Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 156 of 235
Found at i:52558575 original size:39 final size:40
Alignment explanation
Indices: 52558510--52558720 Score: 157
Period size: 39 Copynumber: 5.3 Consensus size: 40
52558500 CCCGAATCAC
* ** *
52558510 ATACCTTCGGAATTTAA-CCGGATATAGCT-ACTCGCTCAA
1 ATACCTTCGGGACATAACCCGGATATAG-TAACTCGCACAA
* *
52558549 ATACC-TCGGGACATAGCCCGGTTATAGTAACTCGCACAA
1 ATACCTTCGGGACATAACCCGGATATAGTAACTCGCACAA
* * * *
52558588 ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCA
1 ATACCTTCGGGACATAACCCGGATATAGTAACTCGCACAA
* * *
52558628 ATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAA
1 ATACCTTCGGGACATAACCCGGATA-TAGTAACTCGCACAA
* * ** * *
52558667 ATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAA
1 ATACCTTCGGGA-CATAACCCGGATATAGTAAC-TCGCACAA
52558708 A-AGCCTTCGGGAC
1 ATA-CCTTCGGGAC
52558721 TTAGCCCAGA
Statistics
Matches: 143, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
38 10 0.07
39 59 0.41
40 56 0.39
41 15 0.10
42 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
ATACCTTCGGGACATAACCCGGATATAGTAACTCGCACAA
Found at i:52558609 original size:40 final size:40
Alignment explanation
Indices: 52558527--52558733 Score: 235
Period size: 40 Copynumber: 5.2 Consensus size: 40
52558517 CGGAATTTAA
* * *
52558527 CCGGATATAGCT-ACTCGCTCAAATACC-TCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52558566 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52558606 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52558645 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52558685 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
*
52558726 CCAGATAT
1 CCGGATAT
52558734 CATTCGAATA
Statistics
Matches: 143, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.02
39 54 0.38
40 56 0.39
41 27 0.19
42 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52558645 original size:79 final size:81
Alignment explanation
Indices: 52558554--52558727 Score: 221
Period size: 79 Copynumber: 2.2 Consensus size: 81
52558544 CTCAAATACC
* * *
52558554 TCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAGT
1 TCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGT
* * *
52558617 AAC-TCGCACCAATGCCT
64 AACTTAGCACAAAAGCCT
** *
52558634 TCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTCA
1 TCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAA
52558698 CTTAGCACAAAAGCCT
66 CTTAGCACAAAAGCCT
52558714 TCGGGACTTAGCCC
1 TCGGGACTTAGCCC
52558728 AGATATCATT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.04
79 48 0.59
80 22 0.27
81 8 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
TCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAA
CTTAGCACAAAAGCCT
Found at i:52566855 original size:39 final size:40
Alignment explanation
Indices: 52566734--52566926 Score: 196
Period size: 40 Copynumber: 4.8 Consensus size: 40
52566724 GGATATAGCT
* * * * *
52566734 ACTCGCTCAAATGCCTTCGGGACATATCCCAG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * *
52566774 ACTCACACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
52566814 ACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* * *
52566853 ACTCGTACAAATGCCTTC-GGATCTTAGTCCGG-ATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTA
* *
52566893 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
52566927 TATCATTCGA
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 34 0.26
40 66 0.51
41 24 0.19
42 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:52566863 original size:79 final size:81
Alignment explanation
Indices: 52566769--52566926 Score: 205
Period size: 79 Copynumber: 2.0 Consensus size: 81
52566759 ATCCCAGTTA
* * * *
52566769 TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTC
1 TAGTAACTCACACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTC
52566832 GGG-CTTAGCCCGGAAT
65 GGGACTTAGCCCGGAAT
** ** *
52566848 TAGTAACTCGTACAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCG
1 TAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTCG
52566913 GGACTTAGCCCGGA
66 GGACTTAGCCCGGA
52566927 TATCATTCGA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 3 0.04
79 37 0.55
80 16 0.24
81 11 0.16
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (81 bp):
TAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAAGCCTTCG
GGACTTAGCCCGGAAT
Found at i:52572353 original size:28 final size:28
Alignment explanation
Indices: 52572313--52572522 Score: 341
Period size: 28 Copynumber: 7.5 Consensus size: 28
52572303 TAAATTGTAC
*
52572313 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
52572341 AGCACTAAATGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
52572369 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
52572397 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
52572425 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
52572453 AGCACTAAGTGGGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
52572481 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
52572508 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52572523 GACTTAATAT
Statistics
Matches: 173, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
27 24 0.14
28 149 0.86
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:52576018 original size:22 final size:22
Alignment explanation
Indices: 52575990--52576111 Score: 59
Period size: 22 Copynumber: 5.3 Consensus size: 22
52575980 TTCCACATCC
52575990 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
*** *** *
52576012 ATCACATATATACACTTTTACATT
1 ATCACAT-TGGCCA-TTCGGCCTT
52576036 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
52576059 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
52576083 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52576106 ATCACA
1 ATCACA
52576112 CATACACATG
Statistics
Matches: 68, Mismatches: 22, Indels: 20
0.62 0.20 0.18
Matches are distributed among these distances:
22 22 0.32
23 15 0.22
24 15 0.22
25 16 0.24
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52576025 original size:47 final size:47
Alignment explanation
Indices: 52575962--52576271 Score: 363
Period size: 47 Copynumber: 6.3 Consensus size: 47
52575952 CCCTTCGGGA
* * *
52575962 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
52576009 CTTATCACATATATACACT-TTTACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
52576056 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52576103 CTTATCACACATACACATGTTTTCACATTTATTTCACATTCATCACATTGGCCATTCGGC
1 CTTAT--CACAT----A---TAT-ACA--T-GTTCACATTCATCACATTGGCCATTCGGC
* *
52576163 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
52576210 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
52576257 CTTATCACATATATA
1 CTTATCACATATATA
52576272 TACACTTTCA
Statistics
Matches: 232, Mismatches: 17, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
46 1 0.00
47 178 0.77
48 1 0.00
49 4 0.02
50 3 0.01
51 1 0.00
53 1 0.00
54 1 0.00
56 2 0.01
57 2 0.01
58 4 0.02
59 1 0.00
60 33 0.14
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:52576174 original size:33 final size:33
Alignment explanation
Indices: 52576077--52576174 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
52576067 TATGCATGTT
52576077 CACATTCATCACATTGGCCATTCGGCCTTATCA
1 CACATTCATCACATTGGCCATTCGGCCTTATCA
** * * **
52576110 CACA-T-A-CACA-T-G-TTTTC-ACATTTATTT
1 CACATTCATCACATTGGCCATTCGGC-CTTATCA
52576137 CACATTCATCACATTGGCCATTCGGCCTTATCA
1 CACATTCATCACATTGGCCATTCGGCCTTATCA
52576170 CACAT
1 CACAT
52576175 ACACATGTTC
Statistics
Matches: 45, Mismatches: 12, Indels: 16
0.62 0.16 0.22
Matches are distributed among these distances:
26 1 0.02
27 11 0.24
28 2 0.04
29 2 0.04
30 8 0.18
31 2 0.04
32 2 0.04
33 16 0.36
34 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.34
Consensus pattern (33 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCA
Found at i:52576189 original size:154 final size:154
Alignment explanation
Indices: 52575983--52576265 Score: 478
Period size: 154 Copynumber: 1.8 Consensus size: 154
52575973 TATACACTTC
* * *
52575983 CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTTACATTCATCACATTGGC
1 CACATCCATCACATTGGCCATTCGGCCTTATCACACATACACACTTTCACATTCATCACATTGGC
* * **
52576048 CATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
66 CATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
52576113 ATACACATGTTTTCACATTTATTT
131 ATACACATGTTTTCACATTTATTT
*
52576137 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCATCACATTGG
1 CACATCCATCACATTGGCCATTCGGCCTTATCACACATACACACT-TTCACATTCATCACATTGG
52576201 CCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
65 CCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
52576266 TATATATACA
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
153 1 0.01
154 119 0.99
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (154 bp):
CACATCCATCACATTGGCCATTCGGCCTTATCACACATACACACTTTCACATTCATCACATTGGC
CATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
ATACACATGTTTTCACATTTATTT
Found at i:52576217 original size:107 final size:107
Alignment explanation
Indices: 52576031--52576230 Score: 364
Period size: 107 Copynumber: 1.9 Consensus size: 107
52576021 ATACACTTTT
* * **
52576031 ACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCC
52576096 ATTCGGCCTTATCACACATACACATGTTTTCACATTTATTTC
66 ATTCGGCCTTATCACACATACACATGTTTTCACATTTATTTC
52576138 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCC
1 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCC
52576203 ATTCGGCCTTATCACACATACACATGTT
66 ATTCGGCCTTATCACACATACACATGTT
52576231 CACATTCATC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 89 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (107 bp):
ACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCC
ATTCGGCCTTATCACACATACACATGTTTTCACATTTATTTC
Found at i:52576604 original size:31 final size:31
Alignment explanation
Indices: 52576569--52576630 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52576559 TTATAACCGG
* *
52576569 AGCTACAAAACTCCAAATCACTTGCCATTAA
1 AGCTAAAAAACTCCAAACCACTTGCCATTAA
*
52576600 AGCTAAAAAACTCCAAACCACTTGCCGTTAA
1 AGCTAAAAAACTCCAAACCACTTGCCATTAA
52576631 TTTTTCCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (31 bp):
AGCTAAAAAACTCCAAACCACTTGCCATTAA
Found at i:52579377 original size:41 final size:39
Alignment explanation
Indices: 52579268--52579385 Score: 128
Period size: 39 Copynumber: 2.9 Consensus size: 39
52579258 CACGTGTGTG
* * * *
52579268 CATTCAAGGGTACTGAAGTACAAATAGGGACACGTATGCT
1 CATTC-AGGGTACCGAAGTACAAATAGGGGCACATATGCA
* * **
52579308 CATTTAGGGTACCAAAGTATGAATAGGGGCACATATGCA
1 CATTCAGGGTACCGAAGTACAAATAGGGGCACATATGCA
*
52579347 CATTCAGGGGTAACCGAAGTACAAACAGGGGCACATATG
1 CATTCA-GGGT-ACCGAAGTACAAATAGGGGCACATATG
52579386 TGCATTCATC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 32 0.51
40 8 0.13
41 23 0.37
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (39 bp):
CATTCAGGGTACCGAAGTACAAATAGGGGCACATATGCA
Found at i:52580589 original size:6 final size:6
Alignment explanation
Indices: 52580551--52580588 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
52580541 AATTCCAACC
52580551 AAAATT -AAATT AAAATT AAAATT AAAATT AAAA-T AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
52580589 AAATTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:52581515 original size:30 final size:30
Alignment explanation
Indices: 52581468--52581527 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52581458 TTTCCCAGCC
*
52581468 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
* *
52581498 TAGGGGAAAAA-TGGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGT-GTAATTATGCAAAAGTT
52581528 CGTATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATGCAAAAGTT
Found at i:52582245 original size:49 final size:50
Alignment explanation
Indices: 52582182--52582420 Score: 232
Period size: 49 Copynumber: 4.8 Consensus size: 50
52582172 TGAGGTCACG
* *
52582182 TGTGTAGTAGTAAGTGCAGGCTACTACGTGTACCAGATTGTT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCA
* * * * * * * *
52582231 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AGTTAGGTCGCA
* * * * *
52582282 TGTGTAGTACTAAGTACAGACTACTACGTGTATCAGATGGTTAGGTC-AA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCA
* * *
52582331 GTGTATAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTAGCA
1 -TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCA
* * * * *
52582381 TCTGTAGTACTAAGTGCCGGCCACTATGCGTACCAGATAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
52582421 CTTCAGCTAC
Statistics
Matches: 150, Mismatches: 36, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
49 70 0.47
50 44 0.29
51 36 0.24
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCA
Found at i:52587273 original size:30 final size:30
Alignment explanation
Indices: 52587226--52587285 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52587216 ATTCCCAGCC
*
52587226 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
* *
52587256 TAGGGGAAAAA-TGGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGT-GTAATTATGCAAAAGTT
52587286 CGTATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATGCAAAAGTT
Found at i:52605910 original size:28 final size:28
Alignment explanation
Indices: 52605878--52605942 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
52605868 ATTTACTAGA
*
52605878 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
52605906 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52605934 ATACCCCTA
1 ATACCCCTA
52605943 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52606092 original size:28 final size:29
Alignment explanation
Indices: 52606048--52606110 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
52606038 AGGAAGCGTC
*
52606048 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
*
52606076 CTGGTGGC-ATTGTCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
52606105 CTGGTG
1 CTGGTG
52606111 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:52606118 original size:29 final size:28
Alignment explanation
Indices: 52606061--52606121 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
52606051 GTGGCTATGC
* *
52606061 CACAAATTATCTGTTCTGGTGGCATTGT
1 CACAAAATATCTGTTCTGGTGACATTGT
52606089 CACAAAATATCTGTATCTGGTGAC-TCTGT
1 CACAAAATATCTGT-TCTGGTGACAT-TGT
52606118 CACA
1 CACA
52606122 TTTTCTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (28 bp):
CACAAAATATCTGTTCTGGTGACATTGT
Found at i:52613727 original size:28 final size:28
Alignment explanation
Indices: 52613696--52613760 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
52613686 ATTTACTAGA
* *
52613696 ATACCCTTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* * *
52613724 ATACCCCTATGTGTGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52613752 ATACCCCTA
1 ATACCCCTA
52613761 GGTTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52613906 original size:28 final size:28
Alignment explanation
Indices: 52613865--52613919 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
52613855 AGGAAGCGTC
*
52613865 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTT
52613893 CTGGTGGC-ACTGCCACAAAATATCTGT
1 CTGGTGGCTA-TGCCACAAAATATCTGT
52613920 ATCCGGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (28 bp):
CTGGTGGCTATGCCACAAAATATCTGTT
Found at i:52613938 original size:29 final size:28
Alignment explanation
Indices: 52613875--52613938 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
52613865 CTGGTGGCTA
* * *
52613875 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCCGGTGACAC
*
52613903 TGCCACAAAATATCTGTATCCGGTGACTC
1 TGCCACAAAATATCTGT-TCCGGTGACAC
*
52613932 TGTCACA
1 TGCCACA
52613939 TTTTCTGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCCGGTGACAC
Found at i:52619279 original size:28 final size:28
Alignment explanation
Indices: 52619247--52619316 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
52619237 AATGAGATTG
52619247 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
* *
52619275 GCACTAAGGGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
52619303 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52619317 GACTTACTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 32 0.86
29 4 0.11
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:52626785 original size:19 final size:20
Alignment explanation
Indices: 52626756--52626800 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
52626746 CGAAATTTTA
* *
52626756 ATTAGTATTATGAGATAAAT
1 ATTATTATTATGAGAAAAAT
*
52626776 -TTATTATTATTAGAAAAAT
1 ATTATTATTATGAGAAAAAT
52626795 ATTATT
1 ATTATT
52626801 GCATGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (20 bp):
ATTATTATTATGAGAAAAAT
Found at i:52626920 original size:87 final size:87
Alignment explanation
Indices: 52626820--52627000 Score: 344
Period size: 87 Copynumber: 2.1 Consensus size: 87
52626810 TTTGAAAATT
52626820 TTTTATGAAAATTATTATTATTATTTACTGTATTATTGATATTTGAAATTTTTATTATTAGATTT
1 TTTTATGAAAATTATTATTATTATTTACTGTATTATTGATATTTGAAATTTTTATTATTAGATTT
*
52626885 ATTTATAAAATTATTATTCTAA
66 ATTTATAAAATTATTATTATAA
52626907 TTTTATGAAAATTATTATTATTATTTACTGTATTATTGATATTTGAAATTTTTATTATTAGATTT
1 TTTTATGAAAATTATTATTATTATTTACTGTATTATTGATATTTGAAATTTTTATTATTAGATTT
52626972 ATTTATAAAATTATTATTATAA
66 ATTTATAAAATTATTATTATAA
52626994 TTATTAT
1 TT-TTAT
52627001 TATTATTAGA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 88 0.96
88 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (87 bp):
TTTTATGAAAATTATTATTATTATTTACTGTATTATTGATATTTGAAATTTTTATTATTAGATTT
ATTTATAAAATTATTATTATAA
Found at i:52626932 original size:23 final size:22
Alignment explanation
Indices: 52626886--52626932 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
52626876 ATTAGATTTA
*
52626886 TTTATAAAATTATTATTCTAAT
1 TTTATAAAATTATTATTATAAT
*
52626908 TTTATGAAAATTATTATTATTAT
1 TTTAT-AAAATTATTATTATAAT
52626931 TT
1 TT
52626933 ACTGTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATAAAATTATTATTATAAT
Found at i:52627003 original size:12 final size:12
Alignment explanation
Indices: 52626958--52627008 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
52626948 TTTGAAATTT
* *
52626958 TTATTATTAGAT
1 TTATTATTATAA
*
52626970 TTATT-TATAAAA
1 TTATTAT-TATAA
52626982 TTATTATTATAA
1 TTATTATTATAA
*
52626994 TTATTATTATTA
1 TTATTATTATAA
52627006 TTA
1 TTA
52627009 GATAGGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTATAA
Found at i:52629434 original size:60 final size:60
Alignment explanation
Indices: 52629370--52629506 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
52629360 CCAACTCTGT
** *
52629370 TGATATGGGC-AAGGCTGAATATA-TCTCGACT-TGTAATAGGGCTATGGCCCAGATTGATAC
1 TGATATGGGCTAAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTATGGCCCAGATTAATAC
* *
52629430 TGATATGGGCTAA-GCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATAT
1 TGATATGGGCTAAGGCCCAATATACTCTGATA-TGTAAAGGGCTATGGCCCAGATTAATAC
52629490 TGATATGGGCTAAGGCC
1 TGATATGGGCTAAGGCC
52629507 TAGTAAAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
59 1 0.01
60 53 0.79
61 13 0.19
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (60 bp):
TGATATGGGCTAAGGCCCAATATACTCTGATATGTAAAGGGCTATGGCCCAGATTAATAC
Found at i:52630169 original size:16 final size:17
Alignment explanation
Indices: 52630137--52630169 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52630127 CATCAAGAAG
52630137 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
52630155 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
52630170 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:52631497 original size:17 final size:19
Alignment explanation
Indices: 52631455--52631498 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
52631445 ACGAAATTTT
*
52631455 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
52631474 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
52631492 AA-TATTA
1 AATTATTA
52631499 CTGCATGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:52631616 original size:12 final size:12
Alignment explanation
Indices: 52631571--52631621 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
52631561 TTTGAAATTT
* *
52631571 TTATTATTAGAT
1 TTATTATTATAA
*
52631583 TTATT-TATAAAA
1 TTATTAT-TATAA
52631595 TTATTATTATAA
1 TTATTATTATAA
*
52631607 TTATTATTATTA
1 TTATTATTATAA
52631619 TTA
1 TTA
52631622 GATAGGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTATAA
Found at i:52634025 original size:60 final size:60
Alignment explanation
Indices: 52633961--52634095 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
52633951 CCAACTGTGT
* ** * *
52633961 TGATATGGGCAAGGCCGAATATA-TCTCGACTTGTA-ATAGGGCTATGGCCCAGATTGATAC
1 TGATATGGGCAAGGCCCAATATACT-TCGA-TACTATATAGGGCTACGGCCCAGATTAATAC
* * * *
52634021 TGATATGGGCTAGGCCCAATATACTTTGATACTATATGGGGCTACGGCCCAGATTAATAT
1 TGATATGGGCAAGGCCCAATATACTTCGATACTATATAGGGCTACGGCCCAGATTAATAC
52634081 TGATATGGGCTAAGG
1 TGATATGGGC-AAGG
52634096 TCCAGTTAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.05
60 55 0.89
61 4 0.06
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (60 bp):
TGATATGGGCAAGGCCCAATATACTTCGATACTATATAGGGCTACGGCCCAGATTAATAC
Found at i:52637248 original size:46 final size:47
Alignment explanation
Indices: 52637102--52637308 Score: 160
Period size: 46 Copynumber: 4.5 Consensus size: 47
52637092 TTTGTGTGCT
* * * * *
52637102 AGTGTAAGACATGCCTGGGACATGCATTGGCCAC-A-TTTTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-AGAGCC
* * * * * ** *
52637148 AGTGTAAGACCATATATGGGACATGGCATCGACATTGAGA-CAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCC
*
52637196 AATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAG-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
* * *
52637242 AGTGTAAGACATGTTTGGGACATGCATCGG-CTACAAGATGT---GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCC
52637286 AGTGTAAGACCATGTCTGGGACA
1 AGTGTAAGA-CATGTCTGGGACA
52637309 AGGCATCAGC
Statistics
Matches: 128, Mismatches: 26, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
44 11 0.09
45 14 0.11
46 58 0.45
47 25 0.20
48 19 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
Found at i:52638649 original size:20 final size:21
Alignment explanation
Indices: 52638610--52638649 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52638600 GTTATAATGA
*
52638610 CCACACAGGCGTGTTGCCCTT
1 CCACACAGGCATGTTGCCCTT
*
52638631 CCACACGGGCATG-TGCCCT
1 CCACACAGGCATGTTGCCCT
52638650 ATTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (21 bp):
CCACACAGGCATGTTGCCCTT
Found at i:52645120 original size:141 final size:138
Alignment explanation
Indices: 52644866--52645135 Score: 348
Period size: 141 Copynumber: 1.9 Consensus size: 138
52644856 GGGTTATTTG
52644866 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTTTGAGAGCCAGTGTAAGACCAT
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTTTGAGAGCCAGTGTAAGACCAT
* ** * *
52644931 GTATGGGACATGGCATCGGCATTGAGACGAGAGCTAGTATAAGACATGTCTGGGACAT-GCATCA
66 GTATGGAACATGGCATCAACATTGAGA-GAGAGCCAATATAAGACATGTCTGGGACATAGCATCA
52644995 GCTACGAGA
130 GCTACGAGA
* * * * *
52645004 TGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCTATTTTGATAGTCAGTGTAAGAC
1 TGTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCAC-ATTTTGAGAGCCAGTGTAAGAC
* *
52645069 CATGTCTGGAACATGGCATCAAC-TTGATG-GATGAGCCAATGTAAGACCATGTCTGGGACATAG
63 CATGTATGGAACATGGCATCAACATTGA-GAGA-GAGCCAATATAAGA-CATGTCTGGGACATAG
52645132 CATC
125 CATC
52645136 GGCATTATAC
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
138 14 0.12
139 16 0.14
140 24 0.21
141 54 0.48
142 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (138 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTTTGAGAGCCAGTGTAAGACCAT
GTATGGAACATGGCATCAACATTGAGAGAGAGCCAATATAAGACATGTCTGGGACATAGCATCAG
CTACGAGA
Found at i:52654670 original size:27 final size:27
Alignment explanation
Indices: 52654637--52654785 Score: 108
Period size: 27 Copynumber: 5.5 Consensus size: 27
52654627 CACACTAAAA
* *
52654637 AGATGGAAGCTTTTTTGGTGATCTAAG
1 AGATGGAAGCCTTTATGGTGATCTAAG
*
52654664 AGATGGAACCCTTTATGGTGATCTAAG
1 AGATGGAAGCCTTTATGGTGATCTAAG
* * *
52654691 AGATGAAAGCC--TAGTCGG-CAACTTAAG
1 AGATGGAAGCCTTTA-T-GGTGATC-TAAG
* * **
52654718 AGATGGAAACCTTTGTGGCAATCTAAG
1 AGATGGAAGCCTTTATGGTGATCTAAG
* *
52654745 AGATGGAAGCCTTTCTGGCTG-TCTATG
1 AGATGGAAGCCTTTATGG-TGATCTAAG
* *
52654772 AAAAGGAAGCCTTT
1 AGATGGAAGCCTTT
52654786 TTGGCAATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
25 2 0.02
26 3 0.03
27 87 0.91
28 3 0.03
29 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (27 bp):
AGATGGAAGCCTTTATGGTGATCTAAG
Found at i:52654792 original size:81 final size:80
Alignment explanation
Indices: 52654657--52654815 Score: 176
Period size: 81 Copynumber: 2.0 Consensus size: 80
52654647 TTTTTTGGTG
* *
52654657 ATCTAAGAGATGGAACCCTTTATGGTGATCTAAGAGATGAAAGCCTAGTCGGCAACTTAAGAGAT
1 ATCTAAGAGATGGAACCCTTTATGGTGATCTAAGAAAAGAAAGCCTAGTCGGCAACTTAAGA-AT
52654722 GGAAACCTTTGTGGCA
65 GGAAACCTTTGTGGCA
* * * * ** * * *
52654738 ATCTAAGAGATGGAAGCCTTTCTGGCTG-TCTATGAAAAGGAAGCCTTTTTGGCAATTTACGAAT
1 ATCTAAGAGATGGAACCCTTTATGG-TGATCTAAGAAAAGAAAGCCTAGTCGGCAACTTAAGAAT
**
52654802 GGATGCCTTTGTGG
65 GGAAACCTTTGTGG
52654816 GGCACTCTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
80 14 0.22
81 48 0.75
82 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (80 bp):
ATCTAAGAGATGGAACCCTTTATGGTGATCTAAGAAAAGAAAGCCTAGTCGGCAACTTAAGAATG
GAAACCTTTGTGGCA
Found at i:52658759 original size:29 final size:29
Alignment explanation
Indices: 52658717--52658789 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
52658707 TGAAAGCATG
*
52658717 TATATGAATGTGATTTGGGCCTAATGGGC
1 TATATGAATGTGATTTGGGCCTAATAGGC
*
52658746 TATACGAATGTGATTTGGGCCTAATAGGC
1 TATATGAATGTGATTTGGGCCTAATAGGC
* *
52658775 CATATGAATGAGATT
1 TATATGAATGTGATT
52658790 GAGCTTAGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (29 bp):
TATATGAATGTGATTTGGGCCTAATAGGC
Found at i:52659851 original size:27 final size:27
Alignment explanation
Indices: 52659821--52659873 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
52659811 TCCACAACTT
52659821 AATTTTTTCTTAAAATGATAGGCTTTA
1 AATTTTTTCTTAAAATGATAGGCTTTA
52659848 AATTTTTTCTTAAAATGATAGGCTTT
1 AATTTTTTCTTAAAATGATAGGCTTT
52659874 CATAAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (27 bp):
AATTTTTTCTTAAAATGATAGGCTTTA
Found at i:52660689 original size:27 final size:27
Alignment explanation
Indices: 52660673--52660757 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
52660663 TTACCCTATG
*
52660673 AGGGTAAAATCGTCATTTTATCACTTA
1 AGGGCAAAATCGTCATTTTATCACTTA
*
52660700 AGGGCAATATCGTCATTTTATCACTTA
1 AGGGCAAAATCGTCATTTTATCACTTA
* * *
52660727 AGGGCAATATCATCATTTTATCACATA
1 AGGGCAAAATCGTCATTTTATCACTTA
52660754 AGGG
1 AGGG
52660758 TTTAGGTACA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (27 bp):
AGGGCAAAATCGTCATTTTATCACTTA
Found at i:52660885 original size:18 final size:18
Alignment explanation
Indices: 52660862--52660900 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52660852 ATAATGTGGG
52660862 CCATGTGTGCCCAC-AAGC
1 CCATGTG-GCCCACGAAGC
*
52660880 CCATGTGGCTCACGAAGC
1 CCATGTGGCCCACGAAGC
52660898 CCA
1 CCA
52660901 ATTATGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (18 bp):
CCATGTGGCCCACGAAGC
Found at i:52671803 original size:8 final size:8
Alignment explanation
Indices: 52671790--52671846 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
52671780 ATTTTTAATT
52671790 TTATTTAA
1 TTATTTAA
52671798 TTATTTAA
1 TTATTTAA
52671806 TTATTTAA
1 TTATTTAA
*
52671814 TTTATTGAA
1 -TTATTTAA
*
52671823 TCA-TTAA
1 TTATTTAA
*
52671830 TAATTT--
1 TTATTTAA
52671836 TTATTTAA
1 TTATTTAA
52671844 TTA
1 TTA
52671847 AATTTTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 23 0.57
9 7 0.17
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (8 bp):
TTATTTAA
Found at i:52671807 original size:25 final size:25
Alignment explanation
Indices: 52671779--52671855 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
52671769 TTTTCTCCTA
*
52671779 AATTTTTAATTTTATTTAATTATTT
1 AATTTTTAATTTTATTAAATTATTT
* *
52671804 AATTATTTAA-TTTATTGAATCATTAAT
1 AATT-TTTAATTTTATTAAATTATT--T
* *
52671831 AATTTTT-ATTTAATTAAATTTTTT
1 AATTTTTAATTTTATTAAATTATTT
52671855 A
1 A
52671856 GAAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 18 0.43
27 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
AATTTTTAATTTTATTAAATTATTT
Found at i:52677859 original size:37 final size:37
Alignment explanation
Indices: 52677818--52677899 Score: 137
Period size: 39 Copynumber: 2.2 Consensus size: 37
52677808 GATGTAAGAA
52677818 ATGCCAAAGAACTGGAAGTACATAAAAAAGAGACGAT
1 ATGCCAAAGAACTGGAAGTACATAAAAAAGAGACGAT
*
52677855 ATGCCCCAAAGAACTGGAAGTATATAAAAAAGAGACGAT
1 ATG--CCAAAGAACTGGAAGTACATAAAAAAGAGACGAT
52677894 ATGCCA
1 ATGCCA
52677900 CAAATCGAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
37 6 0.14
39 36 0.86
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.15
Consensus pattern (37 bp):
ATGCCAAAGAACTGGAAGTACATAAAAAAGAGACGAT
Found at i:52681665 original size:27 final size:27
Alignment explanation
Indices: 52681634--52681691 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
52681624 ACTAAGGTCT
52681634 GTGGTTAGTGTAGGGGAGGTAACGAAA
1 GTGGTTAGTGTAGGGGAGGTAACGAAA
*
52681661 GTGG-TAGTGTAGGGGAGTTAACGAAA
1 GTGGTTAGTGTAGGGGAGGTAACGAAA
52681687 GTGGT
1 GTGGT
52681692 CATGGTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.28, C:0.03, G:0.45, T:0.24
Consensus pattern (27 bp):
GTGGTTAGTGTAGGGGAGGTAACGAAA
Found at i:52688136 original size:56 final size:56
Alignment explanation
Indices: 52688047--52688214 Score: 237
Period size: 56 Copynumber: 3.0 Consensus size: 56
52688037 TCTTACATGT
* * * * * * *
52688047 AATCACATATCGATGCCAATGCACTAGATGTGGTCTTACTCACACACATATATCGG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGA
*
52688103 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATTTATCGA
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGA
* * *
52688159 AATCACATATCGATGCCAACATATTAAACGTGGTCTTACTTGTACACATATATCGA
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGA
52688215 TACCATGGTC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 100 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGA
Found at i:52689121 original size:21 final size:21
Alignment explanation
Indices: 52689096--52689138 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52689086 ATCATTTTAC
* * *
52689096 ATATATAACCTTTATGAAATA
1 ATATAAAACCATTATAAAATA
52689117 ATATAAAACCATTATAAAATA
1 ATATAAAACCATTATAAAATA
52689138 A
1 A
52689139 GGTCACAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAAAACCATTATAAAATA
Found at i:52696653 original size:34 final size:34
Alignment explanation
Indices: 52696610--52696677 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
52696600 CGATGTGGAA
*
52696610 GTGGGAAAGAGGAACTATGGACTTTGTGAGTGGG
1 GTGGGAAAGAGAAACTATGGACTTTGTGAGTGGG
52696644 GTGGGAAAGAGAAACTATGGACTTTGTGAGTGGG
1 GTGGGAAAGAGAAACTATGGACTTTGTGAGTGGG
52696678 CTACCCCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.43, T:0.24
Consensus pattern (34 bp):
GTGGGAAAGAGAAACTATGGACTTTGTGAGTGGG
Found at i:52705071 original size:16 final size:17
Alignment explanation
Indices: 52705039--52705071 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52705029 AAATAAGAAG
52705039 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
52705057 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
52705072 CTTCATTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:52706136 original size:25 final size:25
Alignment explanation
Indices: 52706108--52706156 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
52706098 GTTGCTTAAG
*
52706108 GACTATGATTTCACGATAAAGTATT
1 GACTATGATTGCACGATAAAGTATT
*
52706133 GACTATGATTGCATGATAAAGTAT
1 GACTATGATTGCACGATAAAGTAT
52706157 CATCCTAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (25 bp):
GACTATGATTGCACGATAAAGTATT
Found at i:52708151 original size:27 final size:28
Alignment explanation
Indices: 52708121--52708191 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
52708111 TGCACTACAA
*
52708121 AGGTATTTCGATAATTTTACAA-ACCGG
1 AGGTATTTCGATAATTTTACAAGACAGG
**
52708148 AGGTATTTC-AGTAATTTTACAAGTTAGG
1 AGGTATTTCGA-TAATTTTACAAGACAGG
52708176 A-GTATTTCGATAATTT
1 AGGTATTTCGATAATTT
52708192 CAAAAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.03
27 33 0.87
28 4 0.11
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (28 bp):
AGGTATTTCGATAATTTTACAAGACAGG
Found at i:52708181 original size:54 final size:54
Alignment explanation
Indices: 52708123--52708232 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
52708113 CACTACAAAG
* * *
52708123 GTATTTCGATAATTTTACAAACCGGA-GGTATTTCAGTAATTTTACAAGTTAGGA
1 GTATTTCGATAATTTCA-AAAACGGACGGTATTTCAGTAATTTTACAAATTAGGA
** * *
52708177 GTATTTCGATAATTTCAAAAATTGACGGTATTTTAGTAATTTTACAAATTGGGA
1 GTATTTCGATAATTTCAAAAACGGACGGTATTTCAGTAATTTTACAAATTAGGA
52708231 GT
1 GT
52708233 CTTAACGACC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.10
54 43 0.90
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (54 bp):
GTATTTCGATAATTTCAAAAACGGACGGTATTTCAGTAATTTTACAAATTAGGA
Found at i:52708589 original size:17 final size:18
Alignment explanation
Indices: 52708567--52708607 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
52708557 TACCCAAGTG
*
52708567 AGCCCATA-GGCCCATTT
1 AGCCCATACGACCCATTT
52708584 AGCCCATACGACCCATTT
1 AGCCCATACGACCCATTT
52708602 AGCCCA
1 AGCCCA
52708608 GAACTATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.20
Consensus pattern (18 bp):
AGCCCATACGACCCATTT
Found at i:52713475 original size:9 final size:9
Alignment explanation
Indices: 52713461--52713489 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
52713451 AATCAAATCG
52713461 GTTGCAATT
1 GTTGCAATT
52713470 GTTGCAATT
1 GTTGCAATT
52713479 GTTGCAATT
1 GTTGCAATT
52713488 GT
1 GT
52713490 GCTTTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (9 bp):
GTTGCAATT
Found at i:52719888 original size:50 final size:50
Alignment explanation
Indices: 52719813--52720047 Score: 258
Period size: 50 Copynumber: 4.7 Consensus size: 50
52719803 CTCTATTACG
*
52719813 CATAGTAGGCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACA
* ***
52719863 CATAGTAGCCTGCACTTAGTACTACACATGTGACTTAATC-ATCTAAAACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCT-ATCAATCTGGTACA
* * * ** * * *
52719913 CATAATAGCCTACACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCTGGTACA
* **
52719964 CATAGTAGCCTGCACTTAGTACTATACATGCAACCTATCAATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACA
** *
52720014 TGTAGTAGCCTGCACTTAGTACTACACACGTGAC
1 CATAGTAGCCTGCACTTAGTACTACACATGTGAC
52720048 TTACAACGGA
Statistics
Matches: 147, Mismatches: 33, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
49 3 0.02
50 108 0.73
51 35 0.24
52 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACA
Found at i:52720023 original size:101 final size:101
Alignment explanation
Indices: 52719857--52720046 Score: 256
Period size: 101 Copynumber: 1.9 Consensus size: 101
52719847 CTATCAATCT
** *
52719857 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACTTAATCATCTAAAACACATAATAGC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTAATCATCTAAAACACATAATAGC
52719922 CTACACTTAGTACTACACACGTGATCGAAGTTAACG
66 CTACACTTAGTACTACACACGTGATCGAAGTTAACG
* * *** ** *
52719958 GGTACGCATAGTAGCCTGCACTTAGTACTATACATGCAACCT-ATCAATCTGGTACATGTAGTAG
1 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTAATC-ATCTAAAACACATAATAG
*
52720022 CCTGCACTTAGTACTACACACGTGA
65 CCTACACTTAGTACTACACACGTGA
52720047 CTTACAACGG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 3 0.04
101 73 0.96
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (101 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCTAATCATCTAAAACACATAATAGC
CTACACTTAGTACTACACACGTGATCGAAGTTAACG
Found at i:52720424 original size:19 final size:20
Alignment explanation
Indices: 52720396--52720442 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
52720386 AAGAACATGT
52720396 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
52720417 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
52720436 TATATAT
1 TATATAT
52720443 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:52720705 original size:30 final size:30
Alignment explanation
Indices: 52720648--52720706 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
52720638 CAAAAATCAT
* * *
52720648 ACTTTTACAAATTTTCATTTTGACCCCTAA
1 ACTTTCACAAATTTGCACTTTGACCCCTAA
* *
52720678 ACTTTCACATATTTGCACTTTGGCCCCTA
1 ACTTTCACAAATTTGCACTTTGACCCCTA
52720707 GGCTCGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (30 bp):
ACTTTCACAAATTTGCACTTTGACCCCTAA
Found at i:52722125 original size:34 final size:34
Alignment explanation
Indices: 52722087--52722176 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
52722077 GTGGATACTG
*
52722087 TACTGAAATGGGCTAAGGCCCACATTGATATTGT
1 TACTGAAATGGGCTAAGGCCCACATTGATATTGC
* * * *
52722121 TACTGTATTGAGCTAAGGCCCATATTGATATTGC
1 TACTGAAATGGGCTAAGGCCCACATTGATATTGC
* * *
52722155 GACTGATATGGGCTTAGGCCCA
1 TACTGAAATGGGCTAAGGCCCA
52722177 GACTGTTCAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (34 bp):
TACTGAAATGGGCTAAGGCCCACATTGATATTGC
Found at i:52724182 original size:15 final size:15
Alignment explanation
Indices: 52724162--52724207 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
52724152 TTATTATTCT
52724162 TTTATATATACATTA
1 TTTATATATACATTA
52724177 TTTATAT-T--ATTA
1 TTTATATATACATTA
52724189 TTTTATATATACATTA
1 -TTTATATATACATTA
52724205 TTT
1 TTT
52724208 CAAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 2 0.07
15 10 0.37
16 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATATATACATTA
Found at i:52724193 original size:28 final size:28
Alignment explanation
Indices: 52724153--52724207 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
52724143 TTTCTTATAT
*
52724153 TATTATTCTTTTATATATACATTATTTA
1 TATTATTATTTTATATATACATTATTTA
52724181 TATTATTATTTTATATATACATTATTT
1 TATTATTATTTTATATATACATTATTT
52724208 CAAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTATTATTTTATATATACATTATTTA
Found at i:52724215 original size:28 final size:27
Alignment explanation
Indices: 52724156--52724220 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
52724146 CTTATATTAT
*
52724156 TATTCTTTTATATATACATTATTTATAT
1 TATT-TTTTATATATACATTATTTATAA
52724184 TATTATTTTATATATACATTATTTCA-AA
1 TATT-TTTTATATATACATTATTT-ATAA
52724212 TATTTTTTA
1 TATTTTTTA
52724221 AAAATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 5 0.15
28 28 0.82
29 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTTTTTATATATACATTATTTATAA
Found at i:52725082 original size:21 final size:20
Alignment explanation
Indices: 52725048--52725086 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
52725038 AAAATTGTAT
**
52725048 ATCTATCATCAAACATTCATA
1 ATCTATCAAAAAAC-TTCATA
52725069 ATCTATCAAAAAACTTCA
1 ATCTATCAAAAAACTTCA
52725087 AAACTCATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCTATCAAAAAACTTCATA
Found at i:52729072 original size:27 final size:27
Alignment explanation
Indices: 52729032--52729172 Score: 153
Period size: 27 Copynumber: 5.2 Consensus size: 27
52729022 AGGAAGCGTC
*
52729032 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
52729059 CTGGTGGCTCTGCCA-AATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* ** *
52729086 CTGGTGGCTATGCCACGGTTATCAGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* * *
52729113 ATGGTGGCTCTGCCAC-ATATGTCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
52729140 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
52729167 CTGGTG
1 CTGGTG
52729173 ACTTCGTCAC
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
26 9 0.10
27 82 0.88
28 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:52729172 original size:54 final size:53
Alignment explanation
Indices: 52729032--52729172 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 53
52729022 AGGAAGCGTC
52729032 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCAAATATATCTGTT
1 CTGGTGGCTATGCCACAA-TATCTGATCTGGTGGCTCTGCCAAATATATCTGTT
** * * * *
52729086 CTGGTGGCTATGCCACGGTTATCAGATATGGTGGCTCTGCCACATATGTCTGTT
1 CTGGTGGCTATGCCAC-AATATCTGATCTGGTGGCTCTGCCAAATATATCTGTT
*
52729140 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACAATATCTG-ATCTGGTG
52729173 ACTTCGTCAC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
53 5 0.07
54 69 0.93
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.34
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATATCTGATCTGGTGGCTCTGCCAAATATATCTGTT
Found at i:52746704 original size:43 final size:43
Alignment explanation
Indices: 52746664--52746745 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
52746654 AGTATCGAAG
*
52746664 CCTCTGTCCCAGACAAGGTCTTACACGAA-ATCTCAAATCGAGA
1 CCTCTGTCCCAGACAAGGTCTTACAC-AATATCACAAATCGAGA
* * *
52746707 CCTGTGTCCCAGACACGGTCTTGCACAATATCACAAATC
1 CCTCTGTCCCAGACAAGGTCTTACACAATATCACAAATC
52746746 AATGTCAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (43 bp):
CCTCTGTCCCAGACAAGGTCTTACACAATATCACAAATCGAGA
Found at i:52752786 original size:18 final size:18
Alignment explanation
Indices: 52752763--52752806 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
52752753 AATAGTTTCA
52752763 TTAAAAATATGAATT-ATT
1 TTAAAAATAT-AATTAATT
*
52752781 TT-AAAATATATTTAATT
1 TTAAAAATATAATTAATT
52752798 TTAAAAATA
1 TTAAAAATA
52752807 GGAAGAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTAAAAATATAATTAATT
Found at i:52757072 original size:55 final size:55
Alignment explanation
Indices: 52756946--52757074 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
52756936 ATTTCCTTAG
* *
52756946 CCCGTGTGCAACACTGACTTCAACACACGGCCATGGCACACGCCCGTGTGACCTG
1 CCCGTGTACAACACTGACTTCAACACACGGCCATGGCACACGCCCGTGTGACCTA
* *** * * * *
52757001 CCCATGTACGGTACTGACTTTAAGACACGGCCATGGTACACGCCCGTGTGGCCTA
1 CCCGTGTACAACACTGACTTCAACACACGGCCATGGCACACGCCCGTGTGACCTA
52757056 CCCGTGTACAACACTGACT
1 CCCGTGTACAACACTGACT
52757075 AAAAAGTTTA
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.19
Consensus pattern (55 bp):
CCCGTGTACAACACTGACTTCAACACACGGCCATGGCACACGCCCGTGTGACCTA
Found at i:52758064 original size:47 final size:46
Alignment explanation
Indices: 52757834--52758153 Score: 210
Period size: 47 Copynumber: 6.8 Consensus size: 46
52757824 GGGATAAGTT
*
52757834 GCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTA-GCATCATCGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACTCATCATC-AG
* * * * *
52757883 GTCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCTTGTAT-AT-ACG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCAC-T-CATCATCA-G
* * * * * *
52757932 TGCTGATGCATGTCCCAGGCATGTCTTACACTAGCA--CAACTTTTA-
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATC-ATCAG
* *
52757977 -CTCGATGCGTGTCCCAGACATGTCTTCCACTGGCTA-TCATCATCGAG
1 GC-CGATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATCATC-AG
* * *
52758024 GCCGGTGCATGTCCGAGACATGTCTTACACTGGCACTCATC-TCTAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCATC-AG
* * * *
52758070 GCCGATTCCATGTCCCAGACATGGTCTTATACTGGCACACATAAT-ATG
1 GCCGA-TGCATGTCCCAGACAT-GTCTTACACTGGCACTCATCATCA-G
*
52758118 GCCGATGCATGTCCCAGAAATGTCTTACACTGGCAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCAC
52758154 ACAAGAAATC
Statistics
Matches: 213, Mismatches: 39, Indels: 41
0.73 0.13 0.14
Matches are distributed among these distances:
43 1 0.00
44 28 0.13
45 2 0.01
46 27 0.13
47 63 0.30
48 36 0.17
49 47 0.22
50 7 0.03
51 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCATCAG
Found at i:52758127 original size:94 final size:92
Alignment explanation
Indices: 52757834--52758154 Score: 274
Period size: 94 Copynumber: 3.4 Consensus size: 92
52757824 GGGATAAGTT
* * *
52757834 GCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTAGCATCATCGAGGTCGATGCCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-A-CATCATCTACGTCGATTCCATGTCCC
* * ***
52757899 AGACATGGTCTTATACTAGCTCTTGTATATACG
62 AGACATGGTCTTATACTGGCACACATA-ATA-G
* * * * * * * *
52757932 TGCTGATGCATGTCCCAGGCATGTCTTACACTAGCACAACTTTTAC-TCGA-TGCGTGTCCCAGA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCATCTACGTCGATTCCATGTCCCAGA
** **
52757995 CAT-GTCTTCCACTGGCTATCATCAT-CGAG
65 CATGGTCTTATACTGGC-A-CA-CATAATAG
* * *
52758024 GCCGGTGCATGTCCGAGACATGTCTTACACTGGCAC-TCATCTCTACGCCGATTCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCA--TCTACGTCGATTCCATGTCCCAG
52758088 ACATGGTCTTATACTGGCACACATAATATG
64 ACATGGTCTTATACTGGCACACATAATA-G
*
52758118 GCCGATGCATGTCCCAGAAATGTCTTACACTGGCACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACA
52758155 CAAGAAATCC
Statistics
Matches: 173, Mismatches: 38, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
90 1 0.01
91 31 0.18
92 18 0.10
93 20 0.12
94 54 0.31
95 17 0.10
96 1 0.01
97 12 0.07
98 13 0.08
99 6 0.03
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCACATCATCTACGTCGATTCCATGTCCCAGAC
ATGGTCTTATACTGGCACACATAATAG
Found at i:52766894 original size:39 final size:40
Alignment explanation
Indices: 52766690--52766912 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
52766680 TTGAATGCTG
* * * * * *
52766690 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
52766730 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
52766770 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
52766810 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
52766850 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
52766889 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52766913 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:52766932 original size:79 final size:80
Alignment explanation
Indices: 52766765--52766947 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
52766755 GTGCGAGATA
* * *
52766765 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
52766830 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
52766845 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
52766909 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
52766924 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
52766948 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:52774842 original size:39 final size:40
Alignment explanation
Indices: 52774638--52774860 Score: 254
Period size: 40 Copynumber: 5.6 Consensus size: 40
52774628 TTGAATGCTG
* * * * * *
52774638 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
52774678 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
52774718 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
52774758 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
52774798 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
52774837 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52774861 TGAACGAGGA
Statistics
Matches: 163, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 36 0.22
40 119 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:52774880 original size:79 final size:80
Alignment explanation
Indices: 52774712--52774895 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
52774702 TGTGCGAGAT
* * *
52774712 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
** *
52774777 GCATTCGTGCGAGTT
66 GCATTCGAACGAGTG
* * * *
52774792 ATTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
*
52774856 GCATTTGAACGAG-G
66 GCATTCGAACGAGTG
* *
52774870 AGCTATATCC-GGTTAAATCCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
52774896 TACGTGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 15 0.17
79 45 0.51
80 28 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAG
GCATTCGAACGAGTG
Found at i:52777383 original size:40 final size:40
Alignment explanation
Indices: 52777338--52777443 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
52777328 ATGACATATT
52777338 AGCTAAATATGGCACTTAGTGTGCGGTTTG-GTATAACTTC
1 AGCTAAATATGGCACTTAGTGTGCGGTTTGAG-ATAACTTC
* * * **
52777378 GGCTAAATTTGGCACTTAGTGTGCGATTTGAGATTGCTTC
1 AGCTAAATATGGCACTTAGTGTGCGGTTTGAGATAACTTC
** *
52777418 AGCTACGTATAGCACTTAGTGTGCGG
1 AGCTAAATATGGCACTTAGTGTGCGG
52777444 GACATCAAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
AGCTAAATATGGCACTTAGTGTGCGGTTTGAGATAACTTC
Found at i:52794177 original size:11 final size:10
Alignment explanation
Indices: 52794145--52794201 Score: 66
Period size: 9 Copynumber: 5.8 Consensus size: 10
52794135 TACGTGGGAT
52794145 ATGATAT-AC
1 ATGATATGAC
52794154 ATGAT-TGAC
1 ATGATATGAC
52794163 ATGATATGCAC
1 ATGATATG-AC
*
52794174 ATGATATG-T
1 ATGATATGAC
52794183 ATGATATGCAC
1 ATGATATG-AC
52794194 ATGATATG
1 ATGATATG
52794202 TATGAAATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 1 0.02
9 20 0.49
10 2 0.05
11 18 0.44
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (10 bp):
ATGATATGAC
Found at i:52794177 original size:20 final size:20
Alignment explanation
Indices: 52794152--52794218 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
52794142 GATATGATAT
52794152 ACATGAT-TGACATGATATGC
1 ACATGATATG-CATGATATGC
*
52794172 ACATGATATGTATGATATGC
1 ACATGATATGCATGATATGC
* *
52794192 ACATGATATGTATGAAATGC
1 ACATGATATGCATGATATGC
*
52794212 ATATGAT
1 ACATGAT
52794219 GTAATCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGCATGATATGC
Found at i:52794338 original size:25 final size:25
Alignment explanation
Indices: 52794268--52794375 Score: 150
Period size: 24 Copynumber: 4.4 Consensus size: 25
52794258 GATGAAGTGC
* *
52794268 AAAAGGGCTATGCCCTAGTTTATTG
1 AAAAGGGCTTTGCCCCAGTTTATTG
52794293 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTATTG
*
52794319 AAAAGGGCTTTGCCCCAGTTTA-TC
1 AAAAGGGCTTTGCCCCAGTTTATTG
52794343 AAAAGGGCTTTGCCCCAG-TTATT-
1 AAAAGGGCTTTGCCCCAGTTTATTG
52794366 AAAAGAGGCT
1 AAAAG-GGCT
52794376 AGGCCTCCAG
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
23 8 0.10
24 24 0.31
25 21 0.27
26 24 0.31
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATTG
Found at i:52794624 original size:31 final size:31
Alignment explanation
Indices: 52794586--52794676 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 31
52794576 CCGTTAAACG
52794586 AAAGGCTTCGGCCCAGTAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTAATATGAAACATGA
*
52794617 AAAGGCTTCGGCCCAGTGTTATGAATTATGAAATATGA
1 AAAGGCTTCGGCCCA--G---T-AA-TATGAAACATGA
52794655 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTAATATG
52794677 TTGAGATTGG
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
30 4 0.08
31 16 0.31
33 2 0.04
36 2 0.04
37 2 0.04
38 26 0.50
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAACATGA
Found at i:52801487 original size:26 final size:28
Alignment explanation
Indices: 52801453--52801508 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
52801443 AATAACCAAT
52801453 TTCTGGTT-ACAACAAAAATCGAATAAA
1 TTCTGGTTAACAACAAAAATCGAATAAA
52801480 TTCT-GTTAACAACAAAAATCGAATAAA
1 TTCTGGTTAACAACAAAAATCGAATAAA
52801507 TT
1 TT
52801509 TTATTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (28 bp):
TTCTGGTTAACAACAAAAATCGAATAAA
Found at i:52801629 original size:78 final size:78
Alignment explanation
Indices: 52801542--52801794 Score: 289
Period size: 77 Copynumber: 3.2 Consensus size: 78
52801532 CCTGGAACTG
* * * ** *
52801542 AATTATTCAATTGATTTCTATTTTTTAAA-AAAGATTGAACAAATCCTATTAAACGGCAGGAATA
1 AATTGTTCAATTGATTTCTA-TTTTAAAACAAAAATCAAACAAATCCTATTAAATGGCAGGAATA
52801606 AAATCCTGAAACAA
65 AAATCCTGAAACAA
* *
52801620 AATTGTTCAATTGATTTTCT-GTTTAAAACAAAAATCAAACAAATCCTGTTAAATGGCAGGAATA
1 AATTGTTCAATTGA-TTTCTATTTTAAAACAAAAATCAAACAAATCCTATTAAATGGCAGGAATA
* *
52801684 AAATCCTAAAACAT
65 AAATCCTGAAACAA
* * * *
52801698 GATTGTTCAATT-ATTTTCTA-TTTGAAACAAAAATCAAACAAATCGTATTAAATGACAGGAATA
1 AATTGTTCAATTGA-TTTCTATTTTAAAACAAAAATCAAACAAATCCTATTAAATGGCAGGAATA
* *
52801761 AAATCTTGAAACAG
65 AAATCCTGAAACAA
*
52801775 AATTGTTTAATTGAATTTCT
1 AATTGTTCAATTG-ATTTCT
52801795 GTTTGAAAGA
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
77 73 0.49
78 71 0.47
79 6 0.04
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (78 bp):
AATTGTTCAATTGATTTCTATTTTAAAACAAAAATCAAACAAATCCTATTAAATGGCAGGAATAA
AATCCTGAAACAA
Found at i:52801750 original size:77 final size:77
Alignment explanation
Indices: 52801579--52801807 Score: 316
Period size: 77 Copynumber: 2.9 Consensus size: 77
52801569 AAAAAGATTG
* *
52801579 AACAAATCCTATTAAACGGCAGGAATAAAATCCTGAAACAAAATTGTTCAATTGATTTTCTGTTT
1 AACAAATCCTATTAAATGGCAGGAATAAAATCCTGAAAC-AGATTGTTCAATTGATTTTCTGTTT
*
52801644 AAAACAAAAATCA
65 GAAACAAAAATCA
* * *
52801657 AACAAATCCTGTTAAATGGCAGGAATAAAATCCTAAAACATGATTGTTCAATT-ATTTTCTATTT
1 AACAAATCCTATTAAATGGCAGGAATAAAATCCTGAAACA-GATTGTTCAATTGATTTTCTGTTT
52801721 GAAACAAAAATCA
65 GAAACAAAAATCA
* * * * *
52801734 AACAAATCGTATTAAATGACAGGAATAAAATCTTGAAACAGAATTGTTTAATTGAATTTCTGTTT
1 AACAAATCCTATTAAATGGCAGGAATAAAATCCTGAAACAG-ATTGTTCAATTGATTTTCTGTTT
*
52801799 GAAAGAAAA
65 GAAACAAAA
52801808 TAAAATTTAT
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
76 1 0.01
77 68 0.51
78 64 0.48
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (77 bp):
AACAAATCCTATTAAATGGCAGGAATAAAATCCTGAAACAGATTGTTCAATTGATTTTCTGTTTG
AAACAAAAATCA
Found at i:52801808 original size:77 final size:78
Alignment explanation
Indices: 52801529--52801807 Score: 330
Period size: 78 Copynumber: 3.6 Consensus size: 78
52801519 ACAAGAAAAG
* * * * * * * **
52801529 AATCCTGGAACTGAATTATTCAATTGATTTCTATTTTTTAAA-AAAGATTGAACAAATCCTATTA
1 AATCCTGAAACAGAATTGTTCAATTGATTT-TCTGTTTGAAACAAAAATCAAACAAATCCTATTA
*
52801593 AACGGCAGGAATAA
65 AATGGCAGGAATAA
* * *
52801607 AATCCTGAAACAAAATTGTTCAATTGATTTTCTGTTTAAAACAAAAATCAAACAAATCCTGTTAA
1 AATCCTGAAACAGAATTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAATCCTATTAA
52801672 ATGGCAGGAATAA
66 ATGGCAGGAATAA
* * *
52801685 AATCCTAAAACATG-ATTGTTCAATT-ATTTTCTATTTGAAACAAAAATCAAACAAATCGTATTA
1 AATCCTGAAACA-GAATTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAATCCTATTA
*
52801748 AATGACAGGAATAA
65 AATGGCAGGAATAA
* * * *
52801762 AATCTTGAAACAGAATTGTTTAATTGAATTTCTGTTTGAAAGAAAA
1 AATCCTGAAACAGAATTGTTCAATTGATTTTCTGTTTGAAACAAAA
52801808 TAAAATTTAT
Statistics
Matches: 172, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
76 1 0.01
77 75 0.44
78 96 0.56
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (78 bp):
AATCCTGAAACAGAATTGTTCAATTGATTTTCTGTTTGAAACAAAAATCAAACAAATCCTATTAA
ATGGCAGGAATAA
Found at i:52804301 original size:49 final size:49
Alignment explanation
Indices: 52804229--52804416 Score: 259
Period size: 49 Copynumber: 3.8 Consensus size: 49
52804219 TGAGGTCACG
*
52804229 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * *
52804278 TGTGTAGTACTAAGTACAGGCTACTATGCGTACCAGAAAACTGTGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCGCA
*
52804329 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
52804378 TGTGTAGTACTAAGTTCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
52804417 GCTTCGGCTA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 76 0.64
50 2 0.02
51 41 0.34
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:52804402 original size:100 final size:100
Alignment explanation
Indices: 52804224--52804414 Score: 346
Period size: 100 Copynumber: 1.9 Consensus size: 100
52804214 TATTTTGAGG
* *
52804224 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
52804289 AAGTACAGGCTACTATGCGTACCAGAAAACTGTGA
66 AAGTACAGGCTACTATGCGTACCAGAAAACTGTGA
*
52804324 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
*
52804389 AAGTTCAGGCTACTATGCGTACCAGA
66 AAGTACAGGCTACTATGCGTACCAGA
52804415 TAGCTTCGGC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTACAGGCTACTATGCGTACCAGAAAACTGTGA
Found at i:52814609 original size:41 final size:43
Alignment explanation
Indices: 52814513--52814633 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 43
52814503 TGTCAACGTG
* *
52814513 CCAGACATGGTCTTGCATGTAATCACATATCGATGCCACTATC
1 CCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTATC
* * *
52814556 CCAGACAGGGTCTTACATG-AATCAAATAT-GATGCTGA-TGTC
1 CCAGACATGGTCTTACATGTAATCAAATATCGATGC-CACTATC
* * *
52814597 CCATACATGGTCTTACACGTAACCATATATATCGATG
1 CCAGACATGGTCTTACATGTAATCA-A-ATATCGATG
52814634 ACAATGTCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 24 0.38
42 14 0.22
43 18 0.28
44 4 0.06
45 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
CCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTATC
Found at i:52819425 original size:28 final size:30
Alignment explanation
Indices: 52819388--52819443 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
52819378 TACTTATAAA
* *
52819388 TAACAACTAACA-CATAAA-ATTCATCATT
1 TAACAACTAAAATCACAAATATTCATCATT
*
52819416 TAACATCTAAAATCACAAATATTCATCA
1 TAACAACTAAAATCACAAATATTCATCA
52819444 ATGGAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 5 0.22
30 8 0.35
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (30 bp):
TAACAACTAAAATCACAAATATTCATCATT
Found at i:52824100 original size:27 final size:28
Alignment explanation
Indices: 52824061--52824117 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
52824051 ATGATCAAAT
52824061 TTTAATATAAAA-TTAATTATTTTAATAA
1 TTTAATATAAAATTTAATTATTTT-ATAA
52824089 TTTAAT-TAAAATTTAATTATTTTATAA
1 TTTAATATAAAATTTAATTATTTTATAA
52824116 TT
1 TT
52824118 ATTATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAATATAAAATTTAATTATTTTATAA
Found at i:52829851 original size:46 final size:46
Alignment explanation
Indices: 52829726--52830183 Score: 445
Period size: 46 Copynumber: 9.9 Consensus size: 46
52829716 NNNNNNNNNN
* *
52829726 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-T
* * *
52829777 T-ACAT--TTCA-TGAACTCGGACTCAACTCAACGAGTTCGAACAT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
* ** *
52829819 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
* *
52829865 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-T
* * *
52829916 T-ACAT--TTCA-TGAACTCGGACTCAACTCAACGAGTTCGAACAT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
* ** *
52829958 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
* *
52830004 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-T
* * *
52830055 T-ACAT--TTCA-TGAACTCGGACTCAACTCAACGAGTTCGAACAT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
* ** *
52830097 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGT
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
*
52830143 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCG
1 TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
52830184 GATGCCTAGT
Statistics
Matches: 337, Mismatches: 48, Indels: 49
0.78 0.11 0.11
Matches are distributed among these distances:
42 6 0.02
43 12 0.04
44 3 0.01
45 6 0.02
46 208 0.62
47 80 0.24
48 6 0.02
49 2 0.01
50 9 0.03
51 5 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACAT
Found at i:52829929 original size:93 final size:94
Alignment explanation
Indices: 52829786--52830231 Score: 444
Period size: 93 Copynumber: 4.8 Consensus size: 94
52829776 TTACATTTCA
* * *
52829786 TGAACTCGGACTCAACTCAACGAGTTC-GA-ACA-TTCGCATCCATAAGTGAACTCGGACTCAAC
1 TGAACTCAGACTCAACTCAACGAGTTCGGAGCCAGTTCACAT-CATAAGTGAACTCGGACTCAAC
*
52829848 TCAACGAGCTCGGGCGTTCGCATCCATAAG
65 TCAACGAGTTCGGGCGTTCGCATCCATAAG
* *
52829878 TGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-TTCA-TGAACTCGGACTCAA
1 TGAACTCAGACTCAACTCAACGAGTTCGGA-GCC-AGTTCACATCATAAGTGAACTCGGACTCAA
** *
52829940 CTCAACGAGTTCGAACATTCGCATCCATAAG
64 CTCAACGAGTTCGGGCGTTCGCATCCATAAG
* * * *
52829971 TGAACTCGGACTCAACTCAACGAGCTCGG-G-C-GTTCGCATCCATAAGTGAACTCAGACTCAAC
1 TGAACTCAGACTCAACTCAACGAGTTCGGAGCCAGTTCACAT-CATAAGTGAACTCGGACTCAAC
* * *
52830033 TCAACGAGTTCGGATGCCTAGTT-ACAT--TTCA-
65 TCAACGAGTTCGG--G-C--GTTCGCATCCATAAG
* * *
52830064 TGAACTCGGACTCAACTCAACGAGTTC-GA-ACA-TTCGCATCCATAAGTGAACTCGGACTCAAC
1 TGAACTCAGACTCAACTCAACGAGTTCGGAGCCAGTTCACAT-CATAAGTGAACTCGGACTCAAC
*
52830126 TCAACGAGCTCGGGCGTTCGCATCCATAAG
65 TCAACGAGTTCGGGCGTTCGCATCCATAAG
* * *
52830156 TGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-TTCA-CGAACTCGGACTCAA
1 TGAACTCAGACTCAACTCAACGAGTTCGGA-GCC-AGTTCACATCATAAGTGAACTCGGACTCAA
52830218 CTCAACGAGTTCGG
64 CTCAACGAGTTCGG
52830232 ATGCTCAACC
Statistics
Matches: 294, Mismatches: 34, Indels: 51
0.78 0.09 0.13
Matches are distributed among these distances:
88 6 0.02
89 6 0.02
90 2 0.01
91 6 0.02
92 80 0.27
93 168 0.57
94 6 0.02
95 3 0.01
96 11 0.04
97 6 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (94 bp):
TGAACTCAGACTCAACTCAACGAGTTCGGAGCCAGTTCACATCATAAGTGAACTCGGACTCAACT
CAACGAGTTCGGGCGTTCGCATCCATAAG
Found at i:52829976 original size:139 final size:139
Alignment explanation
Indices: 52829726--52830230 Score: 1001
Period size: 139 Copynumber: 3.6 Consensus size: 139
52829716 NNNNNNNNNN
52829726 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
1 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
52829791 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
66 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
52829856 CTCGGGCGT
131 CTCGGGCGT
52829865 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
1 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
52829930 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
66 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
52829995 CTCGGGCGT
131 CTCGGGCGT
52830004 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
1 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
52830069 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
66 TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
52830134 CTCGGGCGT
131 CTCGGGCGT
*
52830143 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCACGAAC
1 TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
52830208 TCGGACTCAACTCAACGAGTTCG
66 TCGGACTCAACTCAACGAGTTCG
52830231 GATGCTCAAC
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 365 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (139 bp):
TCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCATGAAC
TCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAG
CTCGGGCGT
Found at i:52830251 original size:93 final size:94
Alignment explanation
Indices: 52829733--52830251 Score: 359
Period size: 93 Copynumber: 5.6 Consensus size: 94
52829723 NNNTCGCATC
* * * * *
52829733 CATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGC-CTAGTTACAT-TTCA-TGAACTCGG
1 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---CCATCCTAAGTGAACTCAG
* *
52829795 ACTCAACTCAACGAGTTC-GA-ACA-TTCGCAT
62 ACTCAACTCAACGAGTTCGGAGCCAGTTCACAT
* ** * *
52829825 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGTGAACTCAGAC
1 -CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-TAAGTGAACTCAGAC
52829889 TCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
64 TCAACTCAACGAGTTCGGA-GCC-AGTTCACAT
* * * *** * *
52829921 -TTCA-TGAACTCGGACTCAACTCAACGAGTTCGAACATTC-GCATCCATAAGTGAACTCGGACT
1 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-TAAGTGAACTCAGACT
* *
52829983 CAACTCAACGAGCTCGG-G-C-GTTCGCAT
65 CAACTCAACGAGTTCGGAGCCAGTTCACAT
* * * * *
52830010 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGC-CTAGTTACAT-TTCA-TGAACTCG
1 -CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---CCATCCTAAGTGAACTCA
* *
52830072 GACTCAACTCAACGAGTTC-GA-ACA-TTCGCAT
61 GACTCAACTCAACGAGTTCGGAGCCAGTTCACAT
* ** * *
52830103 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGTGAACTCAGAC
1 -CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-TAAGTGAACTCAGAC
52830167 TCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
64 TCAACTCAACGAGTTCGGA-GCC-AGTTCACAT
* * *
52830199 -TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT-AGTGA
1 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAAGTGA
52830252 CATGTCACTT
Statistics
Matches: 344, Mismatches: 50, Indels: 64
0.75 0.11 0.14
Matches are distributed among these distances:
88 3 0.01
89 9 0.03
90 1 0.00
91 8 0.02
92 81 0.24
93 211 0.61
94 9 0.03
95 7 0.02
96 11 0.03
97 4 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (94 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAAGTGAACTCAGACTC
AACTCAACGAGTTCGGAGCCAGTTCACAT
Found at i:52831721 original size:19 final size:19
Alignment explanation
Indices: 52831697--52831741 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52831687 TCATCTTCTC
52831697 TCTTTTCTTCTTTTT-CTTT
1 TCTTTTCTT-TTTTTCCTTT
52831716 TCTTTTCTTTTTTTCCTTT
1 TCTTTTCTTTTTTTCCTTT
*
52831735 TTTTTTC
1 TCTTTTC
52831742 ACGGGCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TCTTTTCTTTTTTTCCTTT
Found at i:52837900 original size:38 final size:37
Alignment explanation
Indices: 52837849--52838190 Score: 506
Period size: 37 Copynumber: 9.1 Consensus size: 37
52837839 TTAAGCTCGA
*
52837849 ATATAATACCAGCACTAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGA-TAAACCCGG
* *
52837887 ATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGA-TAAACCCGG
* * *
52837925 ATATAATGCCAGCACGAAGCCTGCGGGATAAAACCCAG
1 ATATAATACCAGCACTAAGCCTGCGGGAT-AAACCCGG
* *
52837963 ATATAATACCAGCA-TGAAGCTTGTGGGATAAACCCGG
1 ATATAATACCAGCACT-AAGCCTGCGGGATAAACCCGG
* * *
52838000 ATATAATACCAGCACAAAGCCTACGGGATAAACCTGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
52838037 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
52838074 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGAT-AAACCCGG
* * *
52838112 ATATAATATCAGCACGAAGCCTGTGGGATAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
52838149 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
52838186 ATATA
1 ATATA
52838191 CATCAAATAT
Statistics
Matches: 276, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
37 149 0.54
38 127 0.46
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (37 bp):
ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
Found at i:52838108 original size:112 final size:111
Alignment explanation
Indices: 52837849--52838190 Score: 524
Period size: 112 Copynumber: 3.0 Consensus size: 111
52837839 TTAAGCTCGA
*
52837849 ATATAATACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACAAAGCCTGCGGG
1 ATATAATACCAGCACTAAGCCTGCGGGA-TAAACCCGGATATAATACCAGCACAAAGCCTGCGGG
* * * *
52837914 ATTTAACCCGGATATAATGCCAGCACGAAGCCTGCGGGATAAAACCCAG
65 A-TAAACCCGGATATAATACCAGCACTAAGCCTGCGGGAT-AAACCCGG
* * *
52837963 ATATAATACCAGCA-TGAAGCTTGTGGGATAAACCCGGATATAATACCAGCACAAAGCCTACGGG
1 ATATAATACCAGCACT-AAGCCTGCGGGATAAACCCGGATATAATACCAGCACAAAGCCTGCGGG
*
52838027 ATAAACCTGGATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
65 ATAAACCCGGATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
* * *
52838074 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGGATATAATATCAGCACGAAGCCTGTGGG
1 ATATAATACCAGCACTAAGCCTGCGGGAT-AAACCCGGATATAATACCAGCACAAAGCCTGCGGG
52838139 ATAAACCCGGATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
65 ATAAACCCGGATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
52838186 ATATA
1 ATATA
52838191 CATCAAATAT
Statistics
Matches: 209, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
111 32 0.15
112 117 0.56
113 36 0.17
114 24 0.11
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (111 bp):
ATATAATACCAGCACTAAGCCTGCGGGATAAACCCGGATATAATACCAGCACAAAGCCTGCGGGA
TAAACCCGGATATAATACCAGCACTAAGCCTGCGGGATAAACCCGG
Found at i:52841509 original size:27 final size:27
Alignment explanation
Indices: 52841479--52841533 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
52841469 TATTATAAAA
52841479 TTAATTAAAACTAAA-TATTTTAATAAT
1 TTAATTAAAACTAAATTATTTT-ATAAT
* *
52841506 TTAATTACAATTAAATTATTTTATAAT
1 TTAATTAAAACTAAATTATTTTATAAT
52841533 T
1 T
52841534 ATTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (27 bp):
TTAATTAAAACTAAATTATTTTATAAT
Found at i:52847109 original size:32 final size:32
Alignment explanation
Indices: 52847065--52847158 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 32
52847055 TCAAGCCCAT
*
52847065 TGGGCCTAAGCCC-ATTCAGATAACAGTGATAC
1 TGGGCC-AAGCCCTATTCAGATAACAGTGAAAC
* * *
52847097 TGGGCCAGAGCCCTTTTCAGATTACA-TTAAAC
1 TGGGCCA-AGCCCTATTCAGATAACAGTGAAAC
*
52847129 TGGGCCTTAGCCCCTTATTCAGATAACAGT
1 TGGGCC-AAG-CCC-TATTCAGATAACAGT
52847159 ATGGCCTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.02
32 23 0.47
33 13 0.27
34 11 0.22
35 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (32 bp):
TGGGCCAAGCCCTATTCAGATAACAGTGAAAC
Found at i:52851724 original size:21 final size:21
Alignment explanation
Indices: 52851700--52851741 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
52851690 ATAACCAGGA
52851700 ACTCGTAATGACCATATCGAG
1 ACTCGTAATGACCATATCGAG
52851721 ACTCGTAATGACCATATCGAG
1 ACTCGTAATGACCATATCGAG
52851742 TCCTAAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
ACTCGTAATGACCATATCGAG
Found at i:52854814 original size:112 final size:112
Alignment explanation
Indices: 52854617--52854839 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 112
52854607 TTCATCAAAC
* *
52854617 GGTAAAAGCATCAGGTCCGCCAGAAAACAGGAACCTCGAATTACTAGGGGACATTTCTTACACAC
1 GGTAAAAGCATCAAGTCCCCCAGAAAACAGGAACCTCGAATTACTAGGGGACATTTCTTACACAC
52854682 CTTATCAAAAAGCACACAACGACCCAAGGGATTTGACACTCTAATAT
66 CTTATCAAAAAGCACACAACGACCCAAGGGATTTGACACTCTAATAT
* *
52854729 GGTAAAAGCATCAAGTCCCCCGGAAAATAGGAACCTCGAATTACTAGGGGACATTTCTTACACAC
1 GGTAAAAGCATCAAGTCCCCCAGAAAACAGGAACCTCGAATTACTAGGGGACATTTCTTACACAC
*
52854794 CTTATCAACAAGCACACAACGACCCAAGGGATTTGACACTCTAATA
66 CTTATCAAAAAGCACACAACGACCCAAGGGATTTGACACTCTAATA
52854840 ACGAACTCAG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (112 bp):
GGTAAAAGCATCAAGTCCCCCAGAAAACAGGAACCTCGAATTACTAGGGGACATTTCTTACACAC
CTTATCAAAAAGCACACAACGACCCAAGGGATTTGACACTCTAATAT
Found at i:52861340 original size:48 final size:48
Alignment explanation
Indices: 52861269--52861363 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
52861259 CCGTACCTCG
*
52861269 TTCTGAAAGAGGTTTTGGGTATATCCAAATCTCGAATTAGCAACTGAA
1 TTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGAA
* * *
52861317 TTCTGAAAGCGGTTTTGAGTATATCCGAATCTTGAATTAGCAACTGA
1 TTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGA
52861364 TTATAACCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (48 bp):
TTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGAA
Found at i:52863389 original size:58 final size:59
Alignment explanation
Indices: 52863273--52863389 Score: 182
Period size: 58 Copynumber: 2.0 Consensus size: 59
52863263 TTCCTAAAAC
* * * * *
52863273 TAGACTCATATATCCATCTACAAATTTTTTTCTAGAATTTTTGGTCGATCCAATTAGTA
1 TAGACTCATATATCCATCTACAAATGTTTTTCTAGAATATTTGGTCAAGCAAATTAGTA
52863332 TAGACTCATATATCCATCTACAAA-GTTTTTCTAGAATATTTGGTCAAGCAAATTAGTA
1 TAGACTCATATATCCATCTACAAATGTTTTTCTAGAATATTTGGTCAAGCAAATTAGTA
52863390 CAGTTTATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 29 0.55
59 24 0.45
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (59 bp):
TAGACTCATATATCCATCTACAAATGTTTTTCTAGAATATTTGGTCAAGCAAATTAGTA
Found at i:52864593 original size:40 final size:40
Alignment explanation
Indices: 52864523--52865140 Score: 989
Period size: 40 Copynumber: 15.5 Consensus size: 40
52864513 AAACCAAGTA
* * *
52864523 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTTGCACAAATG
*
52864562 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864602 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
* * *
52864642 CCTTCGGGACTTAGCCCAGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTTGCACAAATG
** * * * *
52864682 CCTTCGGGACTTAGCCCGG-T-TACCATC-CGAATATTAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTG--CA-CAAATG
52864722 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864762 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864802 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864842 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864882 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864922 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52864962 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52865002 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
52865042 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
* * *
52865082 CCTTCGGGACTTAGCCCAGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTTGCACAAATG
52865122 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
52865141 TTACCATCCG
Statistics
Matches: 544, Mismatches: 24, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 17 0.03
40 516 0.95
41 2 0.00
42 4 0.01
43 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
Found at i:52868270 original size:50 final size:50
Alignment explanation
Indices: 52868195--52868294 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
52868185 ACCGTACCTC
* * *
52868195 GTTCTGAAAGCGGTTTTGAGTATATCCGAATCTTGAATTAGCAACTGATT
1 GTTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGATT
*
52868245 GTTCTGAAAGAGGTTTTGGGTATATCCAAATCTCGAATTAGCAACTGATT
1 GTTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGATT
52868295 ATAACCCGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (50 bp):
GTTCTGAAAGAGGTTTTGAGTATATCCAAATCTCGAATTAGCAACTGATT
Found at i:52871591 original size:40 final size:40
Alignment explanation
Indices: 52871521--52871698 Score: 229
Period size: 40 Copynumber: 4.5 Consensus size: 40
52871511 AAACCAAGTA
* *
52871521 CCTTCGGGATTTAG-CCAGATATAGCT-ACTCGCTA-AAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGC-ACAAATG
*
52871560 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
52871600 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
52871640 CCTTGGGGACTTAGCCTGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
52871680 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
52871699 TTACCATCCG
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.12
40 109 0.88
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:52872288 original size:54 final size:54
Alignment explanation
Indices: 52872206--52872308 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
52872196 TACAAAATGT
*
52872206 TCATACGCATTTTTAGTCACATTAAGCAATTTGATACAATTAATTTAACATTTG
1 TCATACGCATTTTTAATCACATTAAGCAATTTGATACAATTAATTTAACATTTG
52872260 TCATACGCATTTTTAATCACATTAAGCAATTTGATACAATTAATTTAAC
1 TCATACGCATTTTTAATCACATTAAGCAATTTGATACAATTAATTTAAC
52872309 CTTTCCTCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (54 bp):
TCATACGCATTTTTAATCACATTAAGCAATTTGATACAATTAATTTAACATTTG
Found at i:52875209 original size:32 final size:32
Alignment explanation
Indices: 52875165--52875258 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 32
52875155 TCAAGCCCAT
*
52875165 TGGGCCTAAGCCC-ATTCAGATAACAGTGATAC
1 TGGGCC-AAGCCCTATTCAGATAACAGTGAAAC
* * *
52875197 TGGGCCAGAGCCCTTTTCAGATTACA-TTAAAC
1 TGGGCCA-AGCCCTATTCAGATAACAGTGAAAC
*
52875229 TGGGCCTTAGCCCCTTATTCAGATAACAGT
1 TGGGCC-AAG-CCC-TATTCAGATAACAGT
52875259 ATGGCCCATA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.02
32 23 0.47
33 13 0.27
34 11 0.22
35 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (32 bp):
TGGGCCAAGCCCTATTCAGATAACAGTGAAAC
Found at i:52880704 original size:22 final size:21
Alignment explanation
Indices: 52880661--52880705 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
52880651 AATTAGCCGA
*
52880661 AATTAAAAACTGTAAAATAAT
1 AATTAAAAACTGTAAAAAAAT
52880682 AATTATAAAACT-TAATAAAAAT
1 AATTA-AAAACTGTAA-AAAAAT
52880704 AA
1 AA
52880706 GGTGAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AATTAAAAACTGTAAAAAAAT
Found at i:52891914 original size:55 final size:56
Alignment explanation
Indices: 52891854--52891974 Score: 133
Period size: 55 Copynumber: 2.2 Consensus size: 56
52891844 TGACTATTTC
* *
52891854 GAGAGTTACACTGCTTG-GAACACGGGT-GTGTTG-CTTGGCCATGTGACCCAACTCA
1 GAGAGTTACACTGCGTGAGAACA-GGGTCGTG-TGCCTTGGCCATGTGACCCAACACA
* * * * *
52891909 GAGAGTTACA-TGGGTGAGGACATGGTCGTGTGCCTTGGTCGTGTGACCCAACACA
1 GAGAGTTACACTGCGTGAGAACAGGGTCGTGTGCCTTGGCCATGTGACCCAACACA
52891964 GAGAGTTACAC
1 GAGAGTTACAC
52891975 GGGTGAGGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
54 9 0.16
55 46 0.84
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.24
Consensus pattern (56 bp):
GAGAGTTACACTGCGTGAGAACAGGGTCGTGTGCCTTGGCCATGTGACCCAACACA
Found at i:52895081 original size:25 final size:25
Alignment explanation
Indices: 52895042--52895113 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
52895032 CAGGCCTATT
* * *
52895042 TTCACAACTCGTGTGAGCATATCGG
1 TTCACAGCTCGTGTGAGCATACCGA
* *
52895067 TTTACAGCTCGTGTGATCATACCGA
1 TTCACAGCTCGTGTGAGCATACCGA
*
52895092 TTCACAGCTTGTGTGAGCATAC
1 TTCACAGCTCGTGTGAGCATAC
52895114 ATGTACATGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATACCGA
Found at i:52898319 original size:40 final size:40
Alignment explanation
Indices: 52898260--52898367 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
52898250 GGAAAAAAAA
52898260 TATAACCGGGTTAAGTCCCGAAGGCATTCGT-ACGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGA-GGGTTAT
*
52898300 TATTACCGGGTTAAGTCCCGAAGGCATTCGTGAGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGAGGGTTAT
52898340 TATAACCGGGTTAAGTCCCGAAGGCATT
1 TATAACCGGGTTAAGTCCCGAAGGCATT
52898368 TGTGCTGGTT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 64 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGAGGGTTAT
Found at i:52902026 original size:10 final size:10
Alignment explanation
Indices: 52902013--52902051 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
52902003 CTGTTTTATA
52902013 CATGATATGC
1 CATGATATGC
52902023 CATGATATGC
1 CATGATATGC
52902033 ACATGATATGC
1 -CATGATATGC
52902044 CATGATAT
1 CATGATAT
52902052 ATTCATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:52902038 original size:21 final size:21
Alignment explanation
Indices: 52902012--52902051 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
52902002 ACTGTTTTAT
52902012 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
52902033 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
52902052 ATTCATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:52902173 original size:24 final size:25
Alignment explanation
Indices: 52902097--52902166 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
52902087 GAAGAAGTGC
* *
52902097 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
52902122 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
52902147 AAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTTGCCCCAGTT
52902167 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:52902179 original size:24 final size:25
Alignment explanation
Indices: 52902096--52902179 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 25
52902086 GGAAGAAGTG
*
52902096 CAAAAG-GGCTTTGCCCCAGTTTAC
1 CAAAAGAGGCTTTGCCCCAGTTTAT
52902120 CGAAAAG-GGCTTTGCCCCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAGTTTAT
*
52902145 CAAAA-AGGGCTTTGCCCTAG-TTAT
1 CAAAAGA-GGCTTTGCCCCAGTTTAT
*
52902169 TAAAAGAGGCT
1 CAAAAGAGGCT
52902180 AGGCCTTCAG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 17 0.32
25 36 0.68
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
CAAAAGAGGCTTTGCCCCAGTTTAT
Found at i:52909963 original size:10 final size:10
Alignment explanation
Indices: 52909950--52909988 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
52909940 CTGTTTTATA
52909950 CATGATATGC
1 CATGATATGC
52909960 CATGATATGC
1 CATGATATGC
52909970 ACATGATATGC
1 -CATGATATGC
52909981 CATGATAT
1 CATGATAT
52909989 ATTCATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:52909975 original size:21 final size:21
Alignment explanation
Indices: 52909949--52909988 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
52909939 ACTGTTTTAT
52909949 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
52909970 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
52909989 ATTCATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:52910068 original size:25 final size:24
Alignment explanation
Indices: 52910033--52910102 Score: 122
Period size: 25 Copynumber: 2.9 Consensus size: 24
52910023 GGAGGAAGTG
52910033 CAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAGGGCTTTGCCCCAGTTTAC
*
52910057 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAC
52910082 CAAAAGGGCTTTGCCCCAGTT
1 CAAAAGGGCTTTGCCCCAGTT
52910103 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAC
Found at i:52910091 original size:24 final size:24
Alignment explanation
Indices: 52910033--52910115 Score: 123
Period size: 24 Copynumber: 3.4 Consensus size: 24
52910023 GGAGGAAGTG
*
52910033 CAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAGGGCTTTGCCCCAGTTTAT
52910057 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
52910082 CAAAAGGGCTTTGCCCCAG-TTAT
1 CAAAAGGGCTTTGCCCCAGTTTAT
*
52910105 TAAAAGAGGCT
1 CAAAAG-GGCT
52910116 AGGCCTCCAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
23 9 0.16
24 23 0.42
25 23 0.42
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:52910126 original size:49 final size:49
Alignment explanation
Indices: 52910033--52910127 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
52910023 GGAGGAAGTG
**
52910033 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTAT
1 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTAT
**
52910082 CAAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
52910128 ATATGATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 5 0.12
48 10 0.25
49 25 0.62
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (49 bp):
CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTAT
Done.