Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 120 of 310
Found at i:38436267 original size:20 final size:20
Alignment explanation
Indices: 38436227--38436287 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
38436217 ACCAATAAAA
38436227 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
38436247 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
38436267 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
38436287 T
1 T
38436288 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:38436288 original size:20 final size:20
Alignment explanation
Indices: 38436251--38436288 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38436241 TGTAGCTAAA
*
38436251 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
38436271 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
38436289 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:38436478 original size:46 final size:45
Alignment explanation
Indices: 38436408--38436575 Score: 183
Period size: 46 Copynumber: 3.6 Consensus size: 45
38436398 GTATCACAAC
* **
38436408 GCATGTCCCAGACATGTCTAACACTGGCTAACATCTCAAGACCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG-CCGAT
* *** *
38436454 GCATGTCCCAAACATGTCTTACACTGGCTCTCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCAT-CTCAAGCCGAT
* * * *
38436500 GCATGTCCTAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAA-GCCGAT
38436546 GCCATGTCCCAGACATGGTCTTACACTGGC
1 G-CATGTCCCAGACAT-GTCTTACACTGGC
38436576 ACACAAATCT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
45 2 0.02
46 69 0.70
47 16 0.16
48 12 0.12
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (45 bp):
GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAGCCGAT
Found at i:38438653 original size:20 final size:20
Alignment explanation
Indices: 38438613--38438660 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38438603 ATAAGCTGGA
**
38438613 GTTGAGCTAGATGTGAACTT
1 GTTGAGCTAGAACTGAACTT
*
38438633 GTTGAGCTAGAACTGAGCTT
1 GTTGAGCTAGAACTGAACTT
*
38438653 GCTGAGCT
1 GTTGAGCT
38438661 GGTTGTGAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
GTTGAGCTAGAACTGAACTT
Found at i:38439273 original size:12 final size:12
Alignment explanation
Indices: 38439258--38439318 Score: 77
Period size: 12 Copynumber: 5.1 Consensus size: 12
38439248 GAAAAAGAAA
*
38439258 AAAAAGAGAGTG
1 AAAAAGAGATTG
*
38439270 AAAATGAGATTG
1 AAAAAGAGATTG
*
38439282 AAAAAGAAATTG
1 AAAAAGAGATTG
*
38439294 AAAAAGAGAATG
1 AAAAAGAGATTG
*
38439306 AAAAAGAGTTTG
1 AAAAAGAGATTG
38439318 A
1 A
38439319 GAGAGAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:38439308 original size:36 final size:33
Alignment explanation
Indices: 38439247--38439330 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 33
38439237 AAAAAGCCGA
* *
38439247 TGAAAAAGAAAAAAAAGAGAGTGAAAATGAGAT
1 TGAAAAAGAAAAAAAAGAGAATGAAAAAGAGAT
*
38439280 TGAAAAAGAAATTGAAAAAGAGAATGAAAAAGAGTT
1 TGAAAAAGAAA---AAAAAGAGAATGAAAAAGAGAT
* *
38439316 TGAGAGAGAAAAAAA
1 TGAAAAAGAAAAAAA
38439331 GTTGAACAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 15 0.35
36 28 0.65
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAAAGAAAAAAAAGAGAATGAAAAAGAGAT
Found at i:38439318 original size:24 final size:24
Alignment explanation
Indices: 38439247--38439318 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
38439237 AAAAAGCCGA
*
38439247 TGAAAAAGA-AA--AAAAAGAGAG
1 TGAAAAAGAGAATGAAAAAGAGAT
* * *
38439268 TGAAAATGAGATTGAAAAAGAAAT
1 TGAAAAAGAGAATGAAAAAGAGAT
*
38439292 TGAAAAAGAGAATGAAAAAGAGTT
1 TGAAAAAGAGAATGAAAAAGAGAT
38439316 TGA
1 TGA
38439319 GAGAGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.20
22 1 0.03
24 31 0.77
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (24 bp):
TGAAAAAGAGAATGAAAAAGAGAT
Found at i:38440028 original size:14 final size:14
Alignment explanation
Indices: 38440011--38440050 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38440001 CGAATGGAAT
*
38440011 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
38440025 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
38440039 GATACGAACAAA
1 GGTAGGAACAAA
38440051 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:38443308 original size:111 final size:112
Alignment explanation
Indices: 38443131--38443353 Score: 421
Period size: 111 Copynumber: 2.0 Consensus size: 112
38443121 GCATGAGTTA
*
38443131 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGATTGGAATAAATGATGCATAAGTGTGTGTT
1 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGATTGGAATAAATGATGCATAAGTGAGTGTT
38443196 CATTTATTTACGTAGTTGTTAATTTGTTTAAAGTTTAATAATTGAAT
66 CATTTATTTACGTAGTTGTTAATTTGTTTAAAGTTTAATAATTGAAT
38443243 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTG-TTGGAATAAATGATGCATAAGTGAGTGTT
1 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGATTGGAATAAATGATGCATAAGTGAGTGTT
*
38443307 CATTTATTTACGTAGTTGTTAATTTGTTTAAAGTTTAGTAATTGAAT
66 CATTTATTTACGTAGTTGTTAATTTGTTTAAAGTTTAATAATTGAAT
38443354 TAATGTGACG
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 74 0.68
112 35 0.32
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (112 bp):
AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGATTGGAATAAATGATGCATAAGTGAGTGTT
CATTTATTTACGTAGTTGTTAATTTGTTTAAAGTTTAATAATTGAAT
Found at i:38444090 original size:71 final size:71
Alignment explanation
Indices: 38443969--38444115 Score: 276
Period size: 71 Copynumber: 2.1 Consensus size: 71
38443959 AAAGATTTGT
* *
38443969 TGGCTACCTAGTGTTCTAGTTGTGTCATCCATTTTCTTTGTTGAAAACTGAACTTATCACTACTC
1 TGGCGACCTAGTGTTCTAGTTGTGTCATCCATTTTCTTTATTGAAAACTGAACTTATCACTACTC
38444034 GTAGTG
66 GTAGTG
38444040 TGGCGACCTAGTGTTCTAGTTGTGTCATCCATTTTCTTTATTGAAAACTGAACTTATCACTACTC
1 TGGCGACCTAGTGTTCTAGTTGTGTCATCCATTTTCTTTATTGAAAACTGAACTTATCACTACTC
38444105 GTAGTG
66 GTAGTG
38444111 TGGCG
1 TGGCG
38444116 TTCAAACATA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (71 bp):
TGGCGACCTAGTGTTCTAGTTGTGTCATCCATTTTCTTTATTGAAAACTGAACTTATCACTACTC
GTAGTG
Found at i:38447582 original size:30 final size:31
Alignment explanation
Indices: 38447548--38447644 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
38447538 AGCTCACTCC
*
38447548 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
38447578 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
38447608 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
38447638 TAGCTCA
1 TAGCTCA
38447645 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:38448317 original size:20 final size:22
Alignment explanation
Indices: 38448294--38448336 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
38448284 TTTTGTTGTC
38448294 TTTCCTCTCTTT-T-TCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
* *
38448314 TTTCTTTTCTTTCTCTCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
38448336 T
1 T
38448337 GATCTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCCTCTCTTTCTCTCTCATT
Found at i:38452019 original size:23 final size:22
Alignment explanation
Indices: 38451967--38452019 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38451957 TCCACGTCTT
*
38451967 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38451989 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38452012 TTTCTTTT
1 TTTCTTTT
38452020 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:38465436 original size:34 final size:34
Alignment explanation
Indices: 38465393--38465459 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
38465383 GTCTAATATT
38465393 AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
1 AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
38465427 AGTGTGGGCCTTAGCCCATTATAGTAACAGTAT
1 AGTGTGGGCCTTAGCCCATTATAGTAACAGTAT
38465460 TAGAAATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (34 bp):
AGTGTGGGCCTTAGCCCATTATAGTAACAGTATC
Found at i:38466702 original size:15 final size:16
Alignment explanation
Indices: 38466656--38466704 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
38466646 TAACCCCATA
*
38466656 AAGTGAAAAGAGAAGA
1 AAGTGAAAAGAGAAGT
*
38466672 AAGTCAAAAGCAAGAAGT
1 AAGTGAAAAG--AGAAGT
38466690 AAG-GAAAAGAGAAGT
1 AAGTGAAAAGAGAAGT
38466705 CAAGAGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 5 0.18
18 8 0.29
ACGTcount: A:0.59, C:0.04, G:0.29, T:0.08
Consensus pattern (16 bp):
AAGTGAAAAGAGAAGT
Found at i:38470827 original size:15 final size:17
Alignment explanation
Indices: 38470799--38470832 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38470789 TTATTAATTT
38470799 TAAAAGGTTAAAT-ATA
1 TAAAAGGTTAAATAATA
38470815 TAAAAGG-TAAATAATA
1 TAAAAGGTTAAATAATA
38470831 TA
1 TA
38470833 TATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAAGGTTAAATAATA
Found at i:38471782 original size:43 final size:42
Alignment explanation
Indices: 38471721--38471850 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 42
38471711 ATAGGATTTT
*
38471721 GATATGTGTTCTCGTGTAAAACCACGTCTGGGACGTTGGCATC
1 GATATGTGAT-TCGTGTAAAACCACGTCTGGGACGTTGGCATC
* * * *
38471764 GATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATGTGATT-CGTGTAAAACCACGTCTGGGACGTTGGCATC
* * *
38471807 -ATATTTGATTCATGTAAAACC-CTATCTGGGACAG-TGGCATC
1 GATATGTGATTCGTGTAAAACCAC-GTCTGGGAC-GTTGGCATC
38471848 GAT
1 GAT
38471851 TTATCGATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
41 23 0.32
42 12 0.17
43 36 0.51
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
GATATGTGATTCGTGTAAAACCACGTCTGGGACGTTGGCATC
Found at i:38471835 original size:41 final size:42
Alignment explanation
Indices: 38471735--38471850 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 42
38471725 TGTGTTCTCG
** * *
38471735 TGTAAAACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAAACCATATCTGGGAC-ATGGCATCGATATGTGATTACA
* * *
38471778 TGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATT-CA
1 TGTAAAACCATATCTGGGACAT-GGCATCGATATGTGATTACA
*
38471819 TGTAAAACCCTATCTGGGACAGTGGCATCGAT
1 TGTAAAACCATATCTGGGACA-TGGCATCGAT
38471851 TTATCGATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 25 0.40
42 13 0.21
43 24 0.39
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAAACCATATCTGGGACATGGCATCGATATGTGATTACA
Found at i:38475622 original size:15 final size:17
Alignment explanation
Indices: 38475594--38475627 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38475584 TTATTAATTT
38475594 TAAAAGGTTAAAT-ATA
1 TAAAAGGTTAAATAATA
38475610 TAAAAGG-TAAATAATA
1 TAAAAGGTTAAATAATA
38475626 TA
1 TA
38475628 TATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAAGGTTAAATAATA
Found at i:38476577 original size:43 final size:42
Alignment explanation
Indices: 38476516--38476645 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 42
38476506 ATAGGATTTT
*
38476516 GATATGTGTTCTCGTGTAAAACCACGTCTGGGACGTTGGCATC
1 GATATGTGAT-TCGTGTAAAACCACGTCTGGGACGTTGGCATC
* * * *
38476559 GATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATGTGATT-CGTGTAAAACCACGTCTGGGACGTTGGCATC
* * *
38476602 -ATATTTGATTCATGTAAAACC-CTATCTGGGACAG-TGGCATC
1 GATATGTGATTCGTGTAAAACCAC-GTCTGGGAC-GTTGGCATC
38476643 GAT
1 GAT
38476646 TTATCGATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
41 23 0.32
42 12 0.17
43 36 0.51
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
GATATGTGATTCGTGTAAAACCACGTCTGGGACGTTGGCATC
Found at i:38476630 original size:41 final size:42
Alignment explanation
Indices: 38476530--38476645 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 42
38476520 TGTGTTCTCG
** * *
38476530 TGTAAAACCACGTCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAAACCATATCTGGGAC-ATGGCATCGATATGTGATTACA
* * *
38476573 TGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATT-CA
1 TGTAAAACCATATCTGGGACAT-GGCATCGATATGTGATTACA
*
38476614 TGTAAAACCCTATCTGGGACAGTGGCATCGAT
1 TGTAAAACCATATCTGGGACA-TGGCATCGAT
38476646 TTATCGATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 25 0.40
42 13 0.21
43 24 0.39
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAAACCATATCTGGGACATGGCATCGATATGTGATTACA
Found at i:38479859 original size:72 final size:73
Alignment explanation
Indices: 38479776--38479923 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
38479766 TTTAATGCTA
* * *
38479776 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
38479839 TAAATGCCG
65 TAAATGCCG
* * * * * *
38479848 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
38479913 AAATGCCG
66 AAATGCCG
38479921 TCC
1 TCC
38479924 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:38480131 original size:16 final size:16
Alignment explanation
Indices: 38480110--38480141 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38480100 CATTCTGCAT
38480110 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
38480126 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
38480142 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:38484674 original size:12 final size:11
Alignment explanation
Indices: 38484657--38484708 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
38484647 AGTAAGTGAA
38484657 AAAAAAGTTTC
1 AAAAAAGTTTC
38484668 GAAAAAAG-TTC
1 -AAAAAAGTTTC
38484679 AAAAAAAAGTTTC
1 --AAAAAAGTTTC
**
38484692 AAAAAAAATTC
1 AAAAAAGTTTC
38484703 AAAAAA
1 AAAAAA
38484709 AAATTGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 18 0.51
12 14 0.40
13 3 0.09
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAAAAGTTTC
Found at i:38484687 original size:24 final size:24
Alignment explanation
Indices: 38484655--38484710 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
38484645 CAAGTAAGTG
* *
38484655 AAAAAAAAGTTTCGAAAAAAGTTC
1 AAAAAAAAGTTTCAAAAAAAATTC
38484679 AAAAAAAAGTTTCAAAAAAAATTC
1 AAAAAAAAGTTTCAAAAAAAATTC
38484703 AAAAAAAA
1 AAAAAAAA
38484711 ATTGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAAAAAAGTTTCAAAAAAAATTC
Found at i:38484709 original size:12 final size:12
Alignment explanation
Indices: 38484669--38484713 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
38484659 AAAAGTTTCG
*
38484669 AAAAAAGTTCAA
1 AAAAAAATTCAA
*
38484681 AAAAAAGTTTC-A
1 AAAAAA-ATTCAA
38484693 AAAAAAATTCAA
1 AAAAAAATTCAA
38484705 AAAAAAATT
1 AAAAAAATT
38484714 GAAACTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:38488947 original size:17 final size:18
Alignment explanation
Indices: 38488925--38488966 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38488915 CATGTTTACA
38488925 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
38488942 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
38488960 TGGTTGA
1 TGGTTGA
38488967 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:38489930 original size:100 final size:100
Alignment explanation
Indices: 38489757--38489956 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
38489747 GCGGAGAACA
38489757 TAAAGTGACCAAGCAAGTACTCATTTCTTTCACCATTCGAAAGTACTTGGACGAAGTATTATGTG
1 TAAAGTGACCAAGCAAGTACTCATTTCTTTCACCATTCGAAAGTACTTGGACGAAGTATTATGTG
38489822 ACGTTGTTTCGATGCACGCGGGCCACCTACTCCTT
66 ACGTTGTTTCGATGCACGCGGGCCACCTACTCCTT
38489857 TAAAGTGACCAAGCAAGTACTCATTTCTTTCACCATTCGAAAGTACTTGGACGAAGTATTATGTG
1 TAAAGTGACCAAGCAAGTACTCATTTCTTTCACCATTCGAAAGTACTTGGACGAAGTATTATGTG
38489922 ACGTTGTTTCGATGCACGCGGGCCACCTACTCCTT
66 ACGTTGTTTCGATGCACGCGGGCCACCTACTCCTT
38489957 GGTCGTCCGT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (100 bp):
TAAAGTGACCAAGCAAGTACTCATTTCTTTCACCATTCGAAAGTACTTGGACGAAGTATTATGTG
ACGTTGTTTCGATGCACGCGGGCCACCTACTCCTT
Found at i:38490654 original size:17 final size:18
Alignment explanation
Indices: 38490632--38490673 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38490622 CATGTTTACA
38490632 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
38490649 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
38490667 TGGTTGA
1 TGGTTGA
38490674 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:38496641 original size:30 final size:30
Alignment explanation
Indices: 38496607--38496666 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38496597 ATTTAATACG
38496607 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
38496637 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
38496667 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:38514330 original size:55 final size:54
Alignment explanation
Indices: 38514235--38514384 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
38514225 CTACTTTGTT
* ** * *
38514235 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
38514289 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
38514344 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
38514385 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:38514347 original size:27 final size:27
Alignment explanation
Indices: 38514207--38514384 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
38514197 TAAATTGTAC
38514207 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
38514234 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
38514260 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
38514288 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
38514316 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
38514343 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
38514370 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38514385 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:38514348 original size:82 final size:81
Alignment explanation
Indices: 38514208--38514363 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
38514198 AAATTGTACA
* * * *
38514208 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
38514273 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
38514289 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
38514352 TGTGCGAGTTGA
63 TGTGCGAATTGA
38514364 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:38522304 original size:40 final size:37
Alignment explanation
Indices: 38522260--38522334 Score: 89
Period size: 37 Copynumber: 1.9 Consensus size: 37
38522250 TTAATATATA
38522260 TTTTAACACATATCATTACTTAT-TATTTATTATATTATGT
1 TTTTAACACATA--A-TACTTATATATTT-TTATATTATGT
* *
38522300 TTTTATCACATAATATTTATATATTTTTATATTAT
1 TTTTAACACATAATACTTATATATTTTTATATTAT
38522335 TATATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 15 0.47
38 6 0.19
40 11 0.34
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTAACACATAATACTTATATATTTTTATATTATGT
Found at i:38522581 original size:21 final size:22
Alignment explanation
Indices: 38522549--38522599 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
38522539 TATTTCAAAA
*
38522549 TTCATTATTTATT-ACTATGTT
1 TTCATTATTTATTAAATATGTT
38522570 TTCATGTA-TTATTAAATATG-T
1 TTCAT-TATTTATTAAATATGTT
38522591 TT-ATTATTT
1 TTCATTATTT
38522600 TATATTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 4 0.15
21 13 0.50
22 7 0.27
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (22 bp):
TTCATTATTTATTAAATATGTT
Found at i:38528399 original size:49 final size:43
Alignment explanation
Indices: 38528301--38528402 Score: 174
Period size: 43 Copynumber: 2.4 Consensus size: 43
38528291 ATCTATTATA
38528301 ATTTATATATTAATATTTATCAATTTAGCATAGAATTAGGATT
1 ATTTATATATTAATATTTATCAATTTAGCATAGAATTAGGATT
38528344 ATTTATATATTAATATTTATCAATTTAGCATAGAATTAGGATT
1 ATTTATATATTAATATTTATCAATTTAGCATAGAATTAGGATT
38528387 AGTTT-TA-ATT-ATATTT
1 A-TTTATATATTAATATTT
38528403 TATCTTTGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
41 6 0.10
42 3 0.05
43 46 0.79
44 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (43 bp):
ATTTATATATTAATATTTATCAATTTAGCATAGAATTAGGATT
Found at i:38541558 original size:14 final size:13
Alignment explanation
Indices: 38541532--38541556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38541522 TTTTTTTGAA
38541532 TTTTATTTTTTTC
1 TTTTATTTTTTTC
38541545 TTTTATTTTTTT
1 TTTTATTTTTTT
38541557 TCAATTTTTT
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:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTATTTTTTTC
Found at i:38542619 original size:6 final size:6
Alignment explanation
Indices: 38542533--38542605 Score: 83
Period size: 6 Copynumber: 12.0 Consensus size: 6
38542523 ATATAAAGAC
** * * * *
38542533 AAAATA AACGTA AAAACTT AAAATT AAAATT AAAATA AAGATA AAAATA
1 AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
38542582 AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA
38542606 TACTTAAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
6 53 0.91
7 5 0.09
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:38587411 original size:13 final size:13
Alignment explanation
Indices: 38587389--38587421 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
38587379 TTGCTATAGT
*
38587389 TTAG-TTAGTTGA
1 TTAGTTTAGTTAA
38587401 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
38587414 TTAGTTTA
1 TTAGTTTA
38587422 ATAAACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:38590998 original size:6 final size:6
Alignment explanation
Indices: 38590946--38590997 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
38590936 TCCTCCTATC
* * *
38590946 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTTTAA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
38590994 TTTT
1 TTTT
38590998 ATTATTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:38593939 original size:13 final size:13
Alignment explanation
Indices: 38593917--38593949 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
38593907 TTGCTTTAGT
38593917 TTAG-TTAGTTAA
1 TTAGTTTAGTTAA
38593929 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
38593942 TTAGTTTA
1 TTAGTTTA
38593950 ATAAACAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:38603621 original size:60 final size:60
Alignment explanation
Indices: 38603554--38603673 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
38603544 ATCCAGCTAT
* * * *
38603554 TATCAGTTGCGAGTTGAGGAGTCGGGCGTGCCTAAGACAGCTTTCGGAATGAGGTATGGC
1 TATCAGTTGCGAGTTAAAGAGTCGGGCATGCCTAAGACAGCTTTCAGAATGAGGTATGGC
38603614 TATCAGTTGCGAGTTAAAGAGTCGGGCATGCCTAAGACAGCTTTCAGAATGAGGTATGGC
1 TATCAGTTGCGAGTTAAAGAGTCGGGCATGCCTAAGACAGCTTTCAGAATGAGGTATGGC
38603674 CACTATGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (60 bp):
TATCAGTTGCGAGTTAAAGAGTCGGGCATGCCTAAGACAGCTTTCAGAATGAGGTATGGC
Found at i:38620672 original size:23 final size:23
Alignment explanation
Indices: 38620645--38620698 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
38620635 TGTTCTTAAG
38620645 CACACAGACATGTGCTTTGCCTC
1 CACACAGACATGTGCTTTGCCTC
* * * *
38620668 TACACGGGCGTGTGCTTTGCCTC
1 CACACAGACATGTGCTTTGCCTC
38620691 CACACAGA
1 CACACAGA
38620699 AGTGTGAGGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.24
Consensus pattern (23 bp):
CACACAGACATGTGCTTTGCCTC
Found at i:38626285 original size:75 final size:75
Alignment explanation
Indices: 38626162--38626306 Score: 272
Period size: 75 Copynumber: 1.9 Consensus size: 75
38626152 AATTACCATG
*
38626162 TTAGAGTGTTTGGTATTTAAGTAGTATTAATTGTTAACTAAGAAATGTAATAATGTGTTGTACTT
1 TTAGAGTGTTTGGTATTTAAGTAGTATAAATTGTTAACTAAGAAATGTAATAATGTGTTGTACTT
38626227 TTTTTATAAA
66 TTTTTATAAA
*
38626237 TTAGAGTGTTTGGTATTTAAGTAGTGTAAATTGTTAACTAAGAAATGTAATAATGTGTTGTACTT
1 TTAGAGTGTTTGGTATTTAAGTAGTATAAATTGTTAACTAAGAAATGTAATAATGTGTTGTACTT
38626302 TTTTT
66 TTTTT
38626307 TTTATAAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47
Consensus pattern (75 bp):
TTAGAGTGTTTGGTATTTAAGTAGTATAAATTGTTAACTAAGAAATGTAATAATGTGTTGTACTT
TTTTTATAAA
Found at i:38627416 original size:26 final size:26
Alignment explanation
Indices: 38627385--38627434 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
38627375 TCTGATTAGA
38627385 ATTTTCATATTTTCAAAACATATATC
1 ATTTTCATATTTTCAAAACATATATC
*
38627411 ATTTTCATATTTTCAGAACATATA
1 ATTTTCATATTTTCAAAACATATA
38627435 GCATATCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTTCATATTTTCAAAACATATATC
Found at i:38629432 original size:40 final size:39
Alignment explanation
Indices: 38629384--38629686 Score: 426
Period size: 40 Copynumber: 7.6 Consensus size: 39
38629374 CTACTTGCTC
* *
38629384 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACA
*
38629424 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACA
* *
38629464 AATGCCTTTGGGACTTAGCCCGGAAATAGTAACTCGTACA
1 AATGCCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACA
38629504 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACA
* * *
38629544 AATGCCTTCGGGACTTAGCCCGGAACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACA
* * *
38629584 AATGCCTTCGGGACTTAGCCCGGAACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACA
* *
38629624 AATGCCTTCGGGACTTAGCCCGGAACTAGTAACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACA
38629664 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
38629687 NNNNNNNNNN
Statistics
Matches: 248, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
39 2 0.01
40 245 0.99
41 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACA
Found at i:38635853 original size:40 final size:40
Alignment explanation
Indices: 38635791--38636088 Score: 485
Period size: 40 Copynumber: 7.5 Consensus size: 40
38635781 AAGCCAAGTA
* * * *
38635791 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCCAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
38635830 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38635870 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38635910 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38635950 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38635990 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38636030 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38636070 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38636089 TTATCATCCA
Statistics
Matches: 247, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
39 13 0.05
40 234 0.95
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38642701 original size:23 final size:23
Alignment explanation
Indices: 38642675--38642723 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
38642665 AATTACAAAA
*
38642675 TCCTAC-CCAACCAGCCTCTACAC
1 TCCTACTCCAACCAACC-CTACAC
* *
38642698 TCCTTCTCCATCCAACCCTACAC
1 TCCTACTCCAACCAACCCTACAC
38642721 TCC
1 TCC
38642724 ATGTAGGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.22, C:0.53, G:0.02, T:0.22
Consensus pattern (23 bp):
TCCTACTCCAACCAACCCTACAC
Found at i:38645658 original size:46 final size:46
Alignment explanation
Indices: 38645608--38645789 Score: 364
Period size: 46 Copynumber: 4.0 Consensus size: 46
38645598 TGGTTGAGCA
38645608 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
38645654 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
38645700 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
38645746 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
38645790 CACCTATTTG
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 136 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:38654059 original size:17 final size:18
Alignment explanation
Indices: 38654027--38654061 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38654017 CCGCGTTGTT
38654027 CACCCGTATGGGCCCACA
1 CACCCGTATGGGCCCACA
*
38654045 CACCCGTGT-GGCCCACA
1 CACCCGTATGGGCCCACA
38654062 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.46, G:0.23, T:0.11
Consensus pattern (18 bp):
CACCCGTATGGGCCCACA
Found at i:38667448 original size:40 final size:40
Alignment explanation
Indices: 38667393--38667591 Score: 287
Period size: 40 Copynumber: 5.0 Consensus size: 40
38667383 NNNTGACCAT
38667393 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
38667433 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
38667473 ATCCGAACTAAGATCTGAAGGCATTTATGTGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
*
38667513 ATCCAGG-TTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
**
38667553 ATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
1 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
38667592 TAACCGGNNN
Statistics
Matches: 147, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
39 3 0.02
40 143 0.97
41 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:38679516 original size:16 final size:16
Alignment explanation
Indices: 38679497--38679528 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38679487 AATTGTTTTA
38679497 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
38679513 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
38679529 ACTTCATTCT
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:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:38683577 original size:22 final size:23
Alignment explanation
Indices: 38683552--38683597 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
38683542 CAACCAAACC
38683552 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
38683574 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
38683597 A
1 A
38683598 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:38683603 original size:23 final size:23
Alignment explanation
Indices: 38683559--38683603 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38683549 ACCAATTCAA
*
38683559 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
38683582 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
38683604 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:38687824 original size:27 final size:27
Alignment explanation
Indices: 38687783--38687857 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
38687773 CTTTGTGGTA
* *
38687783 AAATGACTGTATTGCCCCTGTATA-G-T
1 AAATGACTATTTTGCCCCT-TATATGCT
38687809 AGAATGACTATTTTG-CCCTTATATGCT
1 A-AATGACTATTTTGCCCCTTATATGCT
38687836 AAGATGACTATTTTG-CCCTTAT
1 AA-ATGACTATTTTGCCCCTTAT
38687858 GTGATGTATG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 4 0.09
26 7 0.16
27 32 0.74
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (27 bp):
AAATGACTATTTTGCCCCTTATATGCT
Found at i:38688199 original size:19 final size:19
Alignment explanation
Indices: 38688175--38688216 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
38688165 TGGGTAGGAC
38688175 CTGCATACTACACTAATTA
1 CTGCATACTACACTAATTA
* *
38688194 CTGCATACTGCACTATTTA
1 CTGCATACTACACTAATTA
38688213 CTGC
1 CTGC
38688217 TACAGTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (19 bp):
CTGCATACTACACTAATTA
Found at i:38693804 original size:24 final size:24
Alignment explanation
Indices: 38693777--38693856 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
38693767 TTCCTGTTAA
*
38693777 TGGCTCTCTAGAGCTTCCCGATAT
1 TGGCTCTCTAGAGCTTCCCAATAT
* * * *
38693801 TGGCTCGCTTGAACCTTCCCAACAT
1 TGGCTCTCTAG-AGCTTCCCAATAT
* *
38693826 TGGCTC-ATATGAGCTTCCCAATAA
1 TGGCTCTCTA-GAGCTTCCCAATAT
38693850 TGGCTCT
1 TGGCTCT
38693857 TCGGAGCTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
24 26 0.60
25 17 0.40
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (24 bp):
TGGCTCTCTAGAGCTTCCCAATAT
Found at i:38693863 original size:24 final size:24
Alignment explanation
Indices: 38693725--38693868 Score: 67
Period size: 24 Copynumber: 5.8 Consensus size: 24
38693715 GTCCTGATAT
38693725 ATGGCTCTTCGTGAGCTTCCCAATTA
1 ATGGCTCTTCG-GAGCTTCCCAA-TA
* *** ***
38693751 AAGGCTCTTATTAAGCTTCCTGTTA
1 ATGGCTCTT-CGGAGCTTCCCAATA
* *
38693776 ATGGCTC-TCTAGAGCTTCCCGATA
1 ATGGCTCTTC-GGAGCTTCCCAATA
* * * *
38693800 TTGGCTCGCTT-GAACCTTCCCAACA
1 ATGGCT--CTTCGGAGCTTCCCAATA
* * **
38693825 TTGGCTCATATGAGCTTCCCAATA
1 ATGGCTCTTCGGAGCTTCCCAATA
38693849 ATGGCTCTTCGGAGCTTCCC
1 ATGGCTCTTCGGAGCTTCCC
38693869 GTTATATGGC
Statistics
Matches: 84, Mismatches: 28, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
23 2 0.02
24 42 0.50
25 23 0.27
26 16 0.19
27 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (24 bp):
ATGGCTCTTCGGAGCTTCCCAATA
Found at i:38694645 original size:22 final size:22
Alignment explanation
Indices: 38694617--38694662 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
38694607 GCTTGAATTA
* *
38694617 ATTGTCTTGTATTGTTTTGTTT
1 ATTGTCTTGTATTCTTTTATTT
38694639 ATTGTCTTGTATTCTTTTATTT
1 ATTGTCTTGTATTCTTTTATTT
38694661 AT
1 AT
38694663 GTGTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (22 bp):
ATTGTCTTGTATTCTTTTATTT
Found at i:38705635 original size:50 final size:50
Alignment explanation
Indices: 38705571--38705913 Score: 327
Period size: 50 Copynumber: 6.8 Consensus size: 50
38705561 AACAATCCGG
* * *
38705571 TACATGTAGTAGCCTGCACTTAGTCCTACACACGTGACCTAACCATCTGA
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGA
* * * * *
38705621 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGG
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CTATCTGA
* * * * * * *
38705672 TACGCATAGTATCTTGCACTTAGTACTACACATGCGA-CTAACTATCTGG
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGA
* * * * *
38705721 TACATGTAGTAGCCTGCACATAGTACTTCACACATGACCTAACCATCTGA
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGA
* * *
38705771 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCATGTA
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CTATC-TG-A
* * * * * *
38705824 TGCA--TAGTAGACTGCACTTAGTACAACACATGCGACCTAACTATCTGG
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGA
*
38705872 TACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
38705914 AACCATGTTA
Statistics
Matches: 231, Mismatches: 52, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
48 3 0.01
49 36 0.16
50 119 0.52
51 66 0.29
52 3 0.01
53 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGA
Found at i:38705753 original size:150 final size:149
Alignment explanation
Indices: 38705520--38705951 Score: 594
Period size: 150 Copynumber: 2.9 Consensus size: 149
38705510 GAAGCTATCT
* * * * * * * * *
38705520 GGTACGCATAGTAGCCTGAAGTTCGTAATACACATGCAACCAACAATCCGGTACATGTAGTAGCC
1 GGTACGCATAGTA-ACTGCACTTAGTACTACACATGCGACTAACTATCTGGTACATGTAGTAGCC
*
38705585 TGCACTTAGTCCTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
65 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
*
38705650 ACACGTGATTGAAGTTGTCG
130 ACACGTGATTGAAGTTGTCA
*
38705670 GGTACGCATAGTATCTTGCACTTAGTACTACACATGCGACTAACTATCTGGTACATGTAGTAGCC
1 GGTACGCATAGTAAC-TGCACTTAGTACTACACATGCGACTAACTATCTGGTACATGTAGTAGCC
* * *
38705735 TGCACATAGTACTTCACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
65 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
38705800 ACACGTGATTGAAGTTGTCA
130 ACACGTGATTGAAGTTGTCA
* * *
38705820 TGTATGCATAGTAGACTGCACTTAGTACAACACATGCGACCTAACTATCTGGTACATGTAGTAGC
1 GGTACGCATAGTA-ACTGCACTTAGTACTACACATGCGA-CTAACTATCTGGTACATGTAGTAGC
* * * * * *
38705885 CTGCACTTAGTACTACACACGTGACCTAAAACCATGTTAAACACATAGTATCCTGCACATAGTAC
64 CTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACGTAGTAGCCTGCACTTAGTAC
38705950 TA
127 TA
38705952 TACATGTGTT
Statistics
Matches: 250, Mismatches: 27, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
149 1 0.00
150 167 0.67
151 50 0.20
153 32 0.13
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (149 bp):
GGTACGCATAGTAACTGCACTTAGTACTACACATGCGACTAACTATCTGGTACATGTAGTAGCCT
GCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
CACGTGATTGAAGTTGTCA
Found at i:38716498 original size:168 final size:168
Alignment explanation
Indices: 38716215--38716555 Score: 673
Period size: 168 Copynumber: 2.0 Consensus size: 168
38716205 TACATAAGCT
*
38716215 TAATAGCTTAACAGATTATATCATTCAGTCAAACATTCTCATATCTTATAACTCAAATATGCAAT
1 TAATTGCTTAACAGATTATATCATTCAGTCAAACATTCTCATATCTTATAACTCAAATATGCAAT
38716280 TACAAACTCAATCAAACATTCATACTTTCAAACTAGTAGTTTTGCCAACATGCCAATCTTTTAAG
66 TACAAACTCAATCAAACATTCATACTTTCAAACTAGTAGTTTTGCCAACATGCCAATCTTTTAAG
38716345 GCTCGAAACATACCTAGTTCGGCCACTCACAAAATCAA
131 GCTCGAAACATACCTAGTTCGGCCACTCACAAAATCAA
38716383 TAATTGCTTAACAGATTATATCATTCAGTCAAACATTCTCATATCTTATAACTCAAATATGCAAT
1 TAATTGCTTAACAGATTATATCATTCAGTCAAACATTCTCATATCTTATAACTCAAATATGCAAT
38716448 TACAAACTCAATCAAACATTCATACTTTCAAACTAGTAGTTTTGCCAACATGCCAATCTTTTAAG
66 TACAAACTCAATCAAACATTCATACTTTCAAACTAGTAGTTTTGCCAACATGCCAATCTTTTAAG
38716513 GCTCGAAACATACCTAGTTCGGCCACTCACAAAATCAA
131 GCTCGAAACATACCTAGTTCGGCCACTCACAAAATCAA
38716551 TAATT
1 TAATT
38716556 TGGCTATTAA
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 172 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (168 bp):
TAATTGCTTAACAGATTATATCATTCAGTCAAACATTCTCATATCTTATAACTCAAATATGCAAT
TACAAACTCAATCAAACATTCATACTTTCAAACTAGTAGTTTTGCCAACATGCCAATCTTTTAAG
GCTCGAAACATACCTAGTTCGGCCACTCACAAAATCAA
Found at i:38727902 original size:23 final size:21
Alignment explanation
Indices: 38727849--38727902 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
38727839 AAAGGAAATT
* *
38727849 AAAGAAGGAAGAGATGAGATA
1 AAAGAAGAAAGAAATGAGATA
38727870 AAAGAAAAGAAAGAAATGAAGAGTA
1 AAAG--AAGAAAGAAATG-AGA-TA
38727895 AAAGAAGA
1 AAAGAAGA
38727903 TAATTTCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.15
23 14 0.52
24 3 0.11
25 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (21 bp):
AAAGAAGAAAGAAATGAGATA
Found at i:38745554 original size:32 final size:32
Alignment explanation
Indices: 38745517--38745580 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
38745507 AAGAGAGAAA
38745517 ACCAAGAAGTGACCAAAAATCCCTTGATTTTC
1 ACCAAGAAGTGACCAAAAATCCCTTGATTTTC
* **
38745549 ACCAAGATGTGACTGAAAATCCCTTGATTTTC
1 ACCAAGAAGTGACCAAAAATCCCTTGATTTTC
38745581 TCCCACTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (32 bp):
ACCAAGAAGTGACCAAAAATCCCTTGATTTTC
Found at i:38746477 original size:16 final size:16
Alignment explanation
Indices: 38746456--38746514 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
38746446 AATGCCATTA
38746456 TTCTAAATAATAGTTG
1 TTCTAAATAATAGTTG
*
38746472 TTCTAAACT-TTAGTTG
1 TTCTAAA-TAATAGTTG
* **
38746488 TTCTCAATAGGAGTTG
1 TTCTAAATAATAGTTG
38746504 TTCTCAAATAA
1 TTCT-AAATAA
38746515 CAACACTGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.82
17 5 0.15
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (16 bp):
TTCTAAATAATAGTTG
Found at i:38751089 original size:3 final size:3
Alignment explanation
Indices: 38751081--38751124 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
38751071 ACTTTGAGGA
*
38751081 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
38751125 CATTAACTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.30, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:38753613 original size:25 final size:25
Alignment explanation
Indices: 38753585--38753633 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
38753575 CTTATAATCA
* *
38753585 AAAAATGACTATTTTACCCCTAGGT
1 AAAAATGACCATTGTACCCCTAGGT
38753610 AAAAATGACCATTGTACCCCTAGG
1 AAAAATGACCATTGTACCCCTAGG
38753634 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (25 bp):
AAAAATGACCATTGTACCCCTAGGT
Found at i:38753782 original size:25 final size:25
Alignment explanation
Indices: 38753746--38753840 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
38753736 GAGGAAGTGC
*
38753746 AAAAGGGTTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
38753771 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
38753796 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
38753821 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
38753841 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:38753853 original size:24 final size:25
Alignment explanation
Indices: 38753745--38753853 Score: 111
Period size: 25 Copynumber: 4.4 Consensus size: 25
38753735 GGAGGAAGTG
* *
38753745 CAAAAG-GGTTTTGCCCCAGTTTAC
1 CAAAAGAGGCTTTGCCCCAGTTTAT
* *
38753769 CGAAAAG-GGCTTTGCCCTAGTTTAC
1 C-AAAAGAGGCTTTGCCCCAGTTTAT
38753794 CGAAAAG-GGCTTTGCCCCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAGTTTAT
38753819 CAAAA-AGGGCTTTGCCCCAG-TTAT
1 CAAAAGA-GGCTTTGCCCCAGTTTAT
*
38753843 TAAAAGAGGCT
1 CAAAAGAGGCT
38753854 AGGCCTCAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
24 17 0.22
25 59 0.78
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
CAAAAGAGGCTTTGCCCCAGTTTAT
Found at i:38754095 original size:30 final size:31
Alignment explanation
Indices: 38754061--38754143 Score: 125
Period size: 30 Copynumber: 2.7 Consensus size: 31
38754051 CGTTTACAGT
38754061 AAAGGCTTTGGCCCAGTGATATG-ATAATGA
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
* * *
38754091 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
38754122 AAAGGCTTTGGCCCAGT-ATATG
1 AAAGGCTTTGGCCCAGTGATATG
38754144 TTGAGATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGAATAATGA
Found at i:38754126 original size:31 final size:30
Alignment explanation
Indices: 38754061--38754138 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 30
38754051 CGTTTACAGT
*
38754061 AAAGGCTTTGGCCCAGTGATATGATAATGA
1 AAAGGCTTTGGCCCAGTGACATGATAATGA
* *
38754091 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTTGGCCCAGTGACATG-ATAATGA
38754122 AAAGGCTTTGGCCCAGT
1 AAAGGCTTTGGCCCAGT
38754139 ATATGTTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (30 bp):
AAAGGCTTTGGCCCAGTGACATGATAATGA
Found at i:38755833 original size:35 final size:35
Alignment explanation
Indices: 38755781--38755861 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
38755771 TAGAGACAGT
* * *
38755781 CAGACACAGATTCAGGCTTAAGCCCATTACTGATC
1 CAGATACAGATTCAGGCTTAAGCCCATTACAGATA
* *
38755816 CAGATGCAGATTCAGGCTTAAGCCCATTCCAGATA
1 CAGATACAGATTCAGGCTTAAGCCCATTACAGATA
38755851 CAGATACAGAT
1 CAGATACAGAT
38755862 ACAAATACAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (35 bp):
CAGATACAGATTCAGGCTTAAGCCCATTACAGATA
Found at i:38755856 original size:6 final size:6
Alignment explanation
Indices: 38755845--38755874 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
38755835 AAGCCCATTC
*
38755845 CAGATA CAGATA CAGATA CAAATA CAGATA
1 CAGATA CAGATA CAGATA CAGATA CAGATA
38755875 TGCAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (6 bp):
CAGATA
Found at i:38757549 original size:43 final size:43
Alignment explanation
Indices: 38757429--38757591 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 43
38757419 AGCTCGTACA
*
38757429 ATGCCAACGTCCCAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAATCAAATA-CG
** * *
38757472 ATGCCATTGTCCTAGATAG-GGTCTTACAC-AAAATCAAATACG
1 ATGCCAACGTCCCAGAT-GTGGTCTTACACGTAAATCAAATACG
* *
38757514 ATGCCAACGTCTCATATGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAATCA-AA-TACG
* *
38757558 ATGCCAACGTCCCAGACGAGGTCTTACACAGTAA
1 ATGCCAACGTCCCAGATGTGGTCTTACAC-GTAA
38757592 CACATATCAA
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 24 0.24
43 38 0.39
44 30 0.31
45 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGTAAATCAAATACG
Found at i:38757586 original size:86 final size:85
Alignment explanation
Indices: 38757429--38757587 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 85
38757419 AGCTCGTACA
* ** * *
38757429 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAATATCGATGCCATTGTCCTAGATAGGGT
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAATCAAATATCGATGCCAACGTCCCAGAGAGGGT
38757494 CTTACACAAAATCAAATACG
66 CTTACACAAAATCAAATACG
* * *
38757514 ATGCCAACGTCTCATATGTGGTCTTACACGTAAATCATAA-GTCGATGCCAACGTCCCAGACGA-
1 ATGCCAACGTCCCAGATGTGGTCTTACACGT-AATCA-AATATCGATGCCAACGTCCCAGA-GAG
38757577 GGTCTTACACA
63 GGTCTTACACA
38757588 GTAACACATA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
85 28 0.44
86 32 0.51
87 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (85 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGTAATCAAATATCGATGCCAACGTCCCAGAGAGGGT
CTTACACAAAATCAAATACG
Found at i:38762936 original size:25 final size:25
Alignment explanation
Indices: 38762908--38763046 Score: 145
Period size: 25 Copynumber: 5.6 Consensus size: 25
38762898 ATAATAGATT
*
38762908 GGCACATAGCCATCAATATCATATC
1 GGCACAAAGCCATCAATATCATATC
* *** * *
38762933 GGCACAAAGACAAGGATAACAGATC
1 GGCACAAAGCCATCAATATCATATC
*
38762958 GGCACATAGCCATCAATATCATATC
1 GGCACAAAGCCATCAATATCATATC
* ** *
38762983 GGGACAAAGCCATTGATAAT-AGATC
1 GGCACAAAGCCATCAAT-ATCATATC
*
38763008 GGCACATAGCCATCAATATCATATC
1 GGCACAAAGCCATCAATATCATATC
38763033 GGCACAAAGCCATC
1 GGCACAAAGCCATC
38763047 GATAACAGAA
Statistics
Matches: 87, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
24 2 0.02
25 83 0.95
26 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (25 bp):
GGCACAAAGCCATCAATATCATATC
Found at i:38762962 original size:50 final size:50
Alignment explanation
Indices: 38762880--38763055 Score: 255
Period size: 50 Copynumber: 3.5 Consensus size: 50
38762870 TGATAATACG
* * *
38762880 ATCGGTACAAAGCCA-CTGATAATAGATTGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATC-GATAACAGATCGGCACATAGCCATCAATATCAT
* **
38762930 ATCGGCACAAAGACAAGGATAACAGATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
* * *
38762980 ATCGGGACAAAGCCATTGATAATAGATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
38763030 ATCGGCACAAAGCCATCGATAACAGA
1 ATCGGCACAAAGCCATCGATAACAGA
38763056 ATAATTGGCT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 112 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (50 bp):
ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
Found at i:38763242 original size:41 final size:41
Alignment explanation
Indices: 38763197--38763317 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 41
38763187 AAAAGCCACT
** *
38763197 GTGGATCCACGGTAATCAAGCAACCATGCGATCCTTAATCA
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATCA
* * *
38763238 GTGGATCCACGATCGTCAAGTAACCATGCGATCCTCAATCG
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATCA
** *
38763279 GTGGATCCAAAGTCGTCAAACAACCATGCGATCCTCAAT
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
38763318 TTCTTCCTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (41 bp):
GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATCA
Found at i:38763598 original size:27 final size:27
Alignment explanation
Indices: 38763568--38763619 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38763558 GGGTGTTTTG
38763568 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * * *
38763595 GTAATTTTGCAAACCAATGGTATTT
1 GTAAATCTACAAACCAAGGGTATTT
38763620 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:38763625 original size:27 final size:27
Alignment explanation
Indices: 38763577--38763797 Score: 203
Period size: 27 Copynumber: 8.2 Consensus size: 27
38763567 GGTAAATCTA
*
38763577 CAAACCAAGGGTATTTCAGTAATTTTG
1 CAAACCAAGGGTATTTTAGTAATTTTG
* *
38763604 CAAACCAATGGTATTTTTGTAATTTTTG
1 CAAACCAAGGGTATTTTAGTAA-TTTTG
* *
38763632 -AAAGTCAAGGGTATTTTTGTAATTTTG
1 CAAA-CCAAGGGTATTTTAGTAATTTTG
* * * * *
38763659 TAAATCAAGAGTATTTTTGTAATTTTC
1 CAAACCAAGGGTATTTTAGTAATTTTG
* * *
38763686 CAAATCAAGGGTATTTCAGTAATTTTC
1 CAAACCAAGGGTATTTTAGTAATTTTG
** * * *
38763713 CAAATTAGGGGTATTTTGGTAATTTTA
1 CAAACCAAGGGTATTTTAGTAATTTTG
* * *
38763740 CAAACTAGGGGTATTTTGGTAATTTTG
1 CAAACCAAGGGTATTTTAGTAATTTTG
*
38763767 TAAACCAAGGGTA-TTTAGTAATTTTG
1 CAAACCAAGGGTATTTTAGTAATTTTG
*
38763793 TAAAC
1 CAAAC
38763798 TAATGGTCAG
Statistics
Matches: 169, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.10
27 128 0.76
28 24 0.14
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (27 bp):
CAAACCAAGGGTATTTTAGTAATTTTG
Found at i:38763727 original size:54 final size:54
Alignment explanation
Indices: 38763555--38763791 Score: 226
Period size: 54 Copynumber: 4.4 Consensus size: 54
38763545 TTTCACCCTA
* * * * * *
38763555 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGCAAAC
1 CAAGGGTATTTTTGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTGCAAAT
* ** ** *
38763609 CAATGGTATTTTTGTAATTTTTGAAAGTCAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTTGTAATTTTACAAA-TCAAGGGTATTTCAGTAATTTTGCAAAT
* * *
38763664 CAAGAGTATTTTTGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTCCAAAT
1 CAAGGGTATTTTTGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTGCAAAT
* * * * ** * *
38763718 TAGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTTGTAATTTTACAAATC-AAGGGTATTTCAGTAATTTTGCAAAT
*
38763772 CAAGGGTA-TTTAGTAATTTT
1 CAAGGGTATTTTTGTAATTTT
38763792 GTAAACTAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 12 0.08
54 90 0.61
55 45 0.31
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
CAAGGGTATTTTTGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTGCAAAT
Found at i:38766908 original size:41 final size:41
Alignment explanation
Indices: 38766846--38766968 Score: 183
Period size: 41 Copynumber: 3.0 Consensus size: 41
38766836 TTAAAGCCAC
*
38766846 CGGTGGATCCATAGTCATCAAGCAACCATGCGATCCTTAAT
1 CGGTGGATCCATAGTCGTCAAGCAACCATGCGATCCTTAAT
* * * *
38766887 CGGTGGGTCCATAGTCGTCAAGCAACCGTGCTATCCTGAAT
1 CGGTGGATCCATAGTCGTCAAGCAACCATGCGATCCTTAAT
* *
38766928 CAGTGGATCCACAGTCGTCAAGCAACCATGCGATCCTTAAT
1 CGGTGGATCCATAGTCGTCAAGCAACCATGCGATCCTTAAT
38766969 TTCTTCCTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
CGGTGGATCCATAGTCGTCAAGCAACCATGCGATCCTTAAT
Found at i:38767224 original size:26 final size:27
Alignment explanation
Indices: 38767194--38767249 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
38767184 TATAAGGGTG
38767194 TTTTGGTAAATCTACAAACCAA-GGTA
1 TTTTGGTAAATCTACAAACCAATGGTA
* * *
38767220 TTTTGGTAATTTTGCAAACCAATGGTA
1 TTTTGGTAAATCTACAAACCAATGGTA
38767247 TTT
1 TTT
38767250 CTGTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (27 bp):
TTTTGGTAAATCTACAAACCAATGGTA
Found at i:38767255 original size:27 final size:27
Alignment explanation
Indices: 38767187--38767519 Score: 225
Period size: 27 Copynumber: 12.4 Consensus size: 27
38767177 TTCACCCTAT
* * * * *
38767187 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTGCAAATC
*
38767214 AA-GGTATTTTGGTAATTTTGCAAACC
1 AAGGGTATTTTGGTAATTTTGCAAATC
*
38767240 AATGGTATTTCT-GTAATTTTTG-AAAGTC
1 AAGGGTATTT-TGGTAA-TTTTGCAAA-TC
* *
38767268 AAGGGTATTTCT-GTAATTTTGTAAATT
1 AAGGGTATTT-TGGTAATTTTGCAAATC
* *
38767295 AGGGGTATTTCT-GTAATTTT-CTAAATT
1 AAGGGTATTT-TGGTAATTTTGC-AAATC
** *
38767322 AAGGGTATTTCAGTAATTTTCCAAATC
1 AAGGGTATTTTGGTAATTTTGCAAATC
* * *
38767349 AAGGATATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTGCAAATC
* ***
38767376 GAGGGTATTTTGGTAATTTCAAAAAT-
1 AAGGGTATTTTGGTAATTTTGCAAATC
** * *
38767402 TTGAGGTATTTTGGTAATTTTACAAACC
1 AAG-GGTATTTTGGTAATTTTGCAAATC
* *
38767430 AAGGGTATTTTGGTAATTTTGCTAATT
1 AAGGGTATTTTGGTAATTTTGCAAATC
* *
38767457 GAGGGTATTTTGGTAATTTTGTAAA-C
1 AAGGGTATTTTGGTAATTTTGCAAATC
*** * *
38767483 TAAGGGTA-TCCAGTAATTTTGTAAACC
1 -AAGGGTATTTTGGTAATTTTGCAAATC
38767510 AAGGGTATTT
1 AAGGGTATTT
38767520 CAGTAATTCT
Statistics
Matches: 252, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
26 44 0.17
27 181 0.72
28 27 0.11
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTGCAAATC
Found at i:38767384 original size:81 final size:81
Alignment explanation
Indices: 38767216--38767519 Score: 298
Period size: 81 Copynumber: 3.8 Consensus size: 81
38767206 TACAAACCAA
** * * **
38767216 GGTATTTTGGTAATTTTGC-AAACCAATGGTATTTCTGTAATTTTTGAAAGTCAAGGGTATTTCT
1 GGTATTTTGGTAATTTT-CTAAATTAAGGGTATTTCAGTAATTTTACAAA-TCAAGGGTATTT-T
*
38767280 -GTAATTTTGTAAATT-AGG
63 GGTAATTTTGCAAATTGA-G
* *
38767298 GGTATTTCT-GTAATTTTCTAAATTAAGGGTATTTCAGTAATTTTCCAAATCAAGGATATTTTGG
1 GGTATTT-TGGTAATTTTCTAAATTAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGG
*
38767362 TAATTTTACAAATTGAG
65 TAATTTTGCAAATTGAG
* * ** *
38767379 GGTATTTTGGTAA-TTTCAAAAATT-TGAGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTG
1 GGTATTTTGGTAATTTTC-TAAATTAAG-GGTATTTCAGTAATTTTACAAATCAAGGGTATTTTG
*
38767442 GTAATTTTGCTAATTGAG
64 GTAATTTTGCAAATTGAG
* * * ** *
38767460 GGTATTTTGGTAATTTTGTAAACTAAGGGTA-TCCAGTAATTTTGTAAACCAAGGGTATTT
1 GGTATTTTGGTAATTTTCTAAATTAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTT
38767520 CAGTAATTCT
Statistics
Matches: 186, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
80 31 0.17
81 110 0.59
82 44 0.24
83 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.43
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTCTAAATTAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGT
AATTTTGCAAATTGAG
Found at i:38767504 original size:26 final size:27
Alignment explanation
Indices: 38767469--38767527 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
38767459 GGGTATTTTG
*
38767469 GTAATTTTGTAAACTAAGGGTA-TCCA
1 GTAATTTTGTAAACCAAGGGTATTCCA
*
38767495 GTAATTTTGTAAACCAAGGGTATTTCA
1 GTAATTTTGTAAACCAAGGGTATTCCA
38767522 GTAATT
1 GTAATT
38767528 CTACCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
GTAATTTTGTAAACCAAGGGTATTCCA
Found at i:38767546 original size:27 final size:27
Alignment explanation
Indices: 38767516--38767619 Score: 145
Period size: 27 Copynumber: 3.9 Consensus size: 27
38767506 AACCAAGGGT
38767516 ATTTCAGTAATTCTACCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* ** *
38767543 ATTTTAGTAATTCTATTCTATAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
*
38767570 ATTTTAGTAATTCTACCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
38767597 ATTTCAGTAATACTAGCCTACAG
1 ATTTCAGTAATTCTACCCTACAG
38767620 ATATGAGATT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:38772707 original size:25 final size:25
Alignment explanation
Indices: 38772679--38772728 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38772669 CCTTATATTA
* * *
38772679 TGAAAATGACTGTTTTGCCCCTAGG
1 TGAAAATGACCGTTATACCCCTAGG
38772704 TGAAAATGACCGTTATACCCCTAGG
1 TGAAAATGACCGTTATACCCCTAGG
38772729 GTTTACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
TGAAAATGACCGTTATACCCCTAGG
Found at i:38772789 original size:20 final size:20
Alignment explanation
Indices: 38772764--38772810 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
38772754 ATTTTGATAT
38772764 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
38772784 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
38772804 ACATGAT
1 ACATGAT
38772811 GTATTCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:38772923 original size:26 final size:26
Alignment explanation
Indices: 38772860--38773009 Score: 243
Period size: 27 Copynumber: 5.8 Consensus size: 26
38772850 GAGGAAGTGC
38772860 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
38772886 TAAAAGGGCTTATGCCCCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
*
38772913 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
38772939 AAAAAGGGCTTATGCCCCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
*
38772966 AAAAGGG-TT-TGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
38772990 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
38773010 ATTAAAGAAG
Statistics
Matches: 118, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
24 21 0.18
25 14 0.12
26 32 0.27
27 51 0.43
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:38772944 original size:53 final size:52
Alignment explanation
Indices: 38772860--38773009 Score: 243
Period size: 53 Copynumber: 2.9 Consensus size: 52
38772850 GAGGAAGTGC
38772860 AAAAGGGCTTATGCCCCAGTTTATTGTAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG-AAAAGGGCTTATGCCCCAGTTTATTG
*
38772913 AAAAGGGCTTATGCCCTAGTTTATTGAAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG-AAAAGGGCTTATGCCCCAGTTTATTG
*
38772966 AAAAGGG-TT-TGCCCCAGTTTACTGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTT
38773010 ATTAAAGAAG
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
49 10 0.11
50 10 0.11
51 13 0.14
52 2 0.02
53 58 0.62
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:38775682 original size:44 final size:40
Alignment explanation
Indices: 38775634--38775733 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 40
38775624 TAGAACGATT
*
38775634 TCGCACACTTAGTGCCATTTCAATTAACCGAAGCTATCTCAGTA
1 TCGCACACTTAGTGCCA-TT-AA-TAACCGAAGCTAT-TCAGAA
* **
38775678 TCGCACACTTAGTGCC-TTAATAGCCGAAGCTATTTTGAA
1 TCGCACACTTAGTGCCATTAATAACCGAAGCTATTCAGAA
*
38775717 TTGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
38775734 AATACCATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 18 0.36
40 12 0.24
41 2 0.04
42 2 0.04
44 16 0.32
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (40 bp):
TCGCACACTTAGTGCCATTAATAACCGAAGCTATTCAGAA
Found at i:38779319 original size:10 final size:10
Alignment explanation
Indices: 38779304--38779346 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
38779294 CAATTTACCA
38779304 ACCAAATCAT
1 ACCAAATCAT
*
38779314 ACCAAATCTAA
1 ACCAAATC-AT
38779325 ACCAAAATCAT
1 ACC-AAATCAT
*
38779336 ACCAAAGCAT
1 ACCAAATCAT
38779346 A
1 A
38779347 TATTTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 15 0.54
11 8 0.29
12 5 0.18
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.16
Consensus pattern (10 bp):
ACCAAATCAT
Found at i:38785188 original size:79 final size:81
Alignment explanation
Indices: 38785052--38785236 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
38785042 TTGAATGATG
* *
38785052 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
38785116 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
38785131 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
38785193 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
38785211 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38785237 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:38785250 original size:40 final size:40
Alignment explanation
Indices: 38785053--38785236 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
38785043 TGAATGATGT
* * * *
38785053 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
38785093 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
38785133 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
38785171 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
38785212 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
38785237 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:38785258 original size:79 final size:79
Alignment explanation
Indices: 38785105--38785269 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
38785095 GGACTAAGAT
* * **
38785105 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
38785170 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
38785184 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
38785247 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
38785263 CCGAAGG
1 CCGAAGG
38785270 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:38792731 original size:40 final size:41
Alignment explanation
Indices: 38792635--38792739 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 41
38792625 TGAATGATGT
*
38792635 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
* * * *
38792675 CCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCATAA
*
38792715 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
38792740 AACGAGTAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.84
41 8 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
Found at i:38795441 original size:19 final size:19
Alignment explanation
Indices: 38795419--38795456 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
38795409 ATACCAAACT
38795419 CAAAATT-AAAGTTCCAAAA
1 CAAAATTAAAAG-TCCAAAA
38795438 CAAAATTAAAAGTCCAAAA
1 CAAAATTAAAAGTCCAAAA
38795457 GTTCGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (19 bp):
CAAAATTAAAAGTCCAAAA
Found at i:38795679 original size:26 final size:26
Alignment explanation
Indices: 38795650--38795699 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
38795640 TTAGATCAAA
*
38795650 ATTTTCATTTTTTTAGAACATATATC
1 ATTTTCATATTTTTAGAACATATATC
38795676 ATTTTCATATTTTTAGAACATATA
1 ATTTTCATATTTTTAGAACATATA
38795700 ACATATTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTTCATATTTTTAGAACATATATC
Found at i:38796875 original size:10 final size:11
Alignment explanation
Indices: 38796850--38796880 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
38796840 AGAATACTCA
38796850 AAAAGAAAAAG
1 AAAAGAAAAAG
38796861 AAAAGAAAAAG
1 AAAAGAAAAAG
38796872 -AAAGAAAAA
1 AAAAGAAAAA
38796881 ACGTAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:38806063 original size:393 final size:393
Alignment explanation
Indices: 38805338--38806123 Score: 1563
Period size: 393 Copynumber: 2.0 Consensus size: 393
38805328 TGTTTAATAA
38805338 AAATTTAATTATGCATATTTGAATGATAAATTGATACTTTGGCCATAAATACTTTAGTATTGAGT
1 AAATTTAATTATGCATATTTGAATGATAAATTGATACTTTGGCCATAAATACTTTAGTATTGAGT
*
38805403 TTTAGATATAATGATTAATGTTCGATAATAATTCGATATTGGAAAGAGAACTTGTATAATTTATA
66 TTCAGATATAATGATTAATGTTCGATAATAATTCGATATTGGAAAGAGAACTTGTATAATTTATA
38805468 TGTAAGACCATATTTTGTATTATGGCTTTGTATGATAACAAGAAAGTATTGACTAGCATAGTTTG
131 TGTAAGACCATATTTTGTATTATGGCTTTGTATGATAACAAGAAAGTATTGACTAGCATAGTTTG
38805533 ATGAGAATAAGTTAAGTTGATGATATGATGAGATTGAGAATGTAAGAATGTAAGTTGAGTAGCAT
196 ATGAGAATAAGTTAAGTTGATGATATGATGAGATTGAGAATGTAAGAATGTAAGTTGAGTAGCAT
38805598 TTTATTATTATGCAATTATTGTTATTAGTATTGTTATTATTGAGTTATGCGACTAGCCTTGAGAA
261 TTTATTATTATGCAATTATTGTTATTAGTATTGTTATTATTGAGTTATGCGACTAGCCTTGAGAA
38805663 TTTGAGTAAGTAAGTTTCAGCTATGACTTGACAAGGCATTGATATCTCAAAGTCCATGGTTGTAC
326 TTTGAGTAAGTAAGTTTCAGCTATGACTTGACAAGGCATTGATATCTCAAAGTCCATGGTTGTAC
38805728 CAT
391 CAT
38805731 AAATTTAATTATGCATATTTGAATGATAAATTGATACTTTGGCCATAAATACTTTAGTATTGAGT
1 AAATTTAATTATGCATATTTGAATGATAAATTGATACTTTGGCCATAAATACTTTAGTATTGAGT
38805796 TTCAGATATAATGATTAATGTTCGATAATAATTCGATATTGGAAAGAGAACTTGTATAATTTATA
66 TTCAGATATAATGATTAATGTTCGATAATAATTCGATATTGGAAAGAGAACTTGTATAATTTATA
38805861 TGTAAGACCATATTTTGTATTATGGCTTTGTATGATAACAAGAAAGTATTGACTAGCATAGTTTG
131 TGTAAGACCATATTTTGTATTATGGCTTTGTATGATAACAAGAAAGTATTGACTAGCATAGTTTG
38805926 ATGAGAATAAGTTAAGTTGATGATATGATGAGATTGAGAATGTAAGAATGTAAGTTGAGTAGCAT
196 ATGAGAATAAGTTAAGTTGATGATATGATGAGATTGAGAATGTAAGAATGTAAGTTGAGTAGCAT
38805991 TTTATTATTATGCAATTATTGTTATTAGTATTGTTATTATTGAGTTATGCGACTAGCCTTGAGAA
261 TTTATTATTATGCAATTATTGTTATTAGTATTGTTATTATTGAGTTATGCGACTAGCCTTGAGAA
38806056 TTTGAGTAAGTAAGTTTCAGCTATGACTTGACAAGGCATTGATATCTCAAAGTCCATGGTTGTAC
326 TTTGAGTAAGTAAGTTTCAGCTATGACTTGACAAGGCATTGATATCTCAAAGTCCATGGTTGTAC
38806121 CAT
391 CAT
38806124 GTCAATTAAG
Statistics
Matches: 392, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
393 392 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (393 bp):
AAATTTAATTATGCATATTTGAATGATAAATTGATACTTTGGCCATAAATACTTTAGTATTGAGT
TTCAGATATAATGATTAATGTTCGATAATAATTCGATATTGGAAAGAGAACTTGTATAATTTATA
TGTAAGACCATATTTTGTATTATGGCTTTGTATGATAACAAGAAAGTATTGACTAGCATAGTTTG
ATGAGAATAAGTTAAGTTGATGATATGATGAGATTGAGAATGTAAGAATGTAAGTTGAGTAGCAT
TTTATTATTATGCAATTATTGTTATTAGTATTGTTATTATTGAGTTATGCGACTAGCCTTGAGAA
TTTGAGTAAGTAAGTTTCAGCTATGACTTGACAAGGCATTGATATCTCAAAGTCCATGGTTGTAC
CAT
Found at i:38806615 original size:294 final size:294
Alignment explanation
Indices: 38806086--38806674 Score: 1133
Period size: 294 Copynumber: 2.0 Consensus size: 294
38806076 CTATGACTTG
38806086 ACAAGGCATTGATATCTCAAAGTCCATGGTTGTACCATGTCAATTAAGGAAGAATTGACGGAGAA
1 ACAAGGCATTGATATCTCAAAGTCCATGGTTGTACCATGTCAATTAAGGAAGAATTGACGGAGAA
38806151 GTCCATGTTCATAACATGACATTTAAGCAGGAATTGACAGTTAATGATACCATGTAAGACCATGT
66 GTCCATGTTCATAACATGACATTTAAGCAGGAATTGACAGTTAATGATACCATGTAAGACCATGT
* *
38806216 CAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAATACCATGTCAAGACATGGCATTAGCATT
131 CAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCAGCATT
38806281 GATTAAAGACTCCATGTAAAACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGT
196 GATTAAAGACTCCATGTAAAACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGT
38806346 AAGACCATGTTTGGAACATGGCATTTGGTAAGAT
261 AAGACCATGTTTGGAACATGGCATTTGGTAAGAT
38806380 ACAAGGCATTGATATCTCAAAGTCCATGGTTGTACCATGTCAATTAAGGAAGAATTGACGGAGAA
1 ACAAGGCATTGATATCTCAAAGTCCATGGTTGTACCATGTCAATTAAGGAAGAATTGACGGAGAA
38806445 GTCCATGTTCATAACATGACATTTAAGCAGGAATTGACAGTTAATGATACCATGTAAGACCATGT
66 GTCCATGTTCATAACATGACATTTAAGCAGGAATTGACAGTTAATGATACCATGTAAGACCATGT
*
38806510 CAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCGGCATT
131 CAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCAGCATT
* *
38806575 GATTAAGGACTCCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGT
196 GATTAAAGACTCCATGTAAAACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGT
38806640 AAGACCATGTTTGGAACATGGCATTTGGTAAGAT
261 AAGACCATGTTTGGAACATGGCATTTGGTAAGAT
38806674 A
1 A
38806675 AGGATATCAT
Statistics
Matches: 290, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
294 290 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (294 bp):
ACAAGGCATTGATATCTCAAAGTCCATGGTTGTACCATGTCAATTAAGGAAGAATTGACGGAGAA
GTCCATGTTCATAACATGACATTTAAGCAGGAATTGACAGTTAATGATACCATGTAAGACCATGT
CAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCAGCATT
GATTAAAGACTCCATGTAAAACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGT
AAGACCATGTTTGGAACATGGCATTTGGTAAGAT
Found at i:38806803 original size:55 final size:54
Alignment explanation
Indices: 38806674--38806867 Score: 221
Period size: 55 Copynumber: 3.6 Consensus size: 54
38806664 TTGGTAAGAT
* ** *
38806674 AAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * *
38806728 AAGGAAATCATGTAAGACCATGTCAACACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * * *
38806783 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGACATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
** *
38806836 AAGGATACCACATAAGACCATGTCAAGACATG
1 AAGGATACCATGTAAGACCATGCCAAGACATG
38806868 ACAATGGTAA
Statistics
Matches: 118, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.03
53 29 0.25
54 40 0.34
55 41 0.35
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:38806882 original size:53 final size:54
Alignment explanation
Indices: 38806674--38806881 Score: 213
Period size: 53 Copynumber: 3.9 Consensus size: 54
38806664 TTGGTAAGAT
* ** *
38806674 AAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
* * * * * *
38806728 AAGGAAATCATGTAAGACCATGTCAACACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTT-CTATAAGGC
* * * *
38806783 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGACATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
** * * *
38806836 AAGGATACCACATAAGACCATGTCAAGACATGACAATGGTAAGTTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTC
38806882 AAAAAGGAAA
Statistics
Matches: 130, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
52 4 0.03
53 41 0.32
54 40 0.31
55 41 0.32
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
Found at i:38810485 original size:30 final size:30
Alignment explanation
Indices: 38810451--38810510 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38810441 TCCTTAACTC
38810451 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
38810481 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
38810511 GGGCTCGGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:38812039 original size:41 final size:41
Alignment explanation
Indices: 38811982--38812062 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
38811972 GTCTTATTAA
*
38811982 AAATCATATGAACTTACAATTTCCCATAATATCCATAATCG
1 AAATCATATGAACTTACAATTTCCCATAATAACCATAATCG
38812023 AAATCATATGAACTTACAATTTCCCATAATAACCATAATC
1 AAATCATATGAACTTACAATTTCCCATAATAACCATAATC
38812063 ATAGAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (41 bp):
AAATCATATGAACTTACAATTTCCCATAATAACCATAATCG
Found at i:38813550 original size:65 final size:65
Alignment explanation
Indices: 38813446--38813576 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
38813436 AGTCCCATGC
* *
38813446 ATCAGATAATAATAACATGGCATACAGTAAATAGTAACAGTCAAATATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
* *
38813511 ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTTAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
38813576 A
1 A
38813577 ACCCTAGGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (65 bp):
ATCAGATAATAATAACATGGAATACAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
Found at i:38820739 original size:43 final size:43
Alignment explanation
Indices: 38820678--38820876 Score: 258
Period size: 43 Copynumber: 4.6 Consensus size: 43
38820668 AAGTGTGCGA
* *
38820678 GTAAGACCACATCTGGGACGTTGGCATCGATTTGTGATTACGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
*
38820721 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTATGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
* * * * *
38820764 GTAAGACCACGTCTAGGATGTTGGCATCGATATGTGTTTATGA
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
* * *
38820807 GTAAGACC-CTGTTTGGGACAG-TGGGATCGATATGTGATTACAT
1 GTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACGT
*
38820850 GTAAGACCATGTCTGGGACGTTGGCAT
1 GTAAGACCACGTCTGGGACGTTGGCAT
38820877 TGTACGATAT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
42 2 0.01
43 131 0.98
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (43 bp):
GTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACGT
Found at i:38827285 original size:40 final size:41
Alignment explanation
Indices: 38827206--38827314 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
38827196 TATAATGATA
* * * *
38827206 TTCAACTATGATTGGCACTAAGTGTACG-GTTTAATATAGC
1 TTCAACTATAAATGGCACTAAGTGTGCGAGTTTAACATAGC
**
38827246 TTCAACTATAAATGGCACTAAGTGTGCGAG-TTGGCATAGC
1 TTCAACTATAAATGGCACTAAGTGTGCGAGTTTAACATAGC
**
38827286 TTCGGCTATAGAA-GGCACTAAGTGTGCGA
1 TTCAACTATA-AATGGCACTAAGTGTGCGA
38827315 TACTGATTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 56 0.95
41 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (41 bp):
TTCAACTATAAATGGCACTAAGTGTGCGAGTTTAACATAGC
Found at i:38830938 original size:39 final size:40
Alignment explanation
Indices: 38830838--38831022 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
38830828 TTGAATGATG
* * * *
38830838 TCCGGACTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
38830877 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
38830918 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
38830957 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
38830996 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
38831023 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:38831044 original size:79 final size:79
Alignment explanation
Indices: 38830891--38831055 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
38830881 GGACTAAGAT
* * ** *
38830891 CCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
38830956 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
38830970 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C
* * *
38831033 TATAT-CTGGTTAAATT
63 TAAATCCGGGTTAAATC
38831049 CCGAAGG
1 CCGAAGG
38831056 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:38838935 original size:40 final size:39
Alignment explanation
Indices: 38838851--38839035 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
38838841 TTGAATGATG
* * * *
38838851 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
38838891 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
38838931 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
38838970 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
38839011 -CCGGGCTATGGCCCGAAGGCATTTG
1 TCCGGGCTA-AGTCCGAAGGCATTTG
38839036 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 35 0.28
40 77 0.63
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:38838987 original size:79 final size:80
Alignment explanation
Indices: 38838851--38839035 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
38838841 TTGAATGATG
*
38838851 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
38838915 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
38838930 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
38838993 TTGTGTGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
38839010 ACCGGGCTATGGCCCGAAGGCATTTG
1 TCCGGGCTA-AGCCCGAAGGCATTTG
38839036 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:38839058 original size:79 final size:79
Alignment explanation
Indices: 38838904--38839068 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
38838894 GGACTAAGAT
* ** *
38838904 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
* *
38838969 ATCCGGGTTAAGTC
66 ATCCGAGTTAAATC
* * *
38838983 CCGAAGGCATTTGTGTGAGTTACT-ATAACCGGGCTATGGCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTA-AGCCCGAAGGCATTTGAACGAGTGA-C
* *
38839046 TATATCC-AGTTAAATT
63 TAAATCCGAGTTAAATC
38839062 CCGAAGG
1 CCGAAGG
38839069 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 44 0.61
80 26 0.36
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGAGTTAAATC
Found at i:38841088 original size:77 final size:77
Alignment explanation
Indices: 38840982--38841190 Score: 319
Period size: 77 Copynumber: 2.7 Consensus size: 77
38840972 AGAACTATTT
** ** * * **
38840982 TCATGGCCTAAAGCCAAAACATCCTATATGCATGGCCCAAAGCCAAATTTGTATAACTCACACCC
1 TCATGGCCCGAAGCCAACTCATCCGATATGCATGGCCCGAAGCCAAATCGGTATAACTCACACCC
38841047 GAAGTGCTAATA
66 GAAGTGCTAATA
* *
38841059 TCATGGCCCGAAGCCAGCTCATTCGATATGCATGGCCCGAAGCCAAATCGGTATAACTCACACCC
1 TCATGGCCCGAAGCCAACTCATCCGATATGCATGGCCCGAAGCCAAATCGGTATAACTCACACCC
38841124 GAAGTGCTAATA
66 GAAGTGCTAATA
*
38841136 TCATGGCCCGAAGCCAACTCATCCGATATGCATGGTCCGAAGCCAAATCGGTATA
1 TCATGGCCCGAAGCCAACTCATCCGATATGCATGGCCCGAAGCCAAATCGGTATA
38841191 TCATCTTATA
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 119 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (77 bp):
TCATGGCCCGAAGCCAACTCATCCGATATGCATGGCCCGAAGCCAAATCGGTATAACTCACACCC
GAAGTGCTAATA
Found at i:38842918 original size:29 final size:28
Alignment explanation
Indices: 38842833--38842926 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
38842823 AAGTCTACAT
* *
38842833 ACATGCATATGGTCCACTAGG-CCCAATC
1 ACATTCATATGG-CCATTAGGCCCCAATC
* *
38842861 TCATTCATATGGCCATTAGGCCCAAATC
1 ACATTCATATGGCCATTAGGCCCCAATC
*
38842889 ACATTCATATGGCCCA-TCGGCCCCCAATC
1 ACATTCATATGG-CCATTAGG-CCCCAATC
38842918 ACATTCATA
1 ACATTCATA
38842927 GTCATGCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
27 7 0.12
28 30 0.54
29 19 0.34
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (28 bp):
ACATTCATATGGCCATTAGGCCCCAATC
Found at i:38843167 original size:16 final size:16
Alignment explanation
Indices: 38843146--38843177 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38843136 AAACTTCCGG
38843146 CTTTTCGGCATTTCGA
1 CTTTTCGGCATTTCGA
38843162 CTTTTCGGCATTTCGA
1 CTTTTCGGCATTTCGA
38843178 GATTTGCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTTTCGGCATTTCGA
Found at i:38853665 original size:18 final size:18
Alignment explanation
Indices: 38853623--38853665 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
38853613 ATGGTAGCTT
*
38853623 GGCTACATGATTTCCACA
1 GGCTACTTGATTTCCACA
*
38853641 GGCTACTTGATTTCCGCA
1 GGCTACTTGATTTCCACA
38853659 GGCTACT
1 GGCTACT
38853666 GAGTTTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (18 bp):
GGCTACTTGATTTCCACA
Found at i:38854230 original size:28 final size:28
Alignment explanation
Indices: 38854190--38854245 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
38854180 GGAAATGTTT
38854190 GAGAATGATTAGCTATTGCAGTGGCTAA
1 GAGAATGATTAGCTATTGCAGTGGCTAA
**
38854218 GAGAATGATTAGCTATTGGTGTGGCTAA
1 GAGAATGATTAGCTATTGCAGTGGCTAA
38854246 TCAAGATTAT
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:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (28 bp):
GAGAATGATTAGCTATTGCAGTGGCTAA
Found at i:38857846 original size:6 final size:6
Alignment explanation
Indices: 38857828--38857940 Score: 97
Period size: 6 Copynumber: 18.3 Consensus size: 6
38857818 TAAGAACATT
* *
38857828 ATCAGA A-CTAGA ATCAGA ATCAAA ATCAGA ATCAGGTA A-CAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * *
38857877 ATCAGA ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGA TAACAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA -ATCAGA
*
38857927 ATCAAA ATCAGA AT
1 ATCAGA ATCAGA AT
38857941 GTGAATGCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
5 5 0.06
6 65 0.76
7 12 0.14
8 4 0.05
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (6 bp):
ATCAGA
Done.