Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 120 of 132
Found at i:36681354 original size:2 final size:2
Alignment explanation
Indices: 36681349--36681389 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
36681339 TCTCTCTCTC
*
36681349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36681390 CAAGATTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36683773 original size:15 final size:15
Alignment explanation
Indices: 36683736--36683774 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
36683726 CTACAGCTTT
*
36683736 CTTCTCCTCCGCAGG
1 CTTCTTCTCCGCAGG
*
36683751 CTTCTTCTCCGCTGG
1 CTTCTTCTCCGCAGG
*
36683766 CTTTTTCTC
1 CTTCTTCTC
36683775 AGCTTTTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.41, G:0.15, T:0.41
Consensus pattern (15 bp):
CTTCTTCTCCGCAGG
Found at i:36688944 original size:20 final size:21
Alignment explanation
Indices: 36688921--36688959 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36688911 CTTATTCTCA
*
36688921 GTTTTTTT-ATAATTTTTATG
1 GTTTTTTTAATAAGTTTTATG
36688941 GTTTTTTTAATAAGTTTTA
1 GTTTTTTTAATAAGTTTTA
36688960 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
GTTTTTTTAATAAGTTTTATG
Found at i:36693722 original size:25 final size:24
Alignment explanation
Indices: 36693689--36693738 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
36693679 AAAGTGTGCA
*
36693689 TAATAAAATTATTAAAATAAATTTT
1 TAATAAAA-TAGTAAAATAAATTTT
* *
36693714 TAATTAAATAGTAAATTAAATTTT
1 TAATAAAATAGTAAAATAAATTTT
36693738 T
1 T
36693739 TTAATACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TAATAAAATAGTAAAATAAATTTT
Found at i:36694108 original size:43 final size:43
Alignment explanation
Indices: 36694060--36694147 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
36694050 TCCAAACTCA
*
36694060 TATTATAAATGAAACTATGGTCCAAGCAAAATTTTTGAAACAC
1 TATTATAAATGAAACTATGGTCCAAGCAAAATTTTTAAAACAC
* *
36694103 TATTATAAATGAAACTATGGTCCAAGCACAATTTTTAAAATAC
1 TATTATAAATGAAACTATGGTCCAAGCAAAATTTTTAAAACAC
36694146 TA
1 TA
36694148 ATTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (43 bp):
TATTATAAATGAAACTATGGTCCAAGCAAAATTTTTAAAACAC
Found at i:36697115 original size:29 final size:30
Alignment explanation
Indices: 36697071--36697134 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
36697061 AATGATCTAT
*
36697071 ATTTTTATAATTTTTAAAAAATTAAATTA-A
1 ATTTTTATAATTTTT-AAAAATTAAAATATA
* *
36697101 ATTTTTATTA-TTTTAAAGATTAAAATATA
1 ATTTTTATAATTTTTAAAAATTAAAATATA
36697130 ATTTT
1 ATTTT
36697135 ACCATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 10 0.33
30 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAATTAAAATATA
Found at i:36711361 original size:39 final size:40
Alignment explanation
Indices: 36711318--36711398 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
36711308 ATTACAAAAT
36711318 AATTCAAAATAATTTTTAAAAA-TTCAAAATAAT-TTTTAA
1 AATTCAAAAT-ATTTTTAAAAATTTCAAAATAATATTTTAA
* *
36711357 AATTCAAAATATTTTTAAAAATTTTAAAATTATATTTTAA
1 AATTCAAAATATTTTTAAAAATTTCAAAATAATATTTTAA
36711397 AA
1 AA
36711399 AATTATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 11 0.29
39 19 0.50
40 8 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (40 bp):
AATTCAAAATATTTTTAAAAATTTCAAAATAATATTTTAA
Found at i:36711377 original size:19 final size:20
Alignment explanation
Indices: 36711318--36711399 Score: 114
Period size: 20 Copynumber: 4.1 Consensus size: 20
36711308 ATTACAAAAT
36711318 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTTTAAA
36711338 AATTCAAAATAATTTTT-AA
1 AATTCAAAATAATTTTTAAA
36711357 AATTCAAAAT-ATTTTTAAA
1 AATTCAAAATAATTTTTAAA
* *
36711376 AATTTTAAAATTATATTTTAAA
1 AA-TTCAAAATAAT-TTTTAAA
36711398 AA
1 AA
36711400 ATTATAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
18 6 0.11
19 16 0.28
20 24 0.42
21 2 0.04
22 9 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTCAAAATAATTTTTAAA
Found at i:36711392 original size:23 final size:23
Alignment explanation
Indices: 36711365--36711408 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36711355 AAAATTCAAA
* *
36711365 ATATTTTTAAAAATTTTAAAATT
1 ATATTTTAAAAAATTATAAAATT
36711388 ATATTTTAAAAAATTATAAAA
1 ATATTTTAAAAAATTATAAAA
36711409 ATCCTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTTTAAAAAATTATAAAATT
Found at i:36711435 original size:19 final size:17
Alignment explanation
Indices: 36711393--36711436 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
36711383 AAATTATATT
36711393 TTAAAAAATTATAAAAA
1 TTAAAAAATTATAAAAA
36711410 TCCTAAAAAATATATAAAAAA
1 T--TAAAAAAT-TAT-AAAAA
36711431 TTAAAA
1 TTAAAA
36711437 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
19 13 0.57
20 3 0.13
21 6 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAAAATTATAAAAA
Found at i:36716466 original size:14 final size:14
Alignment explanation
Indices: 36716447--36716492 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
36716437 AAATTTGATA
36716447 TTTAATTTTTATAT
1 TTTAATTTTTATAT
* *
36716461 TTTAATTTAATATAA
1 TTTAATTT-TTATAT
*
36716476 TTTAGTTTTTATAT
1 TTTAATTTTTATAT
36716490 TTT
1 TTT
36716493 TATAATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:36717243 original size:36 final size:34
Alignment explanation
Indices: 36717203--36717299 Score: 106
Period size: 36 Copynumber: 2.8 Consensus size: 34
36717193 CCAAATAACC
36717203 AAAATAACAACCAAAACAGCAACAAAAATAATAGAA
1 AAAATAACAACCAAAACAGCAAC-AAAATAATA-AA
** * *
36717239 AAAATAACAATAAAAACAACAACAAAATAGTAAA
1 AAAATAACAACCAAAACAGCAACAAAATAATAAA
**
36717273 AAAAT-AGTACCAAAACAGCAACCAAAA
1 AAAATAACAACCAAAACAGCAA-CAAAA
36717300 CAGCACCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 11 0.22
34 12 0.24
35 8 0.16
36 20 0.39
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.09
Consensus pattern (34 bp):
AAAATAACAACCAAAACAGCAACAAAATAATAAA
Found at i:36717296 original size:12 final size:11
Alignment explanation
Indices: 36717281--36717312 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
36717271 AAAAAATAGT
36717281 ACCAAAACAGC
1 ACCAAAACAGC
36717292 AACCAAAACAGC
1 -ACCAAAACAGC
36717304 ACCAAAACA
1 ACCAAAACA
36717313 ATAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.59, C:0.34, G:0.06, T:0.00
Consensus pattern (11 bp):
ACCAAAACAGC
Found at i:36722682 original size:20 final size:20
Alignment explanation
Indices: 36722657--36722698 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
36722647 AAAATGACAC
*
36722657 ATAATTATTCATCTAATATT
1 ATAATTATTCAACTAATATT
* *
36722677 ATAATTGTTCAAGTAATATT
1 ATAATTATTCAACTAATATT
36722697 AT
1 AT
36722699 TTGAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAATTATTCAACTAATATT
Found at i:36727366 original size:36 final size:36
Alignment explanation
Indices: 36727316--36727388 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 36
36727306 CAGTGACTTA
36727316 GCTTCTCTATATCTATGGCCTTTACTGAA-GTCAAGG
1 GCTTCTCTATATCTATGGCCTTTACT-AATGTCAAGG
36727352 GCTTCTCT-TCATCTATGGCCTTTACTAATGTCAAGG
1 GCTTCTCTAT-ATCTATGGCCTTTACTAATGTCAAGG
36727388 G
1 G
36727389 ACACTTCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (36 bp):
GCTTCTCTATATCTATGGCCTTTACTAATGTCAAGG
Found at i:36740857 original size:28 final size:28
Alignment explanation
Indices: 36740825--36740879 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
36740815 TTATGTTATA
36740825 AAATGAT-ATTATATTAATTATATCTATT
1 AAATGATAATTATA-TAATTATATCTATT
*
36740853 AAATGATAATTATATATTTATATCTAT
1 AAATGATAATTATATAATTATATCTAT
36740880 ATTAAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
AAATGATAATTATATAATTATATCTATT
Found at i:36747787 original size:16 final size:16
Alignment explanation
Indices: 36747751--36747802 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
36747741 CTTAAGCCAA
* *
36747751 AAATAATTATAATAAG
1 AAATAAATATAATTAG
*
36747767 AAATATATATAATTAG
1 AAATAAATATAATTAG
* *
36747783 TAATAAATAAAATTATG
1 AAATAAATATAATTA-G
36747800 AAA
1 AAA
36747803 AGCTCACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAATAAATATAATTAG
Found at i:36770290 original size:22 final size:22
Alignment explanation
Indices: 36770235--36770291 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
36770225 TTTAAAATAC
36770235 TGGATTTTCCATGTTTGTTACCAA
1 TGGA-TTTCC-TGTTTGTTACCAA
*
36770259 TGGGATTTCCTGTTTGTTACAGAA
1 T-GGATTTCCTGTTTGTTAC-CAA
36770283 T-GATTTCCT
1 TGGATTTCCT
36770292 TTTTAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.27
23 10 0.33
24 9 0.30
25 3 0.10
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (22 bp):
TGGATTTCCTGTTTGTTACCAA
Found at i:36772630 original size:15 final size:15
Alignment explanation
Indices: 36772610--36772639 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36772600 AACTAATAGC
*
36772610 ATCATCTTTATCATG
1 ATCATCTTCATCATG
36772625 ATCATCTTCATCATG
1 ATCATCTTCATCATG
36772640 GAACATAGCA
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:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (15 bp):
ATCATCTTCATCATG
Found at i:36790655 original size:21 final size:21
Alignment explanation
Indices: 36790612--36790658 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
36790602 CCTATGACAG
* * *
36790612 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
36790633 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
36790654 TTCTA
1 TTCTA
36790659 TCGGTACCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:36791410 original size:36 final size:36
Alignment explanation
Indices: 36791360--36791460 Score: 175
Period size: 36 Copynumber: 2.8 Consensus size: 36
36791350 TTGATATCTG
**
36791360 ATTTACTCTATGTTGACCCAAAGGTCATGATGCTCA
1 ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
*
36791396 TTTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
1 ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
36791432 ATTTACTCCCTGTTGACCCAAAGGTCATG
1 ATTTACTCCCTGTTGACCCAAAGGTCATG
36791461 CCTATTACCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (36 bp):
ATTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
Found at i:36801768 original size:31 final size:31
Alignment explanation
Indices: 36801730--36801792 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
36801720 TCGTCCCCTA
36801730 ATTCATTTTATACAATTCTTAACAATTTTTC
1 ATTCATTTTATACAATTCTTAACAATTTTTC
36801761 ATTCATTTTATACAATTCTTAACAATTTTTC
1 ATTCATTTTATACAATTCTTAACAATTTTTC
36801792 A
1 A
36801793 AAGTCGTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTCATTTTATACAATTCTTAACAATTTTTC
Found at i:36805010 original size:23 final size:23
Alignment explanation
Indices: 36804984--36805082 Score: 112
Period size: 23 Copynumber: 4.2 Consensus size: 23
36804974 GAACACTAGC
36804984 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
* * *
36805007 GTGCTCTCAGTTTAGCAC-GTCT
1 GTGCTCTCTGATTAGCACTGTGT
36805029 CGTGCTCTCTGTTATTAGCACT-TCGT
1 -GTGCTCTCTG--ATTAGCACTGT-GT
*
36805055 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
36805078 GTGCT
1 GTGCT
36805083 TACTGTTTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.05
23 41 0.64
24 1 0.02
25 18 0.28
26 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:36805089 original size:48 final size:47
Alignment explanation
Indices: 36804983--36805072 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 47
36804973 GGAACACTAG
*
36804983 CGTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCAGTTTAGCACGTCT
1 CGTGCTCTCTGTTATTAGCACT-TGTGTGCTCTCAGATTAGCACGTCT
*
36805029 CGTGCTCTCTGTTATTAGCACTTCGTGTGCTCTCTGATTAGCAC
1 CGTGCTCTCTGTTATTAGCACTT-GTGTGCTCTCAGATTAGCAC
36805073 TTTGTGTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 11 0.28
47 1 0.03
48 27 0.69
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (47 bp):
CGTGCTCTCTGTTATTAGCACTTGTGTGCTCTCAGATTAGCACGTCT
Found at i:36805124 original size:46 final size:46
Alignment explanation
Indices: 36805069--36805184 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
36805059 TCTCTGATTA
* * *
36805069 GCACTTTGTGTGCTTACTGTTTCACACTTTGTGTGCTTATTGTTT-C
1 GCACCTTGTGTGCTTACTGTTT-ACACTATGTGTGCTTACTGTTTCC
* *
36805115 GCACCTTGTGTGCCTACTGATTTGCACTATGTGTGCTTACTGTTTCC
1 GCACCTTGTGTGCTTACTG-TTTACACTATGTGTGCTTACTGTTTCC
*
36805162 CCAGCACTTGTGTGCTTACTGTT
1 GCA-C-CTTGTGTGCTTACTGTT
36805185 AAGTACTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 36 0.61
47 6 0.10
48 3 0.05
49 14 0.24
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (46 bp):
GCACCTTGTGTGCTTACTGTTTACACTATGTGTGCTTACTGTTTCC
Found at i:36805126 original size:25 final size:23
Alignment explanation
Indices: 36805070--36805184 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 23
36805060 CTCTGATTAG
36805070 CACTTTGTGTGCTTACTGTTTCA
1 CACTTTGTGTGCTTACTGTTTCA
* *
36805093 CACTTTGTGTGCTTATTGTTTCG
1 CACTTTGTGTGCTTACTGTTTCA
* * *
36805116 CACCTTGTGTGCCTACTGATTT-G
1 CACTTTGTGTGCTTACTG-TTTCA
*
36805139 CACTATGTGTGCTTACTGTTTCCCCA
1 CACTTTGTGTGCTTACTGTTT---CA
36805165 GCAC-TTGTGTGCTTACTGTT
1 -CACTTTGTGTGCTTACTGTT
36805185 AAGTACTTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.04
23 52 0.68
24 3 0.04
26 15 0.20
27 3 0.04
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (23 bp):
CACTTTGTGTGCTTACTGTTTCA
Found at i:36812436 original size:23 final size:24
Alignment explanation
Indices: 36812410--36812625 Score: 147
Period size: 23 Copynumber: 9.4 Consensus size: 24
36812400 ACACTAGCGC
36812410 GCTCT-CTGATTAGCACTGTGTGT
1 GCTCTACTGATTAGCACTGTGTGT
* * *
36812433 GCTCT-TTGTTTAGCAC-GTCTCGT
1 GCTCTACTGATTAGCACTGTGT-GT
36812456 GCTCT-CTGTTATTAGCACT-TCGTGT
1 GCTCTACTG--ATTAGCACTGT-GTGT
*
36812481 GCTCT-CTGATTAGCACTTTGTGT
1 GCTCTACTGATTAGCACTGTGTGT
* * * *
36812504 GCT-TACTGTTTCGCACTTTGTGA
1 GCTCTACTGATTAGCACTGTGTGT
* *
36812527 GCT-TACTGTTTCGCACCT-TGTGT
1 GCTCTACTGATTAGCA-CTGTGTGT
* * * *
36812550 GC-CTACTGATTTGCGCTATGTGC
1 GCTCTACTGATTAGCACTGTGTGT
36812573 GC-CTACTGATT-GCACTGTGTGT
1 GCTCTACTGATTAGCACTGTGTGT
36812595 GC-CTACTGGATT-GCACTGTGTGT
1 GCTCTACT-GATTAGCACTGTGTGT
36812618 GCT-TACTG
1 GCTCTACTG
36812626 TTTCCCCAGC
Statistics
Matches: 164, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
22 22 0.13
23 120 0.73
24 3 0.02
25 18 0.11
26 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (24 bp):
GCTCTACTGATTAGCACTGTGTGT
Found at i:36814012 original size:6 final size:6
Alignment explanation
Indices: 36813996--36814037 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
36813986 GACGAGGAAT
*
36813996 TCGAGG CCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG
1 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG
36814038 CAGAGGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.50, T:0.14
Consensus pattern (6 bp):
TCGAGG
Found at i:36814013 original size:12 final size:12
Alignment explanation
Indices: 36813996--36814044 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
36813986 GACGAGGAAT
36813996 TCGAGGCCGAGG
1 TCGAGGCCGAGG
*
36814008 TCGAGGTCGAGG
1 TCGAGGCCGAGG
*
36814020 TCGAGGTCGAGG
1 TCGAGGCCGAGG
*
36814032 TCGAGGCAGAGG
1 TCGAGGCCGAGG
36814044 T
1 T
36814045 AGATTTCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.14
Consensus pattern (12 bp):
TCGAGGCCGAGG
Found at i:36814019 original size:18 final size:18
Alignment explanation
Indices: 36813996--36814044 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
36813986 GACGAGGAAT
36813996 TCGAGGCCGAGGTCGAGG
1 TCGAGGCCGAGGTCGAGG
*
36814014 TCGAGGTCGAGGTCGAGG
1 TCGAGGCCGAGGTCGAGG
*
36814032 TCGAGGCAGAGGT
1 TCGAGGCCGAGGT
36814045 AGATTTCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.14
Consensus pattern (18 bp):
TCGAGGCCGAGGTCGAGG
Found at i:36817667 original size:109 final size:108
Alignment explanation
Indices: 36817484--36817679 Score: 259
Period size: 109 Copynumber: 1.8 Consensus size: 108
36817474 TGTATGCTTG
* * * * * *
36817484 TGAAAATCACGTATTTAGAGTATAAGTATGAATTTAAAAAATAATATATAATAAATTATAAATTA
1 TGAAAATCACGTATTCAGAATATAAGTATGAATTTAAAAAATAACATACAATAAATAATAAAATA
*
36817549 TATAGTTTGAAACTAATAATAACAGATACTAGAAATTCTATCA
66 TACAGTTTGAAACTAATAATAACAGATACTAGAAATTCTATCA
* * *
36817592 TGAATAATCACGTATTCAGAATATAGGTATGCATTT-AAAAATAGCATACAATAAATAATAAAAT
1 TGAA-AATCACGTATTCAGAATATAAGTATGAATTTAAAAAATAACATACAATAAATAATAAAAT
* *
36817656 GTACGGTTTTGAAACTAATAATAA
65 ATACAG-TTTGAAACTAATAATAA
36817680 TAACAACACA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
108 30 0.41
109 44 0.59
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.33
Consensus pattern (108 bp):
TGAAAATCACGTATTCAGAATATAAGTATGAATTTAAAAAATAACATACAATAAATAATAAAATA
TACAGTTTGAAACTAATAATAACAGATACTAGAAATTCTATCA
Found at i:36818677 original size:18 final size:19
Alignment explanation
Indices: 36818650--36818685 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36818640 TTTTTATCTT
36818650 ATATTATAATGTTATTATA
1 ATATTATAATGTTATTATA
*
36818669 ATATT-TAATTTTATTAT
1 ATATTATAATGTTATTAT
36818686 TACTCTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
ATATTATAATGTTATTATA
Found at i:36828158 original size:105 final size:105
Alignment explanation
Indices: 36828028--36828217 Score: 294
Period size: 104 Copynumber: 1.8 Consensus size: 105
36828018 ACTGACACGC
* *
36828028 TTTTTTATATATTTTTATTATATTTATATATT-AAAAATAAAAAATAATATTATTATATTAGTAG
1 TTTTTTATATATTTTTATTATATTTATATATTAAAAAAT-AAAAA-AATAATATTATATTAATAG
* * *
36828092 AGGGTTATTAAATGACGGCACTTCGAAGTTTTTTTACACGAA
64 AAGGTTATCAAATGACGACACTTCGAAGTTTTTTTACACGAA
*
36828134 TTTTTT-TATTTTTTTATTATATTTATATATTAAAAAATAAAAAAATAATATTATATTAATAGAA
1 TTTTTTATATATTTTTATTATATTTATATATTAAAAAATAAAAAAATAATATTATATTAATAGAA
36828198 GGTTATCAAATGACGACACT
66 GGTTATCAAATGACGACACT
36828218 ATAAGGAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
104 36 0.47
105 29 0.38
106 12 0.16
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (105 bp):
TTTTTTATATATTTTTATTATATTTATATATTAAAAAATAAAAAAATAATATTATATTAATAGAA
GGTTATCAAATGACGACACTTCGAAGTTTTTTTACACGAA
Found at i:36828573 original size:30 final size:32
Alignment explanation
Indices: 36828511--36828575 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
36828501 TAAATTTATA
*
36828511 TTTTGTTTAGTATTTATTGTTTTAAGTTATTTG
1 TTTTGTTTAG-ATTTAATGTTTTAAGTTATTTG
36828544 TTTTGTTTA-ATTTAAT-TTTTAA-TTGATTTG
1 TTTTGTTTAGATTTAATGTTTTAAGTT-ATTTG
36828574 TT
1 TT
36828576 ATTTAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (32 bp):
TTTTGTTTAGATTTAATGTTTTAAGTTATTTG
Found at i:36828574 original size:25 final size:24
Alignment explanation
Indices: 36828545--36828720 Score: 102
Period size: 23 Copynumber: 7.4 Consensus size: 24
36828535 AGTTATTTGT
36828545 TTTGTTTAATTTAATTTTTAATTGA
1 TTTG-TTAATTTAATTTTTAATTGA
* *
36828570 TTTGTT-ATTTAATGTTTTTATTTA
1 TTTGTTAATTTAAT-TTTTAATTGA
* * *
36828594 GTTGAGTAAATTTAATTTTTAGTTGA
1 -TT-TGTTAATTTAATTTTTAATTGA
* *
36828620 TTTGTT-ATTTAATATTTTTATTTA
1 TTTGTTAATTTAAT-TTTTAATTGA
* * *
36828644 GTTGAGTAAATTTAATTTTTAATTGG
1 -TT-TGTTAATTTAATTTTTAATTGA
* *
36828670 TTTATT-ATTTAATATTT--TT-A
1 TTTGTTAATTTAATTTTTAATTGA
36828690 TTTGTT-ATTTAA-TTTTAAGTT-A
1 TTTGTTAATTTAATTTTTAA-TTGA
36828712 TTT-TTAATT
1 TTTGTTAATT
36828721 GATATGTTAT
Statistics
Matches: 115, Mismatches: 24, Indels: 27
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.03
20 11 0.10
21 4 0.03
22 9 0.08
23 24 0.21
24 20 0.17
25 12 0.10
26 18 0.16
27 14 0.12
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (24 bp):
TTTGTTAATTTAATTTTTAATTGA
Found at i:36828591 original size:50 final size:50
Alignment explanation
Indices: 36828552--36828739 Score: 247
Period size: 50 Copynumber: 3.7 Consensus size: 50
36828542 TGTTTTGTTT
*
36828552 AATTTAATTTTTAATTGATTTGTTATTTAATGTTTTTATTTAGTTGAGTA
1 AATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTAGTTGAGTA
*
36828602 AATTTAATTTTTAGTTGATTTGTTATTTAATATTTTTATTTAGTTGAGTA
1 AATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTAGTTGAGTA
* * *
36828652 AATTTAATTTTTAATTGGTTTATTATTTAATATTTTTATTT-GTT-ATTTA
1 AATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTAGTTGA-GTA
* *
36828701 ATTTTAAGTTATTTTTAATTGATATGTTATTTAAT-TTTT
1 AATTT-A---ATTTTTAATTGATTTGTTATTTAATATTTT
36828740 CGTGTATTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
48 1 0.01
49 9 0.07
50 87 0.71
52 4 0.03
53 22 0.18
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (50 bp):
AATTTAATTTTTAATTGATTTGTTATTTAATATTTTTATTTAGTTGAGTA
Found at i:36828598 original size:29 final size:28
Alignment explanation
Indices: 36828561--36828648 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 28
36828551 TAATTTAATT
*
36828561 TTTAATTGATTTGTTATTTAATGTTTTTA
1 TTTAGTTGATTTGTTATTTAAT-TTTTTA
*
36828590 TTTAGTTGA---G-TA---AATTTAATT-
1 TTTAGTTGATTTGTTATTTAATTT-TTTA
36828611 TTTAGTTGATTTGTTATTTAATATTTTTA
1 TTTAGTTGATTTGTTATTTAAT-TTTTTA
36828640 TTTAGTTGA
1 TTTAGTTGA
36828649 GTAAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 20
0.67 0.04 0.29
Matches are distributed among these distances:
21 11 0.24
22 5 0.11
24 1 0.02
25 4 0.09
26 1 0.02
28 5 0.11
29 19 0.41
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.61
Consensus pattern (28 bp):
TTTAGTTGATTTGTTATTTAATTTTTTA
Found at i:36828758 original size:21 final size:21
Alignment explanation
Indices: 36828732--36828801 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
36828722 ATATGTTATT
36828732 TAATTTTTCGTGTATTTTGTA
1 TAATTTTTCGTGTATTTTGTA
* ***
36828753 TAATTTTTTAGTGT-TGAGGTA
1 TAA-TTTTTCGTGTATTTTGTA
* *
36828774 T-TTTTTTCGTGTATTTTATA
1 TAATTTTTCGTGTATTTTGTA
36828794 TAATTTTT
1 TAATTTTT
36828802 TCCTGTAATA
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 9 0.26
20 4 0.11
21 13 0.37
22 9 0.26
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (21 bp):
TAATTTTTCGTGTATTTTGTA
Found at i:36828803 original size:22 final size:22
Alignment explanation
Indices: 36828727--36828808 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 22
36828717 AATTGATATG
*
36828727 TTATTTAA-TTTTTCGTGTATT
1 TTATATAATTTTTTCGTGTATT
* *
36828748 TTGTATAATTTTTTAGTG---T
1 TTATATAATTTTTTCGTGTATT
* ** *
36828767 TGAGGTATTTTTTTCGTGTATT
1 TTATATAATTTTTTCGTGTATT
*
36828789 TTATATAATTTTTTCCTGTA
1 TTATATAATTTTTTCGTGTA
36828809 ATACTGTCAT
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
19 13 0.30
21 6 0.14
22 24 0.56
ACGTcount: A:0.20, C:0.05, G:0.13, T:0.62
Consensus pattern (22 bp):
TTATATAATTTTTTCGTGTATT
Found at i:36828871 original size:51 final size:51
Alignment explanation
Indices: 36828797--36828960 Score: 211
Period size: 51 Copynumber: 3.1 Consensus size: 51
36828787 TTTTATATAA
* * *
36828797 TTTTTTCCTGTAATACTGTCATTTGATAACCCTCTACTAATATAATATTAT
1 TTTTTTCTTGTAATACCGTCATTTGATAATCCTCTACTAATATAATATTAT
*
36828848 TTTTTTCTTGTAATACCGTCATTTGATAATCTTCTACTAATATAATTTTATTTTAT
1 TTTTTTCTTGTAATACCGTCATTTGATAATCCTCTACTAATATAA---TA--TTAT
* * *
36828904 TTTTTTTTCTGTAATACCGTCATTTGATAATTCTCTATTAATATAATATTAT
1 TTTTTTCT-TGTAATACCGTCATTTGATAATCCTCTACTAATATAATATTAT
36828956 TTTTT
1 TTTTT
36828961 AATTTTTTAA
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
51 41 0.41
52 9 0.09
54 4 0.04
56 11 0.11
57 34 0.34
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.54
Consensus pattern (51 bp):
TTTTTTCTTGTAATACCGTCATTTGATAATCCTCTACTAATATAATATTAT
Found at i:36828931 original size:57 final size:59
Alignment explanation
Indices: 36828842--36828968 Score: 190
Period size: 57 Copynumber: 2.2 Consensus size: 59
36828832 ACTAATATAA
*
36828842 TATTATTTTTTTCTTGTAATACCGTCATTTGATAA-TCTTCTACTAATATAATTTTATTT
1 TATTATTTTTTTCTTGTAATACCGTCATTTGATAATTC-TCTACTAATATAATATTATTT
*
36828901 TATT-TTTTTTTC-TGTAATACCGTCATTTGATAATTCTCTATTAATATAATATTATTT
1 TATTATTTTTTTCTTGTAATACCGTCATTTGATAATTCTCTACTAATATAATATTATTT
*
36828958 T-TTAATTTTTT
1 TATTATTTTTTT
36828969 AATATATAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
56 2 0.03
57 47 0.75
58 10 0.16
59 4 0.06
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.58
Consensus pattern (59 bp):
TATTATTTTTTTCTTGTAATACCGTCATTTGATAATTCTCTACTAATATAATATTATTT
Found at i:36836263 original size:20 final size:20
Alignment explanation
Indices: 36836233--36836271 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
36836223 AATTAAAAAC
36836233 ATTTATTAAATTTATCATTTA
1 ATTTATTAAATTTAT-ATTTA
36836254 ATTT-TTAAATTTATATTT
1 ATTTATTAAATTTATATTT
36836272 TTTTAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATTAAATTTATATTTA
Found at i:36837498 original size:32 final size:31
Alignment explanation
Indices: 36837438--36837500 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
36837428 TCTAATAGCC
*
36837438 TAGTGACTTAAATAAAAAAATTTGAATAGTT
1 TAGTGACTTAAATAAAAAAATTTCAATAGTT
*
36837469 TAGTGACTTAAA-AGAAAAACTTTCCAATAGTT
1 TAGTGACTTAAATA-AAAAAATTT-CAATAGTT
36837501 CAATAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 1 0.04
31 20 0.71
32 7 0.25
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAAAATTTCAATAGTT
Found at i:36838835 original size:14 final size:14
Alignment explanation
Indices: 36838777--36838835 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
36838767 AATTTTGTTA
*
36838777 TTAATTTTTATAGAT
1 TTAATTTTTATA-TT
* *
36838792 TTAATTTGTGTATT
1 TTAATTTTTATATT
*
36838806 TTAATTAATTAT-TT
1 TTAATT-TTTATATT
36838820 TTAATTTTTATATT
1 TTAATTTTTATATT
36838834 TT
1 TT
36838836 TTGAATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 4 0.11
14 19 0.54
15 12 0.34
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (14 bp):
TTAATTTTTATATT
Found at i:36840054 original size:20 final size:18
Alignment explanation
Indices: 36840010--36840045 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36840000 GAAACTCCAA
* *
36840010 AACTTTATATTTTTTCCC
1 AACTTTTTATTTTTCCCC
36840028 AACTTTTTATTTTTCCCC
1 AACTTTTTATTTTTCCCC
36840046 TGAACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (18 bp):
AACTTTTTATTTTTCCCC
Found at i:36855824 original size:40 final size:39
Alignment explanation
Indices: 36855736--36855825 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 39
36855726 GCACTCAATG
* * * *
36855736 AACACTTTTTGAAGAGTCATAACCCTTTCATATTAGATG
1 AACACCTTTTGAAAAGTCACAACCCTTTCATATTAGATA
* * *
36855775 GACATCTTTTGAAAAGTCACAACCCTTTTCATATTGGATA
1 AACACCTTTTGAAAAGTCACAACCC-TTTCATATTAGATA
36855815 AACACCTTTTG
1 AACACCTTTTG
36855826 GAAATGACTT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 20 0.49
40 21 0.51
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (39 bp):
AACACCTTTTGAAAAGTCACAACCCTTTCATATTAGATA
Found at i:36859953 original size:39 final size:40
Alignment explanation
Indices: 36859899--36859985 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
36859889 CTCAATGGAT
*
36859899 ACCTTTTGAAGAGTCACAACCC-TTTCATATTAGATGAAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTAGATGAAC
* *
36859938 ACCTTTTGAAAAGTCACAACCCTTTTCATATTTGATGGAC
1 ACCTTTTGAAAAGTCACAACCCTTTTCATATTAGATGAAC
36859978 ACCTTTTG
1 ACCTTTTG
36859986 GAGAAGACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 21 0.48
40 23 0.52
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (40 bp):
ACCTTTTGAAAAGTCACAACCCTTTTCATATTAGATGAAC
Found at i:36859980 original size:40 final size:39
Alignment explanation
Indices: 36859893--36859985 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
36859883 TATGCACTCA
* *
36859893 ATGGATACCTTTTGAAGAGTCACAACCCTTTCATATTAG
1 ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTAG
* *
36859932 ATGAACACCTTTTGAAAAGTCACAACCCTTTTCATATTTG
1 ATGGACACCTTTTGAAAAGTCACAACCC-TTTCATATTAG
36859972 ATGGACACCTTTTG
1 ATGGACACCTTTTG
36859986 GAGAAGACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 25 0.52
40 23 0.48
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (39 bp):
ATGGACACCTTTTGAAAAGTCACAACCCTTTCATATTAG
Found at i:36861066 original size:25 final size:25
Alignment explanation
Indices: 36861038--36861090 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
36861028 GTATTTATTT
36861038 TATTTTAATATTTAAT-AATTTTATA
1 TATTTT-ATATTTAATAAATTTTATA
* * *
36861063 TATTTTTTATTTATTAAATTTTTTA
1 TATTTTATATTTAATAAATTTTATA
36861088 TAT
1 TAT
36861091 AATCATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTTTATATTTAATAAATTTTATA
Found at i:36861650 original size:28 final size:29
Alignment explanation
Indices: 36861597--36861651 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
36861587 ATTTTATATT
36861597 TTTTAATAACATAAAAACTAAATTAATAC
1 TTTTAATAACATAAAAACTAAATTAATAC
* *
36861626 TTTTAATAATA-AAAAACTAATTTAAT
1 TTTTAATAACATAAAAACTAAATTAAT
36861652 CTATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
TTTTAATAACATAAAAACTAAATTAATAC
Found at i:36861658 original size:29 final size:29
Alignment explanation
Indices: 36861597--36861668 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
36861587 ATTTTATATT
*
36861597 TTTTAATAACATAAAAACTAAATTAATAC
1 TTTTAATAATATAAAAACTAAATTAATAC
*
36861626 TTTTAATAATA-AAAAACTAATTTAAT-C
1 TTTTAATAATATAAAAACTAAATTAATAC
36861653 TATTTTATATAATATA
1 --TTTTA-ATAATATA
36861669 GAGACCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 1 0.03
28 14 0.38
29 15 0.41
30 6 0.16
31 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (29 bp):
TTTTAATAATATAAAAACTAAATTAATAC
Found at i:36866195 original size:4 final size:4
Alignment explanation
Indices: 36866186--36866260 Score: 71
Period size: 4 Copynumber: 18.2 Consensus size: 4
36866176 AAATAAACGG
* * *
36866186 GAAA GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA GAAA GAAA GGAGAG
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA -GA-AA
* *
36866237 GAAA AAAA G-AA GAAT GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
36866261 GTAATGTGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
3 3 0.05
4 47 0.80
5 8 0.14
6 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:36866224 original size:25 final size:22
Alignment explanation
Indices: 36866194--36866247 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
36866184 GGGAAAGAAA
36866194 GAAAGAAAGAAAG-AAGGAGAG
1 GAAAGAAAGAAAGAAAGGAGAG
36866215 GAAAGAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGAAAGGAGAG
*
36866237 GAAAAAAAGAA
1 GAAAGAAAGAA
36866248 GAATGAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAGAAAGGAGAG
Found at i:36866249 original size:25 final size:25
Alignment explanation
Indices: 36866190--36866256 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
36866180 AAACGGGAAA
*
36866190 GAAAGAAAGAAAGAAAG-AAGGAGAG
1 GAAAAAAAG-AAGAAAGAAAGGAGAG
*
36866215 G--AAAGA-AAGAAAGAAAGGAGAG
1 GAAAAAAAGAAGAAAGAAAGGAGAG
*
36866237 GAAAAAAAGAAGAATGAAAG
1 GAAAAAAAGAAGAAAGAAAG
36866257 AAAGGTAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 7 0.21
22 9 0.26
23 3 0.09
24 4 0.12
25 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (25 bp):
GAAAAAAAGAAGAAAGAAAGGAGAG
Found at i:36866345 original size:19 final size:19
Alignment explanation
Indices: 36866300--36866345 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
36866290 GTATGATATC
*
36866300 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
36866319 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
36866339 TTTTTAA
1 TTTTTAA
36866346 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:36869557 original size:21 final size:21
Alignment explanation
Indices: 36869531--36869577 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
36869521 TTAGGGTCCA
36869531 ATTGCCTC-GGAGGAGTAGAGT
1 ATTGCC-CGGGAGGAGTAGAGT
*
36869552 ATTGCCCGGGAGGAGTATAGT
1 ATTGCCCGGGAGGAGTAGAGT
36869573 ATTGC
1 ATTGC
36869578 GGTGACTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (21 bp):
ATTGCCCGGGAGGAGTAGAGT
Found at i:36869718 original size:12 final size:12
Alignment explanation
Indices: 36869686--36869722 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
36869676 TGCCTTTTCC
36869686 TCTTCCTCCTC-
1 TCTTCCTCCTCT
36869697 -C-TCCTCCTCT
1 TCTTCCTCCTCT
36869707 TCTTCCTCCTCT
1 TCTTCCTCCTCT
36869719 TCTT
1 TCTT
36869723 GTTGCTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.35
10 1 0.04
11 1 0.04
12 13 0.57
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTTCCTCCTCT
Found at i:36871606 original size:16 final size:16
Alignment explanation
Indices: 36871585--36871634 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
36871575 TGATGGGGGT
36871585 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
36871601 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
36871616 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
36871631 ATTA
1 ATTA
36871635 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:36871942 original size:95 final size:94
Alignment explanation
Indices: 36871828--36872095 Score: 409
Period size: 95 Copynumber: 2.9 Consensus size: 94
36871818 TATATTATTT
* *
36871828 TTTTAAATCAATAAATATGAATAATATTTTTTACTTACTACTACTTACTAATAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
***
36871893 TACTAACTA-ATTTTTTTAAACATTATTAAA
65 TACTAACTACA-AAATTTAAACATTATTAAA
* *
36871923 TTTTAAATCAATAAATATGAACAATGTTTTTTACTTACTACTACTACTAACAATAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
36871988 ACTAACTAGCAAAATTTAAACATTATTAAA
66 ACTAACTA-CAAAATTTAAACATTATTAAA
36872018 TTTTAAATCAATAAATATGAACAATATTTTTTA-TT--TACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
36872080 ACTAACTAGCAAAATT
66 ACTAACTA-CAAAATT
36872096 AAATTAAAGT
Statistics
Matches: 162, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
92 42 0.26
94 29 0.18
95 90 0.56
96 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (94 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTACAAAATTTAAACATTATTAAA
Found at i:36872084 original size:20 final size:21
Alignment explanation
Indices: 36872059--36872101 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
36872049 TATTTACTAC
36872059 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
36872079 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
36872100 TA
1 TA
36872102 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:36872479 original size:7 final size:7
Alignment explanation
Indices: 36872449--36872495 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
36872439 TTTTTCTTTC
36872449 TCCTTCT
1 TCCTTCT
*
36872456 TCC-CCT
1 TCCTTCT
36872462 T-CTTC-
1 TCCTTCT
36872467 TCCTTCT
1 TCCTTCT
36872474 TCCTTCT
1 TCCTTCT
36872481 TCCTTCT
1 TCCTTCT
*
36872488 TCTTTCT
1 TCCTTCT
36872495 T
1 T
36872496 TCTTTCTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 2 0.06
6 8 0.24
7 24 0.71
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TCCTTCT
Found at i:36875747 original size:22 final size:22
Alignment explanation
Indices: 36875722--36875781 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
36875712 TAAAAATAAT
36875722 AAAATTTTAATTTAATCATC-TA
1 AAAATTTTAATTTAAT-ATCATA
*
36875744 AAAATATATT--TTTACTATCATA
1 AAAAT-T-TTAATTTAATATCATA
*
36875766 AAAATTATAATTTAAT
1 AAAATTTTAATTTAAT
36875782 TTCGACCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 22 0.73
23 1 0.03
24 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATTTTAATTTAATATCATA
Found at i:36882570 original size:21 final size:21
Alignment explanation
Indices: 36882527--36882571 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36882517 ACCTGATTCT
* *
36882527 TTTACTGTTATGTTGCTGCTG
1 TTTACTGTCATGTTGATGCTG
* *
36882548 TTTACTGTCATTTTGATGTTG
1 TTTACTGTCATGTTGATGCTG
36882569 TTT
1 TTT
36882572 TGTTACCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (21 bp):
TTTACTGTCATGTTGATGCTG
Found at i:36885793 original size:19 final size:19
Alignment explanation
Indices: 36885769--36885806 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
36885759 TTGAAACACC
36885769 TTATTCTAATTAAAATAAA
1 TTATTCTAATTAAAATAAA
36885788 TTATTCTAATTAAAATAAA
1 TTATTCTAATTAAAATAAA
36885807 ATAGATGACT
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:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTCTAATTAAAATAAA
Found at i:36888931 original size:28 final size:28
Alignment explanation
Indices: 36888891--36888946 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
36888881 GTTGAAACAC
* *
36888891 CTTATTCTAATTAAAATAAAATAGATGA
1 CTTATTCAAATTAAAATAAAATAAATGA
36888919 CTTATTCAAATTAAAATAAAATAAATGA
1 CTTATTCAAATTAAAATAAAATAAATGA
36888947 AGTCTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (28 bp):
CTTATTCAAATTAAAATAAAATAAATGA
Found at i:36889876 original size:8 final size:9
Alignment explanation
Indices: 36889838--36889905 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 9
36889828 ATGCAGCAAA
36889838 AAAAATTAT
1 AAAAATTAT
36889847 AAAAA--AT
1 AAAAATTAT
*
36889854 AAAAATAAGT
1 AAAAATTA-T
36889864 AAAAATTAT
1 AAAAATTAT
36889873 AAAAATTATT
1 AAAAATTA-T
**
36889883 AAATTTTAAT
1 AAAAATT-AT
36889893 AAAAA-TAT
1 AAAAATTAT
36889901 AAAAA
1 AAAAA
36889906 AATTTAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.14
8 7 0.14
9 16 0.33
10 18 0.37
11 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:36889923 original size:28 final size:29
Alignment explanation
Indices: 36889863--36889926 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
36889853 TAAAAATAAG
* *
36889863 TAAAAATTATAAAAATTATTAAATTTTAA
1 TAAAAATTAAAAAAATTATAAAATTTTAA
*
36889892 TAAAAATATAAAAAAATT-TAAAATTTT-T
1 TAAAAAT-TAAAAAAATTATAAAATTTTAA
36889920 TAAAAAT
1 TAAAAAT
36889927 CGTAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 15 0.48
30 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAATTAAAAAAATTATAAAATTTTAA
Found at i:36890086 original size:19 final size:19
Alignment explanation
Indices: 36890064--36890151 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
36890054 TCTATATATC
36890064 TTATAATTTTTTACGATTT
1 TTATAATTTTTTACGATTT
** *
36890083 TTATAAAATTTTAC-A-CT
1 TTATAATTTTTTACGATTT
*
36890100 TTATATATTTTTTACGATTC
1 TTATA-ATTTTTTACGATTT
**
36890120 TTATAATTTTTTAATACTTT
1 TTATAATTTTTTACGA-TTT
36890140 TTAATAATTTTT
1 TT-ATAATTTTT
36890152 ATTAAAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.11
18 8 0.15
19 22 0.41
20 9 0.17
21 9 0.17
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATAATTTTTTACGATTT
Found at i:36890142 original size:10 final size:10
Alignment explanation
Indices: 36890122--36890181 Score: 66
Period size: 10 Copynumber: 5.9 Consensus size: 10
36890112 TACGATTCTT
36890122 ATAATTTTTTA
1 ATAA-TTTTTA
*
36890133 ATACTTTTTA
1 ATAATTTTTA
36890143 ATAATTTTTA
1 ATAATTTTTA
* **
36890153 TTAAAATTTA
1 ATAATTTTTA
*
36890163 ATAATTTTTT
1 ATAATTTTTA
36890173 ATAATTTTT
1 ATAATTTTT
36890182 TTGCCACATG
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
10 37 0.93
11 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:36890375 original size:87 final size:84
Alignment explanation
Indices: 36890266--36890461 Score: 216
Period size: 83 Copynumber: 2.3 Consensus size: 84
36890256 TCAACTGTTA
* * * **
36890266 AAGTACCAAATTGAGTGCAAAAAAAGTAGGGGTTTAATT-AATTTTTTAAAAAAGTTTTAGGTTT
1 AAGTACCTAATTGAGTGCAAAAAAA--A--GGCTTAATTGAATTTTTTAAAAAAGTTTGAGGACT
* * *
36890330 TTTTTTATACATTTTGACAGTTC
62 TTTTTAATACATTTTAAAAGTTC
* ** *
36890353 AAGTACCTAATTGAGTAC-AAAAAAAGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGACTTTTT
1 AAGTACCTAATTGAGTGCAAAAAAAAGGCTTAATTGAATTTTTTAAAAAAGTTTGAGGACTTTTT
*
36890417 TAATTCATTTTAAAAGTTC
66 TAATACATTTTAAAAGTTC
*
36890436 AAGTACCTAATTGAGTGTAAAAAAAA
1 AAGTACCTAATTGAGTGCAAAAAAAA
36890462 AATAAAGGCT
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
82 8 0.09
83 54 0.59
84 8 0.09
86 6 0.07
87 16 0.17
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (84 bp):
AAGTACCTAATTGAGTGCAAAAAAAAGGCTTAATTGAATTTTTTAAAAAAGTTTGAGGACTTTTT
TAATACATTTTAAAAGTTC
Found at i:36890426 original size:83 final size:83
Alignment explanation
Indices: 36890307--36890460 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 83
36890297 GTTTAATTAA
* ** * * *
36890307 TTTTTTAAAAAAGTTTTAGGTTTTTTTTTATACATTTTGACAGTTCAAGTACCTAATTGAGTACA
1 TTTTTTAAAAAAGTTTGAGGACTTTTTTAATACATTTTAAAAGTTCAAGTACCTAATTGAGTACA
36890372 AAAAAAGGCTTAATTGCT
66 AAAAAAGGCTTAATTGCT
* * **
36890390 TTTTTTGAAAAAGTTTGAGGACTTTTTTAATTCATTTTAAAAGTTCAAGTACCTAATTGAGTGTA
1 TTTTTTAAAAAAGTTTGAGGACTTTTTTAATACATTTTAAAAGTTCAAGTACCTAATTGAGTACA
36890455 AAAAAA
66 AAAAAA
36890461 AAATAAAGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 61 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (83 bp):
TTTTTTAAAAAAGTTTGAGGACTTTTTTAATACATTTTAAAAGTTCAAGTACCTAATTGAGTACA
AAAAAAGGCTTAATTGCT
Found at i:36896197 original size:13 final size:13
Alignment explanation
Indices: 36896179--36896203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36896169 CTTCCATATC
36896179 ACAGATTAGCAAA
1 ACAGATTAGCAAA
36896192 ACAGATTAGCAA
1 ACAGATTAGCAA
36896204 TAAAGAAAAA
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
ACAGATTAGCAAA
Found at i:36902912 original size:88 final size:88
Alignment explanation
Indices: 36902759--36902999 Score: 380
Period size: 88 Copynumber: 2.7 Consensus size: 88
36902749 AACTTCATCA
* * *
36902759 CAAA-TTTTTTGAAA-AAACAATTAAGCTCATGTTTTTATTTTACACTCAATTGGGTACTTGAAC
1 CAAACTTTTTTAAAAGAAACAATTAAGCTCATGTTTTTATTTTACACTCAATTGGATACTTTAAC
36902822 TATCAAAATGCATCAAAAAGACT
66 TATCAAAATGCATCAAAAAGACT
36902845 CAAACTTTTTTAAAAGAAACAATTAAGCTCATGTTTTTATTTTACACTCAATTGGATACTTTAAC
1 CAAACTTTTTTAAAAGAAACAATTAAGCTCATGTTTTTATTTTACACTCAATTGGATACTTTAAC
36902910 TATCAAAATGCATCAAAAAGACT
66 TATCAAAATGCATCAAAAAGACT
* * *
36902933 CAAACTTTTTTAAAAGAAACAATTAAGCTCATATTTTTTTTTTTTGA-ATTCAATTGGATACTTT
1 CAAACTTTTTTAAAAGAAACAATTAAGCTC--ATGTTTTTATTTT-ACACTCAATTGGATACTTT
36902997 AAC
63 AAC
36903000 AGTTGACGGT
Statistics
Matches: 144, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
86 4 0.03
87 9 0.06
88 100 0.69
90 30 0.21
91 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (88 bp):
CAAACTTTTTTAAAAGAAACAATTAAGCTCATGTTTTTATTTTACACTCAATTGGATACTTTAAC
TATCAAAATGCATCAAAAAGACT
Found at i:36903112 original size:9 final size:9
Alignment explanation
Indices: 36903075--36903221 Score: 66
Period size: 10 Copynumber: 15.4 Consensus size: 9
36903065 ACATGCAGCA
36903075 AAAAATTAT
1 AAAAATTAT
36903084 AAAAA--AT
1 AAAAATTAT
*
36903091 AAAAAATAGT
1 AAAAATTA-T
*
36903101 AAAAGTTAT
1 AAAAATTAT
36903110 AAAAATTATT
1 AAAAATTA-T
**
36903120 AAATTTTAAT
1 AAAAATT-AT
*
36903130 AAAAATATAA
1 AAAAAT-TAT
*
36903140 AAAAATATTT
1 AAAAAT-TAT
*
36903150 AAAATTTATT
1 AAAAATTA-T
36903160 AAAAATCGTA-
1 AAAAAT--TAT
*
36903170 AAAAAATAT
1 AAAAATTAT
*
36903179 AAAAAATTGTT
1 -AAAAATT-AT
**
36903190 AAATTTTAT
1 AAAAATTAT
*
36903199 AAAAATCAT
1 AAAAATTAT
36903208 AAAAAATTAT
1 -AAAAATTAT
36903218 AAAA
1 AAAA
36903222 TGCATAAAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
7 7 0.07
8 2 0.02
9 26 0.25
10 62 0.61
11 3 0.03
12 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:36903152 original size:30 final size:31
Alignment explanation
Indices: 36903110--36903178 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
36903100 TAAAAGTTAT
* *
36903110 AAAAATTA-TTAAATTTTAATAAAAAT-ATA
1 AAAAAATATTTAAAATTTAATAAAAATCATA
* *
36903139 AAAAAATATTTAAAATTTATTAAAAATCGTA
1 AAAAAATATTTAAAATTTAATAAAAATCATA
36903170 AAAAAATAT
1 AAAAAATAT
36903179 AAAAAATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.21
30 16 0.47
31 11 0.32
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (31 bp):
AAAAAATATTTAAAATTTAATAAAAATCATA
Found at i:36903185 original size:31 final size:30
Alignment explanation
Indices: 36903124--36903186 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
36903114 ATTATTAAAT
**
36903124 TTTAATAAAAATATAAAAAAATATTTAAAA
1 TTTAATAAAAATATAAAAAAATATAAAAAA
* *
36903154 TTTATTAAAAATCGTAAAAAAATATAAAAAA
1 TTTAATAAAAAT-ATAAAAAAATATAAAAAA
36903185 TT
1 TT
36903187 GTTAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
TTTAATAAAAATATAAAAAAATATAAAAAA
Found at i:36903194 original size:39 final size:40
Alignment explanation
Indices: 36903130--36903221 Score: 118
Period size: 39 Copynumber: 2.3 Consensus size: 40
36903120 AAATTTTAAT
*
36903130 AAAAATATAAAAAAATATTTAAAA-TTTATTAAAAATCGTAA
1 AAAAATAT-AAAAAATATTTAAAATTTTA-TAAAAATCATAA
36903171 AAAAATATAAAAAAT-TGTT-AAATTTTATAAAAATCATAA
1 AAAAATATAAAAAATAT-TTAAAATTTTATAAAAATCATAA
*
36903210 AAAATTATAAAA
1 AAAAATATAAAA
36903222 TGCATAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
39 26 0.55
40 13 0.28
41 8 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (40 bp):
AAAAATATAAAAAATATTTAAAATTTTATAAAAATCATAA
Found at i:36903228 original size:28 final size:28
Alignment explanation
Indices: 36903171--36903232 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
36903161 AAAATCGTAA
* * **
36903171 AAAAATATAAAAAATTGTTAAATTTTAT
1 AAAAATATAAAAAATTGATAAAATGCAT
36903199 AAAAATCATAAAAAATT-ATAAAATGCAT
1 AAAAAT-ATAAAAAATTGATAAAATGCAT
36903227 AAAAAT
1 AAAAAT
36903233 GCCTTTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATATAAAAAATTGATAAAATGCAT
Found at i:36903434 original size:83 final size:87
Alignment explanation
Indices: 36903326--36903502 Score: 238
Period size: 83 Copynumber: 2.1 Consensus size: 87
36903316 AGTTTTGGGG
* * ** *
36903326 TTTTTCATGCATTTTGACAGTTCAAGTATTTAATTGAGTG-A-AAAAAAT-AG-GCTTAATTG-T
1 TTTTTAATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGAAGAAAAAATAAGAGCTTAATTGCT
* *
36903386 TTTTTTGAAAAAGTTTGAGAGCC
66 TTTTTTGAAAAAATTTGAGA-AC
36903409 TTTTTAATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAGAAAAAATAAGAGCTTAATTGC
1 TTTTTAATGCATTTTGAAAGTTCAAGTACCTAATTAAGTG-AAGAAAAAATAAGAGCTTAATTGC
36903474 TTTTTTTGAAAAAATTTGAGAAC
65 TTTTTTTGAAAAAATTTGAGAAC
36903497 TTTTTA
1 TTTTTA
36903503 CACCCTTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
83 35 0.43
85 1 0.01
86 7 0.09
87 2 0.02
88 16 0.20
89 20 0.25
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (87 bp):
TTTTTAATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGAAGAAAAAATAAGAGCTTAATTGCT
TTTTTTGAAAAAATTTGAGAAC
Found at i:36907058 original size:2 final size:2
Alignment explanation
Indices: 36907011--36907043 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36907001 AAAGTGAAGG
36907011 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
36907044 AAATGATGAT
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:36910862 original size:9 final size:10
Alignment explanation
Indices: 36910850--36910886 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
36910840 ATTTGTATTT
36910850 ATAAAATA-A
1 ATAAAATATA
36910859 ATAAAATAATA
1 ATAAAAT-ATA
36910870 ATAAAA-ATA
1 ATAAAATATA
36910879 ATAAAATA
1 ATAAAATA
36910887 AAAACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 16 0.64
10 2 0.08
11 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAAATATA
Found at i:36910875 original size:20 final size:20
Alignment explanation
Indices: 36910852--36910899 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
36910842 TTGTATTTAT
36910852 AAAATAAATAAAATAATAATA
1 AAAAT-AATAAAATAATAATA
* *
36910873 AAAATAATAAAATAAAAACA
1 AAAATAATAAAATAATAATA
36910893 AAAATAA
1 AAAATAA
36910900 GAAATGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAATAAAATAATAATA
Found at i:36912580 original size:2 final size:2
Alignment explanation
Indices: 36912575--36912604 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36912565 ATATATAAAT
36912575 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36912605 TTGATACACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36926936 original size:135 final size:129
Alignment explanation
Indices: 36926662--36926936 Score: 277
Period size: 135 Copynumber: 2.1 Consensus size: 129
36926652 CTTACTCTTG
* *
36926662 AAGCTAAAGTAAACAATTCATAATAAATAAATCCAAAAATATATAAGACGTAATAAATACGTAAT
1 AAGCTAAAGTAAACAATTCATAATAAATAAATCCAAAAAAATATAAAACGTAATAAATACGTAAT
* * * ** * ** *
36926727 TGCCCTTATACATAATCAAAATAAGTAATATAAACTTCCTTAAACCTATTTAAACTCTTATTCTT
66 TGCACTTATACATAATCAAAATAAG-AATATAAAATTCC-TAAACATATTTAAAAGCTAAGACTA
*
36926792 G
129 A
*
36926793 AAGGTAAAGTAAACAATTCATAATAAATAAATCCAAAAAAAAAAATATAAAACGTAATAAATACG
1 AAGCTAAAGTAAACAATTCATAATAAATAAATCC----AAAAAAATATAAAACGTAATAAATACG
* * *
36926858 TAATTGCACTTATACATAATCAAAATTA-AATCTTAAAATTGAACC-AAATATGATTTAAAAGCT
62 TAATTGCACTTATACATAATCAAAATAAGAAT-ATAAAATT---CCTAAACAT-ATTTAAAAGCT
36926921 AAGAC-AA
122 AAGACTAA
*
36926928 AATCTAAAG
1 AAGCTAAAG
36926937 CTCATCATTC
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
131 33 0.28
133 3 0.03
134 6 0.05
135 62 0.53
136 11 0.09
137 2 0.02
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (129 bp):
AAGCTAAAGTAAACAATTCATAATAAATAAATCCAAAAAAATATAAAACGTAATAAATACGTAAT
TGCACTTATACATAATCAAAATAAGAATATAAAATTCCTAAACATATTTAAAAGCTAAGACTAA
Found at i:36950240 original size:14 final size:15
Alignment explanation
Indices: 36950221--36950250 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36950211 AAGTTTGATA
36950221 ATTTT-ATTTTTTTT
1 ATTTTAATTTTTTTT
36950235 ATTTTAATTTTTTTT
1 ATTTTAATTTTTTTT
36950250 A
1 A
36950251 CAACTACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTAATTTTTTTT
Found at i:36950998 original size:20 final size:21
Alignment explanation
Indices: 36950970--36951008 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
36950960 TCTGACTTTC
*
36950970 ATGATATAT-ATGAACAAAAT
1 ATGAAATATGATGAACAAAAT
*
36950990 ATGAAATATGATGATCAAA
1 ATGAAATATGATGAACAAA
36951009 TCATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (21 bp):
ATGAAATATGATGAACAAAAT
Found at i:36953867 original size:34 final size:34
Alignment explanation
Indices: 36953819--36953921 Score: 102
Period size: 34 Copynumber: 3.0 Consensus size: 34
36953809 AAGAATATGA
**
36953819 AAAGTTAAAAAAGATGAAAGGTTAAAGATC-AAG
1 AAAGTTAAGGAAGATGAAAGGTTAAAGATCAAAG
* *
36953852 AGAGGTTAAGGAAGATGGAAA-GTTAAAGATTAAAG
1 A-AAGTTAAGGAAGAT-GAAAGGTTAAAGATCAAAG
* * *
36953887 AAAGTTAAGGAAAATGGAAGGTTAAAAGATGAAAG
1 AAAGTTAAGGAAGATGAAAGGTT-AAAGATCAAAG
36953922 GTTGAACATC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
33 4 0.07
34 35 0.61
35 18 0.32
ACGTcount: A:0.53, C:0.01, G:0.27, T:0.18
Consensus pattern (34 bp):
AAAGTTAAGGAAGATGAAAGGTTAAAGATCAAAG
Found at i:36953876 original size:17 final size:17
Alignment explanation
Indices: 36953856--36953911 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
36953846 ATCAAGAGAG
*
36953856 GTTAAGGAAGATGGAAA
1 GTTAAGGAAAATGGAAA
*
36953873 GTTAAAGATTAAA--GAAA
1 GTTAAGGA--AAATGGAAA
*
36953890 GTTAAGGAAAATGGAAG
1 GTTAAGGAAAATGGAAA
36953907 GTTAA
1 GTTAA
36953912 AAGATGAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.10
17 26 0.84
19 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAGGAAAATGGAAA
Found at i:36956547 original size:34 final size:34
Alignment explanation
Indices: 36956509--36956602 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
36956499 CCTTTCATCT
* *
36956509 TTTAACCTTCCATTTTCCTTAACTTTCTTTGACC
1 TTTAACCTTCCATTTTCCTTAACTTTCCTTAACC
* * * *
36956543 TTTAACCTTCCATCTTCCTTAACCTCCCTTAATC
1 TTTAACCTTCCATTTTCCTTAACTTTCCTTAACC
*
36956577 TTTAACCTTTCATCTTT-CTTAACTTT
1 TTTAACCTTCCAT-TTTCCTTAACTTT
36956603 TCATATTCTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
34 47 0.96
35 2 0.04
ACGTcount: A:0.19, C:0.31, G:0.01, T:0.49
Consensus pattern (34 bp):
TTTAACCTTCCATTTTCCTTAACTTTCCTTAACC
Found at i:36956564 original size:17 final size:17
Alignment explanation
Indices: 36956497--36956599 Score: 54
Period size: 17 Copynumber: 6.2 Consensus size: 17
36956487 ATGGATGTTC
*
36956497 AACCTTTCATCTT--TT
1 AACCTTCCATCTTCCTT
*
36956512 AACCTTCCATTTTCCTT
1 AACCTTCCATCTTCCTT
*
36956529 AA-CTTTC-T-TTGACCTTT
1 AACCTTCCATCTT--CC-TT
36956546 AACCTTCCATCTTCCTT
1 AACCTTCCATCTTCCTT
* * ** *
36956563 AACCTCCCTTAATCTTT
1 AACCTTCCATCTTCCTT
* *
36956580 AACCTTTCATCTTTCTT
1 AACCTTCCATCTTCCTT
36956597 AAC
1 AAC
36956600 TTTTCATATT
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
14 2 0.03
15 12 0.19
16 6 0.09
17 35 0.55
18 6 0.09
19 1 0.02
20 2 0.03
ACGTcount: A:0.20, C:0.32, G:0.01, T:0.47
Consensus pattern (17 bp):
AACCTTCCATCTTCCTT
Found at i:36957854 original size:6 final size:6
Alignment explanation
Indices: 36957843--36957867 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36957833 TTGTGATCGA
36957843 GGACGT GGACGT GGACGT GGACGT G
1 GGACGT GGACGT GGACGT GGACGT G
36957868 AACGAGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGACGT
Found at i:36960405 original size:21 final size:22
Alignment explanation
Indices: 36960358--36960404 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
36960348 GATTAGGTTA
*
36960358 AAAATATTTTAATTATGATTTG
1 AAAATATTTTAATTATGAATTG
*
36960380 AAAAT-TTTTTATTATGAAATTG
1 AAAATATTTTAATTATG-AATTG
36960402 AAA
1 AAA
36960405 TGGATAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
AAAATATTTTAATTATGAATTG
Found at i:36961494 original size:27 final size:26
Alignment explanation
Indices: 36961444--36961512 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
36961434 CCTGAATCAC
*
36961444 AAACCTTAAACCCTAAATCTAAAATCTA
1 AAACC-TAAA-CCTAAATCGAAAATCTA
* *
36961472 GAACCTGAAACCTAAATCGAAAATTTA
1 AAACCT-AAACCTAAATCGAAAATCTA
36961499 AAATCCTAAACCTA
1 AAA-CCTAAACCTA
36961513 GACCCTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.23
Consensus pattern (26 bp):
AAACCTAAACCTAAATCGAAAATCTA
Found at i:36981252 original size:29 final size:30
Alignment explanation
Indices: 36981197--36981260 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
36981187 AATAATTTAT
* *
36981197 ATTTTTATAATTGTTAAATGATTAAATTA-A
1 ATTTTTATAATTGTTAAAGGA-TAAAATACA
* *
36981227 ATTTTTATTATT-TTTAAGGATAAAATACA
1 ATTTTTATAATTGTTAAAGGATAAAATACA
36981256 ATTTT
1 ATTTT
36981261 ATCTTTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 6 0.21
29 12 0.41
30 11 0.38
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
ATTTTTATAATTGTTAAAGGATAAAATACA
Found at i:36981618 original size:2 final size:2
Alignment explanation
Indices: 36981611--36981643 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
36981601 TTTGAAATTT
36981611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36981644 GAATTGGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36985797 original size:21 final size:21
Alignment explanation
Indices: 36985773--36985848 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
36985763 GAAATTTAAA
36985773 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
**
36985794 ACAAAACATTGTGAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
* *
36985816 ACAAACATTATGAGGAAAGTT
1 ACAAACATAATGAGGAGAGTT
36985837 ACAAACATAATG
1 ACAAACATAATG
36985849 TTTTGTAGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 30 0.61
22 19 0.39
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:36985808 original size:22 final size:22
Alignment explanation
Indices: 36985775--36985841 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
36985765 AATTTAAAAC
*
36985775 AAACATAATGAGGAGAGTTACA
1 AAACATTATGAGGAGAGTTACA
*
36985797 AAACATTGTGAGGAGAGTTAC-
1 AAACATTATGAGGAGAGTTACA
*
36985818 AAACATTATGAGGAAAGTTACA
1 AAACATTATGAGGAGAGTTACA
36985840 AA
1 AA
36985842 CATAATGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.47
22 21 0.52
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.21
Consensus pattern (22 bp):
AAACATTATGAGGAGAGTTACA
Found at i:36987296 original size:29 final size:28
Alignment explanation
Indices: 36987250--36987304 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
36987240 TAAAGAATTG
* *
36987250 AAAAAAAATTTAAGTATCAATTTGAAGT
1 AAAAAAAATATAAATATCAATTTGAAGT
36987278 AAAAAAATATATAAATATCAATTTGAA
1 AAAAAAA-ATATAAATATCAATTTGAA
36987305 AGAAGAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAAAAAATATAAATATCAATTTGAAGT
Found at i:36988027 original size:27 final size:27
Alignment explanation
Indices: 36987992--36988092 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
36987982 GTAATTTTAA
36987992 AAAT-TATTATCACTTTCATGAATGTT
1 AAATATATTATCACTTTCATGAATGTT
*
36988018 AAATATATTATCTTCCACTATGT-ATTCGTAATTTT
1 AAATATATTA---T-CACT-T-TCA-T-G-AATGTT
*
36988053 AAAAATTATTATCACTTTCATGAATGTT
1 AAATA-TATTATCACTTTCATGAATGTT
36988081 AAATATATTATC
1 AAATATATTATC
36988093 TTCACTCCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 23
0.69 0.05 0.27
Matches are distributed among these distances:
26 4 0.07
27 12 0.20
28 9 0.15
29 1 0.02
30 3 0.05
31 6 0.10
32 6 0.10
33 3 0.05
34 1 0.02
35 9 0.15
36 5 0.08
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (27 bp):
AAATATATTATCACTTTCATGAATGTT
Found at i:36988065 original size:63 final size:63
Alignment explanation
Indices: 36987968--36988095 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
36987958 CTCATCTTGC
36987968 TCCACTATGTATTCGTAATTTTAAAAATTATTATCACTTTCATGAATGTTAAATATATTATCT
1 TCCACTATGTATTCGTAATTTTAAAAATTATTATCACTTTCATGAATGTTAAATATATTATCT
36988031 TCCACTATGTATTCGTAATTTTAAAAATTATTATCACTTTCATGAATGTTAAATATATTATCT
1 TCCACTATGTATTCGTAATTTTAAAAATTATTATCACTTTCATGAATGTTAAATATATTATCT
36988094 TC
1 TC
36988096 ACTCCGTCAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.46
Consensus pattern (63 bp):
TCCACTATGTATTCGTAATTTTAAAAATTATTATCACTTTCATGAATGTTAAATATATTATCT
Found at i:36991138 original size:22 final size:22
Alignment explanation
Indices: 36991063--36991138 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
36991053 GTGCTATTTT
*
36991063 TTGCTATTTTTTGTTGTTTTGGTG
1 TTGCTATTTTTTATTGTTTT-G-G
36991087 TTG-TA-TTTTTATTGTTTTGG
1 TTGCTATTTTTTATTGTTTTGG
* *
36991107 -TGCTTTTTTTTTACTGTTTTGG
1 TTGC-TATTTTTTATTGTTTTGG
36991129 TTGCTATTTT
1 TTGCTATTTT
36991139 GGTGCTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 2 0.05
22 31 0.70
23 5 0.11
24 3 0.07
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (22 bp):
TTGCTATTTTTTATTGTTTTGG
Found at i:36991196 original size:12 final size:12
Alignment explanation
Indices: 36991168--36991237 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
36991158 TTTGACGTTG
*
36991168 TTTTTATTGTTA
1 TTTTTGTTGTTA
*
36991180 TTTTTGTTGCTA
1 TTTTTGTTGTTA
*
36991192 TTTTT-TCTATTA
1 TTTTTGT-TGTTA
*
36991204 TTTTTGTTGTTG
1 TTTTTGTTGTTA
*
36991216 TTTTAGTTGTTA
1 TTTTTGTTGTTA
*
36991228 TTTTGGTTGT
1 TTTTTGTTGT
36991238 CTGGATGTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 1 0.02
12 45 0.96
13 1 0.02
ACGTcount: A:0.10, C:0.03, G:0.16, T:0.71
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:36991705 original size:20 final size:20
Alignment explanation
Indices: 36991685--36991730 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
36991675 AATACATGGG
36991685 AAAAAATCGATTAACAGGGGA
1 AAAAAATCGATT-ACAGGGGA
36991706 AAAAAATCGATTACAGGGGCA
1 AAAAAATCGATTACAGGGG-A
36991727 AAAA
1 AAAA
36991731 CATTTCGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.54, C:0.11, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAAATCGATTACAGGGGA
Found at i:36991709 original size:21 final size:20
Alignment explanation
Indices: 36991685--36991730 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
36991675 AATACATGGG
36991685 AAAAAATCGATTAACAGGGGA
1 AAAAAATCGATT-ACAGGGGA
*
36991706 AAAAAATCGATTACAGGGGC
1 AAAAAATCGATTACAGGGGA
36991726 AAAAA
1 AAAAA
36991731 CATTTCGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.54, C:0.11, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAAATCGATTACAGGGGA
Found at i:36993921 original size:2 final size:2
Alignment explanation
Indices: 36993914--36993943 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36993904 TAGCCAAATA
36993914 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
36993944 GAGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36996310 original size:2 final size:2
Alignment explanation
Indices: 36996303--36996327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36996293 TGGAATCAAC
36996303 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
36996328 CATTGGAGTA
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:37005247 original size:19 final size:18
Alignment explanation
Indices: 37005211--37005251 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
37005201 AGATTAAAGT
*
37005211 TTAATTAATTATGATTAA
1 TTAATTAATTAGGATTAA
*
37005229 GTTAATTAATTAGGTTTAA
1 -TTAATTAATTAGGATTAA
37005248 TTAA
1 TTAA
37005252 AATTAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
TTAATTAATTAGGATTAA
Found at i:37010790 original size:26 final size:27
Alignment explanation
Indices: 37010752--37010804 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
37010742 GGTAATCTTT
*
37010752 TTAACAAAAACAGTTGAGTCGTGACTA
1 TTAACAAAAACAGTTGAGTCATGACTA
37010779 TTAA-AAAAACAGTTGAGTCATGACTA
1 TTAACAAAAACAGTTGAGTCATGACTA
37010805 AGTCAATCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (27 bp):
TTAACAAAAACAGTTGAGTCATGACTA
Found at i:37020118 original size:19 final size:20
Alignment explanation
Indices: 37020096--37020133 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
37020086 AAAGAAGAAG
37020096 AAAGAATAAAAAAA-AAAAT
1 AAAGAATAAAAAAATAAAAT
37020115 AAAGAATAAAAAAATAAAA
1 AAAGAATAAAAAAATAAAA
37020134 AGAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAGAATAAAAAAATAAAAT
Found at i:37038146 original size:7 final size:7
Alignment explanation
Indices: 37038134--37038173 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
37038124 CATTTGTCTT
37038134 TCTTCAA
1 TCTTCAA
37038141 TCTTCAA
1 TCTTCAA
37038148 TCTTCAA
1 TCTTCAA
37038155 TCTTCAA
1 TCTTCAA
37038162 TCTTCAA
1 TCTTCAA
37038169 TCTTC
1 TCTTC
37038174 TCATTACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (7 bp):
TCTTCAA
Found at i:37043277 original size:2 final size:2
Alignment explanation
Indices: 37043270--37043294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37043260 TTAAAACTCG
37043270 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
37043295 GTTCAGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37044954 original size:18 final size:18
Alignment explanation
Indices: 37044922--37044973 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
37044912 CTAGAATGAG
37044922 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
37044938 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
37044956 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
37044974 CAATTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:37046085 original size:28 final size:30
Alignment explanation
Indices: 37046030--37046106 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 30
37046020 ATAATATATT
* * **
37046030 TTTTAAAAAATAATTAAATATTTGAAAA-CA
1 TTTT-AAATATAATAAAATATTAAAAAATCA
*
37046060 TTTTCAAT-TAATAAAATATTAAAAAATCA
1 TTTTAAATATAATAAAATATTAAAAAATCA
37046089 TTTTAAATATAAATAAAA
1 TTTTAAATAT-AATAAAA
37046107 ATAGTAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 15 0.39
29 11 0.29
30 5 0.13
31 7 0.18
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (30 bp):
TTTTAAATATAATAAAATATTAAAAAATCA
Found at i:37047762 original size:24 final size:25
Alignment explanation
Indices: 37047735--37047781 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
37047725 TCCAAATAAT
* *
37047735 ATTTTATTTTATTTATAA-AAAATG
1 ATTTTAATATATTTATAATAAAATG
37047759 ATTTTAATATATTTATAATAAAA
1 ATTTTAATATATTTATAATAAAA
37047782 AATCTGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTTAATATATTTATAATAAAATG
Found at i:37052076 original size:18 final size:18
Alignment explanation
Indices: 37052053--37052095 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
37052043 GAATAATTTT
37052053 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
37052071 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
37052089 TTAATTA
1 TTAATTA
37052096 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:37052714 original size:3 final size:3
Alignment explanation
Indices: 37052706--37052741 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
37052696 TAAAAACTTA
37052706 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
37052742 GTCATTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37054441 original size:25 final size:26
Alignment explanation
Indices: 37054403--37054453 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
37054393 GGTCAGGGGA
37054403 GGGAGGGGGAAAGGGACGGGGGTGGG
1 GGGAGGGGGAAAGGGACGGGGGTGGG
37054429 GGGA-GGGGAAAGGGACGGGGGTGGG
1 GGGAGGGGGAAAGGGACGGGGGTGGG
37054454 AGAGGGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.20, C:0.04, G:0.73, T:0.04
Consensus pattern (26 bp):
GGGAGGGGGAAAGGGACGGGGGTGGG
Found at i:37054466 original size:12 final size:12
Alignment explanation
Indices: 37054451--37054495 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
37054441 GGACGGGGGT
37054451 GGGAGAGGGAGA
1 GGGAGAGGGAGA
37054463 GGGAGAGGGAGA
1 GGGAGAGGGAGA
37054475 GGGAGAGGGAGA
1 GGGAGAGGGAGA
37054487 GGGAGAGGG
1 GGGAGAGGG
37054496 GTATGGGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (12 bp):
GGGAGAGGGAGA
Found at i:37054474 original size:18 final size:18
Alignment explanation
Indices: 37054451--37054495 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
37054441 GGACGGGGGT
37054451 GGGAGAGGGAGAGGGAGA
1 GGGAGAGGGAGAGGGAGA
37054469 GGGAGAGGGAGAGGGAGA
1 GGGAGAGGGAGAGGGAGA
37054487 GGGAGAGGG
1 GGGAGAGGG
37054496 GTATGGGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (18 bp):
GGGAGAGGGAGAGGGAGA
Found at i:37054667 original size:17 final size:19
Alignment explanation
Indices: 37054639--37054673 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
37054629 ATATTTATTT
37054639 ATTTTGATATATT-TTAAA
1 ATTTTGATATATTATTAAA
37054657 ATTTT-ATATATTATTAA
1 ATTTTGATATATTATTAA
37054674 TTTTTGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTGATATATTATTAAA
Done.