Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 56 of 325
Found at i:20343139 original size:41 final size:41
Alignment explanation
Indices: 20343046--20343296 Score: 367
Period size: 41 Copynumber: 6.1 Consensus size: 41
20343036 CAAAAATTGT
* * * *
20343046 AAAACACAGAGCAATAGCGGTGCTTTAGTAAAAAACGCCGCTA
1 AAAAC-CAGAGCATTAGCGGCGCTTTTG-GAAAAACGCCGCTA
* * * *
20343089 AAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACACCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
* *
20343130 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCACTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
* *
20343171 AAAACCAGAGCATTAGCTGCGCTTTTGAAAAAACGCCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
*
20343212 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACACCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
20343253 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
20343294 AAA
1 AAA
20343297 GTCATATAAC
Statistics
Matches: 190, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 166 0.87
42 20 0.11
43 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
Found at i:20343265 original size:123 final size:125
Alignment explanation
Indices: 20343046--20343296 Score: 407
Period size: 123 Copynumber: 2.0 Consensus size: 125
20343036 CAAAAATTGT
*
20343046 AAAACACAGAGCAATAGCGGTGCTTTAGTAAAAAACGCCGCTAAAAAACAGAGCAATAGCGGCGC
1 AAAACACAGAGCAATAGCGGCGCTTTAGTAAAAAACGCCGCTAAAAAACAGAGCAATAGCGGCGC
* *
20343111 TTTTGGTAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCACTA
66 TTTTGGAAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCACTA
* * * * *
20343171 AAAAC-CAGAGCATTAGCTGCGCTTTTG-AAAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGC
1 AAAACACAGAGCAATAGCGGCGCTTTAGTAAAAAACGCCGCTAAAAAACAGAGCAATAGCGGCGC
*
20343234 TTTTGGAAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
66 TTTTGGAAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCACTA
20343294 AAA
1 AAA
20343297 GTCATATAAC
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
123 94 0.80
124 18 0.15
125 5 0.04
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (125 bp):
AAAACACAGAGCAATAGCGGCGCTTTAGTAAAAAACGCCGCTAAAAAACAGAGCAATAGCGGCGC
TTTTGGAAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCACTA
Found at i:20343477 original size:14 final size:14
Alignment explanation
Indices: 20343455--20343538 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
20343445 TTAATTATCA
*
20343455 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
20343469 TTATGGTTTAGGGT
1 TTATGGTTTAAGGT
* *
20343483 TTAGGGTTTATGAGT
1 TTATGGTTTAAG-GT
**
20343498 TAAATATGGTTTAATAT
1 T---TATGGTTTAAGGT
* *
20343515 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
*
20343529 TTAAGGTTTA
1 TTATGGTTTA
20343539 GGAGTTAACT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
14 40 0.77
15 3 0.06
17 1 0.02
18 8 0.15
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:20343604 original size:7 final size:7
Alignment explanation
Indices: 20343575--20343703 Score: 68
Period size: 7 Copynumber: 18.1 Consensus size: 7
20343565 GATGAATTAT
20343575 GGGTTTA
1 GGGTTTA
*
20343582 GGGATTA
1 GGGTTTA
* *
20343589 TGATTTA
1 GGGTTTA
20343596 GGGTTTA
1 GGGTTTA
*
20343603 GGGGTTA
1 GGGTTTA
20343610 GGG-TT-
1 GGGTTTA
20343615 GGAGTTTA
1 GG-GTTTA
* *
20343623 AGGTGTAA
1 GGGT-TTA
20343631 GGGTTT-
1 GGGTTTA
*
20343637 GGTGTTAA
1 GG-GTTTA
*
20343645 GGGTTAA
1 GGGTTTA
20343652 GGGTTTA
1 GGGTTTA
*
20343659 GTGTTTA
1 GGGTTTA
*
20343666 GTGTTTA
1 GGGTTTA
*
20343673 TGGG-ATA
1 -GGGTTTA
*
20343680 GGGGTTAA
1 -GGGTTTA
20343688 GAGGTTTA
1 G-GGTTTA
20343696 GGGTTTA
1 GGGTTTA
20343703 G
1 G
20343704 ATTAATTAGT
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
5 2 0.02
6 5 0.05
7 69 0.74
8 17 0.18
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:20350839 original size:33 final size:32
Alignment explanation
Indices: 20350797--20350864 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
20350787 ATTTTTTTAG
* *
20350797 TTTTTTTTTTACAGATT-TTAGAATATTTTCAA
1 TTTTTTTTTTACAGATTCTTA-AAAATTTTAAA
*
20350829 TTTTTATTTTTATAGATTCTTAAAAATTTTAAA
1 TTTTT-TTTTTACAGATTCTTAAAAATTTTAAA
20350862 TTT
1 TTT
20350865 CATAGTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.16
33 23 0.74
34 3 0.10
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (32 bp):
TTTTTTTTTTACAGATTCTTAAAAATTTTAAA
Found at i:20351438 original size:10 final size:9
Alignment explanation
Indices: 20351423--20351526 Score: 78
Period size: 9 Copynumber: 11.9 Consensus size: 9
20351413 AACCAGAAAG
20351423 TTATAAAAA
1 TTATAAAAA
20351432 TT-TATAAAA
1 TTATA-AAAA
*
20351441 TTAT-TAAA
1 TTATAAAAA
20351449 -TATAAAAA
1 TTATAAAAA
*
20351457 TATATGAAAA
1 T-TATAAAAA
20351467 TTGATATAAAA
1 TT-ATA-AAAA
*
20351478 TTATAAATA
1 TTATAAAAA
20351487 TTATAAAAA
1 TTATAAAAA
20351496 -TAT-AAAA
1 TTATAAAAA
* *
20351503 TTCTAATAA
1 TTATAAAAA
20351512 TTAT--AAA
1 TTATAAAAA
20351519 TTATAAAA
1 TTATAAAA
20351527 TTAATAATAC
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
7 13 0.18
8 13 0.18
9 28 0.38
10 14 0.19
11 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:20351449 original size:17 final size:17
Alignment explanation
Indices: 20351429--20351529 Score: 68
Period size: 17 Copynumber: 5.9 Consensus size: 17
20351419 AAAGTTATAA
20351429 AAATTTATAAAATTATT
1 AAATTTATAAAATTATT
* *
20351446 AAATATA-AAAATATATGA
1 AAATTTATAAAAT-TAT-T
20351464 AAATTGATATAAAATTA-T
1 AAATT--TATAAAATTATT
* *
20351482 AAATATTATAAAAATATA
1 AAAT-TTATAAAATTATT
*
20351500 AAATTCTA-ATAATTA-T
1 AAATT-TATAAAATTATT
20351516 AAA-TTATAAAATTA
1 AAATTTATAAAATTA
20351530 ATAATACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.03
15 7 0.11
16 8 0.12
17 24 0.37
18 14 0.22
19 1 0.02
20 4 0.06
21 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTTATAAAATTATT
Found at i:20351502 original size:7 final size:8
Alignment explanation
Indices: 20351423--20351529 Score: 83
Period size: 8 Copynumber: 12.4 Consensus size: 8
20351413 AACCAGAAAG
20351423 TTATAAAAA
1 TTAT-AAAA
20351432 TTTATAAAA
1 -TTATAAAA
*
20351441 TTATTAAA
1 TTATAAAA
20351449 -TATAAAAA
1 TTAT-AAAA
20351457 TATATGAAAA
1 T-TAT-AAAA
20351467 TTGATATAAAA
1 -T--TATAAAA
20351478 TTATAAATA
1 TTATAAA-A
20351487 TTATAAAA
1 TTATAAAA
*
20351495 ATATAAAA
1 TTATAAAA
*
20351503 TTCTAATAA
1 TTATAA-AA
20351512 TTAT-AAA
1 TTATAAAA
20351519 TTATAAAA
1 TTATAAAA
20351527 TTA
1 TTA
20351530 ATAATACATA
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
7 9 0.11
8 35 0.43
9 17 0.21
10 12 0.15
11 5 0.06
12 4 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (8 bp):
TTATAAAA
Found at i:20351504 original size:25 final size:24
Alignment explanation
Indices: 20351470--20351549 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
20351460 ATGAAAATTG
20351470 ATATAAAATTATAA-ATATTATAAAA
1 ATATAAAATTATAATA-ATTAT-AAA
*
20351495 ATATAAAATTCTAATAATTATAAA
1 ATATAAAATTATAATAATTATAAA
* *
20351519 TTATAAAATTAATAATACATATTTAAA
1 ATATAAAATT-ATAATA-AT-TATAAA
20351546 ATAT
1 ATAT
20351550 TTAAACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
24 12 0.26
25 23 0.50
26 3 0.07
27 8 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAAATTATAATAATTATAAA
Found at i:20351575 original size:21 final size:22
Alignment explanation
Indices: 20351543--20351592 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
20351533 ATACATATTT
*
20351543 AAAAT-AT-TTAAACTTTTGTA
1 AAAATCATATTAAACTTCTGTA
20351563 AAAA-CATATTAAACTTCTGTA
1 AAAATCATATTAAACTTCTGTA
20351584 AAAATCATA
1 AAAATCATA
20351593 AATATTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (22 bp):
AAAATCATATTAAACTTCTGTA
Found at i:20352074 original size:9 final size:9
Alignment explanation
Indices: 20352062--20352282 Score: 79
Period size: 9 Copynumber: 24.7 Consensus size: 9
20352052 TTTATGATTT
20352062 TTTTTATAA
1 TTTTTATAA
*
20352071 TTTTAATAA
1 TTTTTATAA
*
20352080 GTTTATATCAA
1 -TTTTTAT-AA
*
20352091 TTTTAAT-A
1 TTTTTATAA
* *
20352099 TTTGTACAA
1 TTTTTATAA
*
20352108 TTTTTATTAT
1 TTTTTA-TAA
*
20352118 TTTTTAGAA
1 TTTTTATAA
* * *
20352127 TTCTAATAC
1 TTTTTATAA
20352136 TTTTTA-AA
1 TTTTTATAA
*
20352144 ATTTTA-AA
1 TTTTTATAA
*
20352152 TATTTAAATAA
1 T-TTT-TATAA
*
20352163 GTTTTATTAA
1 TTTTTA-TAA
20352173 -TTTTATAA
1 TTTTTATAA
20352181 TTTTTATAA
1 TTTTTATAA
*
20352190 TTTATTA-GA
1 TTT-TTATAA
*
20352199 TTTTT-T-G
1 TTTTTATAA
*
20352206 TTTTTATGAT
1 TTTTTAT-AA
20352216 TTTTTATAA
1 TTTTTATAA
*
20352225 TTTTAATAA
1 TTTTTATAA
*
20352234 GTTTATATCAA
1 -TTTTTAT-AA
20352245 --TTTA-AA
1 TTTTTATAA
20352251 TATTTTAT-A
1 T-TTTTATAA
20352260 TTTTTAT-A
1 TTTTTATAA
* *
20352268 TTTTTTTAT
1 TTTTTATAA
20352277 TTTTTA
1 TTTTTA
20352283 AGATTTTTTA
Statistics
Matches: 155, Mismatches: 36, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
6 2 0.01
7 5 0.03
8 35 0.23
9 68 0.44
10 39 0.25
11 6 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:20352228 original size:25 final size:25
Alignment explanation
Indices: 20352181--20352228 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20352171 AATTTTATAA
*
20352181 TTTTTATAATTTATTAGATTTTTTG
1 TTTTTATAATTTATTAGAATTTTTG
* * *
20352206 TTTTTATGATTTTTTATAATTTT
1 TTTTTATAATTTATTAGAATTTT
20352229 AATAAGTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTTATAATTTATTAGAATTTTTG
Found at i:20352276 original size:18 final size:18
Alignment explanation
Indices: 20352253--20352302 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
20352243 AATTTAAATA
20352253 TTTTATATTTTTATATTT
1 TTTTATATTTTTATATTT
*
20352271 TTTTAT-TTTTTAAGATTT
1 TTTTATATTTTT-ATATTT
* *
20352289 TTTAAGATTTTTAT
1 TTTTATATTTTTAT
20352303 GGGAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTATATTTTTATATTT
Found at i:20352281 original size:8 final size:8
Alignment explanation
Indices: 20352173--20352280 Score: 56
Period size: 8 Copynumber: 12.5 Consensus size: 8
20352163 GTTTTATTAA
20352173 TTTTATAAT
1 TTTTAT-AT
20352182 TTTTATAAT
1 TTTTAT-AT
*
20352191 TTATTAGAT
1 TT-TTATAT
*
20352200 TTTT-TGT
1 TTTTATAT
20352207 TTTTATGATT
1 TTTTAT-A-T
20352217 TTTTATAAT
1 TTTTAT-AT
* *
20352226 TTTAATAA
1 TTTTATAT
*
20352234 GTTTATAT
1 TTTTATAT
* *
20352242 CAATTTAAAT
1 --TTTTATAT
20352252 ATTTTATAT
1 -TTTTATAT
20352261 TTTTATAT
1 TTTTATAT
*
20352269 TTTTTTAT
1 TTTTATAT
20352277 TTTT
1 TTTT
20352281 TAAGATTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
7 5 0.06
8 28 0.36
9 28 0.36
10 17 0.22
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.67
Consensus pattern (8 bp):
TTTTATAT
Found at i:20352299 original size:71 final size:70
Alignment explanation
Indices: 20352145--20352299 Score: 174
Period size: 71 Copynumber: 2.2 Consensus size: 70
20352135 CTTTTTAAAA
*
20352145 TTTTAAATATTTAAATAAGTTTTATTAATTTTATAATTTTTATAATTTATTAGATTTTTTGTTTT
1 TTTTAAAT-TTT-AATAAGTTTTATCAATTTTATAATTTTTATAATTTATTAGATTTTTTGTTTT
*
20352210 TATGATT
64 TAAGATT
* *
20352217 TTTTATAATTTTAATAAGTTTATATCAA-TTTA-AATATTTTAT-ATTT-TTATATTTTTTTATT
1 TTTTA-AATTTTAATAAGTTT-TATCAATTTTATAAT-TTTTATAATTTATTAGA-TTTTTT-GT
20352278 TTTTAAGATT
61 TTTTAAGATT
20352288 TTTTAAGATTTT
1 TTTTAA-ATTTT
20352300 TATGGGAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
69 4 0.05
70 14 0.19
71 39 0.53
72 13 0.18
73 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.63
Consensus pattern (70 bp):
TTTTAAATTTTAATAAGTTTTATCAATTTTATAATTTTTATAATTTATTAGATTTTTTGTTTTTA
AGATT
Found at i:20352301 original size:9 final size:10
Alignment explanation
Indices: 20352275--20352300 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20352265 ATATTTTTTT
20352275 ATTTTTTAAG
1 ATTTTTTAAG
20352285 ATTTTTTAAG
1 ATTTTTTAAG
20352295 ATTTTT
1 ATTTTT
20352301 ATGGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
ATTTTTTAAG
Found at i:20358649 original size:29 final size:28
Alignment explanation
Indices: 20358614--20358694 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
20358604 CACACCCGGA
*
20358614 ATAATATAAATCCTCCATAACACACTAGT
1 ATAATAT-AATCCTCCATAACACACCAGT
*
20358643 ATAATAT-AGCCTCCCA-AACACACCAGT
1 ATAATATAATCCT-CCATAACACACCAGT
* *
20358670 ATATTAT-ATCCTCCCTAACACACCA
1 ATAATATAATCCTCCATAACACACCA
20358695 ATAAGGCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 33 0.73
28 3 0.07
29 7 0.16
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.25
Consensus pattern (28 bp):
ATAATATAATCCTCCATAACACACCAGT
Found at i:20358662 original size:27 final size:27
Alignment explanation
Indices: 20358632--20358694 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
20358622 AATCCTCCAT
*
20358632 AACACACTAGTATAATATAGCCTCCCA
1 AACACACCAGTATAATATAGCCTCCCA
* * *
20358659 AACACACCAGTATATTATATCCTCCCT
1 AACACACCAGTATAATATAGCCTCCCA
20358686 AACACACCA
1 AACACACCA
20358695 ATAAGGCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.22
Consensus pattern (27 bp):
AACACACCAGTATAATATAGCCTCCCA
Found at i:20359666 original size:17 final size:17
Alignment explanation
Indices: 20359644--20359676 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20359634 GTTTTCGTTT
20359644 TGTTCTT-TGTTCTTTTC
1 TGTTCTTCT-TTCTTTTC
20359661 TGTTCTTCTTTCTTTT
1 TGTTCTTCTTTCTTTT
20359677 ATTTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.73
Consensus pattern (17 bp):
TGTTCTTCTTTCTTTTC
Found at i:20359691 original size:22 final size:23
Alignment explanation
Indices: 20359675--20359717 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20359665 CTTCTTTCTT
20359675 TTATTTTCTTTTATTCTATTTTC
1 TTATTTTCTTTTATTCTATTTTC
*
20359698 TTA-TTTCTTTTAGT-TATTTT
1 TTATTTTCTTTTATTCTATTTT
20359718 ATATTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
TTATTTTCTTTTATTCTATTTTC
Found at i:20369219 original size:7 final size:7
Alignment explanation
Indices: 20369207--20369256 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
20369197 ATTTAATTTT
20369207 TTAAATA
1 TTAAATA
20369214 TTAAATTA
1 TTAAA-TA
* *
20369222 ATAAAAA
1 TTAAATA
20369229 TATAAATA
1 T-TAAATA
20369237 TTAAATA
1 TTAAATA
20369244 TTAAATA
1 TTAAATA
20369251 TTAAAT
1 TTAAAT
20369257 TTATCACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 25 0.68
8 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TTAAATA
Found at i:20392466 original size:38 final size:38
Alignment explanation
Indices: 20392415--20392606 Score: 258
Period size: 38 Copynumber: 5.0 Consensus size: 38
20392405 CACTCGATAT
* *
20392415 ATATATTCGGGTTAAGTCTCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
*
20392453 ATATATCCGGGTTAAGTCCCGTAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* *
20392491 ATATATCCGGGTTAAATCCCGCAGGTTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* *
20392529 ATTTATCCGGGTTAAAGTCCCGCAGGCTTAGTGCTGGTA
1 ATATATCCGGGTT-AAGTCCCGCAGGCTTCGTGCTGGTA
* * * *
20392568 TTATATCCGAGTTTAAAGTCTCGCAGGCTTTGTGCTGGT
1 ATATATCCG-GGTT-AAGTCCCGCAGGCTTCGTGCTGGT
20392607 GACTGAATTC
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 82 0.60
39 29 0.21
40 26 0.19
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (38 bp):
ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
Found at i:20394121 original size:22 final size:21
Alignment explanation
Indices: 20394096--20394142 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20394086 ATTATTTAAG
*
20394096 TAAATATTAATGTTATTATTAT
1 TAAATATTAATATTA-TATTAT
*
20394118 T-AA-ATTGATATTATATTAT
1 TAAATATTAATATTATATTAT
20394137 TAAATA
1 TAAATA
20394143 AATTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 3 0.14
22 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TAAATATTAATATTATATTAT
Found at i:20403772 original size:18 final size:19
Alignment explanation
Indices: 20403749--20403786 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20403739 TTTTATCTTA
20403749 AAAT-AAATTATAGATTTT
1 AAATAAAATTATAGATTTT
*
20403767 AAATAAAATTATATATTTT
1 AAATAAAATTATAGATTTT
20403786 A
1 A
20403787 TTGTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAATAAAATTATAGATTTT
Found at i:20411256 original size:16 final size:16
Alignment explanation
Indices: 20411235--20411266 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20411225 GAAATTTTTA
*
20411235 TAAATATTTTTAATTT
1 TAAATATTTGTAATTT
20411251 TAAATATTTGTAATTT
1 TAAATATTTGTAATTT
20411267 ATTTTGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAAATATTTGTAATTT
Found at i:20426088 original size:17 final size:19
Alignment explanation
Indices: 20426061--20426099 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
20426051 CCTTCATTCC
20426061 TTTCTTTTATTCTTTTA-G
1 TTTCTTTTATTCTTTTATG
20426079 TTTC-TTTATTCTTTTATG
1 TTTCTTTTATTCTTTTATG
20426097 TTT
1 TTT
20426100 ATAATTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTCTTTTATTCTTTTATG
Found at i:20431046 original size:78 final size:78
Alignment explanation
Indices: 20430913--20431075 Score: 236
Period size: 78 Copynumber: 2.1 Consensus size: 78
20430903 CTTTATCATA
* * * * *
20430913 ATTAGTCGATTGAATCTTAACTTTATCAATATAAAAAGACGTGAATTCGAGTATACTGAAAGTCT
1 ATTAGTTGATTGAATCTTAACTGTATCAATATAAAAAGACGTAAATTCAAATATACTGAAAGTCT
20430978 TATTCTTCTATTT
66 TATTCTTCTATTT
* * *
20430991 ATTAGTTGATTGAGTCTTAACTGTATCAATATAAAAGGATGTAAATTCAAATATACTGAAAGTCT
1 ATTAGTTGATTGAATCTTAACTGTATCAATATAAAAAGACGTAAATTCAAATATACTGAAAGTCT
*
20431056 TATTTTTCTATTT
66 TATTCTTCTATTT
*
20431069 ATGAGTT
1 ATTAGTT
20431076 AGAGAGAGAC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (78 bp):
ATTAGTTGATTGAATCTTAACTGTATCAATATAAAAAGACGTAAATTCAAATATACTGAAAGTCT
TATTCTTCTATTT
Found at i:20440716 original size:17 final size:19
Alignment explanation
Indices: 20440682--20440749 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
20440672 TGTCATACTT
20440682 TATAATTATAATTATTATA
1 TATAATTATAATTATTATA
20440701 TATAATT-T-ATT-TT-TA
1 TATAATTATAATTATTATA
*
20440716 T-TAATATATTAATTATTGT-
1 TATAAT-TA-TAATTATTATA
*
20440735 TACAATTATAATTAT
1 TATAATTATAATTAT
20440750 GGTTGGTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 2 0.05
17 4 0.10
18 11 0.27
19 12 0.29
20 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (19 bp):
TATAATTATAATTATTATA
Found at i:20445363 original size:13 final size:13
Alignment explanation
Indices: 20445345--20445369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20445335 TTTTGGAAAA
20445345 TTTTTATTTATAT
1 TTTTTATTTATAT
20445358 TTTTTATTTATA
1 TTTTTATTTATA
20445370 AAAATATTTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTATAT
Found at i:20445394 original size:19 final size:17
Alignment explanation
Indices: 20445372--20445413 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
20445362 TATTTATAAA
20445372 AATATTTTAACATAATTTT
1 AATATTTTAA-AT-ATTTT
20445391 AATATTTTAAATATTTT
1 AATATTTTAAATATTTT
20445408 -ATATTT
1 AATATTT
20445414 AGTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 2 0.09
19 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTTAAATATTTT
Found at i:20445405 original size:9 final size:9
Alignment explanation
Indices: 20445371--20445408 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
20445361 TTATTTATAA
20445371 AAATATTTT
1 AAATATTTT
20445380 AACATAATTTT
1 AA-AT-ATTTT
20445391 -AATATTTT
1 AAATATTTT
20445399 AAATATTTT
1 AAATATTTT
20445408 A
1 A
20445409 TATTTAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 3 0.12
11 5 0.19
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
AAATATTTT
Found at i:20446209 original size:2 final size:2
Alignment explanation
Indices: 20446202--20446226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20446192 TAATAATTGA
20446202 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20446227 AAATATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20446344 original size:3 final size:3
Alignment explanation
Indices: 20446336--20446360 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20446326 TTTTCTTTAC
20446336 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
20446361 TACTCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20450126 original size:15 final size:15
Alignment explanation
Indices: 20450106--20450134 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20450096 TCACTTCGAT
20450106 TACTGACAAAAGTAC
1 TACTGACAAAAGTAC
20450121 TACTGACAAAAGTA
1 TACTGACAAAAGTA
20450135 ATTGATGGCA
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:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (15 bp):
TACTGACAAAAGTAC
Found at i:20461192 original size:30 final size:30
Alignment explanation
Indices: 20461151--20461211 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
20461141 TCCTCAAAAC
20461151 TAAGATCTGAATAGCTTTTAACTCCCTCTT
1 TAAGATCTGAATAGCTTTTAACTCCCTCTT
*
20461181 TAAGTTCTGAATAGCTTTTAACTCCCTCTT
1 TAAGATCTGAATAGCTTTTAACTCCCTCTT
20461211 T
1 T
20461212 GTGGCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.43
Consensus pattern (30 bp):
TAAGATCTGAATAGCTTTTAACTCCCTCTT
Found at i:20479417 original size:19 final size:19
Alignment explanation
Indices: 20479369--20479417 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
20479359 AGACATAAGA
*
20479369 TTTTAATATATAGTTGTGT
1 TTTTAATATACAGTTGTGT
20479388 TTATTATATATACATGTTGTG-
1 TT-TTA-ATATACA-GTTGTGT
20479409 TTTTAATAT
1 TTTTAATAT
20479418 GAAAAAGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.23
20 6 0.23
21 8 0.31
22 6 0.23
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (19 bp):
TTTTAATATACAGTTGTGT
Found at i:20480398 original size:19 final size:19
Alignment explanation
Indices: 20480363--20480410 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
20480353 GGCAGTTTCT
20480363 CACCACCACC-ACCTCCAC
1 CACCACCACCTACCTCCAC
* *
20480381 CTCCACCACCTTCCTCCAC
1 CACCACCACCTACCTCCAC
20480400 CACCACCACCT
1 CACCACCACCT
20480411 CCTAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.23, C:0.65, G:0.00, T:0.12
Consensus pattern (19 bp):
CACCACCACCTACCTCCAC
Found at i:20483826 original size:14 final size:15
Alignment explanation
Indices: 20483807--20483836 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20483797 CTTTTTCCAA
20483807 AAGTAT-CCCTATAT
1 AAGTATCCCCTATAT
20483821 AAGTATCCCCTATAT
1 AAGTATCCCCTATAT
20483836 A
1 A
20483837 TTTATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (15 bp):
AAGTATCCCCTATAT
Found at i:20487675 original size:46 final size:45
Alignment explanation
Indices: 20487622--20487794 Score: 161
Period size: 46 Copynumber: 3.8 Consensus size: 45
20487612 TTGGGCATCC
*
20487622 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCA
*** * * *
20487668 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCA
* * * *
20487715 GAACTTGTTGAGTTGAGTCTGAGTTCACCTATGGATGCGAACGCCA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCA
* *
20487761 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20487795 GCGGGTTACA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 60 0.60
47 30 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCA
Found at i:20487774 original size:93 final size:93
Alignment explanation
Indices: 20487615--20487787 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
20487605 AGGATATTTG
* * * *
20487615 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCAGAACTCGTTGAG
20487680 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
20487708 GGCATCCGAACTTGTTGAGTTGAGTCTGAGTTCACCTATGGATGCGAACGCCAGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCAGAACTCGTTGAG
20487773 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
20487788 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCAGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:20500883 original size:25 final size:25
Alignment explanation
Indices: 20500833--20500883 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20500823 TTCCTTATAA
**
20500833 ACTTTAAATTAGGAATTCTATGAGG
1 ACTTTAAATTAGGAATTAGATGAGG
*
20500858 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATGAGG
20500883 A
1 A
20500884 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATGAGG
Found at i:20505549 original size:25 final size:25
Alignment explanation
Indices: 20505499--20505549 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20505489 TTCCTTATAA
**
20505499 ACTTTAAATTAGGAATTCTATGAGG
1 ACTTTAAATTAGGAATTAGATGAGG
*
20505524 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATGAGG
20505549 A
1 A
20505550 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATGAGG
Found at i:20511585 original size:12 final size:12
Alignment explanation
Indices: 20511568--20511594 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20511558 TTAATAGTTG
20511568 ATTGTCAAAATC
1 ATTGTCAAAATC
20511580 ATTGTCAAAATC
1 ATTGTCAAAATC
20511592 ATT
1 ATT
20511595 ACAATCTCTA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTGTCAAAATC
Found at i:20512108 original size:12 final size:12
Alignment explanation
Indices: 20512091--20512115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20512081 ACACACACAC
20512091 ACACGTATATAT
1 ACACGTATATAT
20512103 ACACGTATATAT
1 ACACGTATATAT
20512115 A
1 A
20512116 TATTACTAAG
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ACACGTATATAT
Found at i:20513414 original size:19 final size:18
Alignment explanation
Indices: 20513383--20513422 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
20513373 AGGGCCACCA
20513383 TGCAACAAGCAAAATCCT
1 TGCAACAAGCAAAATCCT
* *
20513401 TGCACACAATCAAAATGCT
1 TGCA-ACAAGCAAAATCCT
20513420 TGC
1 TGC
20513423 CTTCATGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (18 bp):
TGCAACAAGCAAAATCCT
Found at i:20525924 original size:66 final size:66
Alignment explanation
Indices: 20525818--20525943 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
20525808 AGTTGGAAAC
*
20525818 GATGGCATTGTCTTTAAGAGTGGACATTTCATGACCGATAGTCTCTTGAGGCAAGGGAAACCAAA
1 GATGGCATTGTCTTTAAGAGTGGACAATTCATGACCGATAGTCTCTTGAGGCAAGGGAAACCAAA
20525883 G
66 G
* ** *
20525884 GATGGCATTGTTTTTAAGAGTGGACAATTCATGATGGATAGTTTCTTGAGGCAAGGGAAA
1 GATGGCATTGTCTTTAAGAGTGGACAATTCATGACCGATAGTCTCTTGAGGCAAGGGAAA
20525944 GCTTCTGTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (66 bp):
GATGGCATTGTCTTTAAGAGTGGACAATTCATGACCGATAGTCTCTTGAGGCAAGGGAAACCAAA
G
Found at i:20530192 original size:264 final size:264
Alignment explanation
Indices: 20529721--20530254 Score: 797
Period size: 264 Copynumber: 2.0 Consensus size: 264
20529711 AAAAGCATGA
*
20529721 ATATTCATCATAATTTTATTAGATCCAAGATCGATGGAAACATGTGTCTTGCAAATAATGCTACA
1 ATATTCATCATAATTTTATTAGATCCAAGATCGATGGAAACATGTGTCTTGCAAATAATGCGACA
* * * *
20529786 ATACATACTATATTAAAAAATTAAAAATATTTTTCTCATTTGATAATGAGTAATGCTTATATTAA
66 ATACATACTATACTAAAAAATTAAAAATATTCTTCTCATTTGACAAAGAGTAATGCTTATATTAA
*
20529851 TACCATATCAGGTAATTCAAAACTTATTGAAAGCTCCGAAAGAGCTAATATATTATTATCCAAAG
131 TACAATATCAGGTAATTCAAAACTTATTGAAAGCTCCGAAAGAGCTAATATATTATTATCCAAAG
* * *
20529916 GGACAGAAATTGTCACTGATGATGCTTTATTTTCTACTAAATC-TAAAAGAAATTTATTGAGTTT
196 GGACAAAAATTGTCACTGATGATACTTTATTTTCAACTAAATCTTAAAA-AAATTTATTGAGTTT
20529980 TAAAG
260 TAAAG
* * *
20529985 ATATTCA-CTATAATTTTATTAGATCCAAGATCGATGGAAACATGTGTTTTGCAAATAGTGGGAC
1 ATATTCATC-ATAATTTTATTAGATCCAAGATCGATGGAAACATGTGTCTTGCAAATAATGCGAC
* * * * *
20530049 AATACATGCTATACTAAAATAATATATATATATTCTTCTTATTTGACAAAGAGTGATGCTTATAT
65 AATACATACTATACTAAAA-AAT-TAAAAATATTCTTCTCATTTGACAAAGAGTAATGCTTATAT
* * * *
20530114 TAATACAATCTCAGGTAATTC-AAA-TTATTGAAAGCTCTGAAAGAGCTATTATATTATTATCTA
128 TAATACAATATCAGGTAATTCAAAACTTATTGAAAGCTCCGAAAGAGCTAATATATTATTATCCA
* *
20530177 AAGGGATAAAAATTGTCATTGATGATACTTTATTTTCAACTAAATCTTAAAAAAATTTATTGAGT
193 AAGGGACAAAAATTGTCACTGATGATACTTTATTTTCAACTAAATCTTAAAAAAATTTATTGAGT
20530242 TTTAAAG
258 TTTAAAG
20530249 ATATTC
1 ATATTC
20530255 GCCTTAATAG
Statistics
Matches: 243, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
263 1 0.00
264 178 0.73
265 11 0.05
266 53 0.22
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (264 bp):
ATATTCATCATAATTTTATTAGATCCAAGATCGATGGAAACATGTGTCTTGCAAATAATGCGACA
ATACATACTATACTAAAAAATTAAAAATATTCTTCTCATTTGACAAAGAGTAATGCTTATATTAA
TACAATATCAGGTAATTCAAAACTTATTGAAAGCTCCGAAAGAGCTAATATATTATTATCCAAAG
GGACAAAAATTGTCACTGATGATACTTTATTTTCAACTAAATCTTAAAAAAATTTATTGAGTTTT
AAAG
Found at i:20530737 original size:15 final size:15
Alignment explanation
Indices: 20530714--20530743 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20530704 ATGCTTAGTT
*
20530714 ATTTGTTTTTATTTA
1 ATTTATTTTTATTTA
20530729 ATTTATTTTTATTTA
1 ATTTATTTTTATTTA
20530744 GTTTTTCATA
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:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
ATTTATTTTTATTTA
Found at i:20536660 original size:15 final size:15
Alignment explanation
Indices: 20536637--20536666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20536627 GAGTCCTAAG
*
20536637 AAAATAGAAATAGAA
1 AAAACAGAAATAGAA
20536652 AAAACAGAAATAGAA
1 AAAACAGAAATAGAA
20536667 TTTTTAGGTT
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:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (15 bp):
AAAACAGAAATAGAA
Found at i:20553396 original size:6 final size:6
Alignment explanation
Indices: 20553385--20553410 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20553375 TGTCATCGAC
20553385 TCCCTT TCCCTT TCCCTT TCCCTT TC
1 TCCCTT TCCCTT TCCCTT TCCCTT TC
20553411 GTTCACCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCCTT
Found at i:20556014 original size:2 final size:2
Alignment explanation
Indices: 20556007--20556041 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20555997 TACTGCTCCT
* *
20556007 TC TC TC TC TC TC TC TT TC TC TC TT TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20556042 TTGAGAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:20562310 original size:29 final size:29
Alignment explanation
Indices: 20562277--20562332 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
20562267 AGAGAGAGAT
20562277 AGAATATGGTATTTGTTATTCTCTTATAC
1 AGAATATGGTATTTGTTATTCTCTTATAC
20562306 AGAATATGGTATTTGTTATTCTCTTAT
1 AGAATATGGTATTTGTTATTCTCTTAT
20562333 CTGGCCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (29 bp):
AGAATATGGTATTTGTTATTCTCTTATAC
Found at i:20566370 original size:24 final size:24
Alignment explanation
Indices: 20566338--20566385 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20566328 TCATGGGGAA
20566338 GGAAGTAGGCAGATAATTTGGACT
1 GGAAGTAGGCAGATAATTTGGACT
20566362 GGAAGTAGGCAGATAATTTGGACT
1 GGAAGTAGGCAGATAATTTGGACT
20566386 AAGAAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.25
Consensus pattern (24 bp):
GGAAGTAGGCAGATAATTTGGACT
Found at i:20571056 original size:25 final size:25
Alignment explanation
Indices: 20571001--20571058 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
20570991 AAATATGATT
*
20571001 TAAAAATAAAAATAAAAATAACATG
1 TAAAAATAAAAATAAAAATAACATA
20571026 TGAAAAATAAAATATAAAGAA-AACA-A
1 T-AAAAATAAAA-ATAAA-AATAACATA
20571052 TAAAAAT
1 TAAAAAT
20571059 TTGACTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 7 0.24
26 11 0.38
27 9 0.31
28 2 0.07
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (25 bp):
TAAAAATAAAAATAAAAATAACATA
Found at i:20587697 original size:3 final size:3
Alignment explanation
Indices: 20587689--20587715 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20587679 AGAACCCAAA
20587689 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
20587716 CACTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20591796 original size:31 final size:31
Alignment explanation
Indices: 20591758--20591822 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
20591748 TACAAAACAA
* *
20591758 TCATTGAACTATTCAAAATTTTTTATTTAAG
1 TCATTGAACTAGTCAAAAGTTTTTATTTAAG
*
20591789 TCATTGAACTAGTCGAAAGTTTTTATTTAAG
1 TCATTGAACTAGTCAAAAGTTTTTATTTAAG
20591820 TCA
1 TCA
20591823 CTAGACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (31 bp):
TCATTGAACTAGTCAAAAGTTTTTATTTAAG
Found at i:20599376 original size:25 final size:23
Alignment explanation
Indices: 20599322--20599376 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
20599312 ATCCGAGTAA
**
20599322 AATTATTTTAGTTTAATTTTTTTT
1 AATT-TTTTAGTTTAATTTTTAAT
20599346 ATATTTTTTAGGTTTAATATTTTAAT
1 A-ATTTTTTA-GTTTAAT-TTTTAAT
20599372 AATTT
1 AATTT
20599377 AATCGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 6 0.23
25 14 0.54
26 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (23 bp):
AATTTTTTAGTTTAATTTTTAAT
Found at i:20604737 original size:3 final size:3
Alignment explanation
Indices: 20604729--20604758 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20604719 TATATATCAA
20604729 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20604759 CATAGTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20605049 original size:12 final size:12
Alignment explanation
Indices: 20605034--20605077 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
20605024 ATATTATGTT
20605034 TTATATATATTA
1 TTATATATATTA
20605046 TTATATATATT-
1 TTATATATATTA
20605057 TTA-ATATTATTA
1 TTATATA-TATTA
20605069 GTTATATAT
1 -TTATATAT
20605078 TTTTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.11
11 7 0.25
12 11 0.39
13 4 0.14
14 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATATATATTA
Found at i:20605065 original size:20 final size:21
Alignment explanation
Indices: 20605040--20605141 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
20605030 TGTTTTATAT
20605040 ATATTATTATATATATTT-TA
1 ATATTATTATATATATTTCTA
*
20605060 ATATTATTAGTTATATATTTTTA
1 ATATTATTA--TATATATTTCTA
*
20605083 TACTATTA-TATGTATATTTCTA
1 -A-TATTATTATATATATTTCTA
*
20605105 ATATTA-TATTGTATATTTCTA
1 ATATTATTA-TATATATTTCTA
* *
20605126 ATACTATTATTTATAT
1 ATATTATTATATATAT
20605142 ATATGTGTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
20 16 0.23
21 24 0.34
22 21 0.30
23 2 0.03
24 3 0.04
25 5 0.07
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (21 bp):
ATATTATTATATATATTTCTA
Found at i:20605074 original size:36 final size:34
Alignment explanation
Indices: 20605018--20605084 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
20605008 TGTAAATAAA
*
20605018 ATTTTAATATTATGTTTTATATATATTATTATATAT
1 ATTTTAATATTATGTGTTATATAT-TT-TTATATAT
20605054 ATTTTAATATTAT-TAGTTATATATTTTTATA
1 ATTTTAATATTATGT-GTTATATATTTTTATA
20605085 CTATTATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
35 3 0.10
36 21 0.72
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (34 bp):
ATTTTAATATTATGTGTTATATATTTTTATATAT
Found at i:20605092 original size:42 final size:42
Alignment explanation
Indices: 20605039--20605141 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
20605029 ATGTTTTATA
*
20605039 TATATTATTATATATATTT-TAATATTATTAGTTATATATTT-T
1 TATACTATTATATATATTTCTAATATTA-TA-TTATATATTTCT
*
20605081 TATACTATTATATGTATATTTCTAATATTATATTGTATATTTCT
1 TATACTATTATA--TATATTTCTAATATTATATTATATATTTCT
* *
20605125 AATACTATTATTTATAT
1 TATACTATTATATATAT
20605142 ATATGTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 16 0.30
43 9 0.17
44 20 0.38
45 8 0.15
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (42 bp):
TATACTATTATATATATTTCTAATATTATATTATATATTTCT
Found at i:20605119 original size:21 final size:22
Alignment explanation
Indices: 20605040--20605141 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
20605030 TGTTTTATAT
*
20605040 ATATTATTA-TATATATTT-TA
1 ATATTATTATTGTATATTTCTA
* *
20605060 ATATTATTAGTTATATATTT-TT
1 ATATTATTA-TTGTATATTTCTA
*
20605082 ATACTATTATATGTATATTTCTA
1 ATATTATTAT-TGTATATTTCTA
20605105 ATATTA-TATTGTATATTTCTA
1 ATATTATTATTGTATATTTCTA
*
20605126 ATACTATTATT-TATAT
1 ATATTATTATTGTATAT
20605142 ATATGTGTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.13
21 23 0.32
22 33 0.46
23 6 0.08
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (22 bp):
ATATTATTATTGTATATTTCTA
Found at i:20607441 original size:16 final size:16
Alignment explanation
Indices: 20607375--20607446 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
20607365 AAAACATTTA
20607375 TTTATTTTTATATATT
1 TTTATTTTTATATATT
* *
20607391 TTTAAATTGTATATATT
1 TTT-ATTTTTATATATT
* * *
20607408 ATTTATTGCTAACAATATT
1 -TTTATT-TTTA-TATATT
20607427 TTTATTTTTATATATT
1 TTTATTTTTATATATT
20607443 TTTA
1 TTTA
20607447 AAAATATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 12 0.29
17 15 0.36
18 10 0.24
19 5 0.12
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTATTTTTATATATT
Found at i:20607452 original size:28 final size:28
Alignment explanation
Indices: 20607375--20607455 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
20607365 AAAACATTTA
*
20607375 TTTATTTTTATATATTTTT--AAAT-TG
1 TTTATTTTTATATATTTTTAAAAATATT
* * * ** *
20607400 TATA-TATTATTTATTGCTAACAATATT
1 TTTATTTTTATATATTTTTAAAAATATT
20607427 TTTATTTTTATATATTTTTAAAAATATT
1 TTTATTTTTATATATTTTTAAAAATATT
20607455 T
1 T
20607456 ATATATTTCT
Statistics
Matches: 39, Mismatches: 13, Indels: 5
0.68 0.23 0.09
Matches are distributed among these distances:
24 10 0.26
25 3 0.08
26 3 0.08
27 4 0.10
28 19 0.49
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTATTTTTATATATTTTTAAAAATATT
Found at i:20610691 original size:16 final size:16
Alignment explanation
Indices: 20610665--20610705 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
20610655 ATATTTTAAA
* *
20610665 TTAATTTTTAATTTTT
1 TTAACTTTTAATTATT
*
20610681 TTTACTTTTAATTATT
1 TTAACTTTTAATTATT
20610697 TTAACTTTT
1 TTAACTTTT
20610706 CTATAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAACTTTTAATTATT
Found at i:20617180 original size:3 final size:3
Alignment explanation
Indices: 20617172--20617201 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20617162 TTTACAAAGC
20617172 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20617202 GATATAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20624599 original size:2 final size:2
Alignment explanation
Indices: 20624582--20624619 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
20624572 AAGCAACTAC
*
20624582 AT AT AT -T AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20624620 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20629985 original size:28 final size:28
Alignment explanation
Indices: 20629898--20629992 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
20629888 AAAAATTAGT
* *
20629898 GTGCTTATCGT-ATTATTTCGCACTTCG
1 GTGCTTATCGTAATTATTTTGCATTTCG
* *
20629925 GTGCTTATCATTGTAA--AATTTGTACTTT-G
1 GTGCTTATC---GTAATTATTTTGCA-TTTCG
20629954 GTGCTTATCGTAATTATTTTGCATTTCG
1 GTGCTTATCGTAATTATTTTGCATTTCG
20629982 GTGCTTATCGT
1 GTGCTTATCGT
20629993 TATTTGCACT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.07
27 12 0.22
28 18 0.33
29 15 0.28
30 4 0.07
31 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (28 bp):
GTGCTTATCGTAATTATTTTGCATTTCG
Found at i:20630192 original size:30 final size:29
Alignment explanation
Indices: 20630152--20630219 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
20630142 CTTTTTTACT
* **
20630152 AAAATAACCCATCAAATTTAATTAAGTACC
1 AAAATGACCCA-CAAATTTAATTAAACACC
***
20630182 AAAATGACCCACCTTTTTAATTAAACACC
1 AAAATGACCCACAAATTTAATTAAACACC
20630211 AAAATGACC
1 AAAATGACC
20630220 TAAAATCTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (29 bp):
AAAATGACCCACAAATTTAATTAAACACC
Found at i:20630489 original size:24 final size:23
Alignment explanation
Indices: 20630449--20630494 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20630439 TCCATGTCAG
*
20630449 TTTCTTTTTTATTTTTTACTTTTC
1 TTTCTTTTTTATATTTTA-TTTTC
20630473 TTTCTTTATTT-TATTTTATTTT
1 TTTCTTT-TTTATATTTTATTTT
20630495 ATTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTTATATTTTATTTTC
Found at i:20630612 original size:22 final size:22
Alignment explanation
Indices: 20630587--20630666 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 22
20630577 ATATTCTGAA
20630587 ATTACTTTTTAAAATTTTAAAT
1 ATTACTTTTTAAAATTTTAAAT
*
20630609 ATTATTTTTTAAATTATTTTATTTTGAA-
1 ATTACTTTTTAAA--ATTTTA-----AAT
*
20630637 ATTACTTTTTTAAATTTTAAAT
1 ATTACTTTTTAAAATTTTAAAT
20630659 ATTA-TTTT
1 ATTACTTTT
20630667 GAAATTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
21 6 0.13
22 16 0.34
24 6 0.13
26 6 0.13
28 11 0.23
29 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (22 bp):
ATTACTTTTTAAAATTTTAAAT
Found at i:20630623 original size:34 final size:33
Alignment explanation
Indices: 20630558--20630628 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
20630548 TAATCTATAT
20630558 TTTTTAAAATTTTAAATATATATTCTGAAATTA
1 TTTTTAAAATTTTAAATATATATTCTGAAATTA
* *
20630591 CTTTTTAAAATTTTAAATAT-TATTTTTTAAATTA
1 -TTTTTAAAATTTTAAATATATA-TTCTGAAATTA
20630625 TTTT
1 TTTT
20630629 ATTTTGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (33 bp):
TTTTTAAAATTTTAAATATATATTCTGAAATTA
Found at i:20630642 original size:50 final size:49
Alignment explanation
Indices: 20630578--20630683 Score: 176
Period size: 50 Copynumber: 2.1 Consensus size: 49
20630568 TTTAAATATA
* *
20630578 TATTCTGAAATTACTTTTTAAAATTTTAAATATTATTTTTTAAATTATTT
1 TATTTTGAAATTACTTTTTAAAATTTTAAATATTA-TTTTGAAATTATTT
*
20630628 TATTTTGAAATTACTTTTTTAAATTTTAAATATTATTTTGAAATTATTT
1 TATTTTGAAATTACTTTTTAAAATTTTAAATATTATTTTGAAATTATTT
20630677 TATTTTG
1 TATTTTG
20630684 TTTATTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 20 0.38
50 33 0.62
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (49 bp):
TATTTTGAAATTACTTTTTAAAATTTTAAATATTATTTTGAAATTATTT
Found at i:20630710 original size:22 final size:21
Alignment explanation
Indices: 20630675--20630716 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20630665 TTGAAATTAT
*
20630675 TTTATTTTGTTTATTTATTTA
1 TTTATTTTGTTTATTAATTTA
*
20630696 TTTATTTTTTGTTATTAATTT
1 TTTATTTTGT-TTATTAATTT
20630717 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTATTTTGTTTATTAATTTA
Found at i:20630739 original size:23 final size:23
Alignment explanation
Indices: 20630713--20630788 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
20630703 TTTGTTATTA
*
20630713 ATTTTAAAAAATTTAAAATGTAT
1 ATTTTAAAAAATTTAAAATATAT
* *** *
20630736 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAAAAATTTAAAATATAT
*
20630759 TTTTTAAAAAAATTT-AAATAT-T
1 ATTTT-AAAAAATTTAAAATATAT
20630781 ATTTTAAA
1 ATTTTAAA
20630789 TTATTTTTTA
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.08
22 5 0.13
23 25 0.64
24 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTTAAAAAATTTAAAATATAT
Found at i:20630802 original size:12 final size:13
Alignment explanation
Indices: 20630771--20630802 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20630761 TTTAAAAAAA
20630771 TTTAAA-TATTAT
1 TTTAAATTATTAT
20630783 TTTAAATTATT-T
1 TTTAAATTATTAT
20630795 TTTAAATT
1 TTTAAATT
20630803 TTGAATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAAATTATTAT
Found at i:20630830 original size:21 final size:21
Alignment explanation
Indices: 20630792--20630831 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20630782 TTTTAAATTA
** *
20630792 TTTTTTAAATTTTGAATATTG
1 TTTTTTAAACATTAAATATTG
20630813 TTTTTTAAACATTAAATAT
1 TTTTTTAAACATTAAATAT
20630832 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTTAAACATTAAATATTG
Found at i:20631061 original size:18 final size:18
Alignment explanation
Indices: 20631038--20631080 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20631028 TTGAATTAAC
20631038 AAAAAAAAAATATTTGTT
1 AAAAAAAAAATATTTGTT
* **
20631056 AAAAAAGATTTATTTGTT
1 AAAAAAAAAATATTTGTT
20631074 AAAAAAA
1 AAAAAAA
20631081 TATGATGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAAAAAAAATATTTGTT
Found at i:20631118 original size:7 final size:7
Alignment explanation
Indices: 20631106--20631163 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
20631096 TATAATATGT
20631106 ATTTTTA
1 ATTTTTA
20631113 ATTTTTA
1 ATTTTTA
20631120 ATTTTTA
1 ATTTTTA
*
20631127 A-TTTAA
1 ATTTTTA
20631133 ATTTTTA
1 ATTTTTA
*
20631140 TTTTTTA
1 ATTTTTA
*
20631147 ATATTT-
1 ATTTTTA
20631153 ATATTTTA
1 AT-TTTTA
20631161 ATT
1 ATT
20631164 AAATTCATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 7 0.17
7 33 0.79
8 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTTTA
Found at i:20631243 original size:25 final size:25
Alignment explanation
Indices: 20631191--20631255 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 25
20631181 ATAAATCTTT
*
20631191 TTTTATTAATATATA---TTTGAAA
1 TTTTATTAATATATATTTTTTAAAA
20631213 TATTTATTAATATATATTTTTTAAAA
1 T-TTTATTAATATATATTTTTTAAAA
20631239 TTTTA--AATATATATTTT
1 TTTTATTAATATATATTTT
20631256 GAAATTACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 1 0.03
23 26 0.68
25 4 0.11
26 7 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTATTAATATATATTTTTTAAAA
Found at i:20631250 original size:21 final size:22
Alignment explanation
Indices: 20631199--20631261 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
20631189 TTTTTTATTA
*
20631199 ATATATATTTGAAATATTTATTAAT
1 ATATATATTTTAAA-A-TT-TTAAT
*
20631224 ATATATTTTTTAAAATTTTAA-
1 ATATATATTTTAAAATTTTAAT
*
20631245 ATATATATTTTGAAATT
1 ATATATATTTTAAAATT
20631262 ACTTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 15 0.44
22 4 0.12
23 2 0.06
24 1 0.03
25 12 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
ATATATATTTTAAAATTTTAAT
Found at i:20631274 original size:34 final size:34
Alignment explanation
Indices: 20631229--20631293 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
20631219 TTAATATATA
20631229 TTTTTTAAAATTTTAAATATATATTTTGAAATTAC
1 TTTTTTAAAATTTTAAATAT-TATTTTGAAATTAC
*
20631264 TTTTTT-AAATTTTAAATATTATTTTTAAAT
1 TTTTTTAAAATTTTAAATATTATTTTGAAAT
20631294 ATTAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 10 0.34
34 13 0.45
35 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (34 bp):
TTTTTTAAAATTTTAAATATTATTTTGAAATTAC
Found at i:20631289 original size:13 final size:13
Alignment explanation
Indices: 20631273--20631297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20631263 CTTTTTTAAA
20631273 TTTTAAATATTAT
1 TTTTAAATATTAT
20631286 TTTTAAATATTA
1 TTTTAAATATTA
20631298 AATATTTTTT
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:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:20631315 original size:18 final size:20
Alignment explanation
Indices: 20631265--20631309 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20631255 TGAAATTACT
*
20631265 TTTTTAAATTTTAAATATTA
1 TTTTTAAATATTAAATATTA
20631285 TTTTTAAATATTAAATATT-
1 TTTTTAAATATTAAATATTA
20631304 TTTTTA
1 TTTTTA
20631310 GTATTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAATATTAAATATTA
Found at i:20631333 original size:46 final size:46
Alignment explanation
Indices: 20631283--20631383 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 46
20631273 TTTTAAATAT
*
20631283 TATTTTTAAA-TATT-AAATATT-TTTTTAGTATTATAAAACATTTAAA
1 TATTTTTAAACT-TTCAAAT-TTGTTATTAGTATTATAAAA-ATTTAAA
* *
20631329 TA-TTTTAAACTTTCAAATTTGTTATTAGTTTTATAATAATTTAAA
1 TATTTTTAAACTTTCAAATTTGTTATTAGTATTATAAAAATTTAAA
20631374 TATTATTTAA
1 TATT-TTTAA
20631384 TTTGTTTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
45 20 0.43
46 22 0.47
47 5 0.11
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (46 bp):
TATTTTTAAACTTTCAAATTTGTTATTAGTATTATAAAAATTTAAA
Found at i:20631602 original size:22 final size:23
Alignment explanation
Indices: 20631560--20631604 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
20631550 AAATGAATTT
* *
20631560 AATTAAATATATATATTAAAAAA
1 AATTAAATATAAAAATTAAAAAA
20631583 AATTAAAT-TAAAAATTAAAAAA
1 AATTAAATATAAAAATTAAAAAA
20631605 TATATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AATTAAATATAAAAATTAAAAAA
Found at i:20631666 original size:15 final size:15
Alignment explanation
Indices: 20631626--20631668 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 15
20631616 TGGTCACATC
20631626 ATATTTTTTTAACAA
1 ATATTTTTTTAACAA
20631641 ATAAATCTTTTTTTAACAA
1 AT--A--TTTTTTTAACAA
20631660 ATATTTTTT
1 ATATTTTTT
20631669 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 8 0.33
17 2 0.08
19 14 0.58
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTTTTAACAA
Found at i:20631906 original size:20 final size:20
Alignment explanation
Indices: 20631875--20631934 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
20631865 TTTTATATTA
**
20631875 TTAAAAATATATATTTAATGT
1 TTAAAAA-ATATATTTAAAAT
*
20631896 TTAAAAAATATATTAAAAAT
1 TTAAAAAATATATTTAAAAT
*
20631916 TTTAAAAATA-ATTTAAAAT
1 TTAAAAAATATATTTAAAAT
20631935 AATATTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 8 0.24
20 19 0.56
21 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAAAAATATATTTAAAAT
Found at i:20631946 original size:12 final size:11
Alignment explanation
Indices: 20631895--20631945 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
20631885 ATATTTAATG
20631895 TTTAAAAAATA
1 TTTAAAAAATA
20631906 TATT-AAAAAT-
1 T-TTAAAAAATA
20631916 TTT-AAAAATAA
1 TTTAAAAAAT-A
20631927 TTTAAAATAATA
1 TTTAAAA-AATA
20631939 TTTAAAA
1 TTTAAAA
20631946 TTTAAATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.23
10 1 0.03
11 10 0.29
12 13 0.37
13 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:20632000 original size:79 final size:76
Alignment explanation
Indices: 20631915--20632152 Score: 197
Period size: 79 Copynumber: 3.1 Consensus size: 76
20631905 ATATTAAAAA
20631915 TTTTAAAAATAATTTAAAATAATATTTAAAATTTAAATACATATATATTATAAAAAATTTCAAAT
1 TTTTAAAAATAATTTAAAATAATATTTAAAATTTAAATA-ATATATATTATAAAAAATTTCAAAT
20631980 ATACATTTTAATTT
65 ATA-ATTTTAA-TT
* * * ** * *
20631994 TTTTAAAATTAA-TAACAAAAAATAAAT-AAA--TAAATAA-ACA-A-AATAAAATAATTTCAAA
1 TTTTAAAAATAATTTA-AAATAATATTTAAAATTTAAATAATATATATTATAAAA-AATTTCAAA
**
20632052 -ATAATATTTAAAA
64 TATAAT-TTTAATT
* *
20632065 TTTAAAAAAGTAATTTCAAAATATATATTTAAAATTTAAA-AATATATATTAATAAAATATTTCA
1 TTTTAAAAA-TAATTT-AAAATA-ATATTTAAAATTTAAATAATATATATT-ATAAAAAATTTCA
*
20632129 AATATATATTTCAAATT
62 AATATA-ATTT-TAATT
20632146 TTTTAAA
1 TTTTAAA
20632153 GTTAATAATA
Statistics
Matches: 120, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
71 9 0.08
72 17 0.14
73 15 0.12
74 7 0.06
75 4 0.03
76 8 0.07
77 6 0.05
78 6 0.05
79 27 0.22
80 11 0.09
81 10 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (76 bp):
TTTTAAAAATAATTTAAAATAATATTTAAAATTTAAATAATATATATTATAAAAAATTTCAAATA
TAATTTTAATT
Found at i:20632029 original size:22 final size:21
Alignment explanation
Indices: 20631999--20632040 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20631989 AATTTTTTTA
*
20631999 AAATTAATAACAAAAAATAAAT
1 AAATAAATAA-AAAAAATAAAT
*
20632021 AAATAAATAAACAAAATAAA
1 AAATAAATAAAAAAAATAAA
20632041 ATAATTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (21 bp):
AAATAAATAAAAAAAATAAAT
Found at i:20632079 original size:33 final size:33
Alignment explanation
Indices: 20632038--20632106 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
20632028 TAAACAAAAT
20632038 AAAATAATTTCAAAATA-ATATTTAAAATTTAA
1 AAAATAATTTCAAAATATATATTTAAAATTTAA
20632070 AAAAGTAATTTCAAAATATATATTTAAAATTTAA
1 AAAA-TAATTTCAAAATATATATTTAAAATTTAA
20632104 AAA
1 AAA
20632107 TATATATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 4 0.11
33 13 0.37
34 18 0.51
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (33 bp):
AAAATAATTTCAAAATATATATTTAAAATTTAA
Found at i:20632100 original size:21 final size:21
Alignment explanation
Indices: 20632076--20632146 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 21
20632066 TTAAAAAAGT
20632076 AATTTCAAAATATATATTTAA
1 AATTTCAAAATATATATTTAA
*
20632097 AATTTAAAAATATATATTAATAAA
1 AATTTCAAAATATATATT--T-AA
*
20632121 ATATTTC-AAATATATATTTCA
1 A-ATTTCAAAATATATATTTAA
20632142 AATTT
1 AATTT
20632147 TTTAAAGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 4 0.09
21 19 0.44
22 1 0.02
23 1 0.02
24 14 0.33
25 4 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTCAAAATATATATTTAA
Found at i:20632132 original size:152 final size:151
Alignment explanation
Indices: 20631900--20632181 Score: 419
Period size: 152 Copynumber: 1.9 Consensus size: 151
20631890 TAATGTTTAA
*
20631900 AAAATATATTAAAAATTTTAAAAATAATTTAAAATAATATTTAAAATTTAAATACATATATATTA
1 AAAATATATTAAAAATTTAAAAAATAATTTAAAATAATATTTAAAATTTAAATACATATATATTA
* * *
20631965 TAAAAAATTTCAAATATACATTTTAATTTTTTTAAAATTAATAA-CAA-AAAATAAATAAATAAA
66 TAAAAAATTTCAAATATACATTTCAAATTTTTTAAAATTAATAATAAATAAAATAAATAAATAAA
20632028 TAAACAAAATAAAATAATTTC
131 TAAACAAAATAAAATAATTTC
*
20632049 AAAATAATATTTAAAATTTAAAAAAGTAATTTCAAAATATATATTTAAAATTTAAA-A-ATATAT
1 AAAAT-ATATTAAAAATTTAAAAAA-TAATTT-AAAATA-ATATTTAAAATTTAAATACATATAT
* * *
20632112 ATTAATAAAATATTTCAAATATATATTTCAAATTTTTTAAAGTTAATAATAAATAAAATAAATAA
62 ATT-ATAAAAAATTTCAAATATACATTTCAAATTTTTTAAAATTAATAATAAATAAAATAAATAA
20632177 ATAAA
126 ATAAA
20632182 GAAGAGTAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
149 5 0.04
150 17 0.14
151 15 0.13
152 47 0.40
153 18 0.15
154 16 0.14
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (151 bp):
AAAATATATTAAAAATTTAAAAAATAATTTAAAATAATATTTAAAATTTAAATACATATATATTA
TAAAAAATTTCAAATATACATTTCAAATTTTTTAAAATTAATAATAAATAAAATAAATAAATAAA
TAAACAAAATAAAATAATTTC
Found at i:20646809 original size:19 final size:18
Alignment explanation
Indices: 20646787--20646822 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20646777 ATGTAAAAAT
20646787 TATGTATTTAAAACATAAA
1 TATGTATTTAAAA-ATAAA
*
20646806 TATGTGTTTAAAAATAA
1 TATGTATTTAAAAATAA
20646823 CGTACAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (18 bp):
TATGTATTTAAAAATAAA
Found at i:20649756 original size:52 final size:52
Alignment explanation
Indices: 20649679--20649784 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
20649669 GTGATATAAA
20649679 TTAAGTTAAGACTCAATTTATCAAATTTATTAAATATATCTAAAGAAAAAGG
1 TTAAGTTAAGACTCAATTTATCAAATTTATTAAATATATCTAAAGAAAAAGG
* * *
20649731 TTAAGTTAAGACTCAATTTATCAAATTTATTGAATATATCTAGAGGAAAAGG
1 TTAAGTTAAGACTCAATTTATCAAATTTATTAAATATATCTAAAGAAAAAGG
20649783 TT
1 TT
20649785 TTTTTCTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (52 bp):
TTAAGTTAAGACTCAATTTATCAAATTTATTAAATATATCTAAAGAAAAAGG
Found at i:20661828 original size:28 final size:28
Alignment explanation
Indices: 20661796--20661858 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
20661786 TCCCATATTA
20661796 ATGGGGTATAGGAAAAGCTTCATAACTT
1 ATGGGGTATAGGAAAAGCTTCATAACTT
* * *
20661824 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGCTTCATAACTT
20661852 ATGGGGT
1 ATGGGGT
20661859 TGATAATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGCTTCATAACTT
Found at i:20669906 original size:28 final size:28
Alignment explanation
Indices: 20669874--20669933 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
20669864 CATATTAATA
20669874 GGGTATAGGAAAAGTCTCATAACTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
* *
20669902 GGGTATAGGAAGAGTTTCATAACTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
20669930 GGGT
1 GGGT
20669934 TGATAATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGTATAGGAAAAGTCTCATAACTTATG
Found at i:20673002 original size:31 final size:31
Alignment explanation
Indices: 20672968--20673039 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
20672958 TTATTCTAAA
*
20672968 TTTTTAAAATTTTTTT-AACTTTCTTTATATAT
1 TTTTTAAAATTTTTTTGAA-ATT-TTTATATAT
* *
20673000 TTTTTAGATTTTTTTTGAAATTTTTATATAT
1 TTTTTAAAATTTTTTTGAAATTTTTATATAT
20673031 TTTTTAAAA
1 TTTTTAAAA
20673040 ATATAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 16 0.47
32 16 0.47
33 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTTTAAAATTTTTTTGAAATTTTTATATAT
Found at i:20676266 original size:17 final size:18
Alignment explanation
Indices: 20676241--20676286 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
20676231 AATAAACTAA
20676241 AAAAT-ACAATATTA-TT
1 AAAATAACAATATTATTT
*
20676257 AAATTAACAAT-TTATTT
1 AAAATAACAATATTATTT
*
20676274 AAAATAAAAATAT
1 AAAATAACAATAT
20676287 CTTTAAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.29
17 16 0.67
18 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAACAATATTATTT
Found at i:20687344 original size:19 final size:20
Alignment explanation
Indices: 20687317--20687358 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
20687307 TTTTTTTGCA
* *
20687317 TTCATTCATTTGTATTACAT
1 TTCATTCATGTGTATTAAAT
20687337 TTCA-TCATGTGTATTAAAT
1 TTCATTCATGTGTATTAAAT
20687356 TTC
1 TTC
20687359 GCGAAAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTCATTCATGTGTATTAAAT
Found at i:20689668 original size:9 final size:9
Alignment explanation
Indices: 20689656--20689684 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20689646 GAGGCTAAAG
20689656 AATTCTTAA
1 AATTCTTAA
20689665 AATTCTTAA
1 AATTCTTAA
20689674 AATTCTTAA
1 AATTCTTAA
20689683 AA
1 AA
20689685 CACAGCGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTCTTAA
Found at i:20699156 original size:5 final size:5
Alignment explanation
Indices: 20699146--20699187 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
20699136 AATAATTAAG
20699146 TATAT TATAT TATAT TATAT TA-AT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
20699188 TATATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:20699171 original size:19 final size:18
Alignment explanation
Indices: 20699148--20699192 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 18
20699138 TAATTAAGTA
20699148 TATTATATTATATTATAT
1 TATTATATTATATTATAT
20699166 TAATTATATTATATTATAT
1 T-ATTATATTATATTATAT
20699185 TATTATAT
1 TATTATAT
20699193 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATTATATTATAT
Found at i:20699173 original size:24 final size:24
Alignment explanation
Indices: 20699125--20699187 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
20699115 TAAAAAAATA
*
20699125 TATATT-TATT-TAATA-ATTAAG
1 TATATTATATTATATTATATTAAG
*
20699146 TATATTATATTATATTATATTAAT
1 TATATTATATTATATTATATTAAG
20699170 TATATTATATTATATTAT
1 TATATTATATTATATTAT
20699188 TATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 6 0.16
22 4 0.11
23 4 0.11
24 23 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTATATTATATTATATTAAG
Found at i:20700765 original size:21 final size:23
Alignment explanation
Indices: 20700721--20700765 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20700711 CAATATTCCG
*
20700721 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATAATCT
20700744 GGTGTGTTTGGG-TGGA-AATCT
1 GGTGTGTTTGGGTTGGATAATCT
20700765 G
1 G
20700766 CGTATCTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 4 0.19
23 12 0.57
ACGTcount: A:0.11, C:0.04, G:0.42, T:0.42
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATAATCT
Found at i:20702956 original size:25 final size:24
Alignment explanation
Indices: 20702901--20702956 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
20702891 ATTTAGAATG
20702901 ATCTTTACAAATTTAAATCAAAAT
1 ATCTTTACAAATTTAAATCAAAAT
**
20702925 AAATTTA-AAATTGTATAATCAAAAT
1 ATCTTTACAAATT-TA-AATCAAAAT
20702950 ATCTTTA
1 ATCTTTA
20702957 GTTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 7 0.27
25 14 0.54
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (24 bp):
ATCTTTACAAATTTAAATCAAAAT
Found at i:20714391 original size:13 final size:14
Alignment explanation
Indices: 20714375--20714416 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
20714365 TTTCAATTTT
20714375 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
20714388 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
20714403 ATTTTAAATAATAT
1 ATTTT-AATAATAT
20714417 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:20714401 original size:16 final size:16
Alignment explanation
Indices: 20714379--20714415 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20714369 AATTTTATTT
20714379 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
20714396 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
20714411 TAATA
1 TAATA
20714416 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:20715801 original size:46 final size:46
Alignment explanation
Indices: 20715736--20716059 Score: 445
Period size: 46 Copynumber: 7.0 Consensus size: 46
20715726 TTATCTTTGA
* * * * * *
20715736 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* *** *
20715782 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAA
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
20715828 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
20715874 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
20715920 CAGGCTGCCATGGTATCTTTCAACCATGGTCTTGCACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
20715966 C-TGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CAT-GCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
20716012 CAAGCTGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
20716058 CA
1 CA
20716060 GAGAGCACAC
Statistics
Matches: 252, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
45 4 0.02
46 248 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:20721463 original size:22 final size:22
Alignment explanation
Indices: 20721438--20721486 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20721428 TAATATAATT
20721438 ATATATGAAATATAAT-TTTTAA
1 ATATATGAAA-ATAATATTTTAA
**
20721460 ATATATTTAAATAATATTTTAA
1 ATATATGAAAATAATATTTTAA
20721482 A-ATAT
1 ATATAT
20721487 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATATGAAAATAATATTTTAA
Found at i:20721477 original size:59 final size:58
Alignment explanation
Indices: 20721409--20721534 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 58
20721399 TAATTAAGAT
* * *
20721409 ATATGATATTTT-AATATTTTAATATAATT-ATATATGAA-ATATAATTTTTAAATATATTTA
1 ATATAATATTTTAAATATTTTAA-A-AATTAATA-AT-AATAAATAATATTTAAATA-ATTTA
20721469 A-ATAATATTTTAAAATATTTTAAAAATTAATAATAATAAATAATATTTAAATAATTTA
1 ATATAATATTTT-AAATATTTTAAAAATTAATAATAATAAATAATATTTAAATAATTTA
20721527 ATATAATA
1 ATATAATA
20721535 ATATATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
58 8 0.14
59 35 0.60
60 5 0.09
61 10 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (58 bp):
ATATAATATTTTAAATATTTTAAAAATTAATAATAATAAATAATATTTAAATAATTTA
Found at i:20721486 original size:21 final size:21
Alignment explanation
Indices: 20721449--20721533 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
20721439 TATATGAAAT
20721449 ATAATTTTTAAATATATTTAA
1 ATAATTTTTAAATATATTTAA
20721470 ATAATATTTTAAA-ATATTTTAA
1 ATAAT-TTTTAAATATA-TTTAA
**
20721492 A-AATTAAT-AATA-A--TAA
1 ATAATTTTTAAATATATTTAA
*
20721508 ATAATATTTAAATA-ATTTAA
1 ATAATTTTTAAATATATTTAA
20721528 TATAAT
1 -ATAAT
20721534 AATATATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
16 4 0.08
17 4 0.08
18 5 0.10
19 3 0.06
20 6 0.12
21 16 0.31
22 13 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATTTTTAAATATATTTAA
Found at i:20721513 original size:28 final size:28
Alignment explanation
Indices: 20721482--20721578 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
20721472 AATATTTTAA
20721482 AATATTTTAAA-AA-TTAATAATAATAAAT
1 AATA-TTTAAATAATTTAAT-ATAATAAAT
20721510 AATATTTAAATAATTTAATATAAT-AAT
1 AATATTTAAATAATTTAATATAATAAAT
* * * *
20721537 -ATA-TAAAATAA-CTCATATAAATAAAA
1 AATATTTAAATAATTTAATAT-AATAAAT
*
20721563 AATATTTTAATAATTT
1 AATATTTAAATAATTT
20721579 TTAAATACCT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
24 5 0.09
25 10 0.18
26 5 0.09
27 12 0.22
28 17 0.31
29 6 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATTTAAATAATTTAATATAATAAAT
Found at i:20723449 original size:4 final size:4
Alignment explanation
Indices: 20723440--20723466 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20723430 ATAATTACCA
20723440 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
20723467 CAACATCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:20734280 original size:37 final size:38
Alignment explanation
Indices: 20734225--20734299 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
20734215 TCTGATGAAA
20734225 TTGTTTTTCTAAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCTAAGTTTAAAATATGTATTAAATGAATGG
20734263 TTGTTTTTC-AAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCTAAGTTTAAAATATGTATTAAATGAATGG
20734300 CTCAAATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 28 0.76
38 9 0.24
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.47
Consensus pattern (38 bp):
TTGTTTTTCTAAGTTTAAAATATGTATTAAATGAATGG
Found at i:20734829 original size:19 final size:19
Alignment explanation
Indices: 20734805--20734842 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20734795 GTCTTATGAC
20734805 TTTTTAACTTTGAAGCAAA
1 TTTTTAACTTTGAAGCAAA
20734824 TTTTTAACTTTGAAGCAAA
1 TTTTTAACTTTGAAGCAAA
20734843 AATAAGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTTTAACTTTGAAGCAAA
Found at i:20735478 original size:130 final size:131
Alignment explanation
Indices: 20735244--20735527 Score: 489
Period size: 130 Copynumber: 2.2 Consensus size: 131
20735234 TTACTAATAT
* *
20735244 TTATTTAAGGGTTAATATGTAGATTATTTCTTGAACTTATCCAAAGGTATTTAGTTAGTATTTGA
1 TTATTTAAGGGTTAATATGTAGTTTATTTCTTGAACTTATCCAAAGGTATTTAATTAGTATTTGA
*
20735309 TTTTTTTTTTGTATTACCTAAACTTGTATTCCACCACACACAGTCTCAATTTCTTAACAACATTA
66 TTTTTTTTTTGTATTACCTAAACTTGCATTCCACCACACACAGTCTCAATTTCTTAACAACATTA
20735374 A
131 A
*
20735375 TTATTTAATGGTTAATATGTAGTTTATTTCTTGAACTTATCCAAAGGTA-TTAATTAGTATTTGA
1 TTATTTAAGGGTTAATATGTAGTTTATTTCTTGAACTTATCCAAAGGTATTTAATTAGTATTTGA
* *
20735439 TTTTTTTTTTGTATTACCTAAACTTGCATTCCATCACACAGAGTCTCAATTTCTTAACAACATTA
66 TTTTTTTTTTGTATTACCTAAACTTGCATTCCACCACACACAGTCTCAATTTCTTAACAACATTA
20735504 A
131 A
* *
20735505 TTTTTTAAGGGTTAATTTGTAGT
1 TTATTTAAGGGTTAATATGTAGT
20735528 CTGCCACTTA
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
130 97 0.67
131 47 0.33
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (131 bp):
TTATTTAAGGGTTAATATGTAGTTTATTTCTTGAACTTATCCAAAGGTATTTAATTAGTATTTGA
TTTTTTTTTTGTATTACCTAAACTTGCATTCCACCACACACAGTCTCAATTTCTTAACAACATTA
A
Found at i:20737223 original size:18 final size:18
Alignment explanation
Indices: 20737202--20737238 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20737192 TGTTATATAC
20737202 GAGTACCAACTTATTTCG
1 GAGTACCAACTTATTTCG
*
20737220 GAGTACTAACTTATTTCG
1 GAGTACCAACTTATTTCG
20737238 G
1 G
20737239 CGTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
GAGTACCAACTTATTTCG
Done.