Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 141 of 187
Found at i:42552176 original size:38 final size:38
Alignment explanation
Indices: 42552128--42552238 Score: 188
Period size: 38 Copynumber: 2.9 Consensus size: 38
42552118 GGATTTAAGG
* *
42552128 TTTAGGGGTTA-GGTGTTATGCTTTATGGGTTAAGGGGA
1 TTTAAGGGTTATGG-GTTATGCTTTAGGGGTTAAGGGGA
42552166 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
1 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
42552204 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGG
1 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGG
42552239 ATTTAGGGTT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
38 68 0.97
39 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.39, T:0.39
Consensus pattern (38 bp):
TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
Found at i:42552195 original size:21 final size:21
Alignment explanation
Indices: 42552166--42552235 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
42552156 GTTAAGGGGA
42552166 TTTAAGGGTTATGGGTTATGC
1 TTTAAGGGTTATGGGTTATGC
* * *
42552187 TTTAGGGGTTAAGGG----GA
1 TTTAAGGGTTATGGGTTATGC
42552204 TTTAAGGGTTATGGGTTATGC
1 TTTAAGGGTTATGGGTTATGC
*
42552225 TTTAGGGGTTA
1 TTTAAGGGTTA
42552236 AGGATTTAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 14 0.37
21 24 0.63
ACGTcount: A:0.20, C:0.03, G:0.37, T:0.40
Consensus pattern (21 bp):
TTTAAGGGTTATGGGTTATGC
Found at i:42553322 original size:17 final size:17
Alignment explanation
Indices: 42553297--42553341 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
42553287 GGGGTTATGC
42553297 TTTAAGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
*
42553314 TTTAGGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
42553331 TTTAAGGGTTA
1 TTTAAGGGTTA
42553342 TGGGTTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (17 bp):
TTTAAGGGTTAGGGGGA
Found at i:42555871 original size:9 final size:9
Alignment explanation
Indices: 42555859--42555958 Score: 66
Period size: 9 Copynumber: 11.4 Consensus size: 9
42555849 AATTCACATA
42555859 ATAACTTAC
1 ATAACTTAC
42555868 ATAACTTA-
1 ATAACTTAC
*
42555876 ACAACTTA-
1 ATAACTTAC
* *
42555884 ACAACTCAC
1 ATAACTTAC
*
42555893 ATAATTTAC
1 ATAACTTAC
*
42555902 ATAATTTAC
1 ATAACTTAC
*
42555911 ATAATACATA-
1 AT-A-ACTTAC
42555921 ATAACTTA-
1 ATAACTTAC
* *
42555929 ACAACTCAC
1 ATAACTTAC
*
42555938 ATAATTTAC
1 ATAACTTAC
42555947 ATAACTTA-
1 ATAACTTAC
42555955 ATAA
1 ATAA
42555959 TTTTAAAATA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
8 28 0.38
9 39 0.53
10 3 0.04
11 3 0.04
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:42556076 original size:17 final size:17
Alignment explanation
Indices: 42556054--42556125 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
42556044 ATAACTCACA
42556054 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
42556071 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
42556088 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
42556104 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
42556122 TAAT
1 TAAT
42556126 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:42556098 original size:25 final size:26
Alignment explanation
Indices: 42556062--42556125 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
42556052 CATAATAACT
*
42556062 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
42556087 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
42556113 TACATAACTTAAT
1 TACATAACTTAAT
42556126 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:42557889 original size:21 final size:21
Alignment explanation
Indices: 42557863--42557932 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
42557853 CTACAACTTA
*
42557863 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
42557884 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
42557905 AAGCAGAGGTTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
42557926 -AGCAGAG
1 AAGCAGAG
42557933 CAGAGCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 7 0.16
21 38 0.84
ACGTcount: A:0.31, C:0.17, G:0.47, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:42558321 original size:43 final size:43
Alignment explanation
Indices: 42558274--42558454 Score: 249
Period size: 43 Copynumber: 4.2 Consensus size: 43
42558264 CAAAACAATT
** *
42558274 GCGGCGTTTGTGAGA-AAAGGGCTGCTAAAGAACATGACCTTTA
1 GCGGCGTTTGTGA-ATAAAGCACCGCTAAAGAACATGACCTTTA
* * *
42558317 GCGGCGTTTGTGAA-AAATGCGCTGCTAAAGAACATTACCTTTA
1 GCGGCGTTTGTGAATAAA-GCACCGCTAAAGAACATGACCTTTA
* *
42558360 GCGGCGTTTATGAATAAAGCACCGCTAAAGAACATTACCTTTA
1 GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
*
42558403 GCGGCGTTTGTGGATAAAGCACCGCTAAAGAACATGACCTTTA
1 GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
42558446 GCGGCGTTT
1 GCGGCGTTT
42558455 ATAGAAATAA
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
42 4 0.03
43 121 0.95
44 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
Found at i:42558777 original size:41 final size:43
Alignment explanation
Indices: 42558676--42558792 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 43
42558666 GGCTCGTACA
* *
42558676 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAAATATCG
* * * *
42558719 TTGCCACTGTCCCAGACAGGGTCTTACCTG-AATTAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
*
42558760 ATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAA
42558793 AGACAAATCG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 28 0.45
42 9 0.15
43 24 0.39
44 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
Found at i:42560504 original size:29 final size:28
Alignment explanation
Indices: 42560468--42560545 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
42560458 TCATGAGATT
42560468 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
42560498 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
42560525 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
42560546 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:42560764 original size:175 final size:174
Alignment explanation
Indices: 42560498--42560826 Score: 595
Period size: 175 Copynumber: 1.9 Consensus size: 174
42560488 AAATTGTACA
42560498 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
42560563 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGATGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGATGCGACCTTACCGAGGCAA
42560628 TTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
42560673 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
42560738 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGGCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGATGCGACCTTACCGAGGCAA
*
42560803 TTTTGGACAGCGGAATAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
42560827 TCCTTGATGT
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
174 10 0.07
175 138 0.93
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGATGCGACCTTACCGAGGCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:42563816 original size:136 final size:136
Alignment explanation
Indices: 42563649--42563919 Score: 524
Period size: 136 Copynumber: 2.0 Consensus size: 136
42563639 GAAAAATCAC
*
42563649 TAAAAATAGTAGGAGTGGAATTAATTAATGAATAAATTATGTATTCGAAGTTCGATGAGTCTATT
1 TAAAAATAGTAGGAGTGGAATTAATTAATGAATAAATTATGTATTCGAAGCTCGATGAGTCTATT
*
42563714 TTCATAGAGAAGCAACGAAAAGATCATATGGACATTATGTTAAGAGATATTCGGGTTCTCGTGAG
66 TTCATAGAGAAGCAACGAAAAGATCATATGGACAGTATGTTAAGAGATATTCGGGTTCTCGTGAG
42563779 ACAGGA
131 ACAGGA
42563785 TAAAAATAGTAGGAGTGGAATTAATTAATGAATAAATTATGTATTCGAAGCTCGATGAGTCTATT
1 TAAAAATAGTAGGAGTGGAATTAATTAATGAATAAATTATGTATTCGAAGCTCGATGAGTCTATT
42563850 TTCATAGAGAAGCAACGAAAAGATCATATGGACAGTATGTTAAGAGATATTCGGGTTCTCGTGAG
66 TTCATAGAGAAGCAACGAAAAGATCATATGGACAGTATGTTAAGAGATATTCGGGTTCTCGTGAG
42563915 ACAGG
131 ACAGG
42563920 GCCAGAACGG
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (136 bp):
TAAAAATAGTAGGAGTGGAATTAATTAATGAATAAATTATGTATTCGAAGCTCGATGAGTCTATT
TTCATAGAGAAGCAACGAAAAGATCATATGGACAGTATGTTAAGAGATATTCGGGTTCTCGTGAG
ACAGGA
Found at i:42570884 original size:39 final size:40
Alignment explanation
Indices: 42570789--42571050 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
42570779 TTGAATGATG
*
42570789 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
42570827 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
42570868 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
42570907 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42570946 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
42570985 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
42571024 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
42571051 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42572506 original size:28 final size:28
Alignment explanation
Indices: 42572475--42572528 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
42572465 TTGTCTTTTT
* *
42572475 TTATAATAA-GTTTATAATATACTATATA
1 TTATAATAACCTTTATAA-ATAATATATA
*
42572503 TTATTATAACCTTTATAAATAATATA
1 TTATAATAACCTTTATAAATAATATA
42572529 AAAACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (28 bp):
TTATAATAACCTTTATAAATAATATATA
Found at i:42581207 original size:28 final size:28
Alignment explanation
Indices: 42581144--42581969 Score: 1618
Period size: 28 Copynumber: 29.5 Consensus size: 28
42581134 ATATTAAGTC
* *
42581144 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
42581171 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581199 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581227 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581255 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581283 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581311 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581339 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581367 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581395 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581423 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581451 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581479 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581507 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581535 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581563 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581591 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581619 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581647 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581675 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581703 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581731 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581759 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581787 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581815 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581843 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581871 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581899 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581927 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
42581955 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42581970 GTACAATTTA
Statistics
Matches: 796, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
27 22 0.03
28 774 0.97
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:42590938 original size:43 final size:43
Alignment explanation
Indices: 42590891--42591001 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
42590881 AAAAGTTAGT
* * * * *
42590891 AGAATGCCATAAAGGGCATATCAGAATTACCACAGAGGATAAC
1 AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
* * *
42590934 AGAATGCCACAAAGGTCATAT-AAAAATACCACAAACGCTAAG
1 AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
42590976 AGAATGCCACAAA-GGCAATATCAAAA
1 AGAATGCCACAAAGGGC-ATATCAAAA
42591002 TACACCATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.04
42 32 0.56
43 23 0.40
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (43 bp):
AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
Found at i:42595430 original size:17 final size:18
Alignment explanation
Indices: 42595397--42595431 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42595387 CAGCGAAAGT
*
42595397 AAACTTTTTTCCTTTTCC
1 AAACTTTATTCCTTTTCC
42595415 AAACTTTATT-CTTTTCC
1 AAACTTTATTCCTTTTCC
42595432 TTTCTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (18 bp):
AAACTTTATTCCTTTTCC
Found at i:42599590 original size:25 final size:26
Alignment explanation
Indices: 42599562--42599626 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 26
42599552 TGTAGATTGG
42599562 TATGCTCTCATGAGCC-ATAAATCGA
1 TATGCTCTCATGAGCCTATAAATCGA
* *
42599587 TATGCTCTCAGGA-CCTATAAATCGG
1 TATGCTCTCATGAGCCTATAAATCGA
42599612 TATGCTCTCATGAGC
1 TATGCTCTCATGAGC
42599627 TTTGGGTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.06
25 32 0.91
26 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (26 bp):
TATGCTCTCATGAGCCTATAAATCGA
Found at i:42608311 original size:25 final size:25
Alignment explanation
Indices: 42608282--42608372 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
42608272 CGGATACACC
*
42608282 ACAGCTCGT-ATGAGCTTACTGATTT
1 ACAGCTCGTGA-GAGCATACTGATTT
* *
42608307 ACAGCTTGTGAGAGCATATTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* * *
42608332 ACAGCTCAAGAGAGAACATACTAATTT
1 ACAGCTC--GTGAGAGCATACTGATTT
* *
42608359 ACAACTCGAGAGAG
1 ACAGCTCGTGAGAG
42608373 AGCATACCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
25 32 0.60
26 1 0.02
27 20 0.38
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:42608358 original size:27 final size:27
Alignment explanation
Indices: 42608328--42608391 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
42608318 GAGCATATTG
*
42608328 ATTTACAGCTCAAGAGAGAACATACTA
1 ATTTACAGCTCAAGAGAGAACATACCA
* * *
42608355 ATTTACAACTCGAGAGAGAGCATACCA
1 ATTTACAGCTCAAGAGAGAACATACCA
*
42608382 ATTCACAGCT
1 ATTTACAGCT
42608392 TGTATGAGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
ATTTACAGCTCAAGAGAGAACATACCA
Found at i:42610679 original size:26 final size:26
Alignment explanation
Indices: 42610648--42610705 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
42610638 AACTTGTACT
*
42610648 TAAATTATTAACATATTTAATTTTAA
1 TAAATTATTAACATATTGAATTTTAA
42610674 TAAATTATTAACATATTGAATTTTAA
1 TAAATTATTAACATATTGAATTTTAA
*
42610700 TTAATT
1 TAAATT
42610706 TTGTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAATTATTAACATATTGAATTTTAA
Found at i:42614276 original size:951 final size:953
Alignment explanation
Indices: 42612371--42614279 Score: 2564
Period size: 967 Copynumber: 2.0 Consensus size: 953
42612361 CATCATTCCA
* *
42612371 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTTTTTAGTTTTCTTTCTTTCATCCCATGTGTG
1 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
* * * * * * * * *
42612436 CCGCCCCCCAAGCCACCAAGATTTACCATTAATTTCTCTTCTTTTTGCAATGGGTTCTTGAGCCA
66 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
* * ** * * * *
42612501 TTCTTTTCCTCTTCTTTTTTTCATTTAATCATAATATTTCTAGCCTTAAATTTGAGATTTAACCA
131 TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTTAAATATGAAATTTAACCA
* * * *
42612566 CTCAATATCGGCCTCCAATGATTCCCCAAAAGAACTACATTGCTGCACCTATCTTCTTGCTTGAG
196 CTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGAG
** * *
42612631 TAAGTGCCATTTTCTTGGGTTTTTCTTGATGGATCTTTCAATAAAATACCAAGTTTTCTAGATCC
261 TAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATCC
42612696 AAAATTGGGGTAATATTTTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGT
326 ------------ATA--TTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGT
* * ** *
42612761 GGTTTTGAATCAGCCCCAATTTCACCACCGTTGGTGGTGGTGCATCGTGCCTAGAGGCAAAAATG
377 GGTTATGAATCAGCCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATA
** ** * * * *
42612826 GGGGTTGTTGTTTCTTTAGTTTTTCTCATATATTTCCAGCAATAACTTTGCTTCCTGAACTCTTC
442 GGGGTTACTGTTTCTTTAAATTTTCTCATATATTTCCAGAAATAACTTTCCTTCCTCAACCCTTC
* *** *
42612891 CTAATCAGCCTTTAATAATGTGTAAACTAGGAAAAATCAAACTTGGACAATCGGTAACTCAGATC
507 CTAATCAGCCTTTAATAATGTGTAAACTAGGAAAAAGCAAACTTGGACAATCAACAACTCAAATC
* * * *
42612956 TGACAATTCGGGAATCGTAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTGAGTTTTGATGTTG
572 TGAAAATTCGGGAAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTG
**
42613021 GGAAATTGTTAATTGATTGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTT
637 GGAAATTGTTAATTGAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTT
* * * **
42613086 AAATGTGTTCAGTGCCAACTTAAATTGCAAAATTATTTCAAGAATAAGGAAATAACCCAATGGTT
702 AAATGTGGTCAGTGCCAACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTT
* ** * *
42613151 CAAAGAAATATGAGAAAGCATGGAAATTAGATTTACGTTCCAAGTTTGATTCCCTTCCCCTGCAA
767 CAAAGAAATATGAGAAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAA
* * * **
42613216 AATAGCTTCATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCGCCCAATCCTTGAACCCT
832 AATAGCTTAATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCT
42613281 AGGTATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
897 AGGTATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
* *
42613338 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCTTGTGTT
1 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
42613403 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
66 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
* * *
42613468 TTATTTCCCTCTTCTTGCTTTCATTTTATCATAAAATTTCAAGCCTTCAAA-ATGAAATTTTAGC
131 TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTT-AAATATGAAATTTAACC
* * * * * *
42613532 ACTGAAGATTGGCCTCTATTGATGCCCCAAAAGAACTTCATTCCCGCCCCTATCTTCTTGCTTGA
195 ACTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGA
* * * *
42613597 GTAAGTGTCATTTTCTTTCATTTTTCTTGATGGCTCTTTAAATAAAATACAAATTTTTCTAGAT-
260 GTAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATC
* * *
42613661 C-TA-TAAGATTTAATGGTTATTTTTTCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAG
325 CATATTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAG
42613724 CCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTT
390 CCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTT
* * *
42613789 CTTTAAATTTTC-CAATCTATTTCCA-AAATTA-TGCTTCCTTCTTCAACCCTTCCTAATCAGCC
455 CTTTAAATTTTCTC-ATATATTTCCAGAAATAACT--TTCCTTCCTCAACCCTTCCTAATCAGCC
* * *
42613851 TTTAGTAATGTGTAAATTAGGAAAACGCAATA-TT-GATCAATCAACAACTCAAATCTGAAAATT
517 TTTAATAATGTGTAAACTAGGAAAAAGCAA-ACTTGGA-CAATCAACAACTCAAATCTGAAAATT
*
42613914 CGGGTAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTGGGGAAATT
580 CGGGAAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTT-GGGAAATT
*
42613979 GTTAATTGAGCGAATTAATGATTTTTATGATGGAATAGCTACTAGCTTTTT-AGTATTTAAATGT
644 GTTAATTGAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAG-TTTTTCAGTATTTAAATGT
* * * *
42614043 GGT-AGGTGCCGAA-TTAAATTACAAAAGTATTTCAAGGATGACAAAATAGCCCAATGGTTCAAG
708 GGTCA-GTGCC-AACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTTCAAA
* * *
42614106 GAAATATGAGAAAGCACGGAAATTAGATTTAGGGCCCAAGTTCGATTCCCTTCACTTGTAAAATA
771 GAAATATGAGAAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAAAATA
* * *
42614171 GCTTAATTTTTGCTAAAATTTCTCCTTCTCCTTATTTTGTGTCACCCAAGCCTCAAACCCTTGGT
836 GCTTAATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCTAGGT
* * * *
42614236 ATAAATACAACTTTTTCTTGTATTTTTTAGCTTTTAAGTCAATT
901 ATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATT
42614280 TTTGTAACAC
Statistics
Matches: 826, Mismatches: 106, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
948 1 0.00
949 7 0.01
950 261 0.32
951 267 0.32
952 7 0.01
953 2 0.00
966 1 0.00
967 277 0.34
968 3 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (953 bp):
CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTTAAATATGAAATTTAACCA
CTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGAG
TAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATCC
ATATTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAGC
CCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTTC
TTTAAATTTTCTCATATATTTCCAGAAATAACTTTCCTTCCTCAACCCTTCCTAATCAGCCTTTA
ATAATGTGTAAACTAGGAAAAAGCAAACTTGGACAATCAACAACTCAAATCTGAAAATTCGGGAA
GCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTGGGAAATTGTTAATT
GAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTTAAATGTGGTCAGTG
CCAACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTTCAAAGAAATATGAG
AAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAAAATAGCTTAATTTT
TACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCTAGGTATAAATACAA
CTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
Found at i:42615461 original size:27 final size:27
Alignment explanation
Indices: 42615416--42615683 Score: 295
Period size: 27 Copynumber: 9.9 Consensus size: 27
42615406 ATCTGCATCG
* *
42615416 AAATACCCTCATAGTGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* * *
42615443 AAATACCCCCACAAGGTAAAAAGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* *
42615470 AAATACCCCTATAGGATAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* * *
42615497 AAATACCTCCATTGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCA
* *
42615524 AAATACCCCTATAAGGTAAAATGA-CA
1 AAATACCCCCATAGGGTAAAATGACCA
*
42615550 GAAATACCCCCATAGGGTAAAATGACTA
1 -AAATACCCCCATAGGGTAAAATGACCA
* *** *
42615578 GAATACTTTCATAGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCA
* * ** *
42615605 AAATAACCCCATAGGTTAGGATGACCG
1 AAATACCCCCATAGGGTAAAATGACCA
*
42615632 AAATACCCCCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCA
*
42615659 AAATACCCTCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
42615684 TGTTATACCC
Statistics
Matches: 197, Mismatches: 42, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 195 0.99
28 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCA
Found at i:42617131 original size:22 final size:22
Alignment explanation
Indices: 42617101--42617143 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42617091 ATTGGCCTCT
42617101 ATTGACACCCCAAAAGAACTCA
1 ATTGACACCCCAAAAGAACTCA
* *
42617123 ATTGTCACCCTAAAAGAACTC
1 ATTGACACCCCAAAAGAACTC
42617144 CACTACCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (22 bp):
ATTGACACCCCAAAAGAACTCA
Found at i:42637952 original size:28 final size:28
Alignment explanation
Indices: 42637918--42637977 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
42637908 TTCATTAAAC
*
42637918 TAATTAAATTAATTA-TCCTAAAATAACT
1 TAATTAAATGAATTAGT-CTAAAATAACT
42637946 TAATTAAATGAATTAGTCTAAAATAACT
1 TAATTAAATGAATTAGTCTAAAATAACT
42637974 TAAT
1 TAAT
42637978 GGAATTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.38
Consensus pattern (28 bp):
TAATTAAATGAATTAGTCTAAAATAACT
Found at i:42640389 original size:26 final size:26
Alignment explanation
Indices: 42640355--42640406 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42640345 TTTGAGTAAA
42640355 AAAATTTCAAGTCGAATTAACGAATC
1 AAAATTTCAAGTCGAATTAACGAATC
42640381 AAAATTTCAAGTCGAATTAACGAATC
1 AAAATTTCAAGTCGAATTAACGAATC
42640407 TTATTATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (26 bp):
AAAATTTCAAGTCGAATTAACGAATC
Found at i:42640587 original size:21 final size:21
Alignment explanation
Indices: 42640561--42640601 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42640551 TCAAAACGAC
42640561 ATAGTTTTG-CATTTTAACTTG
1 ATAGTTTTGAC-TTTTAACTTG
42640582 ATAGTTTTGACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
42640602 TAGAAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTG
Found at i:42640951 original size:20 final size:20
Alignment explanation
Indices: 42640928--42640965 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42640918 TTTATATATT
*
42640928 TTTATATTTTTTTAAAAAAA
1 TTTATAATTTTTTAAAAAAA
42640948 TTTATAATTTTTTAAAAA
1 TTTATAATTTTTTAAAAA
42640966 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATAATTTTTTAAAAAAA
Found at i:42641042 original size:20 final size:19
Alignment explanation
Indices: 42640981--42641040 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
42640971 ATTTTATAAT
*
42640981 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
42640999 TTTTAAAAATTATTTTCAAA
1 TTTTAAAAATTATTTT-GAA
*
42641019 TTTTGAAAATTATTTTG-A
1 TTTTAAAAATTATTTTGAA
42641037 TTTT
1 TTTT
42641041 TTTTTGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.36
19 6 0.17
20 17 0.47
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:42645170 original size:16 final size:16
Alignment explanation
Indices: 42645122--42645170 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
42645112 AAAAATATTT
*
42645122 AAATAAATA-AAATTA
1 AAATAAATATTAATTA
*
42645137 ACAA-AAAT-TTAATGA
1 A-AATAAATATTAATTA
42645152 AAATAAATATTAATTA
1 AAATAAATATTAATTA
42645168 AAA
1 AAA
42645171 ATTAACACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 2 0.07
15 14 0.52
16 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATAAATATTAATTA
Found at i:42646872 original size:16 final size:16
Alignment explanation
Indices: 42646863--42646897 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42646853 AAACTGAAGC
42646863 AAATAAAAACTAAAAA
1 AAATAAAAACTAAAAA
42646879 AAATAAAAAC-AAAATA
1 AAATAAAAACTAAAA-A
42646895 AAA
1 AAA
42646898 ACATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (16 bp):
AAATAAAAACTAAAAA
Found at i:42646892 original size:11 final size:11
Alignment explanation
Indices: 42646874--42646910 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
42646864 AATAAAAACT
42646874 AAAA-AAAATA
1 AAAACAAAATA
42646884 AAAACAAAATA
1 AAAACAAAATA
*
42646895 AAAAC-ATATA
1 AAAACAAAATA
42646905 AAAACA
1 AAAACA
42646911 CTAGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAACAAAATA
Found at i:42646892 original size:21 final size:21
Alignment explanation
Indices: 42646868--42646910 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
42646858 GAAGCAAATA
42646868 AAAACTAAAAA-AAATAAAAAC
1 AAAA-TAAAAACAAATAAAAAC
*
42646889 AAAATAAAAACATATAAAAAC
1 AAAATAAAAACAAATAAAAAC
42646910 A
1 A
42646911 CTAGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAATAAAAACAAATAAAAAC
Found at i:42647110 original size:68 final size:68
Alignment explanation
Indices: 42646978--42647316 Score: 418
Period size: 68 Copynumber: 5.0 Consensus size: 68
42646968 ACAAATTAAT
* ** * * * *
42646978 AACCCTATGTTTAATGTCTTGGAAGACTCTATTAGTTGGCATAGTT-GAGTTATGGTCTTACACC
1 AACCC-ATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATA-TTCGAGCTATGATCTTACACC
42647042 TTATA
64 TTATA
* * *
42647047 AATCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGGTATGATCTTTCACCTT
1 AACCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGCTATGATCTTACACCTT
42647112 ATA
66 ATA
* * * *
42647115 ACCCCATCTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGGTATGATCTTTCACCTT
1 AACCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGCTATGATCTTACACCTT
42647180 ATA
66 ATA
* * * *
42647183 ACCCCATCTTTAATGTCCTGGTGGACTCTATTGGTTGTCATAGTCGAGCTATGGTCTTACACCTT
1 AACCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGCTATGATCTTACACCTT
42647248 AT-
66 ATA
* * * *
42647250 AA-CC-TGTTTAATGTCCTAGAGGACTCTATTAGTTGTCATAGTCGAGCTATTG-TCTTACACCT
1 AACCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGCTA-TGATCTTACACCT
42647312 TATA
65 TATA
42647316 A
1 A
42647317 CCCTATTGAG
Statistics
Matches: 246, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
65 54 0.22
66 5 0.02
67 3 0.01
68 180 0.73
69 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (68 bp):
AACCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGCTATGATCTTACACCTT
ATA
Found at i:42654083 original size:25 final size:25
Alignment explanation
Indices: 42654049--42654105 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
42654039 AACGGCTTTT
42654049 GCTCCCTTTGAGGGCAGCAGTGTAG
1 GCTCCCTTTGAGGGCAGCAGTGTAG
42654074 GCTCCCTTTGAGGGCAGCAGTGTAG
1 GCTCCCTTTGAGGGCAGCAGTGTAG
42654099 GCTCCCT
1 GCTCCCT
42654106 CCGCTTCGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (25 bp):
GCTCCCTTTGAGGGCAGCAGTGTAG
Found at i:42663064 original size:275 final size:275
Alignment explanation
Indices: 42662573--42663118 Score: 961
Period size: 275 Copynumber: 2.0 Consensus size: 275
42662563 TTGATATATA
* *
42662573 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACGACGTTACGACGAATATTGA
1 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
*
42662638 ACCCCGTATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
66 ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
*
42662703 GGTGCTGGTCTTGAATGTCCTACTGATGTTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
131 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
* *
42662768 TGTGTGAGTGACATTGTGTAGCTTACATTCTGA-TCGTCAGCTTGTGTGAGTAGACCCATTTTAT
196 TGTGTGAGCGACATCGTGTAGCTTACATTCTGACT-GTCAGCTTGTGTGAGTAGACCCATTTTAT
42662832 GGCTCGAGTGAGCAAC
260 GGCTCGAGTGAGCAAC
* *
42662848 TATTATTGTGTTATTTATCATGTAAACGATTGTTGGAAATCCAACAACGTTATGACGAATATTAA
1 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
* * *
42662913 ACCCCATGTGAACCTTAGGAATATATAGGATACAACTGACATGTCACTAGGGTTACCATGTTTCG
66 ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
42662978 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGA-AGCTTGTCAGC
131 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATA-CTTGTCAGC
42663042 TTGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTAT
195 TTGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTAT
42663107 GGCTCGAGTGAG
260 GGCTCGAGTGAG
42663119 AAGCTATCTA
Statistics
Matches: 258, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
274 1 0.00
275 256 0.99
276 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (275 bp):
TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
TGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTATG
GCTCGAGTGAGCAAC
Found at i:42663711 original size:7 final size:7
Alignment explanation
Indices: 42663701--42663731 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42663691 TAAAGTTTGA
42663701 GTTAAAT
1 GTTAAAT
42663708 GTTAAAT
1 GTTAAAT
42663715 GTTAAAT
1 GTTAAAT
42663722 GTTAAAT
1 GTTAAAT
42663729 GTT
1 GTT
42663732 GCTTTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (7 bp):
GTTAAAT
Found at i:42674396 original size:50 final size:51
Alignment explanation
Indices: 42674331--42674440 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
42674321 TTTCAACAGG
*
42674331 CATGAAAAGGGAAAGGAATGGTATGTGTTCAAATGAACTAT-TTCATGAAAT
1 CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTT-ATGAAAT
*
42674382 TA-GAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
1 CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
42674432 CATGAAAAG
1 CATGAAAAG
42674441 AATTGAAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
50 45 0.83
51 9 0.17
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (51 bp):
CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
Found at i:42676974 original size:51 final size:50
Alignment explanation
Indices: 42676888--42677329 Score: 372
Period size: 51 Copynumber: 8.7 Consensus size: 50
42676878 TATCGATGAA
* *
42676888 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * * * * *
42676939 CACTTGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATATGGT
* * * * *
42676990 CACGTGTATAGTACTGTGTGAAGGCTACTATCTGAATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * * * * * *
42677041 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATATGGT
* * * *
42677092 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * *
42677143 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAATCTTCGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-AT-GGT
* * ** * *
42677194 CACGTGTGTGGTACTATGTGATGGCTACTACATGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATA--TGGT
* * * * * * *
42677244 CACATGTGTAGTACAATCTGAAGGCTAGTACGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATA--TGGT
* *
42677294 CACGTGTGTAGTACTATCTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
42677330 TCGAATGATA
Statistics
Matches: 313, Mismatches: 70, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
50 84 0.27
51 227 0.73
52 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATGGT
Found at i:42677064 original size:102 final size:102
Alignment explanation
Indices: 42676888--42677333 Score: 580
Period size: 102 Copynumber: 4.4 Consensus size: 102
42676878 TATCGATGAA
* *
42676888 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACTTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
42676953 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
42676990 CACGTGTATAGTACTGTGTGAAGGCTACTATC-TGAATCGATAAATAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA-CGTGAATCGATAAATAATGGTCACATGTGTAGTA
*
42677054 CTAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
65 CTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
42677092 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* * * *
42677157 TAAGTGAAGGCTACTATGTGTACCGAAAATCTTCGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * * * * *
42677194 CACGTGTGTGGTACTATGTGATGGCTACTACATGAACCG-TAAA-ACTTGATCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* ** * * * *
42677257 C-AATCTGAAGGCTAGTACGTGAACCGTA-AAAC-TTGAT
65 CTAA-GTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
* *
42677294 CACGTGTGTAGTACTATCTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
42677334 ATGATAAAAG
Statistics
Matches: 305, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
100 38 0.12
101 43 0.14
102 223 0.73
103 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:42682489 original size:122 final size:124
Alignment explanation
Indices: 42682067--42682526 Score: 762
Period size: 124 Copynumber: 3.7 Consensus size: 124
42682057 NNNNNNNNNN
*
42682067 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTC
1 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTC
*
42682132 GTGGATACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
66 GTGGACACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
*
42682191 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTC
1 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTC
*
42682256 GTGGATACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
66 GTGGACACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
*
42682315 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTT
1 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTC
* * * * *
42682380 GTGGACGCGCTTTTGCTAAAGTAGGTCATGGATAAAAT-A-TTTTTTTGACGTTTTTGA
66 GTGGACACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
* *
42682437 GCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTAAGAAGAATTTGTAAAAATCGCGCCCT
1 GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCT
* * *
42682502 CGTGGGCGCGTTTTTGCTACAGTAG
65 CGTGGACACGGTTTTGCTACAGTAG
42682527 CATGTTTGGG
Statistics
Matches: 321, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
122 66 0.21
123 35 0.11
124 220 0.69
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
GCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTC
GTGGACACGGTTTTGCTACAGTAGGTCATGGATGAAATAATTTTTTTTGACGTTTCTGA
Found at i:42688381 original size:20 final size:20
Alignment explanation
Indices: 42688334--42688382 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
42688324 TTTTCCTTTT
42688334 AATTTTCTTTTATTGCACCAC
1 AATTTTC-TTTATTGCACCAC
* * * *
42688355 AAATTTCTTTCTTGTACTAC
1 AATTTTCTTTATTGCACCAC
42688375 AATTTTCT
1 AATTTTCT
42688383 AACAGAGGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTTTCTTTATTGCACCAC
Found at i:42691251 original size:29 final size:30
Alignment explanation
Indices: 42691196--42691252 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
42691186 TTTTGTTCTT
*
42691196 TCTTTTGTTTTTCTCTGTTTCCCTTTGCTC
1 TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
*
42691226 TCTTTTCTTCTTTCT-T-TTTCCTTTTGC
1 TCTTTTCTT-TTTCTCTGTTTCCCTTTGC
42691253 GATTGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 9 0.38
31 5 0.21
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (30 bp):
TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
Found at i:42692592 original size:3 final size:3
Alignment explanation
Indices: 42692584--42692613 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42692574 TATGTTAACT
42692584 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42692614 ATAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42697092 original size:65 final size:65
Alignment explanation
Indices: 42696980--42697122 Score: 153
Period size: 65 Copynumber: 2.2 Consensus size: 65
42696970 GTCGTACCAT
* * ** * * ** *
42696980 AGCTCTTTATGAACGTCTTATTATATGATCGGTTGTGATCTTGCATATATTGGGGACACAAATAC
1 AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
* * *
42697045 AGCTCTTTGTGAGCGTCTTGTTTTATGATCAATTGTGATGC-TACATATGTCGCAGACACAAACA
1 AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGAT-CTTACATATATCGCAGACACAAACA
42697109 C
65 C
*
42697110 AACTCTTTGTGAG
1 AGCTCTTTGTGAG
42697123 TGTCCTGATA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 63 0.98
66 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (65 bp):
AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
Found at i:42697206 original size:26 final size:26
Alignment explanation
Indices: 42697177--42697228 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42697167 GAAGCTCTTA
* *
42697177 ATTAAAGGCTCTTCGTGAGCTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
* *
42697203 ATTAAAAGTTCTTTGTGAACTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
42697229 CTTATGCCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (26 bp):
ATTAAAAGCTCTTCGTGAACTTCCTG
Found at i:42712225 original size:26 final size:26
Alignment explanation
Indices: 42712195--42712252 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
42712185 TTGGAGCTCT
*
42712195 TGATTAAAAGCTCTTCATGAGCTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
* **
42712221 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
42712247 TGATTA
1 TGATTA
42712253 TGCCTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (26 bp):
TGATTAAAAGCTCTTCATGAACTTCC
Found at i:42712337 original size:26 final size:26
Alignment explanation
Indices: 42712301--42712357 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42712291 TTTCCCGATA
*
42712301 GGCTCTTTGTGAGCTTCATGATTA-AT
1 GGCTCATTGTGAGCTTCATG-TTATAT
* *
42712327 GGCTCATTGTGAGTTTCCTGTTATAT
1 GGCTCATTGTGAGCTTCATGTTATAT
42712353 GGCTC
1 GGCTC
42712358 GAGAGAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.42
Consensus pattern (26 bp):
GGCTCATTGTGAGCTTCATGTTATAT
Found at i:42717303 original size:44 final size:44
Alignment explanation
Indices: 42717154--42717303 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 44
42717144 TAGGGGTAAG
* * * * **
42717154 ATATGTTATGCTATGATATGTGATAAGAAAAGTTTCGATATG-C
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
* * * * *
42717197 AATATGATATGCTATGACATGTTACTAAG-TAT-ACTCCAATATGAA
1 -ATATGATATGCTATGATATG-TAATAAGATATGTC-CCGATATGAC
* * *
42717242 ATTTGATATGATGTGATATGTAATAAGATATGTCCCGATATGAC
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
42717286 ATATGATATGCTATGATA
1 ATATGATATGCTATGATA
42717304 CATTCCGTTA
Statistics
Matches: 79, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
43 6 0.08
44 67 0.85
45 6 0.08
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (44 bp):
ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
Found at i:42719952 original size:39 final size:36
Alignment explanation
Indices: 42719858--42719955 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 36
42719848 TGGGTGAATT
* * *
42719858 TTACTTCGGACGTTCCGATAAGTGCTAGGCACAATAT
1 TTACTTC-GACGTTCCGATGAGTGCTAGGCAAAATAA
42719895 TTACTTC-A-GTTATACCGATGAGTGCTAGGCATAAATTAA
1 TTACTTCGACG-T-T-CCGATGAGTGCTAGGCA-AAA-TAA
42719934 TTACTTCGAACGTTCCGATGAG
1 TTACTTCG-ACGTTCCGATGAG
42719956 GTACCGAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
34 1 0.02
35 2 0.04
36 1 0.02
37 23 0.46
38 2 0.04
39 17 0.34
40 1 0.02
41 2 0.04
42 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (36 bp):
TTACTTCGACGTTCCGATGAGTGCTAGGCAAAATAA
Found at i:42722616 original size:34 final size:34
Alignment explanation
Indices: 42722573--42722640 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42722563 ATACAAGTAT
42722573 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
1 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
42722607 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
1 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
42722641 TTGAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (34 bp):
GCAAATACAACCAAATTCAAGGTGTGATATGTAA
Found at i:42723816 original size:13 final size:13
Alignment explanation
Indices: 42723800--42723837 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
42723790 TTATCAGAAG
*
42723800 CACTTTTTCACAA
1 CACTTTTTCAAAA
*
42723813 CACTTTTTAAAAA
1 CACTTTTTCAAAA
42723826 CA-TTTTTCAAAA
1 CACTTTTTCAAAA
42723838 GTAATGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
CACTTTTTCAAAA
Found at i:42727017 original size:47 final size:46
Alignment explanation
Indices: 42726948--42727039 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 46
42726938 CTGCCAATTA
*
42726948 ATAATATTATGGACAAGCCACCACTTTTGTAGATAAACTACCACTTT
1 ATAATATTATAGACAAGCCACCAC-TTTGTAGATAAACTACCACTTT
* * *
42726995 ATAATATTGTAGACAAGCCACCACTTTGTATATAAACTGCCACTT
1 ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTT
42727040 CTTGCTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 19 0.46
47 22 0.54
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (46 bp):
ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTTT
Found at i:42727118 original size:20 final size:21
Alignment explanation
Indices: 42727085--42727125 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
42727075 ATATGGCCAC
*
42727085 AAAAATTTACTTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
42727106 AAAAA-TTAATTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
42727126 GGCATGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATTTAATTTTTCACTTT
Found at i:42728480 original size:21 final size:20
Alignment explanation
Indices: 42728456--42728504 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
42728446 TCGGCTCCAT
42728456 TAGATTGA-AGCCTCTTAGTAA
1 TAGATTGAGA-CCTC-TAGTAA
*
42728477 TAGACTTGCGACCTCTAGTAA
1 TAGA-TTGAGACCTCTAGTAA
42728498 TAGATTG
1 TAGATTG
42728505 GCCTCTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 7 0.28
23 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
TAGATTGAGACCTCTAGTAA
Found at i:42735755 original size:51 final size:52
Alignment explanation
Indices: 42735657--42735755 Score: 114
Period size: 53 Copynumber: 1.9 Consensus size: 52
42735647 TAAGTTTTTC
* * *
42735657 TATATATTTTTTATATTTTTAAACATTTTAAAGTTTTTTAAAATTTTTATGTA
1 TATATATTTTTCATATTTTCAAACATTTTAAAG-TTTTGAAAATTTTTATGTA
*
42735710 TATATATTTTTCAT-TTTTCATAA-ATTTTAATA-TTTTGAAACTTTTT
1 TATATATTTTTCATATTTTCA-AACATTTTAA-AGTTTTGAAAATTTTT
42735756 TTTACAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
51 12 0.30
52 12 0.30
53 16 0.40
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (52 bp):
TATATATTTTTCATATTTTCAAACATTTTAAAGTTTTGAAAATTTTTATGTA
Found at i:42735839 original size:10 final size:10
Alignment explanation
Indices: 42735805--42735872 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
42735795 CCCTTTTTTT
42735805 TAATTTTT-A
1 TAATTTTTAA
* *
42735814 CAATTTTACAA
1 TAATTTT-TAA
42735825 T-ATTTTTAA
1 TAATTTTTAA
*
42735834 TAATTTCTTTA
1 TAATTT-TTAA
*
42735845 TAATTTTTTA
1 TAATTTTTAA
42735855 TAATGTTTTAGA
1 TAAT-TTTTA-A
42735867 TAATTT
1 TAATTT
42735873 AATTTTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 9 0.19
10 17 0.36
11 16 0.34
12 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:42735847 original size:11 final size:10
Alignment explanation
Indices: 42735826--42735864 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
42735816 ATTTTACAAT
*
42735826 ATTTTTAATA
1 ATTTTTTATA
42735836 ATTTCTTTATA
1 ATTT-TTTATA
42735847 ATTTTTTATA
1 ATTTTTTATA
*
42735857 ATGTTTTA
1 ATTTTTTA
42735865 GATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:42740557 original size:37 final size:37
Alignment explanation
Indices: 42740507--42740580 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
42740497 TCTTTCTCCA
42740507 ATAGTCATTTTCTTTTTCGTATATATACCCTGCCTAT
1 ATAGTCATTTTCTTTTTCGTATATATACCCTGCCTAT
42740544 ATAGTCATTTTCTTTTTCGTATATATACCCTGCCTAT
1 ATAGTCATTTTCTTTTTCGTATATATACCCTGCCTAT
42740581 TGTTATTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (37 bp):
ATAGTCATTTTCTTTTTCGTATATATACCCTGCCTAT
Found at i:42743054 original size:19 final size:19
Alignment explanation
Indices: 42743030--42743068 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42743020 CAGTTGAGGG
* *
42743030 TAATTAGTGATTTAATTGA
1 TAATTAGGGATTTAAATGA
42743049 TAATTAGGGATTTAAATGA
1 TAATTAGGGATTTAAATGA
42743068 T
1 T
42743069 CATAGGCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (19 bp):
TAATTAGGGATTTAAATGA
Found at i:42743135 original size:18 final size:18
Alignment explanation
Indices: 42743109--42743147 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42743099 AGGAATAAGA
42743109 AATTCAATTAGGTTAATT
1 AATTCAATTAGGTTAATT
* *
42743127 AATTTAATTAGTTTAATT
1 AATTCAATTAGGTTAATT
42743145 AAT
1 AAT
42743148 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
AATTCAATTAGGTTAATT
Found at i:42744741 original size:16 final size:16
Alignment explanation
Indices: 42744720--42744765 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42744710 AAGGGCTTAT
42744720 ATTTTAATTTGTTTTA
1 ATTTTAATTTGTTTTA
42744736 ATTTTAATTT-TCTTTA
1 ATTTTAATTTGT-TTTA
* *
42744752 TTTTTCATTTGTTT
1 ATTTTAATTTGTTT
42744766 GTTTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
ATTTTAATTTGTTTTA
Found at i:42750124 original size:24 final size:24
Alignment explanation
Indices: 42750092--42750139 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42750082 GTGACAAAAT
42750092 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
42750116 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
42750140 CTTTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TTTTGATTTATTTGAGAAATTAAA
Found at i:42750152 original size:24 final size:24
Alignment explanation
Indices: 42750101--42750152 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42750091 TTTTTGATTT
* * ***
42750101 ATTTGAGAAATTAAATTTTGATTT
1 ATTTGAGAAATTAAACTTTAAAAC
42750125 ATTTGAGAAATTAAACTTTAAAAC
1 ATTTGAGAAATTAAACTTTAAAAC
42750149 ATTT
1 ATTT
42750153 TTATAAAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (24 bp):
ATTTGAGAAATTAAACTTTAAAAC
Found at i:42756642 original size:19 final size:19
Alignment explanation
Indices: 42756583--42756642 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
42756573 GAAAAATTTA
**
42756583 TTTATATTAATTTAGCCATT
1 TTTATATTAATTTA-AAATT
**
42756603 TTTATATTAATTTAATGTT
1 TTTATATTAATTTAAAATT
*
42756622 TTTATTTTAATTTAAAATT
1 TTTATATTAATTTAAAATT
42756641 TT
1 TT
42756643 ACATTCTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATATTAATTTAAAATT
Found at i:42759501 original size:24 final size:25
Alignment explanation
Indices: 42759460--42759509 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
42759450 ATTTCATATT
42759460 ATTTTAAAAAATATTTGAAAAAGAA
1 ATTTTAAAAAATATTTGAAAAAGAA
*
42759485 ATTTTGAAAAAA-A-TTGAAAATGAA
1 ATTTT-AAAAAATATTTGAAAAAGAA
42759509 A
1 A
42759510 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 6 0.26
26 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (25 bp):
ATTTTAAAAAATATTTGAAAAAGAA
Found at i:42759559 original size:21 final size:22
Alignment explanation
Indices: 42759535--42759577 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42759525 GATTTTTTTT
42759535 GAAAAA-AATTGGAAAAAAAAA
1 GAAAAATAATTGGAAAAAAAAA
* *
42759556 GAAAAATATTTTGAAAAAAAAA
1 GAAAAATAATTGGAAAAAAAAA
42759578 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (22 bp):
GAAAAATAATTGGAAAAAAAAA
Found at i:42759997 original size:6 final size:6
Alignment explanation
Indices: 42759986--42760031 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
42759976 TTGTCTTTTA
*
42759986 TTTATT TTTATT TTTATT TTTATT TTTATT CTTATT ATTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTT
42760032 TCTTCCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:42760009 original size:18 final size:19
Alignment explanation
Indices: 42759979--42760031 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 19
42759969 TTTCTTATTG
42759979 TCTT-TTATTTATTTTTAT
1 TCTTATTATTTATTTTTAT
*
42759997 TTTTATT-TTTATTTTTAT
1 TCTTATTATTTATTTTTAT
42760015 TCTTATTATTTATTTTT
1 TCTTATTATTTATTTTT
42760032 TCTTCCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTATTATTTATTTTTAT
Found at i:42761201 original size:16 final size:16
Alignment explanation
Indices: 42761180--42761212 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42761170 TGTACTTTTA
42761180 TTTTTATTTTTAGTTG
1 TTTTTATTTTTAGTTG
*
42761196 TTTTTATTTTTATTTG
1 TTTTTATTTTTAGTTG
42761212 T
1 T
42761213 GAGAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTAGTTG
Found at i:42761203 original size:22 final size:23
Alignment explanation
Indices: 42761153--42761210 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
42761143 TTTGCTTTAG
* *
42761153 TTATTTTTACTTTTGGTTGTACTT
1 TTATTTTTATTTTTAGTTGTA-TT
42761177 TTATTTTTATTTTTAGTTGT-TT
1 TTATTTTTATTTTTAGTTGTATT
42761199 TTATTTTTATTT
1 TTATTTTTATTT
42761211 GTGAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 14 0.44
24 18 0.56
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (23 bp):
TTATTTTTATTTTTAGTTGTATT
Found at i:42766733 original size:47 final size:48
Alignment explanation
Indices: 42766668--42766761 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
42766658 TCGCATATCA
* * * *
42766668 CACACCGTAGCCATATCCCGGCTATGGTTTTACACGGAAA-CACATAT
1 CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
42766715 CACACCG-ATGCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
1 CACACCGTA-GCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
42766762 ATCATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
46 1 0.02
47 34 0.83
48 6 0.15
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (48 bp):
CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
Found at i:42769798 original size:9 final size:9
Alignment explanation
Indices: 42769784--42769808 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42769774 AATTTATCAT
42769784 AAGATATTA
1 AAGATATTA
42769793 AAGATATTA
1 AAGATATTA
42769802 AAGATAT
1 AAGATAT
42769809 CCTATGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (9 bp):
AAGATATTA
Found at i:42788069 original size:19 final size:20
Alignment explanation
Indices: 42788033--42788076 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
42788023 TGTCAACATT
42788033 CCAAATACCATAATCACAA-
1 CCAAATACCATAATCACAAG
42788052 CCAAGATACCATAA-CACAAG
1 CCAA-ATACCATAATCACAAG
42788072 CCAAA
1 CCAAA
42788077 CCATATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.52, C:0.32, G:0.05, T:0.11
Consensus pattern (20 bp):
CCAAATACCATAATCACAAG
Found at i:42790803 original size:24 final size:24
Alignment explanation
Indices: 42790758--42790804 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42790748 CATTAAAGTC
* **
42790758 CATAATTCAACCATTTTGTATACT
1 CATAATTCAACCAATTCATATACT
42790782 CATAATTCAACCAATTCATATAC
1 CATAATTCAACCAATTCATATAC
42790805 GTTTGCATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (24 bp):
CATAATTCAACCAATTCATATACT
Found at i:42791196 original size:26 final size:26
Alignment explanation
Indices: 42791160--42791213 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42791150 TGTTGAATTG
42791160 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
42791186 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
42791212 AT
1 AT
42791214 TGTAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (26 bp):
ATAGTTAATTAAGGTACATAGACCAA
Found at i:42792519 original size:17 final size:19
Alignment explanation
Indices: 42792487--42792524 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42792477 ACTGATAACC
42792487 TAACACAAATATATATATT
1 TAACACAAATATATATATT
42792506 TAACACAAATATATATATT
1 TAACACAAATATATATATT
42792525 CAACTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACACAAATATATATATT
Found at i:42796346 original size:49 final size:49
Alignment explanation
Indices: 42796238--42797452 Score: 2242
Period size: 49 Copynumber: 25.1 Consensus size: 49
42796228 GAAATGATAG
*
42796238 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796285 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796334 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796383 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796432 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796479 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796528 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796577 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796626 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796675 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796724 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796773 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796822 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796871 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796920 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42796969 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797018 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797067 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797116 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797165 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
42797214 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
42797261 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797308 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797355 TAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
42797402 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
42797449 TAAG
1 TAAG
42797453 TCCCGAAGGG
Statistics
Matches: 1146, Mismatches: 14, Indels: 16
0.97 0.01 0.01
Matches are distributed among these distances:
45 1 0.00
47 261 0.23
48 1 0.00
49 883 0.77
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:42797627 original size:37 final size:37
Alignment explanation
Indices: 42797571--42797649 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42797561 CCGAGCTCTA
* * *
42797571 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
42797608 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42797645 AAGAC
1 AAGAC
42797650 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42799832 original size:16 final size:16
Alignment explanation
Indices: 42799811--42799843 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42799801 TTTGTTGTAT
42799811 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
42799827 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
42799843 T
1 T
42799844 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:42800094 original size:16 final size:16
Alignment explanation
Indices: 42800057--42800098 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42800047 TTAATCATAT
*
42800057 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
42800073 TT-AAATATATTATAA
1 TTAAAATATATTATAA
42800088 TTAAAATATAT
1 TTAAAATATAT
42800099 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:42800105 original size:14 final size:15
Alignment explanation
Indices: 42800066--42800107 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42800056 TTTAAACATA
*
42800066 ATTATTATTAAATAT
1 ATTATAATTAAATAT
42800081 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
42800095 A-TATAATTTAATA
1 ATTATAATTAAATA
42800108 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:42800219 original size:18 final size:17
Alignment explanation
Indices: 42800179--42800231 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
42800169 AAATATAAAT
42800179 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
42800193 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
42800208 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
42800226 TAAAAT
1 TAAAAT
42800232 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:42800289 original size:60 final size:59
Alignment explanation
Indices: 42800105--42800291 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
42800095 ATATAATTTA
*
42800105 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
42800166 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
42800224 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
42800285 ATAAAAT
1 ATAAAAT
42800292 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:42800290 original size:119 final size:120
Alignment explanation
Indices: 42800057--42800351 Score: 486
Period size: 119 Copynumber: 2.5 Consensus size: 120
42800047 TTAATCATAT
* *
42800057 TTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
42800122 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
42800178 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
42800242 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
42800297 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
42800352 TAAAATAATT
Statistics
Matches: 165, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
119 108 0.65
120 52 0.32
121 5 0.03
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:42802711 original size:38 final size:38
Alignment explanation
Indices: 42802588--42802721 Score: 171
Period size: 46 Copynumber: 3.3 Consensus size: 38
42802578 GACAGAAACT
* *
42802588 GAGCAAATCGGCAGAAAAGAAAGGAAAAG-AATAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
42802625 GAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAG-----AAA-AGA--AACAGAGG
42802671 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
42802709 GAGCAAATCGGCA
1 GAGCAAATCGGCA
42802722 AAAGCTAGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 17
0.82 0.02 0.16
Matches are distributed among these distances:
37 23 0.27
38 21 0.24
40 3 0.03
41 3 0.03
42 3 0.03
43 2 0.02
46 31 0.36
ACGTcount: A:0.54, C:0.11, G:0.30, T:0.04
Consensus pattern (38 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
Found at i:42806353 original size:13 final size:13
Alignment explanation
Indices: 42806335--42806363 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42806325 ATCTAACACC
42806335 TAATATTTTTCCA
1 TAATATTTTTCCA
42806348 TAATATTTTTCCA
1 TAATATTTTTCCA
42806361 TAA
1 TAA
42806364 GAAAAGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATATTTTTCCA
Found at i:42814759 original size:25 final size:25
Alignment explanation
Indices: 42814724--42814790 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
42814714 TCTCGAGCCA
* **
42814724 TATAACAGGAAGCTCATGTAAGCTG
1 TATAACGGGAAGCTCATCCAAGCTG
* * *
42814749 TATAACGGGAAGCTTATCCAGGTTG
1 TATAACGGGAAGCTCATCCAAGCTG
42814774 TATAACGGGAAGCTCAT
1 TATAACGGGAAGCTCAT
42814791 AAGAGTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATAACGGGAAGCTCATCCAAGCTG
Found at i:42814932 original size:25 final size:26
Alignment explanation
Indices: 42814901--42814971 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
42814891 GAGCCATATC
* *
42814901 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGAAGAGCCATTAATCA
* *
42814926 GGAAGCTCACAAAGAGCCTTTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCA
*
42814952 GGAAACTCACGAAGAGCCAT
1 GGAAGCTCACGAAGAGCCAT
42814972 ATATCGGGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 8 0.21
26 30 0.79
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCA
Found at i:42819874 original size:12 final size:12
Alignment explanation
Indices: 42819857--42819881 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42819847 ATTAAGAAAG
42819857 GGAAAGAGTAAA
1 GGAAAGAGTAAA
42819869 GGAAAGAGTAAA
1 GGAAAGAGTAAA
42819881 G
1 G
42819882 CCGAGGAAGA
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:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (12 bp):
GGAAAGAGTAAA
Found at i:42834162 original size:30 final size:31
Alignment explanation
Indices: 42834093--42834170 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
42834083 GAATTATTCG
* * *
42834093 AAAGTTTTTATTTAAGTTATTGAACTATTTA
1 AAAGTTTTTATTTAAGTCAATGAACTAGTTA
42834124 AAAGTTTTTATTTAAGTCAATGAACT-GTTA
1 AAAGTTTTTATTTAAGTCAATGAACTAGTTA
** *
42834154 AATTTTTTTTTTTAAGT
1 AAAGTTTTTATTTAAGT
42834171 TCTGATAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (31 bp):
AAAGTTTTTATTTAAGTCAATGAACTAGTTA
Found at i:42843578 original size:11 final size:11
Alignment explanation
Indices: 42843562--42843588 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42843552 TAGAAATTAG
42843562 TTTGTGAAACT
1 TTTGTGAAACT
42843573 TTTGTGAAACT
1 TTTGTGAAACT
42843584 TTTGT
1 TTTGT
42843589 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:42845124 original size:92 final size:92
Alignment explanation
Indices: 42844988--42845181 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
42844978 TTGATTTTAG
* *
42844988 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
*
42845052 TAT-TAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
42845079 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
42845144 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
42845172 CAAATTCATA
1 TAAATTCATA
42845182 AACTATAATC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 17 0.18
92 43 0.46
93 30 0.32
94 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:42845229 original size:48 final size:52
Alignment explanation
Indices: 42845159--42845257 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
42845149 AATAATTATT
42845159 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
42845207 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
42845258 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:42845239 original size:17 final size:17
Alignment explanation
Indices: 42845214--42845247 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42845204 ATAATTTTAA
*
42845214 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
42845231 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
42845248 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:42845264 original size:17 final size:16
Alignment explanation
Indices: 42845219--42845266 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
42845209 TTTAAATTTT
42845219 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
42845236 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
42845250 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
42845267 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:42845324 original size:61 final size:61
Alignment explanation
Indices: 42845259--42845446 Score: 165
Period size: 61 Copynumber: 3.1 Consensus size: 61
42845249 AGTTATAATC
42845259 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * *
42845320 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
42845378 C
61 T
* * *
42845379 ATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
42845440 ATATATT
1 ATATATT
42845447 TTAATTAAAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 11 0.12
58 7 0.08
59 18 0.19
60 16 0.17
61 25 0.27
62 6 0.06
63 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:42845346 original size:15 final size:15
Alignment explanation
Indices: 42845311--42845362 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42845301 TTAAGAATTT
*
42845311 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42845325 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42845339 TATTTAATAATAAT-
1 TATTTAATTATAATA
42845353 TATGTTAATT
1 TAT-TTAATT
42845363 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42845381 original size:120 final size:120
Alignment explanation
Indices: 42845256--42845478 Score: 410
Period size: 120 Copynumber: 1.9 Consensus size: 120
42845246 ATTAGTTATA
*
42845256 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTATTAAGAATTTTATTAAATTA
*
42845321 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
* *
42845376 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTATTAAGAATTTTATTAAATTA
42845441 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
42845479 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
Found at i:42845455 original size:18 final size:17
Alignment explanation
Indices: 42845427--42845461 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42845417 TTTATTAAGA
*
42845427 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42845444 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42845462 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42845574 original size:144 final size:147
Alignment explanation
Indices: 42845418--42845686 Score: 481
Period size: 144 Copynumber: 1.8 Consensus size: 147
42845408 AGAATTTTAT
*
42845418 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAA
42845483 TATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTACCA
66 TATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCA
42845545 AAACAAATTTCTGCTAA
131 AAACAAATTTCTGCTAA
42845562 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAA
*
42845627 TATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
42845687 CAATAATCAT
Statistics
Matches: 118, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
144 88 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAA
TATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCA
AAACAAATTTCTGCTAA
Found at i:42845599 original size:18 final size:17
Alignment explanation
Indices: 42845571--42845605 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42845561 ATTATTAAGA
*
42845571 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42845588 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42845606 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42845816 original size:44 final size:45
Alignment explanation
Indices: 42845767--42845861 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
42845757 TTACACCTCT
* *
42845767 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
42845811 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
42845856 ATTACA
1 ATTACA
42845862 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:42845861 original size:16 final size:16
Alignment explanation
Indices: 42845840--42845872 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42845830 TTGATTTGCT
*
42845840 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
42845856 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
42845872 A
1 A
42845873 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:42845882 original size:21 final size:21
Alignment explanation
Indices: 42845853--42845895 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42845843 ACACCTCTAT
*
42845853 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
42845874 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
42845895 T
1 T
42845896 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:42849314 original size:25 final size:25
Alignment explanation
Indices: 42849238--42849365 Score: 166
Period size: 25 Copynumber: 5.0 Consensus size: 25
42849228 ATTTTTCTTG
* *
42849238 AAATTTTACCAGGGGCAAAATTGTCA
1 AAATTTTA-CAAGGGTAAAATTGTCA
* **
42849264 AAATTTTACCAGAGACAAAATTGTCA
1 AAATTTTACAAG-GGTAAAATTGTCA
*
42849290 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
42849315 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
42849340 AAATTTTACAGGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
42849365 A
1 A
42849366 TTTTGTTGAG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
25 62 0.67
26 30 0.33
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (25 bp):
AAATTTTACAAGGGTAAAATTGTCA
Found at i:42849377 original size:25 final size:24
Alignment explanation
Indices: 42849280--42849384 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 24
42849270 TACCAGAGAC
* *
42849280 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
* *
42849305 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
**
42849330 AAAATTGTCAAAATTTTACAGGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
42849355 AAAATTGTC-AATTTTGTTGAGGGGT
1 AAAATTGTCAAATTTT-TT-AGGGGT
42849380 AAAAT
1 AAAAT
42849385 AAGGACGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
23 6 0.08
25 68 0.92
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (24 bp):
AAAATTGTCAAATTTTTTAGGGGT
Found at i:42859405 original size:54 final size:54
Alignment explanation
Indices: 42859323--42859431 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
42859313 TTTGAGTTAA
*
42859323 TAATAATTCTCTTTGAGTTTCTTTTAGAAGCTTG-TTTAACAATCATTCAGGTTG
1 TAATAATTCTCTTTGAGTATCTTTTAGAAG-TTGTTTTAACAATCATTCAGGTTG
*
42859377 TAATAATTCTCTTTGAGTATCTTTTAGAAGTTGTTTTAACAATCATTTAGGTTG
1 TAATAATTCTCTTTGAGTATCTTTTAGAAGTTGTTTTAACAATCATTCAGGTTG
42859431 T
1 T
42859432 GGGAATTATC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 3 0.06
54 49 0.94
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.48
Consensus pattern (54 bp):
TAATAATTCTCTTTGAGTATCTTTTAGAAGTTGTTTTAACAATCATTCAGGTTG
Found at i:42862662 original size:27 final size:29
Alignment explanation
Indices: 42862625--42862691 Score: 111
Period size: 27 Copynumber: 2.3 Consensus size: 29
42862615 ACGATCGAAA
42862625 AAAATCAAGATTCACTTT-T-TTTTCAAG
1 AAAATCAAGATTCACTTTCTATTTTCAAG
42862652 AAAATCAAGATTCACTTTCGTATTTTCAAG
1 AAAATCAAGATTCACTTTC-TATTTTCAAG
42862682 AAAATCAAGA
1 AAAATCAAGA
42862692 AATTGAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 18 0.49
29 1 0.03
30 18 0.49
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (29 bp):
AAAATCAAGATTCACTTTCTATTTTCAAG
Found at i:42870020 original size:29 final size:29
Alignment explanation
Indices: 42869978--42870036 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
42869968 TCACAGTCCC
*
42869978 TATGGGTATGATAACTCGACATTTACTAG
1 TATGGGTATGATAACTCAACATTTACTAG
42870007 TATGGGTATGATAACTCAACATTTACTAG
1 TATGGGTATGATAACTCAACATTTACTAG
42870036 T
1 T
42870037 CACTTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (29 bp):
TATGGGTATGATAACTCAACATTTACTAG
Found at i:42880344 original size:27 final size:29
Alignment explanation
Indices: 42880299--42880368 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
42880289 CACAAATTTG
42880299 AAATTTAGTCCATGCAC-TTT-AATTTTA
1 AAATTTAGTCCATGCACTTTTAAATTTTA
* * **
42880326 GAATTTAGTCCCTTTACTTTTTAAATTTTA
1 AAATTTAGTCCATGCAC-TTTTAAATTTTA
42880356 AAATTTAGGTCCA
1 AAATTTA-GTCCA
42880369 ACTATTAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.39
29 3 0.09
30 13 0.39
31 4 0.12
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (29 bp):
AAATTTAGTCCATGCACTTTTAAATTTTA
Found at i:42897565 original size:28 final size:28
Alignment explanation
Indices: 42897534--42897587 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
42897524 TTAAAATTTG
42897534 ATATATAAT-T-TTTAAAAATTAAAATAAA
1 ATATATAATATATTT-AAAA-TAAAATAAA
*
42897562 ATATTTAATATATTTAAAATAAAATA
1 ATATATAATATATTTAAAATAAAATA
42897588 CTTACCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 15 0.65
29 5 0.22
30 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATAATATATTTAAAATAAAATAAA
Found at i:42897568 original size:21 final size:21
Alignment explanation
Indices: 42897521--42897587 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
42897511 AAAGCTTTTT
* * *
42897521 TATTTAAAATTTGATATATAA
1 TATTTAAAATTTAAAATAAAA
* *
42897542 TTTTTAAAAATTAAAATAAAA
1 TATTTAAAATTTAAAATAAAA
42897563 TATTTAATATATTTAAAATAAAA
1 TATTTAA-A-ATTTAAAATAAAA
42897586 TA
1 TA
42897588 CTTACCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 22 0.59
22 1 0.03
23 14 0.38
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
TATTTAAAATTTAAAATAAAA
Found at i:42927233 original size:33 final size:34
Alignment explanation
Indices: 42927186--42927320 Score: 105
Period size: 33 Copynumber: 3.8 Consensus size: 34
42927176 ATGTGAAAGG
*
42927186 GGTTACTAAGTGCTGATTCC-CCGATTCTTTGAT
1 GGTTGCTAAGTGCTGATTCCACCGATTCTTTGAT
42927219 GGTTGCTAAGTGCTGATTCCACCG-TATCATTGAATGTGAAAT
1 GGTTGCTAAGTGCTGATTCCACCGAT-TC--T---T-TG--AT
* ** *
42927261 GGGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 -GGTTGCTAAGTGCTGATTCCACCGATTCTTTGAT
*
42927295 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCCACCGAT
42927321 AACGGATAAC
Statistics
Matches: 82, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
33 39 0.48
34 10 0.12
36 3 0.04
39 1 0.01
40 2 0.02
42 7 0.09
43 20 0.24
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGATTCTTTGAT
Found at i:42927280 original size:76 final size:74
Alignment explanation
Indices: 42927107--42927318 Score: 262
Period size: 76 Copynumber: 2.8 Consensus size: 74
42927097 TGATTCCGCC
* * * * * * *
42927107 AAGGGCTTGCTAACTGCTGATTCCACAATTCATTCGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTC-TTTGTGGTTGCTAAGTGCTGATTCCACCGTATA
42927172 TTAAATGTGA
65 TTAAATGTGA
*
42927182 AAGGGGTTACTAAGTGCTGATTCCCCGATTCTTTGATGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCTTTG-TGGTTGCTAAGTGCTGATTCCACCGTAT-
*
42927247 ATTGAATGTGA
64 ATTAAATGTGA
* * * * *
42927258 AATGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTC-TTTGTGGTTGCTAAGTGCTGATTCCACCG
42927319 ATAACGGATA
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
74 3 0.03
75 53 0.45
76 61 0.51
77 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCTTTGTGGTTGCTAAGTGCTGATTCCACCGTATAT
TAAATGTGA
Found at i:42930619 original size:162 final size:162
Alignment explanation
Indices: 42930435--42930759 Score: 614
Period size: 162 Copynumber: 2.0 Consensus size: 162
42930425 TGCTTATGTG
42930435 TTGAATACTAGTATAACCGAGTCGAAGCTTGAATCAGTGCCGGTAGCCTATGAATTTTCGGATGT
1 TTGAATACTAGTATAACCGAGTCGAAGCTTGAATCAGTGCCGGTAGCCTATGAATTTTCGGATGT
*
42930500 ATTTCTAGAGGAATTGCCTGGGTTACCTCCGATTAGAGAAGTTGAGTTTGTTATTGATTTGTTAC
66 ATTTCTAGAAGAATTGCCTGGGTTACCTCCGATTAGAGAAGTTGAGTTTGTTATTGATTTGTTAC
*
42930565 CTGGTACTACACCAATTTCTATTGCATCGTAT
131 CTGGTACTACACCAATTTCTATTGCACCGTAT
42930597 TTGAATACTAGTATAACCGAGTCGAAGCTTGAATCAGTGCCGGTAGCCTATGAATTTTCGGATGT
1 TTGAATACTAGTATAACCGAGTCGAAGCTTGAATCAGTGCCGGTAGCCTATGAATTTTCGGATGT
42930662 ATTTCTAGAAGAATTGCCTGGGTTACCTCCGATTAGAGAAGTTGAGTTTGTTATTGATTTGTTAC
66 ATTTCTAGAAGAATTGCCTGGGTTACCTCCGATTAGAGAAGTTGAGTTTGTTATTGATTTGTTAC
* *
42930727 CTGGTACTGCATCAATTTCTATTGCACCGTAT
131 CTGGTACTACACCAATTTCTATTGCACCGTAT
42930759 T
1 T
42930760 GGATGGCTCC
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 159 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (162 bp):
TTGAATACTAGTATAACCGAGTCGAAGCTTGAATCAGTGCCGGTAGCCTATGAATTTTCGGATGT
ATTTCTAGAAGAATTGCCTGGGTTACCTCCGATTAGAGAAGTTGAGTTTGTTATTGATTTGTTAC
CTGGTACTACACCAATTTCTATTGCACCGTAT
Found at i:42935296 original size:27 final size:27
Alignment explanation
Indices: 42935257--42935308 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
42935247 TTTAAATGTG
*
42935257 AAGGGGCTGCTAAGTGCTGATTCCCCC
1 AAGGGGCTACTAAGTGCTGATTCCCCC
*
42935284 AAGGGGTTACTAAGTGCTGATTCCC
1 AAGGGGCTACTAAGTGCTGATTCCC
42935309 GGAATCATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (27 bp):
AAGGGGCTACTAAGTGCTGATTCCCCC
Found at i:42935385 original size:42 final size:43
Alignment explanation
Indices: 42935321--42935425 Score: 158
Period size: 43 Copynumber: 2.5 Consensus size: 43
42935311 AATCATTGGT
*
42935321 GGTTGCTAAGTGCTGATCCCACCGTA-TCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTCTTAAATGTGAAAGG
* * *
42935363 GGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAATGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTCTTAAATGTGAAAGG
*
42935406 GGTTGCTAAGAGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
42935426 CCAAATCACT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 25 0.44
43 32 0.56
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTCTTAAATGTGAAAGG
Found at i:42942418 original size:33 final size:33
Alignment explanation
Indices: 42942373--42942578 Score: 142
Period size: 33 Copynumber: 5.6 Consensus size: 33
42942363 AAATGAGTTA
*
42942373 GCTAAGTACTGATTCCCCGATTCATTGGTGGTT
1 GCTAAGTGCTGATTCCCCGATTCATTGGTGGTT
* * *
42942406 GCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTT
1 GCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GTGGTT
*
42942448 GCTAAGTGTTGATTCCCCGATTCATTGGTGGTT
1 GCTAAGTGCTGATTCCCCGATTCATTGGTGGTT
* *
42942481 GCTAAGTGCTGATTCCACGGTATCATTGAATGTGAAAGGAGTT
1 GCTAAGTGCTGATTCCCCGAT-TCATTG---GT-----G-GTT
* *
42942524 GCTAAGTGCTGATTCCCCGAATCACTGGTGGTT
1 GCTAAGTGCTGATTCCCCGATTCATTGGTGGTT
*
42942557 GCTAAGTGCTGAATCCACCGAT
1 GCTAAGTGCTGATTCC-CCGAT
42942579 AACGGATAAC
Statistics
Matches: 136, Mismatches: 17, Indels: 39
0.71 0.09 0.20
Matches are distributed among these distances:
33 55 0.40
34 14 0.10
35 1 0.01
36 2 0.01
37 6 0.04
38 4 0.03
39 4 0.03
40 1 0.01
41 3 0.02
42 25 0.18
43 21 0.15
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GCTAAGTGCTGATTCCCCGATTCATTGGTGGTT
Found at i:42942504 original size:75 final size:76
Alignment explanation
Indices: 42942367--42942576 Score: 323
Period size: 76 Copynumber: 2.8 Consensus size: 76
42942357 AACATTAAAT
* *
42942367 GAGTTAGCTAAGTACTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC-T
1 GAGTT-GCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCAT
42942431 TAAATGTGAAAG
65 TAAATGTGAAAG
* * *
42942443 GGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACGGTATCATT
1 GAGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCATT
*
42942508 GAATGTGAAAG
66 AAATGTGAAAG
* * *
42942519 GAGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 GAGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
42942577 ATAACGGATA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
75 53 0.44
76 68 0.56
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (76 bp):
GAGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCATT
AAATGTGAAAG
Done.