Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 113 of 226
Found at i:38770206 original size:54 final size:54
Alignment explanation
Indices: 38770098--38770199 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
38770088 TCGTTTGTCA
* * * *
38770098 ATTTATGATCGCAACC-TATACTTACAAGGTTTTCAGAATCTTGCGGCTCACCG
1 ATTTAAGATCGCAACCTTTTACTTACAAGATTTTCAGAATCTTGCAGCTCACCG
* * *
38770151 ATTTAAGATCGCAACCTTTTGCTTACAAGATTTTCATAATCTTGTAGCT
1 ATTTAAGATCGCAACCTTTTACTTACAAGATTTTCAGAATCTTGCAGCT
38770200 AGCCGATCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 15 0.37
54 26 0.63
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (54 bp):
ATTTAAGATCGCAACCTTTTACTTACAAGATTTTCAGAATCTTGCAGCTCACCG
Found at i:38770224 original size:54 final size:54
Alignment explanation
Indices: 38770104--38770224 Score: 129
Period size: 54 Copynumber: 2.3 Consensus size: 54
38770094 GTCAATTTAT
* * * * *
38770104 GATCGCAACC-TATACTTACAAGGTTTTCAGAATCTTGCGGCTCACCGATTTAA
1 GATCGCAACCTTTTGCTTACAAGATTTTCAGAATCTTGCAGCTCACCGATCTAA
* * *
38770157 GATCGCAACCTTTTGCTTACAAGATTTTCATAATCTTGTAGCT-AGCCGATCTAG
1 GATCGCAACCTTTTGCTTACAAGATTTTCAGAATCTTGCAGCTCA-CCGATCTAA
* *
38770211 GATTGCAATCTTTT
1 GATCGCAACCTTTT
38770225 TGTAACAGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
53 11 0.20
54 45 0.80
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (54 bp):
GATCGCAACCTTTTGCTTACAAGATTTTCAGAATCTTGCAGCTCACCGATCTAA
Found at i:38774324 original size:28 final size:28
Alignment explanation
Indices: 38774292--38774360 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
38774282 AATGAGATTG
* * *
38774292 GCACTAAGTGTGCAAGTTTAATTGTAAA
1 GCACTAAGTGTGCAAGTTCAACTATAAA
* * *
38774320 GCACTAAGTGTGCGAGTTCGACTATTAA
1 GCACTAAGTGTGCAAGTTCAACTATAAA
38774348 GCACTAAGTGTGC
1 GCACTAAGTGTGC
38774361 GAACTTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCAACTATAAA
Found at i:38787047 original size:31 final size:31
Alignment explanation
Indices: 38787007--38787073 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
38786997 CTCACGAGGC
* *
38787007 GATCTCACCATGCCACACCATCTCGCTAAAT
1 GATCCCACCATGCCACACCATCTCACTAAAT
** *
38787038 GATCCCACCATGCCTTACCATCTCACTAAGT
1 GATCCCACCATGCCACACCATCTCACTAAAT
38787069 GATCC
1 GATCC
38787074 TATCACACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.39, G:0.10, T:0.24
Consensus pattern (31 bp):
GATCCCACCATGCCACACCATCTCACTAAAT
Found at i:38787160 original size:62 final size:62
Alignment explanation
Indices: 38787041--38787176 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 62
38787031 GCTAAATGAT
* *
38787041 CCCACCATGCCTTACCATCTCACTAAGTGATCCTATCACACCTCACCACCTCATGAGGTAAC
1 CCCACCATGCCTTACCATCTCACTAAGTGATCCCATCACACATCACCACCTCATGAGGTAAC
* ** * * * ** * *
38787103 CCCACCGTGCCTTACCATCTCGTTAGGTGATCCCGTCACACATTACCACCTTGTGAGGTGAT
1 CCCACCATGCCTTACCATCTCACTAAGTGATCCCATCACACATCACCACCTCATGAGGTAAC
*
38787165 CCCATCATGCCT
1 CCCACCATGCCT
38787177 CTATCACACA
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.23, C:0.38, G:0.14, T:0.25
Consensus pattern (62 bp):
CCCACCATGCCTTACCATCTCACTAAGTGATCCCATCACACATCACCACCTCATGAGGTAAC
Found at i:38788434 original size:53 final size:53
Alignment explanation
Indices: 38788354--38788461 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
38788344 ATCGCAACGA
*
38788354 TGGTCAGTAGACTCTATGCGGCGACCCGGTGACGGCGGTAAGGTCTTTCAAGG
1 TGGTCAGTAGACTCTATGCGGCGACCCGGTGACGACGGTAAGGTCTTTCAAGG
38788407 TGGTCAGTAGACTCTATGCGGCGACCCGGTGACGACGGTAAGGTCTTTCAAGG
1 TGGTCAGTAGACTCTATGCGGCGACCCGGTGACGACGGTAAGGTCTTTCAAGG
38788460 TG
1 TG
38788462 ACACCTCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.23
Consensus pattern (53 bp):
TGGTCAGTAGACTCTATGCGGCGACCCGGTGACGACGGTAAGGTCTTTCAAGG
Found at i:38794406 original size:21 final size:20
Alignment explanation
Indices: 38794361--38794408 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
38794351 TGCCTAGGCC
*
38794361 ATGTGAAAGCTTACACACCT
1 ATGTGGAAGCTTACACACCT
38794381 ATGTGGAAGC-TACACACGCT
1 ATGTGGAAGCTTACACAC-CT
38794401 AGTGTGGA
1 A-TGTGGA
38794409 GGGGACACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 7 0.28
20 12 0.48
21 6 0.24
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (20 bp):
ATGTGGAAGCTTACACACCT
Found at i:38807151 original size:16 final size:17
Alignment explanation
Indices: 38807130--38807169 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
38807120 ATATCACCGG
38807130 CACAAAGCCTACTA-GA
1 CACAAAGCCTACTAGGA
38807146 CACAAAGCCTACTAGGA
1 CACAAAGCCTACTAGGA
38807163 -ACAAAGC
1 CACAAAGC
38807170 TCAAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.10
Consensus pattern (17 bp):
CACAAAGCCTACTAGGA
Found at i:38807175 original size:54 final size:54
Alignment explanation
Indices: 38807093--38807210 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
38807083 TTACACTAGT
* *
38807093 ACAAAGCCTACTAAGCACAGAGCCCAAATATCACCGGCACAAAGCCTACT-AGAC
1 ACAAAGCCTACTAAGAACAAAGCCCAAATATCACCGGCACAAAGCCTACTAAG-C
* * *
38807147 ACAAAGCCTACTAGGAACAAAGCTCAAATATCACCGGCACAAAGCCTGCTAAGC
1 ACAAAGCCTACTAAGAACAAAGCCCAAATATCACCGGCACAAAGCCTACTAAGC
38807201 ACAAAGCCTA
1 ACAAAGCCTA
38807211 AATATCACTG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 56 0.97
55 2 0.03
ACGTcount: A:0.42, C:0.31, G:0.15, T:0.12
Consensus pattern (54 bp):
ACAAAGCCTACTAAGAACAAAGCCCAAATATCACCGGCACAAAGCCTACTAAGC
Found at i:38807205 original size:38 final size:39
Alignment explanation
Indices: 38807146--38807306 Score: 186
Period size: 38 Copynumber: 4.2 Consensus size: 39
38807136 GCCTACTAGA
* * *
38807146 CACAAAGCCTACTAGGAACAAAGCTC-AAATATCACCGG
1 CACAAAGCCTGCTAGGCACAAAGCCCGAAATATCACCGG
* * *
38807184 CACAAAGCCTGCTAAGCACAAAG-CCTAAATATCACTGG
1 CACAAAGCCTGCTAGGCACAAAGCCCGAAATATCACCGG
**
38807222 CACAAAGCCTGCTAGGGTCAAAGCCCG-AATATCACCGG
1 CACAAAGCCTGCTAGGCACAAAGCCCGAAATATCACCGG
* * *
38807260 CACAAAGCTTGCTAGGCACGAAGCCCGAATTAT-ACCGG
1 CACAAAGCCTGCTAGGCACAAAGCCCGAAATATCACCGG
*
38807298 CATAAAGCC
1 CACAAAGCC
38807307 CGAATTAATG
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
37 1 0.01
38 96 0.93
39 6 0.06
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (39 bp):
CACAAAGCCTGCTAGGCACAAAGCCCGAAATATCACCGG
Found at i:38810299 original size:17 final size:16
Alignment explanation
Indices: 38810277--38810309 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
38810267 TTTATAAAGG
38810277 TTATAATATATATTATA
1 TTATAATATAT-TTATA
38810294 TTATAATATATTTATA
1 TTATAATATATTTATA
38810310 ATAAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAATATATTTATA
Found at i:38820733 original size:53 final size:54
Alignment explanation
Indices: 38820643--38820750 Score: 148
Period size: 53 Copynumber: 2.0 Consensus size: 54
38820633 TTAAAAACCT
* * *
38820643 TATTCCAAAAAACACCATTGTTCAAGGAGAGGCTACTATTCAGGGGGAGACTAC
1 TATTCCAAAAAACACCATTGTTCAAGGAGAAGCTACTACTCAAGGGGAGACTAC
* *
38820697 TATT-CAAAAAACACCATTGTTCAA-GAGGAAGTTACTACTCAATGGGAGACTAC
1 TATTCCAAAAAACACCATTGTTCAAGGA-GAAGCTACTACTCAAGGGGAGACTAC
38820750 T
1 T
38820751 GTTAAGAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 2 0.04
53 42 0.88
54 4 0.08
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (54 bp):
TATTCCAAAAAACACCATTGTTCAAGGAGAAGCTACTACTCAAGGGGAGACTAC
Found at i:38824425 original size:20 final size:19
Alignment explanation
Indices: 38824386--38824423 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38824376 CATAATTTTC
38824386 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
38824405 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
38824423 A
1 A
38824424 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:38825063 original size:60 final size:61
Alignment explanation
Indices: 38824992--38825107 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 61
38824982 TGAGTTAAAT
*
38824992 CACATTTGAGGCCTGAA-TTTTTTATTAGTCCAAGTTAGGCTCTAAACTTGACAATTATTTC
1 CACATTTGAGGCCTGAACTTTTTT-TTAGTCCAAGTTAGGCCCTAAACTTGACAATTATTTC
* * * *
38825053 CACA-TTGAGGCTTGAACTTTTTTTTAGTCCAGGTTAGGCCCTGAACTTGGCAATT
1 CACATTTGAGGCCTGAACTTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATT
38825108 GTCCTTACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 39 0.80
61 10 0.20
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (61 bp):
CACATTTGAGGCCTGAACTTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATTATTTC
Found at i:38825118 original size:60 final size:59
Alignment explanation
Indices: 38824991--38825143 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
38824981 CTGAGTTAAA
* *
38824991 TCACATTTGAGGCCTGAA-TTTTTTATTAGTCCAAGTTAGGCTCTAAACTTGACAATTATT
1 TCACA-TTGAGGCTTGAACTTTTTT-TTAGTCCAAGTTAGGCCCTAAACTTGACAATTATT
* * * *
38825051 TCCACATTGAGGCTTGAACTTTTTTTTAGTCCAGGTTAGGCCCTGAACTTGGCAATTGTCCT
1 T-CACATTGAGGCTTGAACTTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATTAT--T
* *
38825113 T-ACATTAAGGTTTGAAC-TTTTTTT-GTCCAAG
1 TCACATTGAGGCTTGAACTTTTTTTTAGTCCAAG
38825144 ATATTCCTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
58 6 0.08
59 7 0.09
60 55 0.69
61 10 0.12
62 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (59 bp):
TCACATTGAGGCTTGAACTTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATTATT
Found at i:38841983 original size:18 final size:18
Alignment explanation
Indices: 38841940--38841983 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38841930 AGTGAAATTT
* *
38841940 ATATGAAAATCCCTGAAGG
1 ATAT-AAAATCCCAGAACG
*
38841959 ATTTAAAATCCCAGAACG
1 ATATAAAATCCCAGAACG
38841977 ATATAAA
1 ATATAAA
38841984 GTTTCTTGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAGAACG
Found at i:38856206 original size:50 final size:51
Alignment explanation
Indices: 38856029--38856216 Score: 245
Period size: 51 Copynumber: 3.7 Consensus size: 51
38856019 TGCCTATAAA
* ** * *
38856029 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TTGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGAT-TTGGT
* * * *
38856080 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGTTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGT
* *
38856131 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGT
*
38856181 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
38856217 TCGAATGATA
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
50 39 0.32
51 77 0.64
52 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAAGATTTGGT
Found at i:38871414 original size:22 final size:22
Alignment explanation
Indices: 38871383--38871426 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38871373 TACACCAAAA
* *
38871383 TAGGCTTTTAGCGGCGTTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
*
38871405 TAGGCCTTTAGTGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
38871427 ACCGCCGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCGCTTTTT
Found at i:38871573 original size:43 final size:43
Alignment explanation
Indices: 38871520--38871721 Score: 316
Period size: 43 Copynumber: 4.7 Consensus size: 43
38871510 TTATGAAACA
*
38871520 AAACGCCGCTAAAGAACATGATCTTTAGCGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* *
38871563 AAACGCCGCTAAAAAACATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * *
38871606 AAACGCCGCTAAAGATCATGACCTTTAGTGGCGCTTTTA-CCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGC-TTTACCCAC
* *
38871649 AAACGCCACTAAAGAACATGATCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
38871692 AAACGCCGCTAAAGAACATGATCTTTAGCG
1 AAACGCCGCTAAAGAACATGATCTTTAGCG
38871722 TCGTTTTTGA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 4 0.03
43 138 0.95
44 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:38874370 original size:12 final size:12
Alignment explanation
Indices: 38874353--38874380 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38874343 AGGGAAAGCT
38874353 CAAATAAATAAA
1 CAAATAAATAAA
38874365 CAAATAAATAAA
1 CAAATAAATAAA
38874377 CAAA
1 CAAA
38874381 AGACAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAATAAATAAA
Found at i:38874556 original size:20 final size:18
Alignment explanation
Indices: 38874510--38874581 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 18
38874500 CAAGAACATG
38874510 AACATAAAAATAAA-AAATTA
1 AACATAAAAA-AAATAAA--A
*
38874530 AAGATAAAAAAAACTAAAA
1 AACATAAAAAAAA-TAAAA
* *
38874549 GAACATAAAAACAATGAAA
1 -AACATAAAAAAAATAAAA
38874568 AACA-AAAAAAAATA
1 AACATAAAAAAAATA
38874582 GGCAGAAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
17 8 0.19
18 4 0.09
19 8 0.19
20 20 0.47
21 3 0.07
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.12
Consensus pattern (18 bp):
AACATAAAAAAAATAAAA
Found at i:38875667 original size:14 final size:15
Alignment explanation
Indices: 38875640--38875672 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38875630 CTTAACTACT
38875640 AACCCTTAAACCTTA
1 AACCCTTAAACCTTA
*
38875655 AACCC-TAACCCTTA
1 AACCCTTAAACCTTA
38875669 AACC
1 AACC
38875673 ATAATCCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCTTAAACCTTA
Found at i:38875681 original size:21 final size:21
Alignment explanation
Indices: 38875612--38875681 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
38875602 NNNNNNNNTA
* *
38875612 AATCCCTAACTCTTAACCCTT
1 AATCCCTAACCCTTAAACCTT
*
38875633 AA-CTACTAACCCTTAAACCTT
1 AATC-CCTAACCCTTAAACCTT
* *
38875654 AAACCCTAACCCTTAAACCAT
1 AATCCCTAACCCTTAAACCTT
38875675 AATCCCT
1 AATCCCT
38875682 GAATCCATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.36, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
AATCCCTAACCCTTAAACCTT
Found at i:38875949 original size:7 final size:7
Alignment explanation
Indices: 38875937--38876050 Score: 54
Period size: 7 Copynumber: 16.0 Consensus size: 7
38875927 ACTAGTTAAT
38875937 CTAAACC
1 CTAAACC
38875944 CTAAACC
1 CTAAACC
*
38875951 ATAAA-C
1 CTAAACC
*
38875957 TTAAACC
1 CTAAACC
38875964 CTAAAACC
1 CT-AAACC
*
38875972 CAAAACC
1 CTAAACC
38875979 CATAAACC
1 C-TAAACC
* *
38875987 CTTAACA
1 CTAAACC
38875994 C-ATAACC
1 CTA-AACC
*
38876001 TTTAAACC
1 -CTAAACC
*
38876009 TTAAACC
1 CTAAACC
*
38876016 C-CAACC
1 CTAAACC
*
38876022 TTTAAACC
1 -CTAAACC
*
38876030 ATAAACC
1 CTAAACC
* *
38876037 ATAACCC
1 CTAAACC
38876044 CTAAACC
1 CTAAACC
38876051 TATAATCTAT
Statistics
Matches: 81, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
6 9 0.11
7 51 0.63
8 20 0.25
9 1 0.01
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:38876012 original size:21 final size:21
Alignment explanation
Indices: 38875938--38876051 Score: 79
Period size: 21 Copynumber: 5.3 Consensus size: 21
38875928 CTAGTTAATC
* *
38875938 TAAACCCTAAACCATAAAC-T
1 TAAACCTTAAACCATAACCTT
* * **
38875958 TAAACCCTAAAACCCAAAACCCA
1 TAAA-CCTTAAA-CCATAACCTT
38875981 TAAACCCTT-AACACATAACCTT
1 TAAA-CCTTAAAC-CATAACCTT
**
38876003 TAAACCTTAAACCCCAACCTT
1 TAAACCTTAAACCATAACCTT
* **
38876024 TAAACCATAAACCATAACCCC
1 TAAACCTTAAACCATAACCTT
38876045 TAAACCT
1 TAAACCT
38876052 ATAATCTATA
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
20 4 0.06
21 39 0.54
22 21 0.29
23 8 0.11
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCTTAAACCATAACCTT
Found at i:38876352 original size:37 final size:38
Alignment explanation
Indices: 38876299--38876371 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
38876289 TAAATCCTTG
* *
38876299 AGCATTAGCGGTGCTTT-CTCAAAAACGCCGCTAAAGC
1 AGCATTAGCGGCGCTTTACTAAAAAACGCCGCTAAAGC
*
38876336 AGCATTAGCGGCGCTTTATTAAAAAACGCCGCTAAA
1 AGCATTAGCGGCGCTTTACTAAAAAACGCCGCTAAA
38876372 TCCCTGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 16 0.50
38 16 0.50
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (38 bp):
AGCATTAGCGGCGCTTTACTAAAAAACGCCGCTAAAGC
Found at i:38876553 original size:114 final size:114
Alignment explanation
Indices: 38876306--38877126 Score: 1057
Period size: 114 Copynumber: 7.2 Consensus size: 114
38876296 TTGAGCATTA
* *
38876306 GCGGTGCTTTCTCAAAAACGCCGCTAAAG--C--AGCATTAGCGGCGCTTTATTAAAAAACGCCG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAACGCCG
**
38876367 CTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTT
65 CTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * * * * *
38876416 GCGGCACTTTCCCAAAAATGCCGCTAATGCCCTGAGCATTATCAGCGCTTTATTAAAAATGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
38876481 TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* ** * *
38876530 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAACACTTTCCTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* *
38876595 TAAATCCCCAAAACCTCAGAAAACAGCGTCGTTGGGCTTA-GTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * *
38876643 GCGGCACTTT-TAAAAAAACACCGCTAATGCCCTGAGCATTAGCAGCGCTTTCTTAAAAACGCCG
1 GCGGCGCTTTCT-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCG
* *
38876707 CTAAATCCCCAAAAGCTCAAAAAACGGCGTCGTTGGGCATAGGTTTTTTTT
65 CTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTT
* * *
38876758 GCGGCGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGGGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* *
38876823 TAAATCCCCAAAAGCTCAGAAAATGGCATCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * * *
38876872 GCAGTGCTTTTTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAATGTCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * * * *
38876937 TAAATCCCCGAAAGCTCAGAAAACGACATCTTTGGGCTTAGTTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * *
38876986 TCGGCGCTTTCTCAAAAACGCAGCTAAAGCCCTGGGCATTAACGGCGCTTCCTTAAAAAACGCCG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAACGCCG
* *
38877051 CTAAATCCCCGAAAGCTC-GAAAAACGGCGTCGTTGGACTTAGG-TTTTTT
65 CTAAATCCCCAAAAGCTCAG-AAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* ** *
38877100 GCGGCGCTTCCTGGAAAACGCTGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
38877127 TGTTTATTTT
Statistics
Matches: 620, Mismatches: 80, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
110 24 0.04
112 2 0.00
113 149 0.24
114 298 0.48
115 147 0.24
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
TAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
Found at i:38890542 original size:32 final size:32
Alignment explanation
Indices: 38890506--38890570 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
38890496 ATAAAAAAAA
38890506 GGAGAAAAGAAAAAAAAAGGAGAGGCCAAGGT
1 GGAGAAAAGAAAAAAAAAGGAGAGGCCAAGGT
** *
38890538 GGAGAAAAGAAAATCAAAGGAGATGCCAAGGT
1 GGAGAAAAGAAAAAAAAAGGAGAGGCCAAGGT
38890570 G
1 G
38890571 AAAACCCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.34, T:0.06
Consensus pattern (32 bp):
GGAGAAAAGAAAAAAAAAGGAGAGGCCAAGGT
Found at i:38891809 original size:44 final size:45
Alignment explanation
Indices: 38891710--38892212 Score: 253
Period size: 44 Copynumber: 11.1 Consensus size: 45
38891700 ATAAATCAAT
* * * * *
38891710 CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAGATCGCCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AA-A--GCCAACAAAC
*
38891759 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAA-AAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
* * * * *
38891803 CTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAG-TAACAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
* * * ** *
38891847 C-TATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACGATGAATC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAG-ATTAAAGCCAACAAAC
* * * **
38891891 ATT-TAC-CTCTGAAGTTGCAGTAG-GTCAGATTAAATCTACCATGACAAGT
1 CTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGATTAAA---GCCA--ACAAAC
* * * **
38891940 CTTATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGCC-ATGAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
* * * *
38891984 CTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTAAAG-TAATAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
* * * ** *
38892028 CTTATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAG-TTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAC-AAAC
* * * * ** *
38892073 C-TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
* * **
38892117 C-TATAC-CTCTGAAGTTGCAGTAG-GTCAGATTAAATCTACCATGACAAGT
1 CTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGATTAAA---GCCA--ACAAAC
* * * *
38892166 CTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACC-ACAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
38892210 CTT
1 CTT
38892213 GTCCCCCTAC
Statistics
Matches: 349, Mismatches: 77, Indels: 61
0.72 0.16 0.13
Matches are distributed among these distances:
42 1 0.00
43 30 0.09
44 205 0.59
45 12 0.03
47 12 0.03
48 2 0.01
49 37 0.11
50 49 0.14
51 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAACAAAC
Found at i:38892129 original size:226 final size:225
Alignment explanation
Indices: 38891759--38892195 Score: 707
Period size: 226 Copynumber: 1.9 Consensus size: 225
38891749 GCCTACAAAT
* *
38891759 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAAAACCTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAAAACCTTATCTCCCTAAAGTTGCAG
*
38891824 TAGAGTAGGTTGAAGTAACAAACCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAACGATGAA
66 TAGAGCAGGTTGAAGTAACAAACCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAACGATGAA
*
38891889 TCATTTACCTCTGAAGTTGCAGTAGGTCAGATTAAATCTACCATGACAAGTCTTATCTCCCTGAA
131 TCATATACCTCTGAAGTTGCAGTAGGTCAGATTAAATCTACCATGACAAGTCTTATCTCCCTGAA
*
38891954 GTTGCAATGGAGCAGATCAAAGCCATGAAC
196 GTTGCAATGGAACAGATCAAAGCCATGAAC
* * * *
38891984 CTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTAAAG-TAATAAACCTTATCTCCCTAAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAA-AAACCTTATCTCCCTAAAGTTGCA
* * *
38892048 GTAGAGCAGGTTGAAGTTACTAATCCTATCTCCTTGAAGTTGCAGTGGAGC-AGATTAAAACGAT
65 GTAGAGCAGGTTGAAGTAAC-AAACCTATCTCCCTGAAGTTGCAGTGGAGCGA-ATTAAAACGAT
*
38892112 GAATCCTATACCTCTGAAGTTGCAGTAGGTCAGATTAAATCTACCATGACAAGTCTTATCTCCCT
128 GAATCATATACCTCTGAAGTTGCAGTAGGTCAGATTAAATCTACCATGACAAGTCTTATCTCCCT
*
38892177 GAAGTTGCAGTGGAACAGA
193 GAAGTTGCAATGGAACAGA
38892196 CTAAAACCAC
Statistics
Matches: 195, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
224 2 0.01
225 74 0.38
226 119 0.61
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (225 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAAAACCTTATCTCCCTAAAGTTGCAG
TAGAGCAGGTTGAAGTAACAAACCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAACGATGAA
TCATATACCTCTGAAGTTGCAGTAGGTCAGATTAAATCTACCATGACAAGTCTTATCTCCCTGAA
GTTGCAATGGAACAGATCAAAGCCATGAAC
Found at i:38893725 original size:52 final size:53
Alignment explanation
Indices: 38893669--38893772 Score: 138
Period size: 52 Copynumber: 1.9 Consensus size: 53
38893659 TATCATTCTC
* * * *
38893669 TTACTTTTAAAATATTTGAATTTAATATTAGGTAT-TATTTTATCTATTTTTT
1 TTACTCTTAAAATATTTAAACTTAACATTAGGTATATATTTTATCTATTTTTT
*
38893721 TTACTCTTAAAATATTTAAACTTAACATTATGTATAAATATTTTATCTATTT
1 TTACTCTTAAAATATTTAAACTTAACATTAGGTAT--ATATTTTATCTATTT
38893773 CGTTTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
52 30 0.68
55 14 0.32
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.55
Consensus pattern (53 bp):
TTACTCTTAAAATATTTAAACTTAACATTAGGTATATATTTTATCTATTTTTT
Found at i:38893914 original size:4 final size:4
Alignment explanation
Indices: 38893905--38893929 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38893895 ATTGATGTTC
38893905 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
38893930 CTTAACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:38893999 original size:12 final size:12
Alignment explanation
Indices: 38893981--38894015 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
38893971 TTTATTTATT
38893981 TTCTTTTA-TTG
1 TTCTTTTATTTG
38893992 TGTCTTTTATTTG
1 T-TCTTTTATTTG
38894005 TTCTTTTATTT
1 TTCTTTTATTT
38894016 ATTTGCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 17 0.77
13 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (12 bp):
TTCTTTTATTTG
Found at i:38894114 original size:3 final size:3
Alignment explanation
Indices: 38894047--38894104 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
38894037 AAAATTTAGA
38894047 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
*
38894095 TGT TAT TAT T
1 TAT TAT TAT T
38894105 GTCTTATTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38894966 original size:43 final size:43
Alignment explanation
Indices: 38894905--38894989 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
38894895 TGGTTTCGAC
38894905 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
1 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
38894948 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT
1 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT
38894990 AGTGTATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (43 bp):
ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
Found at i:38895004 original size:40 final size:42
Alignment explanation
Indices: 38894909--38895008 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
38894899 TTCGACATTA
* *
38894909 AGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTGATT
1 AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
*
38894951 AAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT-AGT
1 -AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
* *
38894993 -GTATATTCAATTTATT
1 AGAATATACAATTTATT
38895009 GTTAATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 13 0.25
42 2 0.04
43 38 0.72
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (42 bp):
AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
Found at i:38896079 original size:10 final size:10
Alignment explanation
Indices: 38896066--38896137 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
38896056 AGATAAAAGA
38896066 TAAAAATTAT
1 TAAAAATTAT
**
38896076 TAAATTTTAAT
1 TAAAAATT-AT
*
38896087 GAAAAA-TA-
1 TAAAAATTAT
*
38896095 TAAAAAATAT
1 TAAAAATTAT
38896105 TAAAAATCTAT
1 TAAAAAT-TAT
38896116 TAAAAATTA-
1 TAAAAATTAT
38896125 T-AAAATTA-
1 TAAAAATTAT
38896133 TAAAA
1 TAAAA
38896138 TTTTATAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 13 0.26
9 7 0.14
10 15 0.30
11 15 0.30
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:38896128 original size:9 final size:9
Alignment explanation
Indices: 38896065--38896182 Score: 53
Period size: 9 Copynumber: 12.2 Consensus size: 9
38896055 AAGATAAAAG
38896065 ATAAAAATT
1 ATAAAAATT
**
38896074 ATTAAATTTT
1 A-TAAAAATT
38896084 AATGAAAAA-T
1 -AT-AAAAATT
*
38896094 ATAAAAAAT
1 ATAAAAATT
38896103 ATTAAAAATCT
1 A-TAAAAAT-T
38896114 ATTAAAAATT
1 A-TAAAAATT
38896124 AT-AAAATT
1 ATAAAAATT
38896132 AT-AAAATT
1 ATAAAAATT
* * *
38896140 TTATAAAGT
1 ATAAAAATT
38896149 AGTAAGAAAATTGT
1 A-T-A-AAAA-T-T
*
38896163 AAAAAAATT
1 ATAAAAATT
38896172 ATAAAAATT
1 ATAAAAATT
38896181 AT
1 AT
38896183 CATACCAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
8 20 0.24
9 21 0.25
10 18 0.21
11 19 0.23
12 4 0.05
14 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:38896143 original size:18 final size:19
Alignment explanation
Indices: 38896089--38896146 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
38896079 ATTTTAATGA
*
38896089 AAAATATAAAAAATATTA-
1 AAAATATATAAAATATTAT
*
38896107 AAAATCTATTAAAA-ATTAT
1 AAAATATA-TAAAATATTAT
*
38896126 AAAAT-TATAAAATTTTAT
1 AAAATATATAAAATATTAT
38896144 AAA
1 AAA
38896147 GTAGTAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.15
18 20 0.59
19 9 0.26
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATATAAAATATTAT
Found at i:38896399 original size:39 final size:39
Alignment explanation
Indices: 38896356--38896439 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 39
38896346 AAAGAGCCTT
* * **
38896356 TTTTATACA-TTTTATAATTTTTTTTTAATTTTTAATAAA
1 TTTTATACATTTTTAT-ATCTTTTATTAAAGTTTAATAAA
* * *
38896395 TTTTAAATATTTTTATATCTTTTATTAAAGTTTAATAAT
1 TTTTATACATTTTTATATCTTTTATTAAAGTTTAATAAA
38896434 TTTTAT
1 TTTTAT
38896440 TTTTTATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (39 bp):
TTTTATACATTTTTATATCTTTTATTAAAGTTTAATAAA
Found at i:38896417 original size:29 final size:28
Alignment explanation
Indices: 38896377--38896445 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
38896367 TTATAATTTT
*
38896377 TTTTTA-ATTTTTAATAAATTTTAA-ATA
1 TTTTTATATTTTTAATAAAGTTTAATA-A
*
38896404 TTTTTATATCTTTTATTAAAGTTTAATAA
1 TTTTTATAT-TTTTAATAAAGTTTAATAA
38896433 TTTTTAT-TTTTTA
1 TTTTTATATTTTTA
38896446 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 11 0.30
28 3 0.08
29 22 0.59
30 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTATATTTTTAATAAAGTTTAATAA
Found at i:38896469 original size:16 final size:16
Alignment explanation
Indices: 38896429--38896469 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
38896419 TTAAAGTTTA
38896429 ATAATTTTTATTTTTT
1 ATAATTTTTATTTTTT
*
38896445 AT-TTATTTTATTTTTT
1 ATAAT-TTTTATTTTTT
38896461 ATAATTTTT
1 ATAATTTTT
38896470 TTGCCACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATAATTTTTATTTTTT
Found at i:38896704 original size:91 final size:90
Alignment explanation
Indices: 38896575--38896804 Score: 268
Period size: 93 Copynumber: 2.5 Consensus size: 90
38896565 TCAAAGGGCT
* * * *
38896575 TTTTTGATACATTTTGATACTTCAAGTACCCAATTGAGTGCAAAAAAAA-AGTAGGGGCTTAATT
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTG-AAAAAAAACA-T--GGGCTTAATT
**
38896639 GC-T-TTTTGTTTAAAAAGTTTGAGGACC
62 GCTTCTTTTGTTTAAAAAGTTCAAGGACC
*
38896666 TTTTTGATGCATTTTGAAAGTTTAAGTATCCAATTGAGTGAAAAAAAACATGGGCTTAATTGCTT
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAAAACATGGGCTTAATTGC--
* ***
38896731 TTTCTTTTTTTTTTTAAGTTCAAGGACC
64 -TTCTTTTGTTTAAAAAGTTCAAGGACC
*
38896759 TTTTTGATGCATTTTAAAAGTTTAAGTACCCAATTGAGTGAAAAAA
1 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAA
38896805 TATACAATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
88 12 0.10
90 9 0.08
91 36 0.30
92 1 0.01
93 62 0.52
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (90 bp):
TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGAAAAAAAACATGGGCTTAATTGCTT
CTTTTGTTTAAAAAGTTCAAGGACC
Found at i:38899751 original size:26 final size:26
Alignment explanation
Indices: 38899722--38899774 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
38899712 TTGTTAAAAC
* *
38899722 TCTTCTAAAAGAAACTC-AAGAGGAAT
1 TCTTCAAAAAAAAACTCAAAGA-GAAT
*
38899748 TCTTGAAAAAAAAACTCAAAGAGAAT
1 TCTTCAAAAAAAAACTCAAAGAGAAT
38899774 T
1 T
38899775 GTAATACGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (26 bp):
TCTTCAAAAAAAAACTCAAAGAGAAT
Found at i:38900194 original size:17 final size:16
Alignment explanation
Indices: 38900164--38900197 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38900154 TTTGGGGGGA
38900164 TTTTCTTTTGATTTTC
1 TTTTCTTTTGATTTTC
*
38900180 TTTTCATTTTTATTTTC
1 TTTTC-TTTTGATTTTC
38900197 T
1 T
38900198 GTAATTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTGATTTTC
Found at i:38903614 original size:7 final size:7
Alignment explanation
Indices: 38903597--38903635 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
38903587 TTCCTCAAAA
38903597 AAAATATG
1 AAAA-ATG
38903605 AAAAATG
1 AAAAATG
38903612 AAAAAAT-
1 -AAAAATG
38903619 AAAAATG
1 AAAAATG
38903626 AAAAATG
1 AAAAATG
38903633 AAA
1 AAA
38903636 GTAAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.21
7 13 0.45
8 10 0.34
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:38903626 original size:21 final size:20
Alignment explanation
Indices: 38903593--38903635 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
38903583 TTGATTCCTC
*
38903593 AAAAAAAATATGAAAAATGA
1 AAAAAAAAAATGAAAAATGA
38903613 AAAAATAAAAATGAAAAATGA
1 AAAAA-AAAAATGAAAAATGA
38903634 AA
1 AA
38903636 GTAAAAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAAAAAAATGAAAAATGA
Found at i:38904966 original size:44 final size:44
Alignment explanation
Indices: 38904883--38904968 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
38904873 AGCTCCTTGA
* *
38904883 CCAGCAGTGGAATAGGTTGAAGATTGCAAGTCTTATCTCCCTGG
1 CCAGCAGTGGAATAGGTTGAAAATTACAAGTCTTATCTCCCTGG
* *
38904927 CCAGCAGTGGAGTAGGTTGAAAATTAC-AGATCTTGTCTCCCT
1 CCAGCAGTGGAATAGGTTGAAAATTACAAG-TCTTATCTCCCT
38904969 AAGCAGTAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (44 bp):
CCAGCAGTGGAATAGGTTGAAAATTACAAGTCTTATCTCCCTGG
Found at i:38905141 original size:128 final size:128
Alignment explanation
Indices: 38904909--38905435 Score: 772
Period size: 128 Copynumber: 4.1 Consensus size: 128
38904899 TTGAAGATTG
*
38904909 CAAGTCTTATCTCCCTGGCCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
* * * *
38904974 GTAGCGGAGCACATCGAAGACGGTGAATCTTATCTTCAAGTGTAAGGAAGTAGATGTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* * * * *
38905037 CAAATCTTATCTCCCTGGTTAACAGTGGAGTAGGTTGGAAATTACAGATCTTGTCCCCCTAAGCA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
* * *
38905102 GTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* *
38905165 CAAGTCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACATATCTTGTCTCCCTAAGCA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
* *
38905230 GTAGCGGAGCAGATTGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* * * * * *
38905293 CAAGTC--CTGTCCCTGGTTAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGTA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
* * *
38905356 GTAGCGGAACAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAACAGATTGAAGCCGA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC-A
* *
38905420 TAA-TCCTATCTCCCTG
1 CAAGTCTTATCTCCCTG
38905436 AAGTTTTAGT
Statistics
Matches: 356, Mismatches: 40, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
126 109 0.31
127 3 0.01
128 244 0.69
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (128 bp):
CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
Found at i:38905558 original size:44 final size:44
Alignment explanation
Indices: 38905507--38905622 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
38905497 ATCGCATCAG
*
38905507 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAA-AA-CAA
1 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGAC-CA-AAGAAGCAA
* * *** *
38905551 GTCTTATCCCCCTGAAGTCAAAGTGGGGCAGACCAAAGAAGCAA
1 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGAAGCAA
* *
38905595 ATCTTATCTCCCTGAGGTTGCGGTGGAG
1 GTCTTATCTCCCTGAGGTTGCAGTGGAG
38905623 TAGATTGAAG
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
42 2 0.04
43 3 0.05
44 50 0.91
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (44 bp):
GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGAAGCAA
Found at i:38906388 original size:17 final size:16
Alignment explanation
Indices: 38906358--38906391 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38906348 TTTGGGGGGA
38906358 TTTTCTTTTGATTTTC
1 TTTTCTTTTGATTTTC
*
38906374 TTTTCATTTTTATTTTC
1 TTTTC-TTTTGATTTTC
38906391 T
1 T
38906392 GTAATTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTGATTTTC
Found at i:38911292 original size:96 final size:96
Alignment explanation
Indices: 38911177--38911372 Score: 306
Period size: 96 Copynumber: 2.1 Consensus size: 96
38911167 CTTACTTTTT
** *
38911177 TCTCTAGTTGGATATTTAATTGGACATTGGAAACTC-TTATGATCTTTTGAACTATACCAATAAC
1 TCTCTAGTTGGATATTTAATTGGACATTAAAAAC-CGTTATGATCTTTTGAACTACACCAATAAC
*
38911241 ATTGCACAAAAGATGATATCTCAATCGTATTC
65 ATTGCACAAAAGATGATAACTCAATCGTATTC
*
38911273 TCTCTATTTGGATATTTAATTGGACATTAAAAACCGTTATGATCTTTTGAACTACACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGACATTAAAAACCGTTATGATCTTTTGAACTACACCAATAACA
* *
38911338 TTGCACAAAAGGTGGTAACTCAATCGTATTC
66 TTGCACAAAAGATGATAACTCAATCGTATTC
38911369 -CTCT
1 TCTCT
38911373 TTTCGTTTGG
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
95 5 0.05
96 87 0.95
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (96 bp):
TCTCTAGTTGGATATTTAATTGGACATTAAAAACCGTTATGATCTTTTGAACTACACCAATAACA
TTGCACAAAAGATGATAACTCAATCGTATTC
Found at i:38913185 original size:8 final size:8
Alignment explanation
Indices: 38913172--38913200 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38913162 AAAAATTCAG
38913172 AATAATAA
1 AATAATAA
38913180 AATAATAA
1 AATAATAA
38913188 AATAATAA
1 AATAATAA
38913196 AATAA
1 AATAA
38913201 CAAGAGCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:38915958 original size:2 final size:2
Alignment explanation
Indices: 38915951--38915980 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38915941 AAATTGTTAT
38915951 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38915981 TATCCTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38920437 original size:19 final size:19
Alignment explanation
Indices: 38920395--38920461 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 19
38920385 GTATTATGTT
38920395 ATTTTTAATAATACTTATA
1 ATTTTTAATAATACTTATA
*
38920414 A-TTTTAA-AATATTTATA
1 ATTTTTAATAATACTTATA
38920431 ATTTTTTAATAAATTTTACTTATA
1 A-TTTTTAAT-AA---TACTTATA
38920455 ATTTTTA
1 ATTTTTA
38920462 TGATTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 7 0.18
21 2 0.05
23 6 0.15
24 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTAATAATACTTATA
Found at i:38925593 original size:19 final size:19
Alignment explanation
Indices: 38925571--38925623 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
38925561 ATAAAAATCT
38925571 TAAACAATTATAAAAAGTA
1 TAAACAATTATAAAAAGTA
* * *
38925590 TAAAAAATTGTAAAAAATTA
1 TAAACAATTAT-AAAAAGTA
*
38925610 TAGAC-ATTATAAAA
1 TAAACAATTATAAAA
38925624 CAAATNNNNN
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAACAATTATAAAAAGTA
Found at i:38925848 original size:9 final size:9
Alignment explanation
Indices: 38925836--38925867 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
38925826 TTTTAAATTG
38925836 TTTAATAAT
1 TTTAATAAT
38925845 TTTAATAAT
1 TTTAATAAT
38925854 TTTAATAAT
1 TTTAATAAT
38925863 TTTAA
1 TTTAA
38925868 AATAGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAATAAT
Found at i:38925849 original size:18 final size:17
Alignment explanation
Indices: 38925826--38925870 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
38925816 NNNNNNNNNT
*
38925826 TTTTAAATTGTTTAATAA
1 TTTTAAAAT-TTTAATAA
38925844 TTTTAATAATTTTAATAA
1 TTTTAA-AATTTTAATAA
38925862 TTTTAAAAT
1 TTTTAAAAT
38925871 AGTTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 20 0.80
19 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTAAAATTTTAATAA
Found at i:38925876 original size:29 final size:28
Alignment explanation
Indices: 38925839--38925893 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
38925829 TAAATTGTTT
38925839 AATAATTTTAATA-ATTTTAATAATTTTAA
1 AATAATTTTAATATATTTT--TAATTTTAA
* *
38925868 AATAGTTTTTATATATTTTTAATTTT
1 AATAATTTTAATATATTTTTAATTTT
38925894 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.30
29 11 0.48
30 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
AATAATTTTAATATATTTTTAATTTTAA
Found at i:38925877 original size:21 final size:20
Alignment explanation
Indices: 38925836--38925886 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
38925826 TTTTAAATTG
38925836 TTTAATAATTTT--AATAAT
1 TTTAATAATTTTAAAATAAT
*
38925854 TTTAATAATTTTAAAATAGT
1 TTTAATAATTTTAAAATAAT
*
38925874 TTTTATATATTTT
1 TTTAATA-ATTTT
38925887 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAATAATTTTAAAATAAT
Found at i:38932565 original size:44 final size:45
Alignment explanation
Indices: 38932516--38932601 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
38932506 ATAGTGTGAC
38932516 GTTCATC-ATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
1 GTTCATCAATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
*
38932560 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGT
1 GTTCATCA-ATACCAAGGTTCCTATCATCCTTGATAGTGGGT
38932602 TGAAGTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 7 0.18
46 32 0.82
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (45 bp):
GTTCATCAATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
Found at i:38937479 original size:7 final size:7
Alignment explanation
Indices: 38937464--38937495 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38937454 TCGTAATATT
38937464 TTATTTA
1 TTATTTA
*
38937471 TTGTTTA
1 TTATTTA
38937478 TTATTTA
1 TTATTTA
38937485 TTATTTA
1 TTATTTA
38937492 TTAT
1 TTAT
38937496 CGTACTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:38938290 original size:49 final size:50
Alignment explanation
Indices: 38938237--38938349 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 50
38938227 AAGTAGTGGC
* *
38938237 AGTATATCTGCGAATCAGTGGTGGCATGTCTACAAAATTG-TATC-ATGGT
1 AGTATATCTGC-AATCAGTGGTGGCATGTCCACAAAAGTGTTATCAATGGT
* *
38938286 AGTATATCTGCAATTCAGTGGTGGCTTGTCCACAAAAGTGTTATCAATGTT
1 AGTATATCTGCAA-TCAGTGGTGGCATGTCCACAAAAGTGTTATCAATGGT
*
38938337 AGTTTATCTGCAA
1 AGTATATCTGCAA
38938350 ACCAGTGACA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 2 0.04
49 34 0.61
50 4 0.07
51 16 0.29
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (50 bp):
AGTATATCTGCAATCAGTGGTGGCATGTCCACAAAAGTGTTATCAATGGT
Found at i:38939420 original size:19 final size:21
Alignment explanation
Indices: 38939396--38939436 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
38939386 CGGGACTAAA
*
38939396 TTAGG-AATAATTGAAA-ATT
1 TTAGGAAAAAATTGAAATATT
38939415 TTAGGAAAAAATTGAAATATT
1 TTAGGAAAAAATTGAAATATT
38939436 T
1 T
38939437 GGACTGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (21 bp):
TTAGGAAAAAATTGAAATATT
Found at i:38945123 original size:221 final size:221
Alignment explanation
Indices: 38944731--38945171 Score: 648
Period size: 221 Copynumber: 2.0 Consensus size: 221
38944721 TTGTGAAAAA
* * * * *
38944731 TAAAGATGGCTCTTTGAGAATGTGTATAGGTTACAAACAGTTGCATAAAGTCATAATAAAAAATA
1 TAAAGACGACTCTTTGAGAATGTGTATAGATTACAAACAGTTGAATAAAGTCACAATAAAAAATA
* * *
38944796 AGTATCCTTTGACACGTATCGACAATTTGTTTGATCAATTGAAAGGTGCCACAGTGTTTTCAAAG
66 AGTATCATTTGACACGTATCGACAATTTGTTTGATCAATTGAAAGGCGCCACAGTGTTCTCAAAG
* *
38944861 ATAGATCTTAGATATGGGTATTATCAATTGAAAGTTAAAGACTGTGATGTGTCAAAGACTACTTT
131 ATAGATCTCAGATACGGGTATTATCAATTGAAAGTTAAAGACTGTGATGTGTCAAAGACTACTTT
* *
38944926 TAGAACTCGTTGCAGTCATTATGAGT
196 CAGAACTCGTTACAGTCATTATGAGT
* *
38944952 TAAAGACGACTCTTTGAGATTGTGTATAGATTACAGACAGTTGAATAAAGTCACAATAAAAAATA
1 TAAAGACGACTCTTTGAGAATGTGTATAGATTACAAACAGTTGAATAAAGTCACAATAAAAAATA
* * * * * * *
38945017 AGTATCATTTGCCACGTGTCGACGATTTGTTTGATCAATTGAAATGCGGCATAGTGTTCTCGAAG
66 AGTATCATTTGACACGTATCGACAATTTGTTTGATCAATTGAAAGGCGCCACAGTGTTCTCAAAG
* ** *
38945082 ATAGATCTCAGATCCGGGTATTATCAATTGATGGTTAAAGACTGTGATGTGTCAAAGACTGCTTT
131 ATAGATCTCAGATACGGGTATTATCAATTGAAAGTTAAAGACTGTGATGTGTCAAAGACTACTTT
*
38945147 CAGAACTCGTTACGGTCATTATGAG
196 CAGAACTCGTTACAGTCATTATGAG
38945172 GTTTCTGGTA
Statistics
Matches: 194, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
221 194 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (221 bp):
TAAAGACGACTCTTTGAGAATGTGTATAGATTACAAACAGTTGAATAAAGTCACAATAAAAAATA
AGTATCATTTGACACGTATCGACAATTTGTTTGATCAATTGAAAGGCGCCACAGTGTTCTCAAAG
ATAGATCTCAGATACGGGTATTATCAATTGAAAGTTAAAGACTGTGATGTGTCAAAGACTACTTT
CAGAACTCGTTACAGTCATTATGAGT
Found at i:38948675 original size:2 final size:2
Alignment explanation
Indices: 38948668--38948697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38948658 TACTGGATAA
38948668 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
38948698 GAGTTCCATT
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:38953851 original size:25 final size:25
Alignment explanation
Indices: 38953823--38953941 Score: 118
Period size: 25 Copynumber: 4.8 Consensus size: 25
38953813 TCCTGTACAT
*
38953823 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACGAGCTGTAAATCG
* * *
38953848 GTATGCTCACT-CAAGCTATAAATCA
1 GTATGCTCA-TACGAGCTGTAAATCG
*
38953873 GTATGCTC-TCATGAGCTGTAAATCG
1 GTATGCTCAT-ACGAGCTGTAAATCG
* *
38953898 GTACGCTC-TCACGAGCTATAAATCG
1 GTATGCTCAT-ACGAGCTGTAAATCG
*
38953923 GTATGCTCACACGAGCTGT
1 GTATGCTCATACGAGCTGT
38953942 GGGTTGGAAC
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.01
25 74 0.97
26 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAAATCG
Found at i:38953898 original size:50 final size:50
Alignment explanation
Indices: 38953823--38953941 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
38953813 TCCTGTACAT
* * * *
38953823 GTATGCTCATACGAGCTGTGAATCGGTATGCTCACTCAAGCTATAAATCA
1 GTATGCTCACACGAGCTGTAAATCGGTACGCTCACACAAGCTATAAATCA
* * * * *
38953873 GTATGCTCTCATGAGCTGTAAATCGGTACGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTAAATCGGTACGCTCACACAAGCTATAAATCA
38953923 GTATGCTCACACGAGCTGT
1 GTATGCTCACACGAGCTGT
38953942 GGGTTGGAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (50 bp):
GTATGCTCACACGAGCTGTAAATCGGTACGCTCACACAAGCTATAAATCA
Found at i:38953971 original size:41 final size:41
Alignment explanation
Indices: 38953926--38954015 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
38953916 TAAATCGGTA
*
38953926 TGCTCACACGAGCTGTGGGTTGGAACGTAGCTACACGATGC
1 TGCTCACACGAGCTGTGGGTTGGAACATAGCTACACGATGC
* * *
38953967 TGCTCACATGAGCTGTGGGTTGGAACATAGCTATACTATGC
1 TGCTCACACGAGCTGTGGGTTGGAACATAGCTACACGATGC
*
38954008 TACTCACA
1 TGCTCACA
38954016 GAAGTTGTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (41 bp):
TGCTCACACGAGCTGTGGGTTGGAACATAGCTACACGATGC
Found at i:38956053 original size:23 final size:22
Alignment explanation
Indices: 38956001--38956053 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
38955991 GCTAACCCCA
*
38956001 TATATATGTTACATGAGAACCC
1 TATATATGTTACATGAAAACCC
**
38956023 TATATATGTTACATGCAAAACTG
1 TATATATGTTACATG-AAAACCC
38956046 TATATATG
1 TATATATG
38956054 CGAACCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TATATATGTTACATGAAAACCC
Found at i:38960443 original size:24 final size:24
Alignment explanation
Indices: 38960394--38960445 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38960384 TATTTTATCG
* *
38960394 TTATTTTTATTATTAGTAGCAATA
1 TTATTTATATTATTAATAGCAATA
* *
38960418 TTATTTATATTATTAATAGTATTA
1 TTATTTATATTATTAATAGCAATA
38960442 TTAT
1 TTAT
38960446 AATTAATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TTATTTATATTATTAATAGCAATA
Found at i:38960485 original size:9 final size:9
Alignment explanation
Indices: 38960471--38960512 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
38960461 TACTATAGTA
38960471 TTATTACTT
1 TTATTACTT
38960480 TTATTACTT
1 TTATTACTT
38960489 TTATTACTT
1 TTATTACTT
38960498 TTATTA-TT
1 TTATTACTT
38960506 ATTATTA
1 -TTATTA
38960513 TTACTACTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 2 0.06
9 30 0.94
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATTACTT
Found at i:38960859 original size:2 final size:2
Alignment explanation
Indices: 38960852--38960885 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
38960842 TTTTACGCAC
*
38960852 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38960886 TATTTTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38963066 original size:19 final size:18
Alignment explanation
Indices: 38963025--38963067 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
38963015 GTCTCTTTTT
38963025 TGCATTCATTTCATGCATC
1 TGCATTCATTTCATGCA-C
38963044 TGCATTGCATTTCATTGCA-
1 TGCATT-CATTTCA-TGCAC
38963063 TGCAT
1 TGCAT
38963068 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCATTCATTTCATGCAC
Found at i:38964357 original size:17 final size:18
Alignment explanation
Indices: 38964335--38964371 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38964325 TTATTCTTTT
38964335 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
38964352 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
38964370 AT
1 AT
38964372 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:38965132 original size:8 final size:8
Alignment explanation
Indices: 38965121--38965150 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
38965111 TCAAAATAGA
38965121 AAAAAAAG
1 AAAAAAAG
38965129 AAAAAAAG
1 AAAAAAAG
38965137 AAGAAAAAG
1 AA-AAAAAG
38965146 AAAAA
1 AAAAA
38965151 GGAGAGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:38965138 original size:17 final size:17
Alignment explanation
Indices: 38965113--38965150 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
38965103 AATCAAAGTC
*
38965113 AAAATAGAAAAAAAAGA
1 AAAAAAGAAAAAAAAGA
*
38965130 AAAAAAGAAGAAAAAGA
1 AAAAAAGAAAAAAAAGA
38965147 AAAA
1 AAAA
38965151 GGAGAGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGA
Found at i:38965967 original size:5 final size:5
Alignment explanation
Indices: 38965936--38965995 Score: 58
Period size: 5 Copynumber: 12.8 Consensus size: 5
38965926 TTTGAGTCAA
* *
38965936 AAAAC -AAAC -AAAC AAAAAA AAAAC AAAGC AAAAC AAAAC AAAAC -AAA-
1 AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
38965983 AAAAC AAAA- AAAA
1 AAAAC AAAAC AAAA
38965996 ATGAAATGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 18 0.38
5 26 0.55
6 3 0.06
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:38965993 original size:15 final size:15
Alignment explanation
Indices: 38965933--38965986 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
38965923 CACTTTGAGT
*
38965933 CAAAAAACAAACAAA
1 CAAAAAAAAAACAAA
38965948 CAAAAAAAAAACAAA
1 CAAAAAAAAAACAAA
*
38965963 GC-AAAACAAAACAAAA
1 -CAAAAAAAAAAC-AAA
38965979 CAAAAAAA
1 CAAAAAAA
38965987 CAAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 24 0.73
16 9 0.27
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAACAAA
Found at i:38966007 original size:22 final size:24
Alignment explanation
Indices: 38965981--38966032 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
38965971 AAACAAAACA
*
38965981 AAAAAACAAAAAAAAATG-AA-ATG
1 AAAAAA-ATAAAAAAATGAAAGATG
*
38966004 AAAAAAATGAAAAAATGAAAGATG
1 AAAAAAATAAAAAAATGAAAGATG
38966028 AAAAA
1 AAAAA
38966033 TGGAGAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 8 0.32
24 8 0.32
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.10
Consensus pattern (24 bp):
AAAAAAATAAAAAAATGAAAGATG
Found at i:38967352 original size:50 final size:50
Alignment explanation
Indices: 38967276--38967420 Score: 159
Period size: 50 Copynumber: 2.9 Consensus size: 50
38967266 AAACCATAGT
* * * * *
38967276 TTGCAATTAAAAAGATTGAAGTTACAACAACAGATCTTACTTTCCT-AGCG
1 TTGCAATGAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCCTGA-CA
* * * *
38967326 TTGCAGTGGAA-CAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAAT-GAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCCTGACA
* *
38967376 TTGCAATTAAGAAGATTGAAGCCACAACAGCAGATCTTACTTTCC
1 TTGCAATGAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCC
38967421 CCGGCAGTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.03
50 73 0.94
51 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (50 bp):
TTGCAATGAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCCTGACA
Found at i:38967618 original size:50 final size:48
Alignment explanation
Indices: 38967543--38969077 Score: 894
Period size: 50 Copynumber: 31.6 Consensus size: 48
38967533 NNNNGAACAT
38967543 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATTAA-AAG
* * * * * * *
38967593 ATTGAAGCCACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * * *
38967643 ATTAAAGTTACAACAACGGATCTTACTTCCATGACATTGCAATTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATT-AAAAG
* * * * * *
38967693 ATTGAAGCTACAACAGCGGATCTTAATTTCCTAGCGTTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
*
38967743 ATTAAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAGAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATTAA-AAG
* * * * **
38967793 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
*
38967843 ATTGAAGCTACAACAGCGGATCTTACTTCCTTGACATTGCAATTAAGAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATTAA-AAG
*
38967893 ATTGAAGCTACAACAGCGGATCTTACTT-CC--CA-GGCAATTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * * ** * * *
38967938 ATTAAAGCTACAACAGTGGATCTTATTTTCCTAGTGTTGCAGTGAAATGG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAATTAAA-AG
* *
38967988 ATTGAAGCTACAGCAGCGGATCTTGCTT-CC--C-TTGCAATTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * * * * *
38968033 ATTGAATCTACAACAACGGATTTTACTTTCCTAACGTTGCAGTGAAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAATTAAA-AG
* * * *
38968083 ATTGAAGCTACAGCAGCGAATCTTGCTT-CC--C-TGGCAATTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * *
38968128 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAACATTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCT-ACATTGCAAT-TAAAAG
* * *
38968178 ATTGAAGCTACAGCAGCGGATCTTGCTTCCC--CA--GCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* ** * * *
38968223 ATTGAAGCTACAGCAGCGGATCTTACTTTCTTACTTTCTTAGTGTTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTAC-TTC---C---C-TA-CATTGCAAT-TAAAAG
* * * * *
38968281 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACAGTTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTT-CCCTACA-TTGCAAT-TAAAAG
* * *
38968332 ATTGAAGCTACAACAGCGGATCTTGCTT-CC--C-TGGCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* ** * * *
38968377 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * * * *
38968427 ATTGAAGCTATAACAGCGAATCTTGCTT-CC--C-TGGCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * *
38968472 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * *
38968522 ATTGAAGCTACAACAGCGGATCTTGCTTCCC--C--GGCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * ** * * * *
38968567 ATTGAAGCTACAACAGTGGATCTTACTTTCCTAGTGTTGTAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * * *
38968617 ATTGAAGCTACAACAGCGGATCTTGCTTCCC--C--GGTAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * * ** ** * *
38968662 ATGGAAGCTACAACAGCTGATCTTATTTTCCTAGTGTTGCTGTGAAACGG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAATTAAA-AG
* *
38968712 ATTGAAGCTACAACAGCGGATCTTGCTTCCC--C--TGCAGTTGAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* ** * *
38968757 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGAAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAATTAAA-AG
* * * * *
38968807 ATTGAAGCTACAGCAGCGGATATTGCTT-CC--C-TGGCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * * * * *
38968852 ACTGAAGCTACAATAGCAGATCTTACTTTCCTAGCATTGCAGTGGAACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * * * *
38968902 ATTGAAGCTACAGCAGGGGATCTTGCTT---T-CCTTGCAGTTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATT-AAAAG
* * * * * *
38968947 ATTGAAGCTACAACAACGGATCTTACTTTCCTAGCGTTGCAGTGGAATAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTA-CATTGCAAT-TAAAAG
* * *
38968997 ATTGAAGCTACAACGGCGAATCTT-CTTTCCCCGACATTGCAATTAAAAAG
1 ATTGAAGCTACAACAGCGGATCTTAC-TT-CCCTACATTGCAATT-AAAAG
* *
38969047 ATTGAAG-TCACAACGGCGAATCTTACTTCCC
1 ATTGAAGCT-ACAACAGCGGATCTTACTTCCC
38969078 AGGCGGTGTA
Statistics
Matches: 1169, Mismatches: 212, Indels: 209
0.74 0.13 0.13
Matches are distributed among these distances:
45 375 0.32
46 32 0.03
47 5 0.00
48 1 0.00
49 39 0.03
50 625 0.53
51 53 0.05
52 2 0.00
55 1 0.00
57 2 0.00
58 34 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (48 bp):
ATTGAAGCTACAACAGCGGATCTTACTTCCCTACATTGCAATTAAAAG
Found at i:38968443 original size:95 final size:95
Alignment explanation
Indices: 38968279--38969020 Score: 1108
Period size: 95 Copynumber: 7.8 Consensus size: 95
38968269 GCAGTGGAAC
* * * **
38968279 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACAGTTGCAGTGGAACAGATTGAAGCTACA
1 AGATTGAAGCTACAACAGCGGATCTTACTT-TCCTAGTGTTGCAGTGGAACAGATTGAAGCTACA
38968344 ACAGCGGATCTTGCTTCCCTGGCAGTTAAAA
65 ACAGCGGATCTTGCTTCCCTGGCAGTTAAAA
*
38968375 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTATAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
*
38968440 CAGCGAATCTTGCTTCCCTGGCAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
** *
38968470 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
*
38968535 CAGCGGATCTTGCTTCCCCGGCAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
* *
38968565 AGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGTGTTGTAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
* *
38968630 CAGCGGATCTTGCTTCCCCGGTAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
* * * * * *
38968660 AGATGGAAGCTACAACAGCTGATCTTATTTTCCTAGTGTTGCTGTGAAACGGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
*
38968725 CAGCGGATCTTGCTTCCCCT-GCAGTTGAAA
66 CAGCGGATCTTGCTT-CCCTGGCAGTTAAAA
* *
38968755 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGAAACAGATTGAAGCTACAG
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
*
38968820 CAGCGGATATTGCTTCCCTGGCAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
* * * ** *
38968850 AGACTGAAGCTACAATAGCAGATCTTACTTTCCTAGCATTGCAGTGGAACAGATTGAAGCTACAG
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
* * *
38968915 CAGGGGATCTTGCTTTCCTTGCAGTTAAAA
66 CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
* * *
38968945 AGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCGTTGCAGTGGAATAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
* *
38969010 CGGCGAATCTT
66 CAGCGGATCTT
38969021 CTTTCCCCGA
Statistics
Matches: 586, Mismatches: 58, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
94 4 0.01
95 550 0.94
96 32 0.05
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (95 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAA
CAGCGGATCTTGCTTCCCTGGCAGTTAAAA
Found at i:38968534 original size:190 final size:192
Alignment explanation
Indices: 38967537--38969127 Score: 1394
Period size: 190 Copynumber: 8.2 Consensus size: 192
38967527 NNNNNNNNNN
* * * *
38967537 GAACATATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCC
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTG-----GCAGTTAAAAAGATTGAAGCT
* * * *
38967602 ACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTAAAGTTACAACAACGGATCTT
61 ACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTT
* * * *
38967667 ACTTCCATGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTAATTTCCTAGCGTTG
126 ACTTCC-T--CATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTG
38967732 CAGTG
188 CAGTG
* * * *
38967737 GAACAGATTAAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAGAAGATTGAAGCT
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTT-CC---C-TGGCAGTTAAAAAGATTGAAGCT
*
38967802 ACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCAGATTGAAGCTACAACAGCGGATCTT
61 ACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTT
* * * *
38967867 ACTTCCTTGACATTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTAC-TTCC---CA-GG
126 ACTTCC-T--CATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTG
* *
38967927 CAATT
188 CAGTG
* * * * * * * **
38967932 AAAAAGATTAAAGCTACAACAGTGGATCTTATTTTCCTAGTGTTGCAGTGAAATGGATTGAAGCT
1 GAACAGATTGAAGCTACAACAGCGGATCTTA-CTTCC--CTG--GCAGTTAAAAAGATTGAAGCT
* * * ** * * * *
38967997 ACAGCAGCGGATCTTGC-TTCC---C-TTGCAATTAAAAAGATTGAATCTACAACAACGGATTTT
61 ACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTT
* * * * * * * * *
38968057 ACTTTCCTAACGTTGCAGTGAAACAGATTGAAGCTACAGCAGCGAATCTTGCTTCCCTGGCAATT
126 AC-TTCCT--CATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-ATT
38968122 --A---
187 GCAGTG
* * ** *
38968123 -AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAACATTGCAGTGGAACAGATTGAAGCT
1 GAACAGATTGAAGCTACAACAGCGGATCTTAC-TTCC---C-TGGCAGTTAAAAAGATTGAAGCT
* * * * * *
38968187 ACAGCAGCGGATCTTGCTTCCCCAGCAGTT--A----AAAAGATTGAAGCTACAGCAGCGGATCT
61 ACAACAGCGGATCTTACTTTCCTAGC-GTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCT
** * *
38968246 TACTTTCTTACTTTCTTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGC-TTC
125 TAC-TTC---C--TC--A-TG--GCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC
**
38968310 CCCGACAGTTGCAGTG
179 CTAG-CA-TTGCAGTG
*
38968326 GAACAGATTGAAGCTACAACAGCGGATCTTGCTTCCCTGGCAGTTAAAAAGATTGAAGCTACAAC
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCAGTTAAAAAGATTGAAGCTACAAC
* * * *
38968391 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTATAACAGCGAATCTTGCTTC
66 AGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTC
38968456 C-C-TGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
131 CTCATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
* * *
38968516 GAATAGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAAC
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCAGTTAAAAAGATTGAAGCTACAAC
* * * *
38968581 AGTGGATCTTACTTTCCTAGTGTTGTAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTTC
66 AGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTC
* * * * * ** *
38968646 C-C-CGGTAGTTAAAAAGATGGAAGCTACAACAGCTGATCTTATTTTCCTAGTGTTGCTGTG
131 CTCATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
* * * *
38968706 AAACGGATTGAAGCTACAACAGCGGATCTTGCTTCCCCT-GCAGTTGAAAAGATTGAAGCTACAA
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTT-CCCTGGCAGTTAAAAAGATTGAAGCTACAA
* * * * *
38968770 CAGCGGATCTTACTTTCCTAGTGTTGCAGTGAAACAGATTGAAGCTACAGCAGCGGATATTGCTT
65 CAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
* * *
38968835 CC-C-TGGCAGTTAAAAAGACTGAAGCTACAATAGCAGATCTTACTTTCCTAGCATTGCAGTG
130 CCTCATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
* * * * *
38968896 GAACAGATTGAAGCTACAGCAGGGGATCTTGCTTTCCTTGCAGTTAAAAAGATTGAAGCTACAAC
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCAGTTAAAAAGATTGAAGCTACAAC
* * * *
38968961 AACGGATCTTACTTTCCTAGCGTTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTT-CTTT
66 AGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTAC-TT
* * * * * * ** *
38969025 CCCCGACATTGCAATTAAAAAGATTGAAG-TCACAACGGCGAATCTTAC-TTCCCAGGCGGTGTA
130 --CC-TCATGGCAGTTAAAAAGATTGAAGCT-ACAACAGCGGATCTTACTTTCCTA-GCATTGCA
*
38969088 ATG
190 GTG
* * * *
38969091 GAATAGATTGAAGCTACGACGGCGAATCTTACTTCCC
1 GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCC
38969128 CAACATTACA
Statistics
Matches: 1171, Mismatches: 161, Indels: 123
0.80 0.11 0.08
Matches are distributed among these distances:
189 4 0.00
190 625 0.53
191 51 0.04
192 8 0.01
193 5 0.00
194 16 0.01
195 134 0.11
196 6 0.01
197 6 0.01
198 41 0.04
199 44 0.04
200 165 0.14
201 2 0.00
203 7 0.01
204 56 0.05
205 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (192 bp):
GAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGGCAGTTAAAAAGATTGAAGCTACAAC
AGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTC
CTCATGGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTG
Found at i:38969093 original size:100 final size:100
Alignment explanation
Indices: 38967543--38969149 Score: 694
Period size: 95 Copynumber: 16.5 Consensus size: 100
38967533 NNNNGAACAT
* * ** * * *
38967543 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCCACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * *
38967608 GC-AGATCTTACTTTCCTAGCGTTGCAGTGGAACAG
66 ACGA-ATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * ** * *** *
38967643 ATTAAAGTTACAACAACGGATCTTACTTCCATGACATTGCAATTAAAAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * * *
38967708 GCGGATCTTAATTTCCTAGCGTTGCAGTGGAACAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * * *
38967743 ATTAAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAGAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * **
38967808 GCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * *** * *
38967843 ATTGAAGCTACAACAGCGGATCTTACTTCCTTGACATTGCAATTAAGAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * ** *
38967908 GCGGATCTTAC-TTCCCA---G-GCAATTAAAAAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * * * * *** * ** *
38967938 ATTAAAGCTACAACAGTGGATCTTATTTTCCTAGTGTTGCAGTGAAATGGATTGAAGCTACAGCA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * ** *
38968003 GCGGATCTTGC-TT-CC--C-TTGCAATTAAAAAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* ** * * * * * * * *
38968033 ATTGAATCTACAACAACGGATTTTACTTTCCTAACGTTGCAGTGAAACAGATTGAAGCTACAGCA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * ** *
38968098 GCGAATCTTGC-TT-CC--CTG-GCAATTAAAAAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * ** * *
38968128 ATTGAAGCTACAACAGCGGATCTTACTTTCCTAACATTGCAGTGGAACAGATTGAAGCTACAGCA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * *
38968193 GCGGATCTTGCTTCCCCAGCAGT-TAA---AA-AG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * *** ** *
38968223 ATTGAAGCTACAGCAGCGGATCTTACTTTCTTACTTTCTTAGTGTTGCAGTGGAACAGATTGAAG
1 ATTGAAGCTACAACGGCGAATCTTAC-TTC---C---C-CAACATTGCAGTTAAAAAGATTGAAG
* * * * * * *
38968288 CTACAACAGCGGATCTTGC-TTCCCCGACAGTTGCAGTGGAACAG
58 CTACAACAACGAATCTTACTTTCCCAG-C-GGTGCAATGGAATAG
* * * *
38968332 ATTGAAGCTACAACAGCGGATCTTGCTT--CC--C-TGGCAGTTAAAAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * * *
38968392 GCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * *
38968427 ATTGAAGCTATAACAGCGAATCTTGCTT--CC--C-TGGCAGTTAAAAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * ** *
38968487 GCGGATCTTACTTTCCTAGCATTGCAGTGGAATAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * *
38968522 ATTGAAGCTACAACAGCGGATCTTGCTT-CCC--C--GGCAGTTAAAAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
** * * * * * * *
38968582 GTGGATCTTACTTTCCTAGTGTTGTAGTGGAACAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * * *
38968617 ATTGAAGCTACAACAGCGGATCTTGCTT-CCC--C--GGTAGTTAAAAAGATGGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * ** * **
38968677 GCTG-ATCTTATTTTCCTAGTGTTGCTGTGAAACGG
66 AC-GAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * *
38968712 ATTGAAGCTACAACAGCGGATCTTGCTT-CCC--C--TGCAGTTGAAAAGATTGAAGCTACAACA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * * * * * * *
38968772 GCGGATCTTACTTTCCTAGTGTTGCAGTGAAACAG
66 ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * * * * * *
38968807 ATTGAAGCTACAGCAGCGGATATTGCTT--CC--C-TGGCAGTTAAAAAGACTGAAGCTACAATA
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
* * ** * *
38968867 GC-AGATCTTACTTTCCTAGCATTGCAGTGGAACAG
66 ACGA-ATCTTACTTTCCCAGCGGTGCAATGGAATAG
* * * *
38968902 ATTGAAGCTACAGCAGG-GGATCTTGCTT--TC--C-TTGCAGTTAAAAAGATTGAAGCTACAAC
1 ATTGAAGCTACAAC-GGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAAC
* * * *
38968961 AACGGATCTTACTTTCCTAGCGTTGCAGTGGAATAG
65 AACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
* *
38968997 ATTGAAGCTACAACGGCGAATCTT-CTTTCCCCGACATTGCAATTAAAAAGATTGAAG-TCACAA
1 ATTGAAGCTACAACGGCGAATCTTAC-TTCCCCAACATTGCAGTTAAAAAGATTGAAGCT-ACAA
** *
38969060 CGGCGAATCTTAC-TTCCCAGGCGGTGTAATGGAATAG
64 CAACGAATCTTACTTTCCCA-GCGGTGCAATGGAATAG
* * *
38969097 ATTGAAGCTACGACGGCGAATCTTACTTCCCCAACATTACAGTTAAACAGATT
1 ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATT
38969150 AGAGATGGCA
Statistics
Matches: 1315, Mismatches: 150, Indels: 84
0.85 0.10 0.05
Matches are distributed among these distances:
94 9 0.01
95 803 0.61
96 45 0.03
97 8 0.01
99 17 0.01
100 352 0.27
101 1 0.00
102 6 0.00
103 42 0.03
104 1 0.00
105 1 0.00
108 4 0.00
109 26 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (100 bp):
ATTGAAGCTACAACGGCGAATCTTACTTCCCCAACATTGCAGTTAAAAAGATTGAAGCTACAACA
ACGAATCTTACTTTCCCAGCGGTGCAATGGAATAG
Found at i:38969242 original size:21 final size:18
Alignment explanation
Indices: 38969201--38969239 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
38969191 AATCGCATCC
38969201 AGTCCTATCTCCCTAAGT
1 AGTCCTATCTCCCTAAGT
38969219 AGTCCTATCTCCCTAAGT
1 AGTCCTATCTCCCTAAGT
38969237 AGT
1 AGT
38969240 AGTGGAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (18 bp):
AGTCCTATCTCCCTAAGT
Found at i:38970789 original size:3 final size:3
Alignment explanation
Indices: 38970783--38970888 Score: 69
Period size: 3 Copynumber: 35.7 Consensus size: 3
38970773 TTAGTAGCAA
* * * * *
38970783 TAT TAT T-T ATAT TAT TAA TAG TAT TAT TAT TAT TAT TAA TGT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
38970828 CAT TAC TA- TAG TAT TAT TACT T-T TAT TACT T-T TAT TACT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TA-T TAT TAT
38970872 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
38970889 CTACTACTAC
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
2 9 0.11
3 67 0.81
4 7 0.08
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:38970795 original size:24 final size:24
Alignment explanation
Indices: 38970761--38970813 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
38970751 TATTTTATCG
* *
38970761 TTATTTTTATTATTAGTAGCAATA
1 TTATTTATATTATTAATAGCAATA
* *
38970785 TTATTTATATTATTAATAGTATTA
1 TTATTTATATTATTAATAGCAATA
38970809 TTATT
1 TTATT
38970814 ATTATTAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TTATTTATATTATTAATAGCAATA
Found at i:38970819 original size:24 final size:23
Alignment explanation
Indices: 38970765--38970822 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
38970755 TTATCGTTAT
*
38970765 TTTTATTATTAGTAGCAATATTA
1 TTTTATTATTAATAGCAATATTA
38970788 TTTATATTATTAATAG---TATTA
1 TTT-TATTATTAATAGCAATATTA
38970809 TTATTATTATTAAT
1 TT-TTATTATTAAT
38970823 GTCATCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.53
22 1 0.03
23 3 0.09
24 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTATTATTAATAGCAATATTA
Found at i:38973162 original size:25 final size:25
Alignment explanation
Indices: 38973128--38973177 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
38973118 GGTCACTCAT
38973128 TTTATCTTTTAAAAAATTAA-TTTA
1 TTTATCTTTTAAAAAATTAAGTTTA
* *
38973152 TTTATCTTTTTTAAGAATTAAGTTTA
1 TTTATC-TTTTAAAAAATTAAGTTTA
38973178 ATTCTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTATCTTTTAAAAAATTAAGTTTA
Found at i:38973884 original size:64 final size:64
Alignment explanation
Indices: 38973806--38973943 Score: 258
Period size: 64 Copynumber: 2.2 Consensus size: 64
38973796 CAACTGTAAG
* *
38973806 AAAAATATTTAAAATTATATTTTTAATATTTTATGTGTAAAACTATACGTAAACAATTATGTAT
1 AAAAATATTTAAAATTATATTTTTAATATTTTATGTCTAAAACTATAAGTAAACAATTATGTAT
38973870 AAAAATATTTAAAATTATATTTTTAATATTTTATGTCTAAAACTATAAGTAAACAATTATGTAT
1 AAAAATATTTAAAATTATATTTTTAATATTTTATGTCTAAAACTATAAGTAAACAATTATGTAT
38973934 AAAAATATTT
1 AAAAATATTT
38973944 TTTAAATGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 72 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (64 bp):
AAAAATATTTAAAATTATATTTTTAATATTTTATGTCTAAAACTATAAGTAAACAATTATGTAT
Found at i:38976101 original size:18 final size:17
Alignment explanation
Indices: 38976078--38976163 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 17
38976068 AATAATAATG
38976078 TGTATAATAAAATTAAAA
1 TGTATAA-AAAATTAAAA
38976096 TGTATAAAAAA-TAAAA
1 TGTATAAAAAATTAAAA
*
38976112 -ATA-AAAGAAATAATAAAA
1 TGTATAAA-AAAT--TAAAA
*
38976130 TGTGTAATAAAATTAAAA
1 TGTATAA-AAAATTAAAA
38976148 TGTATAAAAATATTAA
1 TGTATAAAAA-ATTAA
38976164 GATAAAACTT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.05
15 5 0.09
16 5 0.09
17 7 0.12
18 28 0.50
19 1 0.02
20 6 0.11
21 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
TGTATAAAAAATTAAAA
Found at i:38976733 original size:22 final size:23
Alignment explanation
Indices: 38976708--38976752 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
38976698 TTAAGACATG
* *
38976708 AACATCTAACATCTA-ACATCAC
1 AACACCTAAAATCTAGACATCAC
38976730 AACACCTAAAATCTAGACATCAC
1 AACACCTAAAATCTAGACATCAC
38976753 CAAATCACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (23 bp):
AACACCTAAAATCTAGACATCAC
Found at i:38982870 original size:27 final size:27
Alignment explanation
Indices: 38982840--38983368 Score: 541
Period size: 27 Copynumber: 19.8 Consensus size: 27
38982830 CCCTAAAATA
* * * *
38982840 GGTAAAATAACTGTAATGCCCCTGTAT
1 GGTAAAATGACCGTAATGCCCCTATAG
*
38982867 GGTAAAATGATCGTAATGCCCCT-TAG
1 GGTAAAATGACCGTAATGCCCCTATAG
** ** *
38982893 GGTAAAATGACTATAATGCCTTTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
38982920 GGTAAAATGACCGTAATACCCC-ATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
38982946 GGTAAAATGACCGTAAT-ACCTTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
38982972 GGTAAAATGACCATAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
38982999 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * * *
38983026 GGTAAAATAATCGTAATGCCTCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
38983053 GGTAAAATGACCGTAATACCCATATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* **
38983080 GGTAAAATGACCATAATAACCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
38983107 GGTAAAATGACCGTAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * * * *
38983134 GCTAAAATAATCGTAATGTCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * * *
38983161 GGTAAAATAATCATAATACCCC-ATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
38983187 GGTAAAATGACAGTAATATCCCC-ATAG
1 GGTAAAATGACCGTAAT-GCCCCTATAG
* *
38983214 GGTAAAATGACCAT-ATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
38983240 GGTAAAATGACCGTAATACCCCCATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
38983267 GGTAAAATGATCGTAATACCTCC-ATAA
1 GGTAAAATGACCGTAATGCC-CCTATAG
* * **
38983294 GGTAAAATGATCGTAATACCCAAATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
38983321 GGTAAAATGACCGTAAAGCCCCTGTAA
1 GGTAAAATGACCGTAATGCCCCTATAG
*
38983348 GGTAAAATTACCGTAATGCCC
1 GGTAAAATGACCGTAATGCCC
38983369 TTGGAGGGTA
Statistics
Matches: 421, Mismatches: 73, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.01
26 95 0.23
27 318 0.76
28 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTATAG
Found at i:38983270 original size:241 final size:240
Alignment explanation
Indices: 38982867--38983368 Score: 688
Period size: 241 Copynumber: 2.1 Consensus size: 240
38982857 GCCCCTGTAT
* * * * *
38982867 GGTAAAATGATCGTAATGCCCCTTAGGGTAAAATGACTATAATGCCTTTGTAGGGTAAAATGACC
1 GGTAAAATGACCGTAATGCCCCTTAGGCTAAAATAACTATAATGCCTCTGTAGGGTAAAATAACC
* * **
38982932 GTAATACCCCATAGGGTAAAATGACCGTAATACCTTATAGGGTAAAATGACCATAATGCCCCTAT
66 ATAATACCCCATAGGGTAAAATGACAGTAATACCCCATAGGGTAAAATGACCATAATGCCCCTAT
* ** * ** *
38982997 AGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATAATCGTAATGCCTCTGTAGGGTAAAATG
131 AGGGTAAAATGACCGTAATACCCCCATAGGGTAAAATAATCGTAATACCTCCATAAGGTAAAATG
* *
38983062 ACCGTAATACCCATATAGGGTAAAATGACCATAATA-ACCCTATAG
196 ACCGTAATACCCAAATAGGGTAAAATGACCATAA-AGACCCTATAA
*
38983107 GGTAAAATGACCGTAATGCCCCTATAGGCTAAAATAA-TCGTAATGTCC-CTGTAGGGTAAAATA
1 GGTAAAATGACCGTAATGCCCCT-TAGGCTAAAATAACT-ATAATG-CCTCTGTAGGGTAAAATA
*
38983170 ATCATAATACCCCATAGGGTAAAATGACAGTAATATCCCCATAGGGTAAAATGACCAT-ATGCCC
63 ACCATAATACCCCATAGGGTAAAATGACAGTAATA-CCCCATAGGGTAAAATGACCATAATGCCC
* *
38983234 CTGTAGGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGATCGTAATACCTCCATAAGGTAA
127 CTATAGGGTAAAATGACCGTAATACCCCCATAGGGTAAAATAATCGTAATACCTCCATAAGGTAA
* * * *
38983299 AATGATCGTAATACCCAAATAGGGTAAAATGACCGTAAAGCCCCTGTAA
192 AATGACCGTAATACCCAAATAGGGTAAAATGACCATAAAGACCCTATAA
*
38983348 GGTAAAATTACCGTAATGCCC
1 GGTAAAATGACCGTAATGCCC
38983369 TTGGAGGGTA
Statistics
Matches: 230, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
240 24 0.10
241 184 0.80
242 22 0.10
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (240 bp):
GGTAAAATGACCGTAATGCCCCTTAGGCTAAAATAACTATAATGCCTCTGTAGGGTAAAATAACC
ATAATACCCCATAGGGTAAAATGACAGTAATACCCCATAGGGTAAAATGACCATAATGCCCCTAT
AGGGTAAAATGACCGTAATACCCCCATAGGGTAAAATAATCGTAATACCTCCATAAGGTAAAATG
ACCGTAATACCCAAATAGGGTAAAATGACCATAAAGACCCTATAA
Found at i:38983574 original size:27 final size:26
Alignment explanation
Indices: 38983525--38983595 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
38983515 ATGAAGGAAG
38983525 TACTG-TACTGGTGGCTCTACCACA-A
1 TACTGTTACTGGTGGCT-TACCACATA
*
38983550 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTT-ACCACATA
* *
38983578 TACTATTACTGGTAGCTT
1 TACTGTTACTGGTGGCTT
38983596 TGCTGTGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 1 0.03
26 5 0.13
27 31 0.79
28 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (26 bp):
TACTGTTACTGGTGGCTTACCACATA
Found at i:38983639 original size:26 final size:26
Alignment explanation
Indices: 38983591--38983640 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
38983581 TATTACTGGT
* *
38983591 AGCTTTGCTGTGATACTATTGATGAC
1 AGCTTTGCTGCGATACTACTGATGAC
**
38983617 AGCTTTGCTGCGATGTTACTGATG
1 AGCTTTGCTGCGATACTACTGATG
38983641 GCTTTGTGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (26 bp):
AGCTTTGCTGCGATACTACTGATGAC
Found at i:38983677 original size:32 final size:32
Alignment explanation
Indices: 38983631--38983789 Score: 160
Period size: 32 Copynumber: 5.0 Consensus size: 32
38983621 TTGCTGCGAT
*
38983631 GTTACTGATGGCTTTGTGCCGATCATATTACC
1 GTTACTGATAGCTTTGTGCCGATCATATTACC
* ***
38983663 ATTACTGATAGCTTTGTATTGATCATATTACC
1 GTTACTGATAGCTTTGTGCCGATCATATTACC
*
38983695 GTTACTGATAGCTTTGTGCCGATCATATTACT
1 GTTACTGATAGCTTTGTGCCGATCATATTACC
* * * * *
38983727 GTTACTGAT-GGTTGTATGTCGATCATATCACT
1 GTTACTGATAGCTT-TGTGCCGATCATATTACC
* * *
38983759 GCTATTGA-AGGCTTTGTGCCAATCATATTAC
1 GTTACTGATA-GCTTTGTGCCGATCATATTAC
38983790 TGTACTTATG
Statistics
Matches: 103, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
31 3 0.03
32 97 0.94
33 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (32 bp):
GTTACTGATAGCTTTGTGCCGATCATATTACC
Found at i:38983790 original size:64 final size:63
Alignment explanation
Indices: 38983633--38983800 Score: 191
Period size: 64 Copynumber: 2.7 Consensus size: 63
38983623 GCTGCGATGT
** * * *
38983633 TACTGAT-GGCTTTGTGCCGATCATATTACCATTACTGATAGCTTTGTATTGATCATATTACCGT
1 TACTGATAGGCTTTGTGCCGATCATATTACTGTTACTGAT-G-GTTGTATTGATCATATCACCGC
*
38983697 TACTGATA-GCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTATGTCGATCATATCACTGC
1 TACTGATAGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTAT-T-GATCATATCACCGC
* * *
38983761 TATTGA-AGGCTTTGTGCCAATCATATTACTG-TACTTATGG
1 TACTGATAGGCTTTGTGCCGATCATATTACTGTTACTGATGG
38983801 CTTATAGCCA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
62 6 0.07
63 11 0.12
64 74 0.81
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (63 bp):
TACTGATAGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTATTGATCATATCACCGC
Found at i:38983820 original size:22 final size:22
Alignment explanation
Indices: 38983795--38983859 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
38983785 ATTACTGTAC
38983795 TTATGGCTTATAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
* * *
38983817 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTTATAGCCATTCTGT
* *
38983839 TTACGGCTCT-TAACCATTCTG
1 TTATGGCT-TATAGCCATTCTG
38983860 GTTACTGACA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:38986669 original size:12 final size:12
Alignment explanation
Indices: 38986652--38986676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38986642 ATAATAATAT
38986652 TTATGAACTTAC
1 TTATGAACTTAC
38986664 TTATGAACTTAC
1 TTATGAACTTAC
38986676 T
1 T
38986677 CGTTAGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TTATGAACTTAC
Found at i:39011545 original size:17 final size:18
Alignment explanation
Indices: 39011523--39011564 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39011513 ATATATGGAT
*
39011523 AAATTA-TTGACTTGATA
1 AAATTAGTTAACTTGATA
*
39011540 AAATTAGTTAATTTGATA
1 AAATTAGTTAACTTGATA
*
39011558 AATTTAG
1 AAATTAG
39011565 AGTTAAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (18 bp):
AAATTAGTTAACTTGATA
Found at i:39011969 original size:39 final size:39
Alignment explanation
Indices: 39011916--39011990 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
39011906 ATATATGCCC
* ** *
39011916 AGCAAGCTGTGTGCCGGTAATTATTCGGGCTATGTGTCT
1 AGCAAGCTGGGTGCCAATAATTATTCAGGCTATGTGTCT
*
39011955 AGCATGCTGGGTGCCAATAATTATTCAGGCTATGTG
1 AGCAAGCTGGGTGCCAATAATTATTCAGGCTATGTG
39011991 CCAGTGATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32
Consensus pattern (39 bp):
AGCAAGCTGGGTGCCAATAATTATTCAGGCTATGTGTCT
Found at i:39013224 original size:19 final size:20
Alignment explanation
Indices: 39013194--39013235 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
39013184 CCCTGCAGTT
* *
39013194 TGAAAAATTTTATCTTTTTC
1 TGAAAAATTTTATATGTTTC
39013214 TGAAAAA-TTTATATGTTTC
1 TGAAAAATTTTATATGTTTC
39013233 TGA
1 TGA
39013236 TTTAGTCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
TGAAAAATTTTATATGTTTC
Found at i:39016584 original size:18 final size:18
Alignment explanation
Indices: 39016540--39016587 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
39016530 AAAATAAAAA
39016540 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAATTGAAT
***
39016558 AACAATTTGTAAA-TGAAT
1 AATGTTTTG-AAATTGAAT
39016576 AATGTTTTGAAA
1 AATGTTTTGAAA
39016588 ACGAACGACA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.40
Consensus pattern (18 bp):
AATGTTTTGAAATTGAAT
Found at i:39026853 original size:43 final size:43
Alignment explanation
Indices: 39026764--39026877 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
39026754 AGCTTGTACA
* * * * *
39026764 ATGCTAACGTCCTAAACGTGGTCTTACATGTAATCACATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
39026807 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAAACACATA-TCG
39026850 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
39026878 CAATAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
42 4 0.07
43 54 0.89
44 3 0.05
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:39026886 original size:43 final size:43
Alignment explanation
Indices: 39026806--39026887 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
39026796 ATCACATATT
**
39026806 GATGCCACTGTCCCAGACAGGGTCTTACATGTAAACACAAGTC
1 GATGCCACTGTCCCAGACAGGGTCTTACAAATAAACACAAGTC
39026849 GATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAT-AACACA
1 GATGCC-ACTGTCCCAGACAG-GGTCTTACA-AATAAACACA
39026888 TATAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 1 0.03
43 30 0.88
44 3 0.09
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (43 bp):
GATGCCACTGTCCCAGACAGGGTCTTACAAATAAACACAAGTC
Found at i:39068246 original size:50 final size:49
Alignment explanation
Indices: 39068181--39068280 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 49
39068171 TATATTGATT
39068181 GATAAAATTTCAAATGGATCTGATTATTTTGTAATACTTTGTAACCCTA
1 GATAAAATTTCAAATGGATCTGATTATTTTGTAATACTTTGTAACCCTA
39068230 GATAAAATGTTCAAATGGATCTGATTATTTTGTAATACTTTGTAACCCTA
1 GATAAAAT-TTCAAATGGATCTGATTATTTTGTAATACTTTGTAACCCTA
39068280 G
1 G
39068281 TTTGGCGACC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 8 0.16
50 42 0.84
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (49 bp):
GATAAAATTTCAAATGGATCTGATTATTTTGTAATACTTTGTAACCCTA
Found at i:39075863 original size:453 final size:452
Alignment explanation
Indices: 39075265--39076120 Score: 1390
Period size: 453 Copynumber: 1.9 Consensus size: 452
39075255 GAGACACGAC
*
39075265 CGTATGTCACCTTATTGTTTTGATATGTAAAAAGTTAAAGTATGATTTTAAGTACAAGTAGTTAA
1 CGTATGTCACCTTATTGTTTTGATATGTAAAAAGTTAAAGTATGATTTAAAGTACAAGTAGTTAA
* * *
39075330 CCTCATATGATATGTGAACTAAGGAAGATGTTTTAGTGCAAATATATGGTATGTATTAATGGAAT
66 CCTAATATGATATATGAACTAAGAAAGATGTTTTAGTGCAAATATATGGTATGTATTAATGGAAT
* * *
39075395 GTTGTGACCGAGGTGCCTAAGTTTGGCATATTGGTTGAATGTTAGATGATGTGATTTAACCTACT
131 GTTGTGACCGAGGTGCCTAAGTTTGACATATTGGTTGAATGTTAAATGATGTGATTTAACATACT
*
39075460 TTGAATGATAATTCTTTTTATTCTAAAATTGTATATACTTGTGGTATCAATGAGGATACATTGGT
196 TTGAATGATAATTCTTTTTATTCTAAAATTGTATATACTTGTGGTATCAATGAAGATACATTGGT
* * *
39075525 TAGGCACCTAGGATTATTGATGTAGCATGTTTTTAACTTTTTTTAATGTCACTTTGAATATGTCT
261 TAAGCACCTAGGATTATTGATGTAGCATGTTTTTAAC-TTGTTTAATGTCACTTTGAATAGGTCT
** * *
39075590 TTTGGCTGGTAAATGGATTTTTTAGAGTCC-AGGTAAGCTTGAAATGGTAAACTAATTGATTAAG
325 TTTGGCTGGTAAATGGATTACTTAGAG-CCTAAGTAACCTTGAAATGGTAAACTAATTGATTAAG
*
39075654 GTTCATTTTGGGTTCACACGGCCTTAGACATGACCATGTGAGACACACGGCCTGGCAACACGGT
389 GTTCATTCTGGGTTCACACGGCCTTAGACATGACCATGTGAGACACACGGCCTGGCAACACGGT
* *
39075718 CGTATGTCACCTTATTGTTTTGATATGTAAAATGTTAAAGTATGATTTAAAGTGCAAGTAGTTAA
1 CGTATGTCACCTTATTGTTTTGATATGTAAAAAGTTAAAGTATGATTTAAAGTACAAGTAGTTAA
*
39075783 CCTAATATGATATATGAACTAAGAAAGATGTTTTAGTGCAAATATATGGTATGTGTTAATGGAAT
66 CCTAATATGATATATGAACTAAGAAAGATGTTTTAGTGCAAATATATGGTATGTATTAATGGAAT
* * *
39075848 GTTGTGACTGAGGTGCCTAAGTTTGACATATTGGTTGAATGTTAAATGGTGTGATTTAACATTCT
131 GTTGTGACCGAGGTGCCTAAGTTTGACATATTGGTTGAATGTTAAATGATGTGATTTAACATACT
* * *
39075913 TTGAATGATATTTCTTTTTGTTGTAAAATTGTATATACTTGTGGTATCAATGAAGATACATTGGT
196 TTGAATGATAATTCTTTTTATTCTAAAATTGTATATACTTGTGGTATCAATGAAGATACATTGGT
* * * *
39075978 TAAGCACTTAGGATTGTTGATTTAGCATGTTTTTAGCTTGTTTAATGTCACTTTGAATAGGTCTT
261 TAAGCACCTAGGATTATTGATGTAGCATGTTTTTAACTTGTTTAATGTCACTTTGAATAGGTCTT
* ** *
39076043 TTGGCTGGTAAATGGATTACTTAGAGCCTAAGTAACCTTGAATTGGTAAACTTGTTGTTTAAGGT
326 TTGGCTGGTAAATGGATTACTTAGAGCCTAAGTAACCTTGAAATGGTAAACTAATTGATTAAGGT
39076108 TCATTCTGGGTTC
391 TCATTCTGGGTTC
39076121 TAACGGCTTA
Statistics
Matches: 369, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
451 2 0.01
452 92 0.25
453 275 0.75
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.39
Consensus pattern (452 bp):
CGTATGTCACCTTATTGTTTTGATATGTAAAAAGTTAAAGTATGATTTAAAGTACAAGTAGTTAA
CCTAATATGATATATGAACTAAGAAAGATGTTTTAGTGCAAATATATGGTATGTATTAATGGAAT
GTTGTGACCGAGGTGCCTAAGTTTGACATATTGGTTGAATGTTAAATGATGTGATTTAACATACT
TTGAATGATAATTCTTTTTATTCTAAAATTGTATATACTTGTGGTATCAATGAAGATACATTGGT
TAAGCACCTAGGATTATTGATGTAGCATGTTTTTAACTTGTTTAATGTCACTTTGAATAGGTCTT
TTGGCTGGTAAATGGATTACTTAGAGCCTAAGTAACCTTGAAATGGTAAACTAATTGATTAAGGT
TCATTCTGGGTTCACACGGCCTTAGACATGACCATGTGAGACACACGGCCTGGCAACACGGT
Found at i:39077189 original size:17 final size:17
Alignment explanation
Indices: 39077167--39077221 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
39077157 AAACATATAG
39077167 TTCTATCAATTAACAAT
1 TTCTATCAATTAACAAT
*
39077184 TTCTATCAAATAACCAA-
1 TTCTATCAATTAA-CAAT
*
39077201 TTCGAGATCAATTAACAAT
1 TTC--TATCAATTAACAAT
39077220 TT
1 TT
39077222 ATACAAGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.48
18 6 0.19
19 10 0.32
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (17 bp):
TTCTATCAATTAACAAT
Found at i:39078625 original size:10 final size:10
Alignment explanation
Indices: 39078593--39078627 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
39078583 AAATTAAGGG
39078593 GAGTTCAATA
1 GAGTTCAATA
*
39078603 GATGTTCAGTA
1 GA-GTTCAATA
39078614 GAGTTCAATA
1 GAGTTCAATA
39078624 GAGT
1 GAGT
39078628 AGTCAGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (10 bp):
GAGTTCAATA
Found at i:39078874 original size:17 final size:17
Alignment explanation
Indices: 39078846--39078879 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
39078836 TCTTTTGTCA
39078846 TTTGTTTGATGA-AATG
1 TTTGTTTGATGAGAATG
39078862 TTTGTTGTGATGAGAATG
1 TTTGTT-TGATGAGAATG
39078880 AGTTTGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (17 bp):
TTTGTTTGATGAGAATG
Found at i:39080046 original size:28 final size:28
Alignment explanation
Indices: 39080015--39080086 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
39080005 ATATTAATAA
39080015 ATTTTTAATTTAATTTAATATTTATATT
1 ATTTTTAATTTAATTTAATATTTATATT
** * **
39080043 ATTTAAAAAATT-ATAAAATATTTATATT
1 ATTT-TTAATTTAATTTAATATTTATATT
39080071 ATTTTTAATTTAATTT
1 ATTTTTAATTTAATTT
39080087 TTTTATTTAT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
27 4 0.12
28 24 0.75
29 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTTAATTTAATTTAATATTTATATT
Found at i:39080201 original size:20 final size:19
Alignment explanation
Indices: 39080157--39080202 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
39080147 ATTTTTTGTG
* *
39080157 TTATAAATTATATAATATA
1 TTATAAATAATATAATAAA
*
39080176 TAATAACATAATATAATAAA
1 TTATAA-ATAATATAATAAA
39080196 TTATAAA
1 TTATAAA
39080203 CATTGAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TTATAAATAATATAATAAA
Found at i:39087091 original size:50 final size:52
Alignment explanation
Indices: 39087029--39087167 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 52
39087019 TGATAATAAC
* * *
39087029 ATGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT-CT-TG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATACTATG
* *
39087079 GTGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCAT-A-CT--ATG
39087135 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
39087168 TGGGATCTCT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
50 41 0.53
53 2 0.03
56 34 0.44
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.24
Consensus pattern (52 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATACTATG
Found at i:39087141 original size:56 final size:50
Alignment explanation
Indices: 39087029--39087177 Score: 190
Period size: 56 Copynumber: 2.9 Consensus size: 50
39087019 TGATAATAAC
* **
39087029 ATGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* *
39087079 GTGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TG
*
39087135 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39087178 TTAGCCAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
50 41 0.48
53 2 0.02
56 42 0.49
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
Found at i:39098606 original size:27 final size:27
Alignment explanation
Indices: 39098567--39098668 Score: 141
Period size: 27 Copynumber: 3.8 Consensus size: 27
39098557 CCCTAAAATA
* *
39098567 GGTATAATAACCGTAATACCCCTATAG
1 GGTAAAATGACCGTAATACCCCTATAG
*
39098594 GGTAAAATGACCGTAATACCTCTATAG
1 GGTAAAATGACCGTAATACCCCTATAG
* * *
39098621 GGAAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATACCCCTATAG
*
39098648 GGTAAAATGACTGTAATACCC
1 GGTAAAATGACCGTAATACCC
39098669 AATTTTAGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTATAG
Found at i:39098812 original size:19 final size:21
Alignment explanation
Indices: 39098711--39098830 Score: 156
Period size: 21 Copynumber: 5.7 Consensus size: 21
39098701 ATTTTCGAGG
* *
39098711 ATATACAATCTTTGATATG--
1 ATATGCAATCTTAGATATGAT
39098730 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
39098751 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
39098772 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
39098793 ATATACAATCTTAGAAGATATGAT
1 ATATGCAATCTT---AGATATGAT
*
39098817 -TTTGCAATCTTAGA
1 ATATGCAATCTTAGA
39098831 GATTTAATTT
Statistics
Matches: 91, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
19 17 0.19
20 3 0.03
21 53 0.58
23 9 0.10
24 9 0.10
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:39098840 original size:22 final size:23
Alignment explanation
Indices: 39098798--39098840 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39098788 ATGATATATA
*
39098798 CAATCTTAGAAGATATGATTTTG
1 CAATCTTAGAAGATATAATTTTG
*
39098821 CAATCTTAG-AGATTTAATTT
1 CAATCTTAGAAGATATAATTT
39098841 GTAGATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (23 bp):
CAATCTTAGAAGATATAATTTTG
Found at i:39099469 original size:28 final size:27
Alignment explanation
Indices: 39099424--39099481 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
39099414 TATACGCATA
39099424 TTTATTTTTTGTAGTATAATATAATTAT
1 TTTATTTTTTGTAGTAT-ATATAATTAT
* *
39099452 TTTATTTTTT-TATTTATATGTAATTAT
1 TTTATTTTTTGTA-GTATATATAATTAT
39099479 TTT
1 TTT
39099482 TTATAACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTATTTTTTGTAGTATATATAATTAT
Done.