTATATCGTA
63 ACTCAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
40673080 AGTA
1 AGTA
40673084 TCTGAAAATC
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
122 25 0.21
125 92 0.79
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (122 bp):
AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
Found at i:40689153 original size:16 final size:16
Alignment explanation
Indices: 40689132--40689167 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40689122 TGTTTAAGAA
*
40689132 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
40689148 ATTATTATAATATTAT
1 ATTATTATAATATTAC
40689164 ATTA
1 ATTA
40689168 ACTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:40689915 original size:3 final size:3
Alignment explanation
Indices: 40689907--40689944 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40689897 GTGAGGTAAG
40689907 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40689945 AGATGAGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40691434 original size:20 final size:20
Alignment explanation
Indices: 40691396--40691434 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40691386 TATTACTCAC
*
40691396 TTTATCATTTTAAATATTTT
1 TTTATCATTTTAAAGATTTT
40691416 TTTATCA-TTTATAAGATTT
1 TTTATCATTTTA-AAGATTT
40691435 ATCACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATCATTTTAAAGATTTT
Found at i:40691599 original size:20 final size:19
Alignment explanation
Indices: 40691574--40691626 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
40691564 AAAAATTCAA
*
40691574 ATTTTATATTAAAATATTT
1 ATTTTATATTAAAATAATT
*
40691593 ATATTTATATTTAAATAATT
1 AT-TTTATATTAAAATAATT
40691613 ATTTT-TCATTAAAA
1 ATTTTAT-ATTAAAA
40691627 AAGAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 17 0.59
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTATATTAAAATAATT
Found at i:40696511 original size:18 final size:18
Alignment explanation
Indices: 40696490--40696527 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40696480 TAGAAACAGC
40696490 AAAAA-AGCACGATAGCAA
1 AAAAATAGCA-GATAGCAA
*
40696508 AAAAATAGTAGATAGCAA
1 AAAAATAGCAGATAGCAA
40696526 AA
1 AA
40696528 GCAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAATAGCAGATAGCAA
Found at i:40697742 original size:3 final size:3
Alignment explanation
Indices: 40697712--40697812 Score: 53
Period size: 3 Copynumber: 33.3 Consensus size: 3
40697702 TTTATCCTTG
* * * *
40697712 TTA TCA TTA TTA TCA TTTA TCTA CTTA TTA TTA TGA -TA TGA TTA TTA
1 TTA TTA TTA TTA TTA -TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
40697759 ATA TTA ATA TTA ATA TTA ATA TTA ATA ATA TTA TTA TTA -CA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
40697806 TTG TTA T
1 TTA TTA T
40697813 AGTATTCCTT
Statistics
Matches: 71, Mismatches: 22, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
2 2 0.03
3 62 0.87
4 6 0.08
5 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:40697763 original size:6 final size:6
Alignment explanation
Indices: 40697754--40697785 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40697744 ATGATATGAT
40697754 TATTAA TATTAA TATTAA TATTAA TATTAA TA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TA
40697786 ATATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:40697793 original size:18 final size:18
Alignment explanation
Indices: 40697752--40697794 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40697742 TTATGATATG
*
40697752 ATTATTAATATTAATATT
1 ATTATTAATATTAATAAT
*
40697770 AATATTAATATTAATAAT
1 ATTATTAATATTAATAAT
40697788 ATTATTA
1 ATTATTA
40697795 TTACATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTAATATTAATAAT
Found at i:40707188 original size:30 final size:30
Alignment explanation
Indices: 40707127--40707188 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
40707117 GGAGTGGAGG
* ** **
40707127 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
*
40707157 GGAGTAAAAGTTTTGAGTAAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
40707187 GG
1 GG
40707189 TTTGGGAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
Found at i:40708419 original size:124 final size:123
Alignment explanation
Indices: 40708275--40708544 Score: 391
Period size: 124 Copynumber: 2.2 Consensus size: 123
40708265 TTTTTTCGAA
* * * ** *
40708275 TTGACGTATCTG-GTCAAATAGTGGGAAATCGTTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGGAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
***
40708339 GAAATCGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGTAAGAAATAATTTTTT
65 GAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAT-ATTTTTT
**
40708398 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGGAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
*
40708463 GAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATATTTTTT
65 GAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATATTTTTT
40708522 TTGACGTTTCTGAGCAAATAGTG
1 TTGACGTTTCTGAGCAAATAGTG
40708545 TCAAATCACG
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
123 22 0.17
124 93 0.71
125 16 0.12
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTGGAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATATTTTTT
Found at i:40708923 original size:28 final size:28
Alignment explanation
Indices: 40708883--40709472 Score: 562
Period size: 28 Copynumber: 22.4 Consensus size: 28
40708873 AGTTCTTCTG
40708883 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40708911 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* **
40708934 TTAATTAAAATAGGTTAGGGTTAGGG--T
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* *
40708961 TT--TT-AACTAAATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40708986 TTAATT--A---AATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* *
40709009 TTAATTAAATTAAATTAGTTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709037 TTAATTAAATTAAATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709065 TTAATTAAATTAAATTAGGTTGGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
40709093 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
40709121 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709149 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
40709172 TTAATTAAATTAGGTTAGTGTTAGGG-TT
1 TTAATTAAATTAAATTAG-GTTAGGGTTT
* * **
40709200 TTCATGTAAAATAGGTTAGGGTTAGGG--T
1 TTAAT-TAAATTAAATTA-GGTTAGGGTTT
* *
40709228 TT--TT-AACTAAATTAGGTTAGGATTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709253 TTAATTAAATTAAATTAGGCTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
40709281 TTAATT--A-T--ATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
40709304 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709332 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
** *
40709355 TTAATTAAATTAGGTTAGGGTAAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
40709384 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
40709412 TTAATTAAGTT--A--A-GTTAGGG-TT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
40709434 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
40709463 TTAATCAAAT
1 TTAATTAAAT
40709473 AATGTCAAAA
Statistics
Matches: 480, Mismatches: 36, Indels: 91
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.03
23 123 0.26
24 18 0.04
25 12 0.03
26 8 0.02
27 10 0.02
28 228 0.47
29 68 0.14
30 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
TTAATTAAATTAAATTAGGTTAGGGTTT
Found at i:40708991 original size:18 final size:21
Alignment explanation
Indices: 40708968--40709020 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 21
40708958 GGTTTTTAAC
40708968 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
40708991 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
40709014 TAAATTA
1 TAAATTA
40709021 AATTAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
TAAATTAGGTTAGGGATTTAT
Found at i:40709040 original size:51 final size:51
Alignment explanation
Indices: 40708890--40709472 Score: 456
Period size: 51 Copynumber: 11.2 Consensus size: 51
40708880 CTGTTAATTA
*
40708890 AATTAAATTAGGTTAGGGTTTTTAATTAAGTT--A--A-GTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * *
40708936 AATTAAAATAGGTTAGGGTTAGGGTTT--TT-AACTAAATTAGGTTAGGGATTTT
1 AATTAAATTAGGTTAGGGTT----TTTAATTAAATTAAATTAGGTTAGGGTTTTT
* *
40708988 AATTAAATTAGGTTAGGGATTTTAATTAAATTAAATTAGTTTAGGGATTTTAATT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT
* *
40709043 AAATTAAATTAGGTTAGGGATTTTAATTAAATTAAATTAGGTTGGGGTTTTTAATT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT
40709099 AAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * **
40709151 AATTAAGTTAAGTTAGGGTTTTTAATTAAATTAGGTTAGTGTTAGGG-TTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAG-GTTAGGGTTTTT
* * * *
40709202 CATGTAAAATAGGTTAGGGTTAGGGTTT--TT-AACTAAATTAGGTTAGGATTTTTAATT
1 AAT-TAAATTAGGTTAGGGTT----TTTAATTAAATTAAATTAGGTTAGG--GTTT--TT
*
40709259 AAATTAAATTAGGCTAGGGTTTTTAATT--A-T--ATTAGGTTAGGGTTTTTAATT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT
*
40709310 AAATTAAATTAGGTTAGGGTTTTTAATTAAGTT--A--A-GTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
*
40709357 AATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGTTTTT
1 AATTAAATTAGG-T----T-AGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * **
40709414 AATTAAGTTAAGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTT
*
40709465 AATCAAAT
1 AATTAAAT
40709473 AATGTCAAAA
Statistics
Matches: 450, Mismatches: 39, Indels: 91
0.78 0.07 0.16
Matches are distributed among these distances:
46 31 0.07
47 5 0.01
48 5 0.01
49 4 0.01
50 23 0.05
51 134 0.30
52 77 0.17
53 14 0.03
54 8 0.02
55 6 0.01
56 102 0.23
57 39 0.09
58 2 0.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (51 bp):
AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
Found at i:40710778 original size:34 final size:35
Alignment explanation
Indices: 40710734--40710800 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40710724 CAGTAAAATA
*
40710734 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
40710768 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
40710801 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:40712256 original size:23 final size:25
Alignment explanation
Indices: 40712220--40712266 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
40712210 ATAACAAAAA
40712220 ATAAATTAATAAATATCTAAAATAC
1 ATAAATTAATAAATATCTAAAATAC
*
40712245 ATAAA-TAA-AAATATCTTAAATA
1 ATAAATTAATAAATATCTAAAATA
40712267 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAATTAATAAATATCTAAAATAC
Found at i:40712496 original size:22 final size:22
Alignment explanation
Indices: 40712466--40712507 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40712456 ATTTGGAGAT
*
40712466 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
40712488 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
40712508 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:40712515 original size:30 final size:30
Alignment explanation
Indices: 40712479--40712537 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
40712469 TTGAAGGAAA
*
40712479 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAATTTGAGAGT
40712509 TTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGGAATTTGAGAG
40712538 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAATTTGAGAGT
Found at i:40712528 original size:52 final size:51
Alignment explanation
Indices: 40712457--40712559 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
40712447 TTAATATGGA
* * *
40712457 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAA-TTGAGAG
* *
40712508 TTTGAGAGAATTTTGGAAGGAATTTGAGAGAATTTTTGAACGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
40712560 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.34
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
Found at i:40712533 original size:22 final size:22
Alignment explanation
Indices: 40712508--40712578 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
40712498 AATTTGAGAG
*
40712508 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
40712530 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
40712553 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
40712574 ATTGA
1 TTTGA
40712579 TATTGAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 4 0.09
22 38 0.83
23 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:40713793 original size:12 final size:12
Alignment explanation
Indices: 40713776--40713800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40713766 TTTTGATATA
40713776 TTTTATAATTTT
1 TTTTATAATTTT
40713788 TTTTATAATTTT
1 TTTTATAATTTT
40713800 T
1 T
40713801 ACGAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:40713861 original size:20 final size:20
Alignment explanation
Indices: 40713786--40713861 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
40713776 TTTTATAATT
* **
40713786 TTTTTTATAATTTTTACGAA
1 TTTTTTATAAATTTTAATAA
* *
40713806 TTTTTCAAAAAATTTTAAT-A
1 TTTTT-TATAAATTTTAATAA
* *
40713826 TTTTTTTTAAAGTTTAATAA
1 TTTTTTATAAATTTTAATAA
*
40713846 TTTTTTATAACTTTTA
1 TTTTTTATAAATTTTA
40713862 TTAACTTTTA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 9 0.21
20 25 0.60
21 8 0.19
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTTATAAATTTTAATAA
Found at i:40719382 original size:21 final size:21
Alignment explanation
Indices: 40719356--40719399 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40719346 ATTGAACAAG
40719356 AAGATTTTAACCACGAAACCT
1 AAGATTTTAACCACGAAACCT
40719377 AAGATTTTAACCACGAAACCT
1 AAGATTTTAACCACGAAACCT
40719398 AA
1 AA
40719400 CCATTCCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (21 bp):
AAGATTTTAACCACGAAACCT
Found at i:40730545 original size:7 final size:7
Alignment explanation
Indices: 40730533--40730563 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40730523 AAGAGGAAGA
40730533 AATAAAG
1 AATAAAG
40730540 AATAAAG
1 AATAAAG
40730547 AATAAAG
1 AATAAAG
40730554 AATAAAG
1 AATAAAG
40730561 AAT
1 AAT
40730564 TTGAGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (7 bp):
AATAAAG
Found at i:40731557 original size:510 final size:511
Alignment explanation
Indices: 40730604--40731615 Score: 1670
Period size: 510 Copynumber: 2.0 Consensus size: 511
40730594 AATAGAAGGC
40730604 TGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGCCAATGATCAATTG
1 TGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGCCAATGATCAATTG
* * *
40730669 CATAATGAGCTTTCTATGCTTCGAGCTGAAAAACTTGGCCTTTAGGAAAGTATGGAAACCATGGG
66 CATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTATGGAAACCATGGG
* *
40730734 TGAGAAGCACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCCCTACGAAGTACTA
131 TGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCCCTACGAAGTACCA
40730799 AGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAACATTTTGTTGCACA
196 AGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAACATTTTGTTGCACA
* * * * *
40730864 CCTAAGTTGTTGGGGGGCCTTTTGATGCTTGGAGGGTAAACCTCGATGCCTTGAGTCATCTTAAA
261 CCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTTAAGTCATCTCAAA
* *
40730929 GATTCTCAACTTGGTTTTGACATCCACTTCCTTTCGGGACCTGCTTGGGAAGAGTTCACTAAAGA
326 GATACTAAACTTGGTTTTGACATCCACTTCCTTTCGGGACCTGCTTGGGAAGAGTTCACTAAAGA
* * * *
40730994 GTGGAAGAACTCAAATAAACTTTTTATGGCTGATAAACTTGTTAAGCATAGTGTTGCTCCCTTTG
391 GTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGTGTTGCTCCATTCG
* *
40731059 TAGATTCTAAGAAAGGT-GAGCGAAAATACAATGGAAGATGTTGATAATAGGAGTT
456 CAGATTCTAAGAAAGGTAGAGCGAAAATACAAGGGAAGATGTTGATAATAGGAGTT
40731114 TGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGCCAATGATCAATTG
1 TGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGCCAATGATCAATTG
* *
40731179 CATAAAGAGATTTCTATGCTTCAAGTTGAAAAACTTGGCTTTTAGGAAAGTATGGAAACCATGGG
66 CATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTATGGAAACCATGGG
40731244 TGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCCCTACGAAGTACCA
131 TGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCCCTACGAAGTACCA
40731309 AGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAACATTTTGTTGCACA
196 AGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAACATTTTGTTGCACA
* * *
40731374 CCTAAGTTGTTGGTAGGCCTTTTGACGCTCGGAGGGTGAACCTTGATGCCTTAAGTCATCTCAAA
261 CCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTTAAGTCATCTCAAA
*** *
40731439 GATACTAAACTTGGTTTTGACATTTGCTTTCC-TTCGGGACCTGCTTGGGAAGAGTTC-CTTGAA
326 GATACTAAACTTGGTTTTGACATCCAC-TTCCTTTCGGGACCTGCTTGGGAAGAGTTCAC-TAAA
* * * *
40731502 GAGTGGAAGAACTCAAACGAACTTTTTGTGGCTGATAAACCTGTTGAGGATAGTGTTGCTCCATT
389 GAGTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGTGTTGCTCCATT
* * *
40731567 CGCAGATTTTGAGAAAGGTGAGAGCGAAGATACAAGGGAAGATGTTGAT
454 CGCAGATTCTAAGAAAGGT-AGAGCGAAAATACAAGGGAAGATGTTGAT
40731616 GATTCAAATG
Statistics
Matches: 464, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
509 1 0.00
510 433 0.93
511 4 0.01
512 26 0.06
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (511 bp):
TGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGCCAATGATCAATTG
CATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTATGGAAACCATGGG
TGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCCCTACGAAGTACCA
AGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAACATTTTGTTGCACA
CCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTTAAGTCATCTCAAA
GATACTAAACTTGGTTTTGACATCCACTTCCTTTCGGGACCTGCTTGGGAAGAGTTCACTAAAGA
GTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGTGTTGCTCCATTCG
CAGATTCTAAGAAAGGTAGAGCGAAAATACAAGGGAAGATGTTGATAATAGGAGTT
Found at i:40732102 original size:134 final size:134
Alignment explanation
Indices: 40731862--40732175 Score: 414
Period size: 134 Copynumber: 2.3 Consensus size: 134
40731852 AACTGTTCAT
* * * *
40731862 GATCGTAAATCAACAAGTTTTAATAATATCAGTCGTGATCATAATTCAGCAAGCTGTTTGAATGA
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGCAAGCTGTTTGAATAA
* * * * * * *
40731927 AGTTGTGGTCGTAAATCAGTGAACTCAAAATAAATTGTTCATGATTGTAAATCAATGAACTTAAG
66 AGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
40731992 TTGC
131 TTGC
* * *
40731996 GATCGTAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAA-CTTTTTGAATA
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGC-AAGCTGTTTGAATA
* * * * *
40732060 AAGTTGCGATTGTAAATTAGAGAACTTAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAA
65 AAGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAA
*
40732125 ATTGT
130 ATTGC
* *
40732130 GATCATAAATCAACAAGTTTTAATAATACCAGTTGTGATCGTAAAT
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAAT
40732176 TGACAAACTA
Statistics
Matches: 155, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
134 153 0.99
135 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (134 bp):
GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCGTAAATCAGCAAGCTGTTTGAATAA
AGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
TTGC
Found at i:40732248 original size:233 final size:232
Alignment explanation
Indices: 40731948--40732392 Score: 620
Period size: 233 Copynumber: 1.9 Consensus size: 232
40731938 TAAATCAGTG
* ** * *
40731948 AACTCAAAATAAATTGTTCATGATTGTAAATCAATGAACTTAAGTTGCGATCGTAAATCAGCAAG
1 AACTAAAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAG
* ** *
40732013 CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTTTTTGAATAAAGTTGCGATTGTAAATT
66 CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATC
* * * * *
40732078 AGAGAACTTAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAATTGTGATCATAAATCAA
131 AGAGAACTCAAAACGAACTATTCATAATCGTAAATCAATGAACTT-AAGTGTGATCATAAATCAA
*
40732143 CAAGTTTTAATAATACCAGTTGTGATCGTAAATTGACA
195 CAAGCTTTAATAATACCAGTTGTGATCGTAAATTGACA
* *
40732181 AACTAAAAATAAATTGTTCGTGATCATAAATCAATGAACTTAAGTTGTGATCATAAATCAACAAG
1 AACTAAAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAG
* * ** *
40732246 CTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATC
66 CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATC
* * * * * *
40732311 AGTGAACTCAAAACGAATTATTCATGATCGTAAATCAATTAACTTAAGTGTGATCTTAAATTAAC
131 AGAGAACTCAAAACGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATCATAAATCAAC
*
40732376 ATGCTTTAATAATACCA
196 AAGCTTTAATAATACCA
40732393 TTCATAATCA
Statistics
Matches: 183, Mismatches: 29, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
232 32 0.17
233 151 0.83
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (232 bp):
AACTAAAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAG
CTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATC
AGAGAACTCAAAACGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATCATAAATCAAC
AAGCTTTAATAATACCAGTTGTGATCGTAAATTGACA
Found at i:40732307 original size:134 final size:134
Alignment explanation
Indices: 40732160--40732809 Score: 653
Period size: 134 Copynumber: 4.9 Consensus size: 134
40732150 TAATAATACC
* * * * * * * *
40732160 AGTTGTGATCGTAAATTGACAAACTAAAAATAAATTGTTCGTGATCATAAATCAATGAACTTAAG
1 AGTTGCGATCGTAAATTGACGAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAG
* * * *
40732225 TTGTGATCATAAATCAACAAGCTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGA
66 CTGTGATCATAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGA
40732290 ATGG
131 ATGG
* * * * * * * *
40732294 AGTTGTGACCGTAAA-TCAGTGAACTCAAAACGAATTATTCATGATCGTAAATCAATTAACTTAA
1 AGTTGCGATCGTAAATTGA-CGAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAA
* * * * * * * *
40732358 G-TGTGATCTTAAATTAACATGCTTTAATAATACCATTCATAATCATAAATCAGCGAACTGTTTG
65 GCTGTGATCATAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTG
40732422 AATGG
130 AATGG
* * ** *
40732427 AGTTGCAATTGTAAATCAAC-AAGCTCAAAATCAACTGTTCATGATCGTAAATCAATAAACTTAA
1 AGTTGCGATCGTAAATTGACGAA-CTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAA
* * * * * * *
40732491 GTTGTGATCGTAAATCAGTAAGCTTTAATAATACTAGTTGTGATCGTAAATCAGTGAACTTTTTG
65 GCTGTGATCATAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTG
40732556 AATGG
130 AATGG
* * * * * *
40732561 AGTTGCGATTGTAAATTGGCGAACTCAAAATGAACTGTTTATGATCATAAATTAATAAACCTAAG
1 AGTTGCGATCGTAAATTGACGAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAG
* * * * * * *
40732626 CTGTGAT-AGCAAATCAGTAAGCTTTAATAATTCTAGTCATGATTGTAAATCAGCGAATTGTTTG
66 CTGTGATCA-TAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTG
40732690 AATGG
130 AATGG
* * * * * * *
40732695 AGTTACAATCATGAA-TGAGCGAACTCATAATGAACTGGTCATGATCGTAAATCAATGAACTTAA
1 AGTTGCGATCGTAAATTGA-CGAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAA
** * *
40732759 GCTGTGATTGTAAATTAGCAAGCTTTAATAATACCAGTTGTGATCGTAAAT
65 GCTGTGATCATAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAAT
40732810 ACCCGAACTC
Statistics
Matches: 422, Mismatches: 86, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
132 2 0.00
133 111 0.26
134 307 0.73
135 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (134 bp):
AGTTGCGATCGTAAATTGACGAACTCAAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAG
CTGTGATCATAAATCAGCAAGCTTTAATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGA
ATGG
Found at i:40732523 original size:267 final size:268
Alignment explanation
Indices: 40732181--40732809 Score: 758
Period size: 268 Copynumber: 2.4 Consensus size: 268
40732171 TAAATTGACA
* * * * * *
40732181 AACTAAAAATAAATTGTTCGTGATCATAAATCAATGAACTTAAGTTGTGATCATAAATCAACAAG
1 AACTCAAAATAAACTGTTCATGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAG
* * *
40732246 CTTTAATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATC
66 CTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAATC
* * * * * *** *
40732311 AGTGAACTCAAAACGAATTATTCATGATCGTAAATCAATTAACTTAAG-TGTGATCTTAAATTAA
131 AGCGAACTCAAAACGAACTATTCATGATCATAAATCAATAAACCTAAGCTGTGATAGCAAATCAA
* * * **
40732375 CATGCTTTAATAATACCATTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTGCAATTGTA
196 CAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCATA
40732440 AATCAAC-
261 AATCAACG
* * *
40732447 AAGCTCAAAATCAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATCGTAAATCAGTAA
1 AA-CTCAAAATAAACTGTTCATGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAA
* * **
40732512 GCTTTAATAATACTAGTTGTGATCGTAAATCAGTGAACTTTTTGAATGGAGTTGCGATTGTAAAT
65 GCTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAAT
** * * * *
40732577 TGGCGAACTCAAAATGAACTGTTTATGATCATAAATTAATAAACCTAAGCTGTGATAGCAAATCA
130 CAGCGAACTCAAAACGAACTATTCATGATCATAAATCAATAAACCTAAGCTGTGATAGCAAATCA
** * * * ** *
40732642 GTAAGCTTTAATAATTCTAGTCATGATTGTAAATCAGCGAATTGTTTGAATGGAGTTACAATCAT
195 ACAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCAT
* * *
40732707 GAATGAGCG
260 AAATCAACG
* * * * * *
40732716 AACTCATAATGAACTGGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATTAGCAAG
1 AACTCAAAATAAACTGTTCATGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAG
40732781 CTTTAATAATACCAGTTGTGATCGTAAAT
66 CTTTAATAATACCAGTTGTGATCGTAAAT
40732810 ACCCGAACTC
Statistics
Matches: 304, Mismatches: 56, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
266 2 0.01
267 149 0.49
268 151 0.50
269 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (268 bp):
AACTCAAAATAAACTGTTCATGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAG
CTTTAATAATACCAGTTGTGATCGTAAATCAGTGAACTGTTTGAATGGAGTTGCGACCGTAAATC
AGCGAACTCAAAACGAACTATTCATGATCATAAATCAATAAACCTAAGCTGTGATAGCAAATCAA
CAAGCTTTAATAATACCAGTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCATA
AATCAACG
Found at i:40732875 original size:71 final size:71
Alignment explanation
Indices: 40732794--40732925 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
40732784 TAATAATACC
* * *
40732794 AGTTGTGATCGTAAAT-ACCCGAACTCAAAATGAACTGTTCATGATCGTAAATCAACGAACTGTT
1 AGTTGCGATCGTAAATCA-CCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACTGTT
40732858 TGAATAG
65 TGAATAG
* * * *
40732865 AGTTGCGATCGTAAATCAGCAAACTCAAAATGAACTATTTATGATCGTTAATCAATGAACT
1 AGTTGCGATCGTAAATCACCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACT
40732926 TAAGTTGTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
71 52 0.98
72 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (71 bp):
AGTTGCGATCGTAAATCACCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACTGTTT
GAATAG
Found at i:40732953 original size:170 final size:170
Alignment explanation
Indices: 40732662--40732979 Score: 447
Period size: 170 Copynumber: 1.9 Consensus size: 170
40732652 ATAATTCTAG
* * * * * * * *
40732662 TCATGATTGTAAATCAGCGAATTGTTTGAATGGAGTTACAATCATGAATGAGCGAACTCATAATG
1 TCATGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATG
* * *
40732727 AACTGGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATTAGCAAGCTTTAATAATA
66 AACTAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATA
* *
40732792 CCAGTTGTGATCGTAAATACCCGAACTCAAAATGAACTGT
131 CCAGTCGTGATCATAAATACCCGAACTCAAAATGAACTGT
* * *
40732832 TCATGATCGTAAATCAACGAACTGTTTGAATAGAGTTGCGATCGTAAATCAGCAAACTCAAAATG
1 TCATGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATG
* * * * *
40732897 AACTATTTATGATCGTTAATCAATGAACTTAAGTTGTGATTGTAAATCAACAAGCTTTAATAATT
66 AACTAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATA
40732962 CCAGTCGTGATCATAAAT
131 CCAGTCGTGATCATAAAT
40732980 CAACGATCTG
Statistics
Matches: 127, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
170 127 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (170 bp):
TCATGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATG
AACTAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATA
CCAGTCGTGATCATAAATACCCGAACTCAAAATGAACTGT
Found at i:40735255 original size:74 final size:74
Alignment explanation
Indices: 40735133--40735277 Score: 168
Period size: 74 Copynumber: 2.0 Consensus size: 74
40735123 CAGGTGAAAG
* * ** * **
40735133 TAATAGTGTCTAGTTACCAGTATGGGTTAAACCTACACAATATTTATCAATTTCTCATTTGAGCT
1 TAATAGTGTCTAGTCACCAGTATGGGTTAAACCTACACAACAAGTATCAATTACTCATCCGAGCT
40735198 AATCATGAA
66 AATCATGAA
* * *
40735207 TAATAGTGTCTAGTCACTC-GT-TCGGGTTGAACCTATACAACAAGTATCAATTACTCGTCCGAG
1 TAATAGTGTCTAGTCAC-CAGTAT-GGGTTAAACCTACACAACAAGTATCAATTACTCATCCGAG
40735270 CTAATCAT
64 CTAATCAT
40735278 AAACAATAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
73 1 0.02
74 57 0.97
75 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (74 bp):
TAATAGTGTCTAGTCACCAGTATGGGTTAAACCTACACAACAAGTATCAATTACTCATCCGAGCT
AATCATGAA
Found at i:40736997 original size:55 final size:55
Alignment explanation
Indices: 40736911--40737023 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 55
40736901 GGATAAAGTG
* * *
40736911 TAAGCCTTTGTATTTTTTGCCTTGGATAATTGTTGAACTTCTGCCTACAGTTCTC
1 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
* *
40736966 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGGACTTCCGCTTACAGTTCGC
1 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
40737021 TAA
1 TAA
40737024 CTATGGCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (55 bp):
TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
Found at i:40749566 original size:15 final size:15
Alignment explanation
Indices: 40749530--40749559 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40749520 TCAAAATAAA
*
40749530 AAATTAATTAAAATT
1 AAATTAACTAAAATT
40749545 AAATTAACTAAAATT
1 AAATTAACTAAAATT
40749560 GAGTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAACTAAAATT
Found at i:40751542 original size:84 final size:84
Alignment explanation
Indices: 40751397--40751702 Score: 310
Period size: 84 Copynumber: 3.6 Consensus size: 84
40751387 TCATTGTAAC
* * * *
40751397 AGGCTTAGTAGTGGTAGGA-AGCAAACTGGTTGCAAGAATCTGAGTGGTTGCATGCTAGTTTAGG
1 AGGCTTAGTAGTGGTAGGAGA-CAAATTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGG
* *
40751461 GCCCTAATTATTGATGCATG
65 GCCCTAATTGTTGATGCAAG
* * * * * *
40751481 AGGCTTAGTAGTGGCAGGAGACAAATTGGTTGTAAGAGTTTGGGTGGTTACTTGCTGGTTTAAGG
1 AGGCTTAGTAGTGGTAGGAGACAAATTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
40751546 CCTTAGTGGTTGATGCAAG
66 CCCTAATTGTTGATGCAAG
* * * * ** * * * *
40751565 AAGCTTAATGGTGGTAGGAGGCCGATTGGTTGTAGGAGTTTGAGTGATTGCTTGCTGGTTTAGGG
1 AGGCTTAGTAGTGGTAGGAGACAAATTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
40751630 -CCTCAATTGTTGCTACACG
66 CCCT-AATTGTTGATGCAAG
* *
40751649 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGCAAGAATTTGAGTGGTTGCTTG
1 AGGCTTAGTAGTGGTAGGAGACAAATTGGTTGCAAGAATTTGAGTGGTTGCTTG
40751703 TCGGCTTGTT
Statistics
Matches: 179, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
83 2 0.01
84 176 0.98
85 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.35, T:0.32
Consensus pattern (84 bp):
AGGCTTAGTAGTGGTAGGAGACAAATTGGTTGCAAGAATTTGAGTGGTTGCTTGCTGGTTTAGGG
CCCTAATTGTTGATGCAAG
Found at i:40752225 original size:13 final size:13
Alignment explanation
Indices: 40752207--40752231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40752197 ATTTAATGGA
40752207 ATATATATATTTC
1 ATATATATATTTC
40752220 ATATATATATTT
1 ATATATATATTT
40752232 GAAGACGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATATATTTC
Found at i:40752374 original size:37 final size:37
Alignment explanation
Indices: 40752318--40752391 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
40752308 CTCTATCTTG
* * * *
40752318 AAAATTTATGTAAAAATCTTAAAGATTGAATTTAAAA
1 AAAAATTAAGTAAAAATCTTAAAAATTGAATTCAAAA
*
40752355 AAAAATTAAGTAAATATCTTAAAAATTGAATTCAAAA
1 AAAAATTAAGTAAAAATCTTAAAAATTGAATTCAAAA
40752392 CTAATTATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (37 bp):
AAAAATTAAGTAAAAATCTTAAAAATTGAATTCAAAA
Found at i:40753926 original size:24 final size:26
Alignment explanation
Indices: 40753894--40753944 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
40753884 ATTTGAAACT
40753894 TATTTTTTTTAAA-AT-TATAAAAAA
1 TATTTTTTTTAAATATCTATAAAAAA
*
40753918 TATTTTTTTTAAATATCTTTAAAAAA
1 TATTTTTTTTAAATATCTATAAAAAA
40753944 T
1 T
40753945 TTTATAGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.54
25 2 0.08
26 9 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TATTTTTTTTAAATATCTATAAAAAA
Found at i:40754147 original size:37 final size:37
Alignment explanation
Indices: 40754049--40754139 Score: 137
Period size: 37 Copynumber: 2.5 Consensus size: 37
40754039 TTACAAAACT
* * * *
40754049 TTTGCAGAGAATCTTCACTCTTAATCTCCGTCTTTTC
1 TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
*
40754086 TTTGCAGATAATCTTTACTATTGATCTCCATCTTTTC
1 TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
40754123 TTTGCAGAGAATCTTTA
1 TTTGCAGAGAATCTTTA
40754140 TTGTTGATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
Found at i:40754416 original size:34 final size:34
Alignment explanation
Indices: 40754326--40754417 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
40754316 CCGAATATAA
40754326 TAAATATATATTTTTT-ATTTTTA-TTTTTTAATTT
1 TAAA-ATA-ATTTTTTAATTTTTATTTTTTTAATTT
* * *
40754360 TAAAAT-ACTTTTAAATTTTTTATTTTTTTATTTT
1 TAAAATAATTTTTTAA-TTTTTATTTTTTTAATTT
*
40754394 TAAAATAATTTTTTAATGTTTATT
1 TAAAATAATTTTTTAATTTTTATT
40754418 AAAAAACGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 5 0.10
32 1 0.02
33 8 0.17
34 27 0.56
35 7 0.15
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (34 bp):
TAAAATAATTTTTTAATTTTTATTTTTTTAATTT
Found at i:40760964 original size:13 final size:13
Alignment explanation
Indices: 40760895--40760954 Score: 84
Period size: 13 Copynumber: 4.5 Consensus size: 13
40760885 TCATACATCT
40760895 ATTTCCATATAACC
1 ATTT-CATATAACC
*
40760909 AATTCATATAACC
1 ATTTCATATAACC
* *
40760922 ATTTCATGTAATC
1 ATTTCATATAACC
40760935 ATTTCATATAACC
1 ATTTCATATAACC
40760948 ATTTCAT
1 ATTTCAT
40760955 TCACACATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
13 37 0.93
14 3 0.08
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:40760964 original size:39 final size:41
Alignment explanation
Indices: 40760895--40760978 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 41
40760885 TCATACATCT
*
40760895 ATTTCCATATAACCAATTCATATAACCATTT-CATGTAATC
1 ATTTCCATATAACCAATTCATATAACCATTTACACGTAATC
* *
40760935 ATTT-CATATAACCATTTCAT-TCACACATTTAACACGTAATC
1 ATTTCCATATAACCAATTCATATAAC-CATTT-ACACGTAATC
40760976 ATT
1 ATT
40760979 CTGTATATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 3 0.08
39 20 0.53
40 4 0.11
41 11 0.29
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (41 bp):
ATTTCCATATAACCAATTCATATAACCATTTACACGTAATC
Found at i:40774456 original size:32 final size:32
Alignment explanation
Indices: 40774403--40774465 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
40774393 AAATTATAAC
* * *
40774403 TATTCAAGTGATATTACTTGAATAGTTATGTT
1 TATTCAAGAGATATTAATTGAATAATTATGTT
*
40774435 TATTTAAGAGATATTAATTGAATAATTATGT
1 TATTCAAGAGATATTAATTGAATAATTATGT
40774466 CTCTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (32 bp):
TATTCAAGAGATATTAATTGAATAATTATGTT
Found at i:40777991 original size:22 final size:22
Alignment explanation
Indices: 40777961--40778002 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
40777951 AACAGTTCAA
40777961 TATTAAAAAAATAAAA-AAAAGG
1 TATT-AAAAAATAAAATAAAAGG
*
40777983 TATTTAAAAATAAAATAAAA
1 TATTAAAAAATAAAATAAAA
40778003 TAATACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
TATTAAAAAATAAAATAAAAGG
Found at i:40781546 original size:26 final size:26
Alignment explanation
Indices: 40781515--40781632 Score: 70
Period size: 26 Copynumber: 4.7 Consensus size: 26
40781505 CTTATGAACG
40781515 TCCCGATATATGGCTCTTCGTGAGCT
1 TCCCGATATATGGCTCTTCGTGAGCT
* * *
40781541 TCCCGATTAAAT-GCTTTTTGTGAGCT
1 TCCCGA-TATATGGCTCTTCGTGAGCT
* ** *
40781567 TCCTGAT-TAATGGCTCCCCG-AAGCT
1 TCCCGATAT-ATGGCTCTTCGTGAGCT
* * *
40781592 TCCCG--ATATGGCTC-GCTTGAACT
1 TCCCGATATATGGCTCTTCGTGAGCT
40781615 TCCCGAT-TAATGGCTCTT
1 TCCCGATAT-ATGGCTCTT
40781633 TGGAGCTATT
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
22 1 0.01
23 15 0.22
24 2 0.03
25 18 0.27
26 27 0.40
27 4 0.06
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCCCGATATATGGCTCTTCGTGAGCT
Found at i:40781591 original size:25 final size:26
Alignment explanation
Indices: 40781563--40781630 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
40781553 GCTTTTTGTG
*
40781563 AGCTTCCTGATTAATGGCTC-CCCGA
1 AGCTTCCCGATTAATGGCTCGCCCGA
**
40781588 AGCTTCCCGA-T-ATGGCTCGCTTGA
1 AGCTTCCCGATTAATGGCTCGCCCGA
40781612 A-CTTCCCGATTAATGGCTC
1 AGCTTCCCGATTAATGGCTC
40781631 TTTGGAGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 15 0.41
24 6 0.16
25 16 0.43
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCTTCCCGATTAATGGCTCGCCCGA
Found at i:40781735 original size:25 final size:25
Alignment explanation
Indices: 40781684--40781747 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
40781674 AGCTCTTATG
* ***
40781684 AGCTTCCCGTTATACAGCCCGGGTA
1 AGCTTCCCGTTATACAACCCACATA
*
40781709 AGCTTCCCGTTATACAACTCACATA
1 AGCTTCCCGTTATACAACCCACATA
40781734 AGC-TCCCTGTTATA
1 AGCTTCCC-GTTATA
40781748 TGGCTCAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (25 bp):
AGCTTCCCGTTATACAACCCACATA
Found at i:40788520 original size:15 final size:16
Alignment explanation
Indices: 40788500--40788532 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40788490 GATCTCTCTA
*
40788500 TTTCTTTT-TTTTTAT
1 TTTCTTTTATCTTTAT
40788515 TTTCTTTTATCTTTAT
1 TTTCTTTTATCTTTAT
40788531 TT
1 TT
40788533 CTGTTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTATCTTTAT
Found at i:40796639 original size:22 final size:22
Alignment explanation
Indices: 40796613--40796705 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 22
40796603 AAAATAAAAT
*
40796613 AAAATAAAAGATATAAATTTAG
1 AAAATAAAAGATATAAATATAG
*
40796635 AAAATAAAAG--ATAAATAAAG
1 AAAATAAAAGATATAAATATAG
* * *
40796655 AAACTAAAAATATATAAATCTAG
1 AAAAT-AAAAGATATAAATATAG
*
40796678 AAAATAAAA-A-ATAAA-ATAA
1 AAAATAAAAGATATAAATATAG
40796697 AAAATAAAA
1 AAAATAAAA
40796706 ATAGGGCTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
19 11 0.19
20 17 0.29
21 5 0.08
22 14 0.24
23 12 0.20
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAATAAAAGATATAAATATAG
Found at i:40796670 original size:43 final size:42
Alignment explanation
Indices: 40796598--40796708 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 42
40796588 ATAAAAAAAC
* *
40796598 ATAATAAAATAAAAT--AAAAT-AAAAGATATAAATTTAGAAA
1 ATAA-AAAATAAAATAAAAAATAAAAATATATAAATCTAGAAA
*
40796638 ATAAAAGAT-AAATAAAGAAACTAAAAATATATAAATCTAGAAA
1 ATAAAAAATAAAATAAA-AAA-TAAAAATATATAAATCTAGAAA
40796681 ATAAAAAATAAAATAAAAAATAAAAATA
1 ATAAAAAATAAAATAAAAAATAAAAATA
40796709 GGGCTTGGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
38 4 0.07
39 4 0.07
40 5 0.08
41 3 0.05
42 9 0.15
43 29 0.48
44 7 0.11
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (42 bp):
ATAAAAAATAAAATAAAAAATAAAAATATATAAATCTAGAAA
Found at i:40796679 original size:23 final size:21
Alignment explanation
Indices: 40796613--40796706 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 21
40796603 AAAATAAAAT
* *
40796613 AAAATAAAAGATATAAATTTAG
1 AAAATAAAAAATA-AAATCTAG
* **
40796635 AAAATAAAAGAT-AAATAAAG
1 AAAATAAAAAATAAAATCTAG
*
40796655 AAACTAAAAATATATAAATCTAG
1 AAAATAAAAA-ATA-AAATCTAG
*
40796678 AAAATAAAAAATAAAA--TAA
1 AAAATAAAAAATAAAATCTAG
40796697 AAAATAAAAA
1 AAAATAAAAA
40796707 TAGGGCTTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 12 0.20
20 14 0.23
21 5 0.08
22 15 0.25
23 15 0.25
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAATAAAATCTAG
Found at i:40796695 original size:12 final size:12
Alignment explanation
Indices: 40796678--40796705 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40796668 ATAAATCTAG
40796678 AAAATAAAAAAT
1 AAAATAAAAAAT
40796690 AAAATAAAAAAT
1 AAAATAAAAAAT
40796702 AAAA
1 AAAA
40796706 ATAGGGCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:40796749 original size:16 final size:15
Alignment explanation
Indices: 40796728--40796758 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40796718 ATAAAGAGGA
40796728 ACAAAAGAATAAAAAG
1 ACAAAAGAA-AAAAAG
40796744 ACAAAAGAAAAAAAG
1 ACAAAAGAAAAAAAG
40796759 CTTTAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.03
Consensus pattern (15 bp):
ACAAAAGAAAAAAAG
Found at i:40803790 original size:19 final size:19
Alignment explanation
Indices: 40803766--40803808 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
40803756 GGTATGCAAC
*
40803766 TTTTTTTGCGCTTTTTGGT
1 TTTTTTTGCGCTTTTTGCT
40803785 TTTTTTTGCGCTTTTTGCT
1 TTTTTTTGCGCTTTTTGCT
40803804 TTTTT
1 TTTTT
40803809 CTGTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (19 bp):
TTTTTTTGCGCTTTTTGCT
Found at i:40804394 original size:31 final size:31
Alignment explanation
Indices: 40804356--40804417 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
40804346 AGGCAAATTA
40804356 CAAGAGTAATTGAATCCAAATAAAACTCTTT
1 CAAGAGTAATTGAATCCAAATAAAACTCTTT
*
40804387 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCAAATAAAACTCTTT
40804418 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCAAATAAAACTCTTT
Found at i:40813091 original size:14 final size:13
Alignment explanation
Indices: 40813061--40813106 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
40813051 AAATTATTAA
40813061 TTAAGTTTAATAAT
1 TTAA-TTTAATAAT
*
40813075 TTAATTTAATAGCT
1 TTAATTTAATA-AT
40813089 TTAATTTAA-AAT
1 TTAATTTAATAAT
40813101 TTAATT
1 TTAATT
40813107 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.24
13 8 0.28
14 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (13 bp):
TTAATTTAATAAT
Found at i:40813113 original size:13 final size:12
Alignment explanation
Indices: 40813061--40813113 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 12
40813051 AAATTATTAA
40813061 TTAAGTTTAATAAT
1 TTAA-TTTAA-AAT
*
40813075 TTAATTTAATAGCT
1 TTAATTTAA-A-AT
40813089 TTAATTTAAAAT
1 TTAATTTAAAAT
40813101 TTAATTATAAAAT
1 TTAATT-TAAAAT
40813114 AATCAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 7 0.20
13 14 0.40
14 14 0.40
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (12 bp):
TTAATTTAAAAT
Found at i:40813627 original size:18 final size:17
Alignment explanation
Indices: 40813581--40813628 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
40813571 ATTTTTATAC
*
40813581 AAATAATATAAAAATTAT
1 AAATAA-ATAAAAATAAT
*
40813599 AAATATGATAAAAATAAT
1 AAATA-AATAAAAATAAT
40813617 AAAATAAATAAA
1 -AAATAAATAAA
40813629 TATTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAAATAAAAATAAT
Found at i:40817905 original size:10 final size:10
Alignment explanation
Indices: 40817890--40817926 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
40817880 GGTGCTGCCG
40817890 GAAAAAGAGA
1 GAAAAAGAGA
40817900 GAAAAAGAGA
1 GAAAAAGAGA
*
40817910 GAAAGAGAAGA
1 GAAAAAG-AGA
40817921 GAAAAA
1 GAAAAA
40817927 AAAGGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:40823892 original size:157 final size:158
Alignment explanation
Indices: 40823378--40823929 Score: 542
Period size: 157 Copynumber: 3.5 Consensus size: 158
40823368 ATTTCCCCAA
* * * *
40823378 ATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACA
1 ATTTTATTACTTT-AATAAAAATATATAATTTCTGAATTTTATTATTTTACATTATTTCAGTACA
* *
40823443 TTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTTAAAAAATTTAGTAAAAGACTCTTAC
65 TTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTTA-
* **
40823508 TTCGGCCCTTTGTTCGTATTTTTTTCTCTAC
129 TTCGGCCCTTTCTTCGTA-TTTTTTCTCCGC
* * *
40823539 ATTTTATTACTTT-A-AAAAATATCATAATTTCT-AATTTTATAATTTTGCATTATTTCAGTGCA
1 ATTTTATTACTTTAATAAAAATAT-ATAATTTCTGAATTTTATTATTTTACATTATTTCAGTACA
* * * * *
40823601 TTATT-TTT--TA-ATTT-TATTAATT-TAGTGTG-TTTTTTAAATTAATTTAGTGTAAAAAAAC
65 TT-TTGTTTGAAATATTTGTATTAATTAT-TTCTGAATTTTTAAA-AAATTTA--GT-AAAAAAC
* * * *
40823659 CCTTATTCTTGCCCTTTGC-TCGTATTATTTT-TTCGA
124 TCTTATTC-GGCCCTTT-CTTCGTATT-TTTTCTCCGC
* * * *
40823695 ATTTTATTACTTTCAATAAAAATATATTACTTT-TGTATTTTATTATTTTATATTATTTCATTAC
1 ATTTTATTACTTT-AATAAAAATATA-TAATTTCTGAATTTTATTATTTTACATTATTTCAGTAC
**
40823759 ATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACTCTCTTA
64 ATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTTA
* *
40823824 TTTCGGCCATTTCTTTGTATTTTTTCTCCGC
129 -TTCGGCCCTTTCTTCGTATTTTTTCTCCGC
* * *
40823855 TTTTTATTACTTT-A-AAAAATATCATAATTTCT-AATTTTATTATTTTACATGATTTTAGTACA
1 ATTTTATTACTTTAATAAAAATAT-ATAATTTCTGAATTTTATTATTTTACATTATTTCAGTACA
*
40823917 TTATGTTTGAAAT
65 TTTTGTTTGAAAT
40823930 TTATTAATTT
Statistics
Matches: 316, Mismatches: 48, Indels: 58
0.75 0.11 0.14
Matches are distributed among these distances:
153 9 0.03
154 17 0.05
155 4 0.01
156 22 0.07
157 76 0.24
158 46 0.15
159 57 0.18
160 36 0.11
161 19 0.06
162 4 0.01
163 17 0.05
164 9 0.03
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.54
Consensus pattern (158 bp):
ATTTTATTACTTTAATAAAAATATATAATTTCTGAATTTTATTATTTTACATTATTTCAGTACAT
TTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTTATT
CGGCCCTTTCTTCGTATTTTTTCTCCGC
Found at i:40824326 original size:36 final size:36
Alignment explanation
Indices: 40824284--40824453 Score: 155
Period size: 36 Copynumber: 4.4 Consensus size: 36
40824274 AAAAATTACC
* *
40824284 TTCTTTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTCT
1 TTCTTTTTTTCCTCTCCTTTCCTTTTCTT-TTCTTCT
* *
40824320 TTCTTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTT
1 TTC--TTTTTTTCCTCTCCTTTCCTTTTCTTTTCTTC--T
* *
40824360 TTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 TTC--T-TTTTTTCCTCTCCTTTCCTTTTCTTTTCTTCT
*
40824399 TTCTTTCTTTCCTCTCCTTTCCTTTTC-TTTCTTTCT
1 TTCTTTTTTTCCTCTCCTTTCCTTTTCTTTTC-TTCT
40824435 TTCTTCTTCTTTCCCTCTC
1 TTCTT-TT-TTT-CCTCTC
40824454 ATTCTCTTCC
Statistics
Matches: 116, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.03
36 33 0.28
37 2 0.02
38 17 0.15
39 23 0.20
40 7 0.06
41 31 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (36 bp):
TTCTTTTTTTCCTCTCCTTTCCTTTTCTTTTCTTCT
Found at i:40824344 original size:5 final size:5
Alignment explanation
Indices: 40824336--40824437 Score: 65
Period size: 5 Copynumber: 21.4 Consensus size: 5
40824326 TTTTTTCTTC
* * * * *
40824336 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT TCTTTT TTCTT CTCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC-CTT TCCTT -TCCTT TCCTT
* * *
40824387 TTCTT TCC-T T-CTT T-CTT T-CTT TCCTC TCCTT TCCTT TTCTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
40824432 T-CTT TC
1 TCCTT TC
40824438 TTCTTCTTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
3 1 0.01
4 23 0.30
5 45 0.59
6 7 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:40824371 original size:41 final size:41
Alignment explanation
Indices: 40824288--40824446 Score: 185
Period size: 41 Copynumber: 4.1 Consensus size: 41
40824278 ATTACCTTCT
* *
40824288 TTTTTTCCT-TCCTTCCCTCTTC-TT-CTTCTTCTTTCTTT-
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTC
*
40824326 TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
*
40824367 TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC--TTTCTTTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
*
40824406 ---TTTCCTCTCCTTTCCTTTTCTTTCTTTCTTTCTTC-TTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTT-TTCTTTC
40824444 TTT
1 TTT
40824447 CCCTCTCATT
Statistics
Matches: 106, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
36 26 0.25
38 12 0.11
39 22 0.21
40 9 0.08
41 37 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (41 bp):
TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
Found at i:40824383 original size:31 final size:32
Alignment explanation
Indices: 40824307--40824448 Score: 132
Period size: 31 Copynumber: 4.4 Consensus size: 32
40824297 TCCTTCCCTC
* * *
40824307 TTCTTCTTC-TTCTTTCTTTTTTTTTCTTCTCCT
1 TTCTTCTCCTTTCCTTCTTTTTCTTTCTT-T-CT
*
40824340 TTCCTT-TTCTTTCCTTCTTTTTCTTTCTTT-T
1 TT-CTTCTCCTTTCCTTCTTTTTCTTTCTTTCT
*
40824371 TTCTTCTCCTTTCCTT-TTCTTTCCTTCTTTCT
1 TTCTTCTCCTTTCCTTCTT-TTTCTTTCTTTCT
* *
40824403 TTCTT-TCCTCTCCTTTCCTTTTCTTTCTTTCT
1 TTCTTCTCCTTTCC-TTCTTTTTCTTTCTTTCT
*
40824435 TTCTTCTTCTTTCC
1 TTCTTCTCCTTTCC
40824449 CTCTCATTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
30 5 0.05
31 29 0.32
32 25 0.27
33 13 0.14
34 20 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (32 bp):
TTCTTCTCCTTTCCTTCTTTTTCTTTCTTTCT
Found at i:40824538 original size:27 final size:27
Alignment explanation
Indices: 40824500--40824589 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
40824490 TAAATAGGCA
40824500 GTGCCGCCTGTGGGAGAGGCACCATCG
1 GTGCCGCCTGTGGGAGAGGCACCATCG
40824527 GTGCCGCCTGTGGGAG-GGCCACCATCG
1 GTGCCGCCTGTGGGAGAGG-CACCATCG
* ** *
40824554 GTGCCGCCTCTGACAGAGGCA-CAACTG
1 GTGCCGCCTGTGGGAGAGGCACCATC-G
40824581 GTGCCGCCT
1 GTGCCGCCT
40824590 ATGGCACCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.09
27 49 0.88
28 2 0.04
ACGTcount: A:0.14, C:0.33, G:0.37, T:0.16
Consensus pattern (27 bp):
GTGCCGCCTGTGGGAGAGGCACCATCG
Found at i:40830892 original size:73 final size:72
Alignment explanation
Indices: 40830746--40830910 Score: 204
Period size: 73 Copynumber: 2.3 Consensus size: 72
40830736 AGATCGATCA
** * * * * *
40830746 TTAGCGGCGTTTTCCAGAAAGCGCCGCAAAAAACCTAAGCCCAACAACGTCATTTTCCGAGCTTT
1 TTAGCGGCGTTTTTAAGAAAACGCCGCAAAAAACATAAGCCCAACAACGCCATTTTACGAACTTT
40830811 CGGGGAT
66 CGGGGAT
* * * * *
40830818 TTAGCGGCATTTTTGAGAAAACGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTATGAACTT
1 TTAGCGGCGTTTTTAAGAAAACGCCGC-AAAAAACATAAGCCCAACAACGCCATTTTACGAACTT
*
40830883 TTGGGGAT
65 TCGGGGAT
40830891 TTAGCGGCGTTTTTAAGAAA
1 TTAGCGGCGTTTTTAAGAAA
40830911 GCGCTGCTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 23 0.29
73 55 0.71
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (72 bp):
TTAGCGGCGTTTTTAAGAAAACGCCGCAAAAAACATAAGCCCAACAACGCCATTTTACGAACTTT
CGGGGAT
Found at i:40830966 original size:114 final size:114
Alignment explanation
Indices: 40830817--40831487 Score: 948
Period size: 114 Copynumber: 5.9 Consensus size: 114
40830807 CTTTCGGGGA
* * * * * *
40830817 TTTAGCGGCATTTTTGAGAAAACGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTATGAACT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * *
40830882 TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* * * * *
40830931 TTTAGCAACGTTTCTGAGAAAGCGCTGCAAAAAAACATAAGCCCAACGACGTCGTTTTGTGAGCT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
*
40830996 TTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* ** * *
40831045 TTTAGCGGCGTTTTTGAGAAAATGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTGTGAGTT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* *
40831110 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGTTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* * * * *
40831159 TTTATCGGCGTTTTTGAGAAAGCGCTGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* * * *
40831224 TTCGGGGATTTAGCAGTGTTTTT-AGTAAAGCACCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGTC
* *
40831273 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
*
40831338 TTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
* * * * * **
40831387 TTTATCGATGTTTTTGAGAAAGTGCAGCAAAAAAACCTAAGCCCAACAACGTTGTTTTGTGAGCT
1 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
*
40831452 TTCGGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
40831488 AAAAAAACCT
Statistics
Matches: 498, Mismatches: 57, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
113 2 0.00
114 494 0.99
115 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (114 bp):
TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
Found at i:40831504 original size:187 final size:186
Alignment explanation
Indices: 40831273--40831655 Score: 561
Period size: 187 Copynumber: 2.0 Consensus size: 186
40831263 TGCTCAGGGC
* **
40831273 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
*** * * * *
40831338 TTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTATCGATGTTTTTG
66 TTCGGGGATTTAGCAACGTTTTTAAGAAAGCGCCGCCAATGCTCAGGGCTTTAGCGACGTTTTTG
** *
40831403 AGAAAGTGCA-GCAAAAAAACCTAAGCCCAACAACGTTGTTTTGTGAGCTTTCGGGGA
131 AG-AA-TGCACGCAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGA
40831460 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
* *
40831525 TTCGGGGATTTAGCAACGTTTTTAAGAAAGTGCCGCCAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCAACGTTTTTAAGAAAGCGCCGCCAATGCTCAGGGCTTTAGCGACGTTTTTG
*** *
40831590 AGAATGCACCGCAAAAAAACCTAAGCCCAATGGCGCCGTTTTCTGGGCTTTCGGGGA
131 AGAATGCA-CGCAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGA
40831647 TTTAGCGGC
1 TTTAGCGGC
40831656 AAAAGATTCT
Statistics
Matches: 175, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
185 4 0.02
186 2 0.01
187 169 0.97
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (186 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
TTCGGGGATTTAGCAACGTTTTTAAGAAAGCGCCGCCAATGCTCAGGGCTTTAGCGACGTTTTTG
AGAATGCACGCAAAAAAACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGGGA
Found at i:40831517 original size:73 final size:73
Alignment explanation
Indices: 40831396--40831560 Score: 240
Period size: 73 Copynumber: 2.3 Consensus size: 73
40831386 CTTTATCGAT
* *** *
40831396 GTTTTTGAGAAAGTGCAGCAAAAAAACCTAAGCCCAACAACGTTGTTTTGTGAGCTTTCGGGGAT
1 GTTTTTGAGAAAGTGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGAGCTTTCGGGGAT
**
40831461 TTAGCGGC
66 TTAGCAAC
* *
40831469 GTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCGGGGAT
1 GTTTTTGAGAAAGTGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGAGCTTTCGGGGAT
40831534 TTAGCAAC
66 TTAGCAAC
*
40831542 GTTTTTAAGAAAGTGCCGC
1 GTTTTTGAGAAAGTGCCGC
40831561 CAATGCTCAG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 81 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (73 bp):
GTTTTTGAGAAAGTGCCGCAAAAAAACCTAAGCCCAACAACACCGTTTTCTGAGCTTTCGGGGAT
TTAGCAAC
Found at i:40832008 original size:15 final size:15
Alignment explanation
Indices: 40831990--40832020 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40831980 CATATTTTAA
40831990 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
40832005 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
40832020 G
1 G
40832021 ATTACGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:40832330 original size:21 final size:22
Alignment explanation
Indices: 40832293--40832345 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
40832283 GAGTATGGAT
*
40832293 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
40832314 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
40832335 TTAGGGGTTTA
1 TTAGGGATTTA
40832346 GGGGTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAAGGG
Found at i:40832338 original size:7 final size:7
Alignment explanation
Indices: 40832328--40832366 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
40832318 GATTTAAGGT
40832328 TTAGGGG
1 TTAGGGG
40832335 TTAGGGG
1 TTAGGGG
40832342 TTTAGGGG
1 -TTAGGGG
**
40832350 TTAGATG
1 TTAGGGG
40832357 TTAGGGG
1 TTAGGGG
40832364 TTA
1 TTA
40832367 AGAGTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:40832345 original size:15 final size:15
Alignment explanation
Indices: 40832324--40832366 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
40832314 TTGGGATTTA
40832324 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
40832339 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
40832354 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
40832367 AGAGTTAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:40832353 original size:22 final size:22
Alignment explanation
Indices: 40832311--40832374 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
40832301 TATGGTTTAA
* *
40832311 GGGTT-GGGATTTAAGGTTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
*
40832332 GGGTTAGGGGTTTAGGGGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
** *
40832354 ATGTTAGGGG-TTAAGAGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
40832375 AGATTTAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.34
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGGTTAG
Found at i:40832373 original size:14 final size:14
Alignment explanation
Indices: 40832328--40832374 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
40832318 GATTTAAGGT
* *
40832328 TTAGGGGTTAGGGG
1 TTAGGGGTTAAGAG
40832342 TTTAGGGGTT-AGATG
1 -TTAGGGGTTAAGA-G
40832357 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
40832371 TTAG
1 TTAG
40832375 AGATTTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Done.