Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 29 of 210
Found at i:9337025 original size:23 final size:22
Alignment explanation
Indices: 9336975--9337051 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
9336965 CTACTTTTTG
*
9336975 TTTTCTTTATTTGTTTATTATT
1 TTTTTTTTATTTGTTTATTATT
9336997 TGTTTTTTTATTTGTTTATTATT
1 T-TTTTTTTATTTGTTTATTATT
* * *
9337020 ATTTTTATAATAT-TTTATGTATCT
1 -TTTTTTTTATTTGTTTAT-TAT-T
9337044 TTTTTTTT
1 TTTTTTTT
9337052 GTAGAGCCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 6 0.13
23 37 0.82
24 2 0.04
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (22 bp):
TTTTTTTTATTTGTTTATTATT
Found at i:9337103 original size:14 final size:15
Alignment explanation
Indices: 9337084--9337123 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
9337074 CACCTGTACT
9337084 TTTTTTTAAATTT-A
1 TTTTTTTAAATTTAA
*
9337098 TTTTTTTATATTTAAA
1 TTTTTTTAAATTT-AA
9337114 TTTTTTTAAA
1 TTTTTTTAAA
9337124 AAATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
16 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTTAAATTTAA
Found at i:9337696 original size:53 final size:52
Alignment explanation
Indices: 9337638--9337741 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 52
9337628 TATTTTTCAA
* * * *
9337638 TTTGTAAGATAGAATGA-TGTCAGTTTTGAACAAAATTGTTTAATTATATTTTG
1 TTTGTAAGACACAAT-ATTGTCAGTCTTGAAAAAAATTGTTTAATTAT-TTTTG
* *
9337691 TTTGTAAGACACAATATTGTTAGTCTTGAAAAAAATTGTTTATTTATTTTT
1 TTTGTAAGACACAATATTGTCAGTCTTGAAAAAAATTGTTTAATTATTTTT
9337742 AGTATTGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
52 5 0.11
53 39 0.89
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (52 bp):
TTTGTAAGACACAATATTGTCAGTCTTGAAAAAAATTGTTTAATTATTTTTG
Found at i:9338319 original size:14 final size:14
Alignment explanation
Indices: 9338302--9338336 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9338292 TAAGGTATAA
*
9338302 TATAGTTTGTATTT
1 TATAGTTTATATTT
*
9338316 TATATTTTATATTT
1 TATAGTTTATATTT
9338330 TATAGTT
1 TATAGTT
9338337 ATTGTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (14 bp):
TATAGTTTATATTT
Found at i:9339628 original size:7 final size:7
Alignment explanation
Indices: 9339580--9339640 Score: 56
Period size: 7 Copynumber: 8.6 Consensus size: 7
9339570 TAGTTAAAAA
9339580 TATATAT
1 TATATAT
9339587 TATAATAT
1 TAT-ATAT
9339595 TATA-AT
1 TATATAT
*
9339601 ATATTTAGT
1 -TATATA-T
9339610 TA-AGTA-
1 TATA-TAT
9339616 TATATAT
1 TATATAT
9339623 TATATAT
1 TATATAT
9339630 TATATAT
1 TATATAT
9339637 TATA
1 TATA
9339641 AATGAATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 6 0.13
7 26 0.58
8 12 0.27
9 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (7 bp):
TATATAT
Found at i:9339637 original size:32 final size:36
Alignment explanation
Indices: 9339556--9339633 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
9339546 AGGTGTATGT
*
9339556 TATTATAAAAT-TTATAGTTAAAAATATATATTATAA
1 TATTATAATATATT-TAGTTAAAAATATATATTATAA
**
9339592 TATTATAATATATTTAGTTAAGTATATATATTAT-A
1 TATTATAATATATTTAGTTAAAAATATATATTATAA
9339627 TATTATA
1 TATTATA
9339634 TATTATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 8 0.21
36 28 0.74
37 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (36 bp):
TATTATAATATATTTAGTTAAAAATATATATTATAA
Found at i:9339699 original size:16 final size:15
Alignment explanation
Indices: 9339652--9339723 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
9339642 ATGAATGAAT
9339652 AAAA-AAAG-AAAAG
1 AAAAGAAAGAAAAAG
** *
9339665 AAAAAGAAAGCCAACG
1 -AAAAGAAAGAAAAAG
9339681 AAACAGAAAGAAAAAG
1 AAA-AGAAAGAAAAAG
*
9339697 -AAAGAAAAGAAAAAT
1 AAAAG-AAAGAAAAAG
9339712 AGAAAGAAAGAA
1 A-AAAGAAAGAA
9339724 GGAGAAAGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.13
15 18 0.39
16 18 0.39
17 4 0.09
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:9339717 original size:17 final size:15
Alignment explanation
Indices: 9339652--9339723 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
9339642 ATGAATGAAT
9339652 AAAA-AAAGAAAAGA
1 AAAAGAAAGAAAAGA
* *
9339666 AAAAGAAAGCCAACGA
1 AAAAGAAAG-AAAAGA
*
9339682 AACAGAAAGAAAA-A
1 AAAAGAAAGAAAAGA
*
9339696 GAAAGAAAAGAAAA-A
1 AAAAG-AAAGAAAAGA
9339711 TAGAAAGAAAGAA
1 -A-AAAGAAAGAA
9339724 GGAGAAAGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 8 0.18
15 15 0.33
16 18 0.40
17 4 0.09
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:9339730 original size:41 final size:39
Alignment explanation
Indices: 9339652--9339732 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 39
9339642 ATGAATGAAT
*
9339652 AAAAAAAGAAAAGAAAAAGAAAGCCAACGAAACAGAAAGA
1 AAAAAAAGAAAAGAAAAAGAAAG-CAAAGAAACAGAAAGA
**
9339692 AAAAGAAAGAAAAGAAAAATAGAAAG-AAAGAAGGAGAAAGA
1 AAAA-AAAGAAAAG-AAAA-AGAAAGCAAAGAAACAGAAAGA
9339733 CACAAAGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 4 0.11
41 21 0.60
42 4 0.11
43 6 0.17
ACGTcount: A:0.73, C:0.05, G:0.21, T:0.01
Consensus pattern (39 bp):
AAAAAAAGAAAAGAAAAAGAAAGCAAAGAAACAGAAAGA
Found at i:9343650 original size:25 final size:25
Alignment explanation
Indices: 9343567--9343726 Score: 181
Period size: 25 Copynumber: 6.6 Consensus size: 25
9343557 TTTTTATGCA
*
9343567 CTAATGAA-CAGAGAGCACTGAAGTG
1 CTAAT-AATCAGAGAGCACTGACGTG
* *
9343592 CT-AT-A-CAGAGAGCACAGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
9343614 CT-A-AA-CAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
* *
9343636 CTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
9343661 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
**
9343686 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
9343711 CTAATATTCAGAGAGC
1 CTAATAATCAGAGAGC
9343727 GCGCTAAAGT
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
22 37 0.31
24 4 0.03
25 77 0.65
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:9344689 original size:5 final size:5
Alignment explanation
Indices: 9344679--9344707 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9344669 TTATTTCTTT
9344679 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
9344708 TAACTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:9348590 original size:37 final size:36
Alignment explanation
Indices: 9348548--9348660 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 36
9348538 TTTAAATATA
9348548 ATTTAAAAAACTTTTGAATAAACAAATATTATAAAAC
1 ATTTAAAAAACTTTTGAATAAA-AAATATTATAAAAC
* * *
9348585 ATTTAAAATA-TTAT-AA-AATAAATA--AT-AAAC
1 ATTTAAAAAACTTTTGAATAAAAAATATTATAAAAC
* *
9348615 AAATTAAAAATACGTTTGAATAAAAAATATTATAAAAC
1 -ATTTAAAAA-ACTTTTGAATAAAAAATATTATAAAAC
9348653 ATTTAAAA
1 ATTTAAAA
9348661 TATTATAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
30 4 0.07
31 9 0.15
32 1 0.02
33 7 0.12
34 4 0.07
35 9 0.15
36 3 0.05
37 18 0.31
38 4 0.07
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (36 bp):
ATTTAAAAAACTTTTGAATAAAAAATATTATAAAAC
Found at i:9348603 original size:10 final size:10
Alignment explanation
Indices: 9348571--9348671 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 10
9348561 TTGAATAAAC
9348571 AAATATTATA
1 AAATATTATA
*
9348581 AAACATT-TA
1 AAATATTATA
9348590 AAATATTATA
1 AAATATTATA
*
9348600 AAATAAATAATA
1 AAAT--ATTATA
*
9348612 AACAAATTA-A
1 AA-ATATTATA
9348622 AAATACGTT-T-
1 AAATA--TTATA
*
9348632 GAATA--A-A
1 AAATATTATA
9348639 AAATATTATA
1 AAATATTATA
*
9348649 AAACATT-TA
1 AAATATTATA
9348658 AAATATTATA
1 AAATATTATA
9348668 AAAT
1 AAAT
9348672 GAATAATAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 26
0.65 0.10 0.25
Matches are distributed among these distances:
7 4 0.06
9 19 0.28
10 32 0.47
11 5 0.07
12 7 0.10
13 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (10 bp):
AAATATTATA
Found at i:9348622 original size:31 final size:31
Alignment explanation
Indices: 9348581--9348691 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
9348571 AAATATTATA
9348581 AAAC-ATTTAAAATATTATAAAATAAATAAT
1 AAACAATTTAAAATATTATAAAATAAATAAT
* *
9348611 AAACAAATTAAAAATACGTTTGAATAAAA-AATATTAT
1 AAAC-AATTTAAAATA---TT--ATAAAATAA-ATAAT
*
9348648 AAA-ACATTTAAAATATTATAAAATGAATAAT
1 AAACA-ATTTAAAATATTATAAAATAAATAAT
9348679 AAACAATTTAAAA
1 AAACAATTTAAAA
9348692 AACAAATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
30 4 0.06
31 21 0.32
32 11 0.17
33 2 0.03
35 3 0.05
36 11 0.17
37 13 0.20
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (31 bp):
AAACAATTTAAAATATTATAAAATAAATAAT
Found at i:9348643 original size:68 final size:68
Alignment explanation
Indices: 9348550--9348694 Score: 247
Period size: 68 Copynumber: 2.1 Consensus size: 68
9348540 TAAATATAAT
*
9348550 TTAAAAAACTTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAATAAATAATAAAC
1 TTAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAATAAATAATAAAC
9348615 AAA
66 AAA
*
9348618 TTAAAAATACGTTTGAATAAA-AAATATTATAAAACATTTAAAATATTATAAAATGAATAATAAA
1 TTAAAAA-ACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAATAAATAATAAA
*
9348682 CAAT
65 CAAA
9348686 TTAAAAAAC
1 TTAAAAAAC
9348695 AAATTTTCAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
67 2 0.03
68 59 0.81
69 12 0.16
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (68 bp):
TTAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAATAAATAATAAAC
AAA
Found at i:9355849 original size:3 final size:3
Alignment explanation
Indices: 9355841--9355900 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
9355831 GTTAAAACAA
9355841 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9355889 AAT AAT AAT AAT
1 AAT AAT AAT AAT
9355901 CTTAAAGAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9356820 original size:15 final size:15
Alignment explanation
Indices: 9356802--9356859 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
9356792 TTCAATATTC
9356802 AATATTTTAATAATA
1 AATATTTTAATAATA
*
9356817 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
9356836 AATATATTAATAATA
1 AATATTTTAATAATA
*
9356851 AATGTTTTA
1 AATATTTTA
9356860 TAGTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:9357252 original size:32 final size:34
Alignment explanation
Indices: 9357214--9357286 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
9357204 CAACTTTTAT
*
9357214 AAAATATTTTTA-A-GAAATCTACCAAACAACAG
1 AAAATATTTTTACATGAAATCAACCAAACAACAG
* * *
9357246 AAAATA-TTTTACATGGATTCAACCAAACACCAG
1 AAAATATTTTTACATGAAATCAACCAAACAACAG
9357279 AAAATATT
1 AAAATATT
9357287 AGTTTTTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 21 0.62
34 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (34 bp):
AAAATATTTTTACATGAAATCAACCAAACAACAG
Found at i:9361866 original size:41 final size:41
Alignment explanation
Indices: 9361821--9361938 Score: 209
Period size: 41 Copynumber: 2.9 Consensus size: 41
9361811 TGATTCAATA
* *
9361821 CACCGGCATTAAACCTGCTAGACGTAAGGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
*
9361862 CACCGGCGTTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
9361903 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAA
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAA
9361939 ATCTCAGATA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
Found at i:9364112 original size:18 final size:19
Alignment explanation
Indices: 9364079--9364121 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
9364069 ACAAATAAAT
9364079 AAAAAGAAAAAGGAAATAG
1 AAAAAGAAAAAGGAAATAG
*
9364098 AAAAAGAAAGA-GAAATAG
1 AAAAAGAAAAAGGAAATAG
*
9364116 AGAAAG
1 AAAAAG
9364122 CCAAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAAAGGAAATAG
Found at i:9372948 original size:3 final size:3
Alignment explanation
Indices: 9372940--9373014 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
9372930 AATCATTAAA
* * * * * * * * *
9372940 AAT AAT AAT AAT TAT TAT ATT AAC AAG AAT AAT AAT TAT TAT TAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
9372988 AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
9373015 TCTTATTCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:9372980 original size:27 final size:27
Alignment explanation
Indices: 9372940--9373005 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
9372930 AATCATTAAA
9372940 AATAATAATAATTATTATATTAACAAG
1 AATAATAATAATTATTATATTAACAAG
* *
9372967 AATAATAATTATTATTATATTAACAAT
1 AATAATAATAATTATTATATTAACAAG
9372994 AATAATAATAAT
1 AATAATAATAAT
9373006 AATAATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
AATAATAATAATTATTATATTAACAAG
Found at i:9373770 original size:5 final size:5
Alignment explanation
Indices: 9373762--9373806 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
9373752 ATTTTTACTT
*
9373762 ATATA ATATA ATACA ATATA ATATA ATATA ATATA ATAT- ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
9373807 AACATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:9377204 original size:41 final size:41
Alignment explanation
Indices: 9377159--9377592 Score: 679
Period size: 41 Copynumber: 10.6 Consensus size: 41
9377149 GGTTTTAAAA
*
9377159 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
** *
9377200 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
9377241 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
9377282 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
*
9377323 CCTAGCAGGCTAAGTGCAGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
*
9377364 CCTAGCAGGCTAAGTGCAGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
** *
9377405 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
* * *
9377446 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
* ** *
9377487 CCTAGCAGGCTAAGTGCTGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
* *
9377528 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
* * *
9377569 CCTAACAAGCTAAGTGCCAGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGAA
9377593 TCTGTTTAAA
Statistics
Matches: 366, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 366 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
Found at i:9381463 original size:25 final size:24
Alignment explanation
Indices: 9381414--9381468 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
9381404 GTCATTAGGG
* * *
9381414 TTACCGATTCCAACTCTTATGAGC
1 TTACCGATACCAACTCGTATAAGC
9381438 TTACCGATACTCAACTCGTATAAGC
1 TTACCGATAC-CAACTCGTATAAGC
9381463 TTACCG
1 TTACCG
9381469 TTATTCAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (24 bp):
TTACCGATACCAACTCGTATAAGC
Found at i:9381511 original size:24 final size:25
Alignment explanation
Indices: 9381431--9381511 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
9381421 TTCCAACTCT
* * *
9381431 TATGAGCTTACCGATACTCAACTCG
1 TATGAGCTTACCGTTATTCAGCTCG
*
9381456 TATAAGCTTACCGTTATTCAGCTCG
1 TATGAGCTTACCGTTATTCAGCTCG
* * *
9381481 GAGGAGCTTAGCGTT-TATC-GCTCG
1 TATGAGCTTACCGTTAT-TCAGCTCG
9381505 TATGAGC
1 TATGAGC
9381512 ATACATGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
24 11 0.24
25 34 0.76
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (25 bp):
TATGAGCTTACCGTTATTCAGCTCG
Found at i:9387656 original size:8 final size:8
Alignment explanation
Indices: 9387643--9387667 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9387633 TTTTTAGGGT
9387643 ATATAATA
1 ATATAATA
9387651 ATATAATA
1 ATATAATA
9387659 ATATAATA
1 ATATAATA
9387667 A
1 A
9387668 CAGCTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATAATA
Found at i:9393322 original size:2 final size:2
Alignment explanation
Indices: 9393315--9393350 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9393305 GAATATAACT
9393315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9393351 GCTGTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9395171 original size:38 final size:37
Alignment explanation
Indices: 9395129--9395212 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 37
9395119 TGATAAATAT
9395129 AAATGATATAATATAA-TTGAAATTTCAAATTTCAACAA
1 AAATGATATAATATAATTTGAAA-TTCAAATTTCAA-AA
* *
9395167 AAATGATATAATATAATTTGAAATTGAAATTTTAAAA
1 AAATGATATAATATAATTTGAAATTCAAATTTCAAAA
9395204 AAATTGATA
1 AAA-TGATA
9395213 ATACATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 5 0.12
38 31 0.74
39 6 0.14
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (37 bp):
AAATGATATAATATAATTTGAAATTCAAATTTCAAAA
Found at i:9397227 original size:18 final size:18
Alignment explanation
Indices: 9397204--9397258 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
9397194 TTAATCCATA
9397204 TAAATCCTTCAGGGATTT
1 TAAATCCTTCAGGGATTT
9397222 TAAATCCTTCAGGGATTT
1 TAAATCCTTCAGGGATTT
* *
9397240 TAAATTCTTCAAGGATTT
1 TAAATCCTTCAGGGATTT
9397258 T
1 T
9397259 CATATAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (18 bp):
TAAATCCTTCAGGGATTT
Found at i:9401080 original size:7 final size:7
Alignment explanation
Indices: 9401068--9401092 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9401058 AACCCAAGCC
9401068 AAAATAT
1 AAAATAT
9401075 AAAATAT
1 AAAATAT
9401082 AAAATAT
1 AAAATAT
9401089 AAAA
1 AAAA
9401093 ATTATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:9401590 original size:32 final size:32
Alignment explanation
Indices: 9401554--9401619 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
9401544 TTAGGACTGA
9401554 GCAAAATGGTTTTTAGTTTATTCTACATTTGT
1 GCAAAATGGTTTTTAGTTTATTCTACATTTGT
*
9401586 GCAAAATGTTTTTTAGTTTATTCTACATTTGT
1 GCAAAATGGTTTTTAGTTTATTCTACATTTGT
9401618 GC
1 GC
9401620 TTTACTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (32 bp):
GCAAAATGGTTTTTAGTTTATTCTACATTTGT
Found at i:9403019 original size:31 final size:31
Alignment explanation
Indices: 9402981--9403039 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9402971 TAAACTGTAT
9402981 GCATTAGGGGATAGT-TCCAGTTATGCATTCA
1 GCATTAGGGGATAGTAT-CAGTTATGCATTCA
9403012 GCATTAGGGGATAGTATCAGTTATGCAT
1 GCATTAGGGGATAGTATCAGTTATGCAT
9403040 CTAGGTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (31 bp):
GCATTAGGGGATAGTATCAGTTATGCATTCA
Found at i:9407638 original size:30 final size:29
Alignment explanation
Indices: 9407593--9407671 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
9407583 GGAAGCTACC
9407593 TAAAAATTTCAAAAAACTTT-AAGAGAAAAA
1 TAAAAATTTCAAAAAA-TTTGAAG-GAAAAA
* * *
9407623 TAAAATTTTCTAAAAATTTGAAGGAAAAG
1 TAAAAATTTCAAAAAATTTGAAGGAAAAA
*
9407652 TAAAAATTCCCAAAAAATTT
1 TAAAAATT-TCAAAAAATTT
9407672 AGGGGTGGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.28
Consensus pattern (29 bp):
TAAAAATTTCAAAAAATTTGAAGGAAAAA
Found at i:9410903 original size:7 final size:7
Alignment explanation
Indices: 9410891--9410928 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
9410881 CTACTCGACT
9410891 TCACAGC
1 TCACAGC
9410898 TCACAGC
1 TCACAGC
9410905 TCACAGC
1 TCACAGC
9410912 TCACAGC
1 TCACAGC
*
9410919 TCACATC
1 TCACAGC
9410926 TCA
1 TCA
9410929 TTTGAGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.18
Consensus pattern (7 bp):
TCACAGC
Found at i:9417336 original size:11 final size:11
Alignment explanation
Indices: 9417320--9417347 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
9417310 AAGTCCACTT
9417320 AATGCCACAGC
1 AATGCCACAGC
9417331 AATGCCACAGC
1 AATGCCACAGC
9417342 AATGCC
1 AATGCC
9417348 GCAAGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.11
Consensus pattern (11 bp):
AATGCCACAGC
Found at i:9417958 original size:31 final size:30
Alignment explanation
Indices: 9417905--9417977 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
9417895 CGGGAAGTAA
* * *
9417905 AAATTAAGGGAACTACCAACTAGCCTAGAGG
1 AAATTAAGGAAACCACCAACTAGCATAGA-G
** *
9417936 AAATTAAGGAAACCACTTACTAGCATGGAG
1 AAATTAAGGAAACCACCAACTAGCATAGAG
9417966 AAATTCAAGGAA
1 AAATT-AAGGAA
9417978 TCGACGCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (30 bp):
AAATTAAGGAAACCACCAACTAGCATAGAG
Found at i:9420950 original size:25 final size:25
Alignment explanation
Indices: 9420922--9420975 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
9420912 ATACAGGTAA
*
9420922 AACAACTCGCATGATAATATGACAT
1 AACAACTCACATGATAATATGACAT
*
9420947 AACAACTCACCTGATAATATGACAT
1 AACAACTCACATGATAATATGACAT
9420972 AACA
1 AACA
9420976 CATAACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.22
Consensus pattern (25 bp):
AACAACTCACATGATAATATGACAT
Found at i:9421422 original size:17 final size:17
Alignment explanation
Indices: 9421400--9421441 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
9421390 TAACCTTATA
* *
9421400 GGTTCGTATGTAACATG
1 GGTTCGCATATAACATG
*
9421417 GGTTCGCATATATCATG
1 GGTTCGCATATAACATG
9421434 GGTTCGCA
1 GGTTCGCA
9421442 CAACATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (17 bp):
GGTTCGCATATAACATG
Found at i:9421458 original size:19 final size:18
Alignment explanation
Indices: 9421434--9421479 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
9421424 ATATATCATG
9421434 GGTTCGCACAACATATATA
1 GGTTCGCACAA-ATATATA
*
9421453 GGTTCGCA-TAATATATA
1 GGTTCGCACAAATATATA
*
9421470 GGTTCACACA
1 GGTTCGCACA
9421480 TGGTGTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 14 0.61
18 1 0.04
19 8 0.35
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (18 bp):
GGTTCGCACAAATATATA
Found at i:9421468 original size:17 final size:17
Alignment explanation
Indices: 9421417--9421474 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
9421407 ATGTAACATG
*
9421417 GGTTCGCAT-ATATCATG
1 GGTTCGCATAATAT-ATA
*
9421434 GGTTCGCACAACATATATA
1 GGTTCGCA-TA-ATATATA
9421453 GGTTCGCATAATATATA
1 GGTTCGCATAATATATA
9421470 GGTTC
1 GGTTC
9421475 ACACATGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 20 0.57
18 1 0.03
19 10 0.29
20 4 0.11
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (17 bp):
GGTTCGCATAATATATA
Found at i:9421488 original size:17 final size:17
Alignment explanation
Indices: 9421468--9421500 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9421458 GCATAATATA
9421468 TAGGTTCACACATGGTG
1 TAGGTTCACACATGGTG
*
9421485 TAGGTTCGCACATGGT
1 TAGGTTCACACATGGT
9421501 TAAGGGCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (17 bp):
TAGGTTCACACATGGTG
Found at i:9421566 original size:23 final size:23
Alignment explanation
Indices: 9421540--9421611 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
9421530 TACATATATC
*
9421540 ATAACAGGGTTCACACATGTTGT
1 ATAACAGGGTTAACACATGTTGT
* * *
9421563 ATAACAGGTTTTACACATGTAGT
1 ATAACAGGGTTAACACATGTTGT
* *
9421586 ATAACACGGTTAACACAT-TTTT
1 ATAACAGGGTTAACACATGTTGT
9421608 ATAA
1 ATAA
9421612 GTTTCGCACA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 6 0.15
23 35 0.85
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACAGGGTTAACACATGTTGT
Found at i:9428404 original size:18 final size:18
Alignment explanation
Indices: 9428376--9428436 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 18
9428366 ATTTATATTA
**
9428376 TTTGTTCTTGTATATGGAC
1 TTTG-TCTTGTATAAAGAC
9428395 TTTGTCTTGTACATAAAGAC
1 TTTGTCTTGT--ATAAAGAC
9428415 TTTGTCTTGTACATAAAGAC
1 TTTGTCTTGT--ATAAAGAC
9428435 TT
1 TT
9428437 AATTTGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 6 0.16
19 4 0.11
20 28 0.74
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (18 bp):
TTTGTCTTGTATAAAGAC
Found at i:9428417 original size:20 final size:20
Alignment explanation
Indices: 9428392--9428436 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
9428382 CTTGTATATG
9428392 GACTTTGTCTTGTACATAAA
1 GACTTTGTCTTGTACATAAA
9428412 GACTTTGTCTTGTACATAAA
1 GACTTTGTCTTGTACATAAA
9428432 GACTT
1 GACTT
9428437 AATTTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (20 bp):
GACTTTGTCTTGTACATAAA
Found at i:9431773 original size:14 final size:15
Alignment explanation
Indices: 9431745--9431777 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
9431735 AGCCCATTAG
*
9431745 TAAAATAAAACCAAT
1 TAAAATAAAAACAAT
9431760 TAAAA-AAAAACAAT
1 TAAAATAAAAACAAT
9431774 TAAA
1 TAAA
9431778 CAGCCCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAAATAAAAACAAT
Found at i:9432679 original size:3 final size:3
Alignment explanation
Indices: 9432671--9432723 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
9432661 ATTAAATTTC
9432671 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9432719 ATT AT
1 ATT AT
9432724 AATATTTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9433405 original size:24 final size:24
Alignment explanation
Indices: 9433347--9433398 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
9433337 TTGAATGTAG
9433347 ATAGTGATATTAGCATGATGTACA
1 ATAGTGATATTAGCATGATGTACA
9433371 ATAGTGATATTAGCATGATGTACA
1 ATAGTGATATTAGCATGATGTACA
9433395 ATAG
1 ATAG
9433399 GAATATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (24 bp):
ATAGTGATATTAGCATGATGTACA
Found at i:9437989 original size:15 final size:14
Alignment explanation
Indices: 9437963--9438002 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
9437953 CAGATCCAAT
9437963 TCAAAA-AAAAAAA
1 TCAAAATAAAAAAA
9437976 TCAAAAATAAAAAAAA
1 TC-AAAAT-AAAAAAA
9437992 TCAAAATAAAA
1 TCAAAATAAAA
9438003 TGAGAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 8 0.33
15 5 0.21
16 9 0.38
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (14 bp):
TCAAAATAAAAAAA
Found at i:9437989 original size:16 final size:15
Alignment explanation
Indices: 9437968--9438002 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
9437958 CCAATTCAAA
9437968 AAAAAAAATCAAAAAT
1 AAAAAAAATC-AAAAT
9437984 AAAAAAAATCAAAAT
1 AAAAAAAATCAAAAT
9437999 AAAA
1 AAAA
9438003 TGAGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAAATCAAAAT
Found at i:9438076 original size:16 final size:16
Alignment explanation
Indices: 9438055--9438098 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
9438045 AATGAAAATG
9438055 AAAAAAGAGAGAAGGA
1 AAAAAAGAGAGAAGGA
* *
9438071 AAAAAAGAAAAAAGGA
1 AAAAAAGAGAGAAGGA
*
9438087 AAAAAGGAGAGA
1 AAAAAAGAGAGA
9438099 TCAAGGCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGAGAAGGA
Found at i:9438921 original size:8 final size:7
Alignment explanation
Indices: 9438908--9438971 Score: 73
Period size: 6 Copynumber: 9.3 Consensus size: 7
9438898 AAAAAAAAGG
9438908 TGAAAAA
1 TGAAAAA
9438915 TGAAAAAA
1 TG-AAAAA
9438923 TG-AAAA
1 TGAAAAA
9438929 TGAAAAAA
1 TG-AAAAA
9438937 TG-AAAA
1 TGAAAAA
9438943 TGAAAAA
1 TGAAAAA
9438950 TG-AAAA
1 TGAAAAA
9438956 TGAAAAA
1 TGAAAAA
9438963 -GTAAAAA
1 TG-AAAAA
9438970 TG
1 TG
9438972 GAGAGGCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
6 19 0.38
7 17 0.34
8 14 0.28
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:9438956 original size:27 final size:28
Alignment explanation
Indices: 9438910--9438971 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
9438900 AAAAAAGGTG
9438910 AAAAATGAAAAAATGAAAATGAAAAAAT
1 AAAAATGAAAAAATGAAAATGAAAAAAT
* *
9438938 GAAAATG-AAAAATGAAAATGAAAAAGT
1 AAAAATGAAAAAATGAAAATGAAAAAAT
9438965 AAAAATG
1 AAAAATG
9438972 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (28 bp):
AAAAATGAAAAAATGAAAATGAAAAAAT
Found at i:9438971 original size:14 final size:14
Alignment explanation
Indices: 9438911--9438962 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
9438901 AAAAAGGTGA
9438911 AAAATGAAAAAATG
1 AAAATGAAAAAATG
9438925 AAAATGAAAAAATG
1 AAAATGAAAAAATG
9438939 AAAATG-AAAAATG
1 AAAATGAAAAAATG
9438952 AAAATGAAAAA
1 AAAATGAAAAA
9438963 GTAAAAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.35
14 24 0.65
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATGAAAAAATG
Found at i:9440315 original size:43 final size:42
Alignment explanation
Indices: 9440268--9440404 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 42
9440258 AGAAGCAGAT
9440268 CTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATT-ACAGTGAAGCAGATCGAAAACAAAGC
* * * * * * *
9440311 CTTGCC-TCCAT-CGGTTGCAGTGGAGCTAG-T-TAAAGATAGCAGAT
1 CTTGCCTTCC-TGC-ATTACAGTGAAGC-AGATCGAAA-ACA-AAG-C
*
9440355 CTTGCCTTCCTGCATTGATAGTGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATT-ACAGTGAAGCAGATCGAAAACAAAGC
9440398 CTTGCCT
1 CTTGCCT
9440405 CCATTGGTTA
Statistics
Matches: 68, Mismatches: 15, Indels: 22
0.65 0.14 0.21
Matches are distributed among these distances:
41 3 0.04
42 15 0.22
43 20 0.29
44 13 0.19
45 14 0.21
46 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (42 bp):
CTTGCCTTCCTGCATTACAGTGAAGCAGATCGAAAACAAAGC
Found at i:9440390 original size:87 final size:87
Alignment explanation
Indices: 9440209--9440598 Score: 602
Period size: 87 Copynumber: 4.5 Consensus size: 87
9440199 AGATCAGTGA
* * *
9440209 AGATCGAAAATAAAACCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGA-AGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
9440273 CTTCCTGCATTAACAGTGAAGC
66 CTTCCTGCATTGACAGCGAAGC
*
9440295 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
9440360 CTTCCTGCATTGATAGTGAAGC
66 CTTCCTGCATTGACAGCGAAGC
* * *
9440382 AGATCGAAAACAAAGCCTTGCCTCCATTGGTTACAGTGGAGCTTGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
9440447 CTTCCTGCATTGACAGCGAAGC
66 CTTCCTGCATTGACAGCGAAGC
* * *
9440469 AGATCGAAGACCCAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTG
1 AGATCGAA-AACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* *
9440534 CCTTCCTGCATTGATAGCAAAGC
65 CCTTCCTGCATTGACAGCGAAGC
**
9440557 AGATCGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
9440599 AGATTGAATT
Statistics
Matches: 280, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
86 48 0.17
87 153 0.55
88 79 0.28
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATTGACAGCGAAGC
Found at i:9440520 original size:175 final size:173
Alignment explanation
Indices: 9440209--9440598 Score: 627
Period size: 175 Copynumber: 2.2 Consensus size: 173
9440199 AGATCAGTGA
* *
9440209 AGATCGAAAATAAAACCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAGAAGCAGATCTTGCC
1 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
*
9440274 TTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTA
66 TTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTA
**
9440339 GTTAAAGATAGCAGATCTTGCCTTCCTGCATTGATAGTGAAGC
131 GTTAAAGATAGCAGATCTTGCCTTCCTGCATTGATAGCAAAGC
* * * *
9440382 AGATCGAAAACAAAGCCTTGCCTCCATTGGTTACAGTGGAGCTTGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
* * *
9440447 CTTCCTGCATTGACAGCGAAGCAGATCGAAGACCCAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
65 CTTCCTGCATTAACAGCGAAGCAGATCGAA-AACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
* *
9440512 TGGTTAAAGATAGTAGATCTTGCCTTCCTGCATTGATAGCAAAGC
129 TAGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGATAGCAAAGC
*
9440557 AGATCGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
1 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
9440599 AGATTGAATT
Statistics
Matches: 197, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
173 46 0.23
174 40 0.20
175 111 0.56
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (173 bp):
AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
TTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTA
GTTAAAGATAGCAGATCTTGCCTTCCTGCATTGATAGCAAAGC
Found at i:9442164 original size:3 final size:3
Alignment explanation
Indices: 9442156--9442214 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
9442146 ATTAAATTTC
*
9442156 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
9442204 ATT ATA ATT AT
1 ATT ATT ATT AT
9442215 ATTTGATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9450595 original size:8 final size:9
Alignment explanation
Indices: 9450565--9450597 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
9450555 ATATATATTA
9450565 TTATTTGAT
1 TTATTTGAT
9450574 TTATTGTGAT
1 TTATT-TGAT
9450584 TTATTT-AT
1 TTATTTGAT
9450592 TTATTT
1 TTATTT
9450598 TGTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (9 bp):
TTATTTGAT
Found at i:9456931 original size:40 final size:40
Alignment explanation
Indices: 9456887--9457053 Score: 155
Period size: 40 Copynumber: 4.2 Consensus size: 40
9456877 TATTGATGAT
*
9456887 TGCACTTATGTGCCCCTGTTTGTACTTCGATATCCCTGAA
1 TGCACTTACGTGCCCCTGTTTGTACTTCGATATCCCTGAA
* * ** *
9456927 TGCACATACGTGCCCCTAG-TTGTACTTTGGCACCCCTG-A
1 TGCACTTACGTGCCCCT-GTTTGTACTTCGATATCCCTGAA
*
9456966 TCGCACTTACGTGCCCTTGTTTGTACTTC-AGT-TCCCCTGAA
1 T-GCACTTACGTGCCCCTGTTTGTACTTCGA-TAT-CCCTGAA
* * * *
9457007 TGCACTTACGTGCCCCTATTTTTACTTCGGTA-CCGTTGAA
1 TGCACTTACGTGCCCCTGTTTGTACTTCGATATCC-CTGAA
9457047 TGCACTT
1 TGCACTT
9457054 CGGTACCCCT
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
39 5 0.05
40 93 0.92
41 3 0.03
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (40 bp):
TGCACTTACGTGCCCCTGTTTGTACTTCGATATCCCTGAA
Found at i:9457004 original size:80 final size:80
Alignment explanation
Indices: 9456883--9457033 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 80
9456873 TAATTATTGA
* *
9456883 TGATTGCACTTATGTGCCCCTGTTTGTACTTCGATATCCCTGAATGCACATACGTGCCCCTAGTT
1 TGATCGCACTTACGTGCCCCTGTTTGTACTTCGATATCCCTGAATGCACATACGTGCCCCTAGTT
9456948 GTACTTTGGCACCCC
66 GTACTTTGGCACCCC
* * *
9456963 TGATCGCACTTACGTGCCCTTGTTTGTACTTC-AGT-TCCCCTGAATGCACTTACGTGCCCCTAT
1 TGATCGCACTTACGTGCCCCTGTTTGTACTTCGA-TAT-CCCTGAATGCACATACGTGCCCCTAG
*
9457026 TTTTACTT
64 TTGTACTT
9457034 CGGTACCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
79 2 0.03
80 61 0.97
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (80 bp):
TGATCGCACTTACGTGCCCCTGTTTGTACTTCGATATCCCTGAATGCACATACGTGCCCCTAGTT
GTACTTTGGCACCCC
Found at i:9457022 original size:20 final size:19
Alignment explanation
Indices: 9456959--9457023 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
9456949 TACTTTGGCA
9456959 CCCCTGATCGCACTTACGTG
1 CCCCTGAT-GCACTTACGTG
* * * *
9456979 CCCTTGTTTGTACTT-CAGTT
1 CCCCTG-ATGCACTTAC-GTG
9456999 CCCCTGAATGCACTTACGTG
1 CCCCTG-ATGCACTTACGTG
9457019 CCCCT
1 CCCCT
9457024 ATTTTTACTT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 1 0.03
20 30 0.91
21 2 0.06
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.32
Consensus pattern (19 bp):
CCCCTGATGCACTTACGTG
Found at i:9457066 original size:20 final size:20
Alignment explanation
Indices: 9457030--9457067 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9457020 CCCTATTTTT
**
9457030 ACTTCGGTACCGTTGAATGC
1 ACTTCGGTACCCCTGAATGC
9457050 ACTTCGGTACCCCTGAAT
1 ACTTCGGTACCCCTGAAT
9457068 TATTTTAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (20 bp):
ACTTCGGTACCCCTGAATGC
Found at i:9472508 original size:22 final size:23
Alignment explanation
Indices: 9472474--9472520 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
9472464 TTAAATATAT
9472474 ATTTATATATTTTTA-TAATTAA
1 ATTTATATATTTTTATTAATTAA
*
9472496 ATTTA-ATATTTTTTATTATTTAA
1 ATTTATATA-TTTTTATTAATTAA
9472519 AT
1 AT
9472521 CAAATTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.50
23 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTATATATTTTTATTAATTAA
Found at i:9472512 original size:28 final size:28
Alignment explanation
Indices: 9472461--9472527 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
9472451 ATGTTAATAA
*
9472461 AAATTAAATATATATTTATATATT-TTT
1 AAATTAAATTTATATTTATATATTATTT
*
9472488 ATAATTAAATTTAATATTT-TTTATTATTT
1 A-AATTAAATTT-ATATTTATATATTATTT
*
9472517 AAATCAAATTT
1 AAATTAAATTT
9472528 GGACCGGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 23 0.68
29 10 0.29
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATTAAATTTATATTTATATATTATTT
Found at i:9472774 original size:37 final size:37
Alignment explanation
Indices: 9472719--9472796 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
9472709 TTTGGTTTTC
*
9472719 AAACAAGACATTAAATAGAATATATAAAAATATAATA
1 AAACAAGACATTAAATAGAATATAGAAAAATATAATA
* *
9472756 AAACAAGACATTAGATAGAATATAGGAAAATATAATA
1 AAACAAGACATTAAATAGAATATAGAAAAATATAATA
9472793 AAAC
1 AAAC
9472797 CTCAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (37 bp):
AAACAAGACATTAAATAGAATATAGAAAAATATAATA
Found at i:9472977 original size:20 final size:20
Alignment explanation
Indices: 9472952--9472991 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9472942 CGTAAAATGA
*
9472952 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
9472972 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
9472992 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:9472981 original size:34 final size:35
Alignment explanation
Indices: 9472937--9473003 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
9472927 CAGTAAAATA
*
9472937 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
9472971 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
9473004 CTGATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:9473909 original size:17 final size:17
Alignment explanation
Indices: 9473857--9473909 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
9473847 TATGGAAACA
* *
9473857 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
9473874 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
9473893 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
9473910 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:9473909 original size:22 final size:23
Alignment explanation
Indices: 9473881--9473925 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9473871 ATGCAATCTT
9473881 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
9473903 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
9473926 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:9473935 original size:22 final size:23
Alignment explanation
Indices: 9473891--9473935 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
9473881 AGATATGATA
*
9473891 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
9473914 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
9473936 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:9474344 original size:14 final size:15
Alignment explanation
Indices: 9474315--9474343 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9474305 AATTTTTAGG
9474315 ATGTAATTATTTTTT
1 ATGTAATTATTTTTT
9474330 ATGTAATTATTTTT
1 ATGTAATTATTTTT
9474344 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
ATGTAATTATTTTTT
Found at i:9480390 original size:35 final size:35
Alignment explanation
Indices: 9480337--9480420 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
9480327 TCTATTGGTC
* *
9480337 ATTCGAGGTGACATTGTGTAATCAATATATAGGTT
1 ATTCGAGGCGACACTGTGTAATCAATATATAGGTT
* *
9480372 ATTCGAGGCGATACTGTGTAATCGATATATAGGTT
1 ATTCGAGGCGACACTGTGTAATCAATATATAGGTT
* * *
9480407 CTACGAAGCGACAC
1 ATTCGAGGCGACAC
9480421 CTTGAAAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (35 bp):
ATTCGAGGCGACACTGTGTAATCAATATATAGGTT
Found at i:9488671 original size:16 final size:18
Alignment explanation
Indices: 9488644--9488676 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9488634 ATAAATTAAT
9488644 TTAAATTAA-TTTCTCAA
1 TTAAATTAATTTTCTCAA
9488661 TTAAA-TAATTTTCTCA
1 TTAAATTAATTTTCTCA
9488677 GCCTGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTAATTTTCTCAA
Found at i:9493240 original size:17 final size:16
Alignment explanation
Indices: 9493214--9493246 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
9493204 TAAATCTCAG
9493214 ATTTTGATACCCATAT
1 ATTTTGATACCCATAT
9493230 ATTTCTGATACCCATAT
1 ATTT-TGATACCCATAT
9493247 CTTTGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTTGATACCCATAT
Found at i:9500147 original size:4 final size:4
Alignment explanation
Indices: 9500138--9500166 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9500128 TTTTACTAAT
9500138 TGAA TGAA TGAA TGAA TGAA TGAA TGAA T
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA T
9500167 TAAATGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (4 bp):
TGAA
Found at i:9503450 original size:16 final size:16
Alignment explanation
Indices: 9503420--9503452 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9503410 AATTTTTATT
*
9503420 TTTATTTTATTTTTGG
1 TTTATTTAATTTTTGG
9503436 TTTATTTAATTTTTGG
1 TTTATTTAATTTTTGG
9503452 T
1 T
9503453 ACATGACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (16 bp):
TTTATTTAATTTTTGG
Found at i:9506620 original size:85 final size:86
Alignment explanation
Indices: 9506467--9506730 Score: 343
Period size: 85 Copynumber: 3.1 Consensus size: 86
9506457 GCAATTTAAT
* * *
9506467 CTGCAAACAGTGTGGTTCAATCACGAACCGAGTAACAATTTGTTTAATCTGCAAATATGTTGTGC
1 CTGCAAATAGTGTGGTTCAATCACGAACCAAGTGACAATTTGTTTAATCTGCAAATATGTTGTGC
*
9506532 ACTCACAATAAGTGGCAGTAA
66 ACTCACAACAAGTGGCAGTAA
* * * * * *
9506553 CTGTAAATA-TGTGGTTCAATCACGAGCCAAGTGGCAGTTTGTTTAATTTGCTAATATGTTGTGC
1 CTGCAAATAGTGTGGTTCAATCACGAACCAAGTGACAATTTGTTTAATCTGCAAATATGTTGTGC
9506617 ACTCACAACAAGTGGCAGTAA
66 ACTCACAACAAGTGGCAGTAA
* * * * * * *
9506638 CTACAAATAGTTTGGTTCAATCACGAACGAAGTGAC-TTTTTTTTAATCTACAAATATGTTGTGT
1 CTGCAAATAGTGTGGTTCAATCACGAACCAAGTGACAATTTGTTTAATCTGCAAATATGTTGTGC
*
9506702 ACCCACAACAAGTGGCAGTAA
66 ACTCACAACAAGTGGCAGTAA
*
9506723 CTGGAAAT
1 CTGCAAAT
9506731 GAACGATGGT
Statistics
Matches: 152, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 123 0.81
86 29 0.19
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (86 bp):
CTGCAAATAGTGTGGTTCAATCACGAACCAAGTGACAATTTGTTTAATCTGCAAATATGTTGTGC
ACTCACAACAAGTGGCAGTAA
Found at i:9509047 original size:43 final size:43
Alignment explanation
Indices: 9508919--9509048 Score: 122
Period size: 43 Copynumber: 3.0 Consensus size: 43
9508909 CATAGGATTC
* *
9508919 CGTTATGTG-TTATCATGTACGACCACGTCTGGGACGTTGGCAT
1 CGTTATGTGATTA-CATGTAAGACCACGTCTGGGACATTGGCAT
* * * * **
9508962 TGACT-TGTGACTTACGTGTAAGACC-CTGTCTAGGACCGTGGCAT
1 CG-TTATGTGA-TTACATGTAAGACCAC-GTCTGGGACATTGGCAT
*
9509006 CGTTATGTGATTACATGTAAGACCACGTTTGGGACATTGGCAT
1 CGTTATGTGATTACATGTAAGACCACGTCTGGGACATTGGCAT
9509049 TGTACGAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
43 33 0.49
44 31 0.46
45 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (43 bp):
CGTTATGTGATTACATGTAAGACCACGTCTGGGACATTGGCAT
Found at i:9522274 original size:69 final size:69
Alignment explanation
Indices: 9522158--9522301 Score: 243
Period size: 69 Copynumber: 2.1 Consensus size: 69
9522148 CATTAGCCTT
* * *
9522158 AGCTAGATATTTATCCAACTCAGATGTTTTATCCTCACCACCGTTTTCCAAGTCACAATTTTTAT
1 AGCTTGATATTTATCCAACTCAGATGTTTTATCCTCACCACCATTTTCCAACTCACAATTTTTAT
9522223 ACAA
66 ACAA
* *
9522227 AGCTTGATATTTATCCAACTTAGATGTTTTATCCTCACCACCATTTTCCAACTCACACTTTTTAT
1 AGCTTGATATTTATCCAACTCAGATGTTTTATCCTCACCACCATTTTCCAACTCACAATTTTTAT
9522292 ACAA
66 ACAA
9522296 AGCTTG
1 AGCTTG
9522302 CATTCACCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (69 bp):
AGCTTGATATTTATCCAACTCAGATGTTTTATCCTCACCACCATTTTCCAACTCACAATTTTTAT
ACAA
Found at i:9524777 original size:30 final size:31
Alignment explanation
Indices: 9524743--9524807 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 31
9524733 CTTTAAGAGA
9524743 TTAAAAATCACTC-CTCTT-AAGTTTTTAAAT
1 TTAAAAATCACTCACTCTTAAAGTTTTT-AAT
9524773 TTAAAAATCACTCACTCTTAAAGTTTTTAAT
1 TTAAAAATCACTCACTCTTAAAGTTTTTAAT
9524804 TTAA
1 TTAA
9524808 GATTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 13 0.39
31 12 0.36
32 8 0.24
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAAAAATCACTCACTCTTAAAGTTTTTAAT
Found at i:9526004 original size:20 final size:21
Alignment explanation
Indices: 9525967--9526010 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
9525957 TGTGTTACTG
9525967 TTTTAGTTTTAGACTTTTA-C
1 TTTTAGTTTTAGACTTTTATC
**
9525987 TTTTAGTTTTAGTTTTTTATC
1 TTTTAGTTTTAGACTTTTATC
9526008 TTT
1 TTT
9526011 ATTTATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.68
Consensus pattern (21 bp):
TTTTAGTTTTAGACTTTTATC
Found at i:9527396 original size:17 final size:17
Alignment explanation
Indices: 9527374--9527406 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9527364 GCACGGGCAC
9527374 TCATGTTTGACGTACTA
1 TCATGTTTGACGTACTA
*
9527391 TCATGTTTGATGTACT
1 TCATGTTTGACGTACT
9527407 GTCACTCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (17 bp):
TCATGTTTGACGTACTA
Found at i:9528969 original size:20 final size:20
Alignment explanation
Indices: 9528944--9528984 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
9528934 GCCTTACAGC
9528944 TTACTTTCTTTCTCGTTCTT
1 TTACTTTCTTTCTCGTTCTT
9528964 TTACTTTCTTTCTCGTTCTT
1 TTACTTTCTTTCTCGTTCTT
9528984 T
1 T
9528985 CCCATCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (20 bp):
TTACTTTCTTTCTCGTTCTT
Found at i:9529935 original size:2 final size:2
Alignment explanation
Indices: 9529928--9529973 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
9529918 TAAGTCATGC
* *
9529928 AT AT AT AT CT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9529970 -T AT A
1 AT AT A
9529974 AAAACCAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9533526 original size:21 final size:22
Alignment explanation
Indices: 9533502--9533544 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9533492 TTACATGTAA
* *
9533502 TTATTTAG-TAAATTATATTGT
1 TTATGTAGTTAAATAATATTGT
9533523 TTATGTAGTTAAATAATATTGT
1 TTATGTAGTTAAATAATATTGT
9533545 ACTTCGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTGT
Found at i:9538272 original size:33 final size:33
Alignment explanation
Indices: 9538235--9538326 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
9538225 GCAATAGAAC
9538235 ATAACATGCTTATAATAAATCAATACAGTAGTA
1 ATAACATGCTTATAATAAATCAATACAGTAGTA
* * * *
9538268 ATAACATACTTATAATAAGTCGATATAGTAGTA
1 ATAACATGCTTATAATAAATCAATACAGTAGTA
* *
9538301 ATTATCATGCTTATAATAGATCAATA
1 A-TAACATGCTTATAATAAATCAATA
9538327 TGGTAGCAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.61
34 19 0.39
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.34
Consensus pattern (33 bp):
ATAACATGCTTATAATAAATCAATACAGTAGTA
Found at i:9542255 original size:67 final size:67
Alignment explanation
Indices: 9542171--9542348 Score: 180
Period size: 67 Copynumber: 2.6 Consensus size: 67
9542161 ATGCAACATG
* * * *
9542171 ACATGCTTATAACAGATCAATACGGAAGTAAT-AACATGCTTATAATAAGTCAATATAA-TAGGA
1 ACATGCCTATAACAGATCAATA-GGAAGCAATAAACATGCTTATAACAAGTCAATA-AAGTAGCA
9542234 ATTA
64 ATTA
* * * *
9542238 TCATGCCTATAATAGATCAATAGGGAGCAATAAACATGCTTATAACAAGTCGATAAAGTAGCAAT
1 ACATGCCTATAACAGATCAATAGGAAGCAATAAACATGCTTATAACAAGTCAATAAAGTAGCAAT
9542303 TA
66 TA
* * * * * *
9542305 ACATGCATTATAACATATCATTACAGTAGCAATAAACTTGCTTA
1 ACATGC-CTATAACAGATCAATA-GGAAGCAATAAACATGCTTA
9542349 ACATGCATTT
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
66 9 0.10
67 53 0.58
68 12 0.13
69 17 0.19
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (67 bp):
ACATGCCTATAACAGATCAATAGGAAGCAATAAACATGCTTATAACAAGTCAATAAAGTAGCAAT
TA
Found at i:9542308 original size:34 final size:34
Alignment explanation
Indices: 9542171--9542348 Score: 116
Period size: 33 Copynumber: 5.3 Consensus size: 34
9542161 ATGCAACATG
** * *
9542171 ACATGCTTATAAC-AGATCAATACGGAAGTAA-TA
1 ACATGCTTATAACAAG-TCAATAAAGTAGCAATTA
* *
9542204 ACATGCTTATAATAAGTCAATATAA-TAGGAATTA
1 ACATGCTTATAACAAGTCAATA-AAGTAGCAATTA
* * * * * *
9542238 TCATGCCTATAA-TAGATCAAT-AGGGAGCAATAA
1 ACATGCTTATAACAAG-TCAATAAAGTAGCAATTA
*
9542271 ACATGCTTATAACAAGTCGATAAAGTAGCAATTA
1 ACATGCTTATAACAAGTCAATAAAGTAGCAATTA
* * *
9542305 ACATGCATTATAACATA-TCATTACAGTAGCAATAA
1 ACATGC-TTATAACA-AGTCAATAAAGTAGCAATTA
*
9542340 ACTTGCTTA
1 ACATGCTTA
9542349 ACATGCATTT
Statistics
Matches: 112, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
32 1 0.01
33 44 0.39
34 39 0.35
35 27 0.24
36 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (34 bp):
ACATGCTTATAACAAGTCAATAAAGTAGCAATTA
Found at i:9542333 original size:35 final size:34
Alignment explanation
Indices: 9542263--9542348 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 34
9542253 ATCAATAGGG
9542263 AGCAATAAACATGCTTATAACAAGTCGATAAAGT
1 AGCAATAAACATGCTTATAACAAGTCGATAAAGT
* *
9542297 AGCAATTAACATGCATTATAACATA-TC-ATTACAGT
1 AGCAATAAACATGC-TTATAACA-AGTCGA-TAAAGT
*
9542332 AGCAATAAACTTGCTTA
1 AGCAATAAACATGCTTA
9542349 ACATGCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 17 0.38
35 27 0.60
36 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (34 bp):
AGCAATAAACATGCTTATAACAAGTCGATAAAGT
Found at i:9547751 original size:2 final size:2
Alignment explanation
Indices: 9547744--9547781 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9547734 TTTCCTAAAT
9547744 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9547782 TACATACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9547786 original size:4 final size:4
Alignment explanation
Indices: 9547779--9547823 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
9547769 ACACACACAC
9547779 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
9547824 TTTGTAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:9548408 original size:22 final size:22
Alignment explanation
Indices: 9548380--9548441 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
9548370 TTTATTGTTC
9548380 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
9548402 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
9548424 AGCCATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
9548442 GTACTAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:9561257 original size:5 final size:5
Alignment explanation
Indices: 9561247--9561271 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9561237 AAAACTTTTA
9561247 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
9561272 AACCCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:9564717 original size:19 final size:19
Alignment explanation
Indices: 9564674--9564717 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
9564664 TTAAAAATAC
9564674 AATTTTTTAAATTTTTAAT
1 AATTTTTTAAATTTTTAAT
* *
9564693 GATTTTTTTAATTTTTAA-
1 AATTTTTTAAATTTTTAAT
9564711 AATTTTT
1 AATTTTT
9564718 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
AATTTTTTAAATTTTTAAT
Found at i:9564718 original size:9 final size:9
Alignment explanation
Indices: 9564674--9564721 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
9564664 TTAAAAATAC
*
9564674 AATTTTTTA
1 AATTTTTAA
9564683 AATTTTTAA
1 AATTTTTAA
* **
9564692 TGATTTTTTT
1 -AATTTTTAA
9564702 AATTTTTAA
1 AATTTTTAA
9564711 AATTTTTAA
1 AATTTTTAA
9564720 AA
1 AA
9564722 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
9 25 0.81
10 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
AATTTTTAA
Found at i:9585279 original size:20 final size:20
Alignment explanation
Indices: 9585239--9585279 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9585229 ATAATGATAT
*
9585239 TAAAATGATAGATAAATAAA
1 TAAAATGATAAATAAATAAA
9585259 TAAAATGATAAAATAAA-AAA
1 TAAAATGAT-AAATAAATAAA
9585279 T
1 T
9585280 TTCTATGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
TAAAATGATAAATAAATAAA
Found at i:9587155 original size:17 final size:19
Alignment explanation
Indices: 9587114--9587155 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
9587104 ACTTCATTCC
9587114 ATTCTTATTTTTATAAACT
1 ATTCTTATTTTTATAAACT
9587133 -TT-TTATTTTT-TAAA-T
1 ATTCTTATTTTTATAAACT
9587148 ATTCTTAT
1 ATTCTTAT
9587156 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.05
16 6 0.29
17 12 0.57
18 2 0.10
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTCTTATTTTTATAAACT
Found at i:9588775 original size:2 final size:2
Alignment explanation
Indices: 9588768--9588800 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9588758 CCAAATTCGG
9588768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9588801 GCATGTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9589679 original size:25 final size:25
Alignment explanation
Indices: 9589647--9589695 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9589637 TTAAATATTT
9589647 TTTTATTTTTAATCAAATATATATA
1 TTTTATTTTTAATCAAATATATATA
9589672 TTTTATTTTTAATCAAATATATAT
1 TTTTATTTTTAATCAAATATATAT
9589696 TTTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATTTTTAATCAAATATATATA
Found at i:9599699 original size:17 final size:17
Alignment explanation
Indices: 9599677--9599714 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
9599667 CAGGAGCTCC
9599677 TGTTAATAAAATCT-GAT
1 TGTTAATAAAAT-TGGAT
9599694 TGTTAATAAAATTGGAT
1 TGTTAATAAAATTGGAT
9599711 TGTT
1 TGTT
9599715 TTTCGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (17 bp):
TGTTAATAAAATTGGAT
Found at i:9600719 original size:97 final size:97
Alignment explanation
Indices: 9600553--9600746 Score: 325
Period size: 97 Copynumber: 2.0 Consensus size: 97
9600543 TGATGCACTC
* *
9600553 ACTCTTGATGAACTTCAAAGCTCCTTGTTGGTCCATGAGCAGAAAATGAACAGAAATTCTACCTC
1 ACTCTTGATGAACTTCAAAGCTCCTTGTTGGTCCATAAGCAGAAAATAAACAGAAATTCTACCTC
9600618 AATAGAACAGGCTTTGAAAGCTTCAACTCATT
66 AATAGAACAGGCTTTGAAAGCTTCAACTCATT
* * *
9600650 ACTCTTGATGAACTTCAGAGCTCCTTGTTGGTCCATAAGCAGAAGATAAACAGAATTTCTACCTC
1 ACTCTTGATGAACTTCAAAGCTCCTTGTTGGTCCATAAGCAGAAAATAAACAGAAATTCTACCTC
**
9600715 AATAGAGTAGGCTTTGAAAGCTTCAACTCATT
66 AATAGAACAGGCTTTGAAAGCTTCAACTCATT
9600747 CTTTCAGAGG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (97 bp):
ACTCTTGATGAACTTCAAAGCTCCTTGTTGGTCCATAAGCAGAAAATAAACAGAAATTCTACCTC
AATAGAACAGGCTTTGAAAGCTTCAACTCATT
Found at i:9604187 original size:17 final size:18
Alignment explanation
Indices: 9604147--9604188 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
9604137 TTTAAAGGAG
9604147 GGATTGTTAATAAAATCT
1 GGATTGTTAATAAAATCT
*
9604165 GG-TTGTTAATAGAATC-
1 GGATTGTTAATAAAATCT
9604181 GGATTGTT
1 GGATTGTT
9604189 TTTCTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (18 bp):
GGATTGTTAATAAAATCT
Found at i:9605244 original size:20 final size:20
Alignment explanation
Indices: 9605221--9605270 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9605211 TTTTAACATG
*
9605221 ATTTTTAATAGTTTCA-ATAT
1 ATTTTTAATAATTT-ATATAT
*
9605241 ATTTTTAATAATTTATATTT
1 ATTTTTAATAATTTATATAT
9605261 ATTTTTAATA
1 ATTTTTAATA
9605271 TTTTGTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTTAATAATTTATATAT
Found at i:9605284 original size:21 final size:24
Alignment explanation
Indices: 9605260--9605308 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 24
9605250 AATTTATATT
*
9605260 TATTTTTAATATT-TTGTT-AG-A
1 TATTTTTAAAATTATTGTTAAGAA
9605281 TA-TTTTAAAATTATTGTTAAGAA
1 TATTTTTAAAATTATTGTTAAGAA
9605304 TATTT
1 TATTT
9605309 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 9 0.39
21 7 0.30
22 2 0.09
23 3 0.13
24 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (24 bp):
TATTTTTAAAATTATTGTTAAGAA
Found at i:9605312 original size:22 final size:20
Alignment explanation
Indices: 9605263--9605314 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
9605253 TTATATTTAT
*
9605263 TTTTAATATTTTGTTAGATA
1 TTTTAAAATTTTGTTAGATA
9605283 TTTTAAAATTATTGTTAAGAATA
1 TTTTAAAATT-TTGTT-AG-ATA
*
9605306 TTTAAAAAT
1 TTTTAAAAT
9605315 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 5 0.19
22 2 0.07
23 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTAAAATTTTGTTAGATA
Found at i:9606475 original size:2 final size:2
Alignment explanation
Indices: 9606468--9606499 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9606458 TCAAAAAGAA
9606468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9606500 GTAGGGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9612557 original size:9 final size:9
Alignment explanation
Indices: 9612543--9612576 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
9612533 TAGGGTTCCA
9612543 TTTCATGAT
1 TTTCATGAT
9612552 TTTCATGAT
1 TTTCATGAT
9612561 TTTCATGAT
1 TTTCATGAT
9612570 TTTCATG
1 TTTCATG
9612577 TAATTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (9 bp):
TTTCATGAT
Found at i:9624503 original size:17 final size:16
Alignment explanation
Indices: 9624478--9624527 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
9624468 AAAGTCAAAG
9624478 ATATGGGTATCAGAAAT
1 ATATGGGTATCA-AAAT
* *
9624495 ATATAGGTATCAAAAAG
1 ATATGGGTATC-AAAAT
9624512 ATATGGGTATCAAAAT
1 ATATGGGTATCAAAAT
9624528 CTGGGATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 23 0.82
18 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (16 bp):
ATATGGGTATCAAAAT
Found at i:9628036 original size:17 final size:17
Alignment explanation
Indices: 9628014--9628063 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
9628004 ATAGAAAGTC
9628014 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
9628031 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
9628048 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
9628064 AAATCTGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:9629597 original size:38 final size:38
Alignment explanation
Indices: 9629555--9629627 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
9629545 AAATAAAAAA
9629555 TTAAATTAATAAAAATAAAACATGACATTTAATATCAC
1 TTAAATTAATAAAAATAAAACATGACATTTAATATCAC
9629593 TTAAATTAATAAAAATAAAACATGACATTTAATAT
1 TTAAATTAATAAAAATAAAACATGACATTTAATAT
9629628 TACTCAACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (38 bp):
TTAAATTAATAAAAATAAAACATGACATTTAATATCAC
Found at i:9630991 original size:11 final size:11
Alignment explanation
Indices: 9630975--9631000 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9630965 AATGTTTCTC
9630975 AATAAATTGAA
1 AATAAATTGAA
9630986 AATAAATTGAA
1 AATAAATTGAA
9630997 AATA
1 AATA
9631001 TATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (11 bp):
AATAAATTGAA
Found at i:9633152 original size:41 final size:41
Alignment explanation
Indices: 9633095--9633182 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
9633085 CCCAGTAAAT
9633095 TCCAAACTTTTATTATTACAGGGTAGCTATAGAAAACCTGG
1 TCCAAACTTTTATTATTACAGGGTAGCTATAGAAAACCTGG
9633136 TCCAAACTTTTATTATTACAGGGTAGCTATAGAAAACCTGG
1 TCCAAACTTTTATTATTACAGGGTAGCTATAGAAAACCTGG
9633177 TCCAAA
1 TCCAAA
9633183 GTTTCATCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
TCCAAACTTTTATTATTACAGGGTAGCTATAGAAAACCTGG
Found at i:9635168 original size:21 final size:21
Alignment explanation
Indices: 9635143--9635239 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
9635133 AAGCTCGAAT
* *
9635143 GCTAAACAGAAGCACATAAGT
1 GCTAAACAGAAGCCCATAAGG
* *
9635164 GCTAAAAAGAAACCCATAAGG
1 GCTAAACAGAAGCCCATAAGG
* * * * *
9635185 GTTGAACGGAAGCTCATAAGA
1 GCTAAACAGAAGCCCATAAGG
*
9635206 GCTAAAC-GAAAACCCATAAGG
1 GCTAAACAG-AAGCCCATAAGG
*
9635227 GTTAAACAGAAGC
1 GCTAAACAGAAGC
9635240 TCAAAAGAGC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (21 bp):
GCTAAACAGAAGCCCATAAGG
Found at i:9635210 original size:42 final size:42
Alignment explanation
Indices: 9635151--9635300 Score: 149
Period size: 42 Copynumber: 3.6 Consensus size: 42
9635141 ATGCTAAACA
* *
9635151 GAAGCACATAAGTGCTAAAAAGAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTAAAAAGAAACCCATAAGGGTTGAACG
* * *
9635193 GAAGCTCATAAGAGCT-AAACGAAAACCCATAAGGGTTAAACA
1 GAAGCTCATAAGAGCTAAAAAG-AAACCCATAAGGGTTGAACG
* * ** * *
9635235 GAAGCTCAAAAGAGCTGAACGGAAACCCATTAGAGTTGAACG
1 GAAGCTCATAAGAGCTAAAAAGAAACCCATAAGGGTTGAACG
* * * *
9635277 GAAACTCATATGAGTTAAACAGAA
1 GAAGCTCATAAGAGCTAAAAAGAA
9635301 GCTCGTAAGA
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.05
42 81 0.92
43 3 0.03
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAAAAGAAACCCATAAGGGTTGAACG
Found at i:9635274 original size:21 final size:21
Alignment explanation
Indices: 9635172--9635322 Score: 104
Period size: 21 Copynumber: 7.2 Consensus size: 21
9635162 GTGCTAAAAA
*
9635172 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGAGTTGAACG
* * * *
9635193 GAAGCTCATAAGAGCTAAACG
1 GAAACCCATAAGAGTTGAACG
* * * *
9635214 AAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGAGTTGAACG
* * * *
9635235 GAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGAGTTGAACG
*
9635256 GAAACCCATTAGAGTTGAACG
1 GAAACCCATAAGAGTTGAACG
* * * *
9635277 GAAACTCATATGAGTTAAACA
1 GAAACCCATAAGAGTTGAACG
* * * *
9635298 GAAGCTCGTAAGAGTTAAACG
1 GAAACCCATAAGAGTTGAACG
9635319 GAAA
1 GAAA
9635323 GTAAACATGA
Statistics
Matches: 96, Mismatches: 34, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 96 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
GAAACCCATAAGAGTTGAACG
Found at i:9644857 original size:7 final size:7
Alignment explanation
Indices: 9644845--9644905 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
9644835 TAATCGATTC
9644845 GTATTTA
1 GTATTTA
9644852 GTATTTA
1 GTATTTA
9644859 GTATTTA
1 GTATTTA
9644866 GTATTTA
1 GTATTTA
9644873 GTATTTA
1 GTATTTA
9644880 GTATTTA
1 GTATTTA
9644887 GTATTTA
1 GTATTTA
9644894 GTATTTA
1 GTATTTA
9644901 GTATT
1 GTATT
9644906 ATGTATATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:9645831 original size:21 final size:21
Alignment explanation
Indices: 9645806--9645861 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
9645796 CCAACACAAA
9645806 CAACCAG-ATCCCCTACTGGAG
1 CAACCAGAATCCCC-ACTGGAG
* *
9645827 GAACCAGAATCCCCGCTGGAG
1 CAACCAGAATCCCCACTGGAG
*
9645848 CAACCACAATCCCC
1 CAACCAGAATCCCC
9645862 GCTGAAAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.30, C:0.41, G:0.18, T:0.11
Consensus pattern (21 bp):
CAACCAGAATCCCCACTGGAG
Found at i:9645862 original size:21 final size:21
Alignment explanation
Indices: 9645821--9645865 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9645811 AGATCCCCTA
* *
9645821 CTGGAGGAACCAGAATCCCCG
1 CTGGAGCAACCACAATCCCCG
9645842 CTGGAGCAACCACAATCCCCG
1 CTGGAGCAACCACAATCCCCG
9645863 CTG
1 CTG
9645866 AAAGCTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.38, G:0.24, T:0.11
Consensus pattern (21 bp):
CTGGAGCAACCACAATCCCCG
Found at i:9649719 original size:41 final size:38
Alignment explanation
Indices: 9649623--9649722 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 38
9649613 GAAGCAATAG
*
9649623 TTGACACCCAGTGTCTCATCG-GCCAAGCCGAAGTAAA
1 TTGACACCCAGTGTCTCATCGAACCAAGCCGAAGTAAA
** ** * * *
9649660 TTGGTACCCAGTACCTCATCGAATCTATCCGAAGTAACA
1 TTGACACCCAGTGTCTCATCGAACCAAGCCGAAGTAA-A
9649699 GTATGACACCCAGTGTCTCATCGA
1 -T-TGACACCCAGTGTCTCATCGA
9649723 CTCGAGGTCG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 17 0.36
38 11 0.23
39 1 0.02
40 1 0.02
41 17 0.36
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (38 bp):
TTGACACCCAGTGTCTCATCGAACCAAGCCGAAGTAAA
Done.