Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 261 of 378
Found at i:78357124 original size:29 final size:29
Alignment explanation
Indices: 78357088--78357250 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
78357078 AATAAACGAT
***
78357088 CTCGCACACTTAGTGCCATGCGATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
78357117 CTCGCACACATAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* *
78357146 TTTGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
78357175 TTCGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* ** *
78357204 TTCGCACACTTAGTGCCATA-CCTTCCAAG
1 CTCGCACACTTAGTGCCATATAATT-TAAG
*
78357233 CCCGCACACTTAGTGCCA
1 CTCGCACACTTAGTGCCA
78357251 ATCTTGTCAC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
28 2 0.02
29 118 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CTCGCACACTTAGTGCCATATAATTTAAG
Found at i:78357283 original size:38 final size:39
Alignment explanation
Indices: 78357232--78357305 Score: 141
Period size: 38 Copynumber: 1.9 Consensus size: 39
78357222 TACCTTCCAA
78357232 GCCCGCACACTTAGTGCCAATCTTGTCACC-TGCCAATT
1 GCCCGCACACTTAGTGCCAATCTTGTCACCGTGCCAATT
78357270 GCCCGCACACTTAGTGCCAATCTTGTCACCGTGCCA
1 GCCCGCACACTTAGTGCCAATCTTGTCACCGTGCCA
78357306 TTTATTGCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (39 bp):
GCCCGCACACTTAGTGCCAATCTTGTCACCGTGCCAATT
Found at i:78357316 original size:38 final size:38
Alignment explanation
Indices: 78357234--78357325 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
78357224 CCTTCCAAGC
*
78357234 CCGCACACTTAGTGCCAATCTTGTCACCTGCCAATTGC
1 CCGCACACTTAGTGCCAATCTTGTCACCTGCCAATTGA
*
78357272 CCGCACACTTAGTGCCAATCTTGTCACCGTGCC-ATTTA
1 CCGCACACTTAGTGCCAATCTTGTCACC-TGCCAATTGA
**
78357310 TTGCACACTTAGTGCC
1 CCGCACACTTAGTGCC
78357326 GAGACCAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 45 0.92
39 4 0.08
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (38 bp):
CCGCACACTTAGTGCCAATCTTGTCACCTGCCAATTGA
Found at i:78361511 original size:29 final size:29
Alignment explanation
Indices: 78361421--78361580 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
78361411 ACTCGATTTC
* * **
78361421 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
78361450 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
78361478 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
78361508 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
78361537 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
78361566 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
78361581 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:78365828 original size:45 final size:45
Alignment explanation
Indices: 78365778--78365864 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
78365768 TAGGGTTCAC
*
78365778 TAGAAAGCTTGGTGAGCTAATGTACT-CTAGAAGTCCTGGTGAATT
1 TAGAAAGCTTGGTGAGCTAATGTA-TGCTAGAAGTCCTAGTGAATT
* *
78365823 TAGAAAGCTTGGTGAGTTGATGTATGCTAGAAGTCCTAGTGA
1 TAGAAAGCTTGGTGAGCTAATGTATGCTAGAAGTCCTAGTGA
78365865 GTTAAAGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (45 bp):
TAGAAAGCTTGGTGAGCTAATGTATGCTAGAAGTCCTAGTGAATT
Found at i:78367838 original size:7 final size:7
Alignment explanation
Indices: 78367826--78367910 Score: 62
Period size: 7 Copynumber: 11.7 Consensus size: 7
78367816 TTATGCATAG
78367826 AACCCTA
1 AACCCTA
78367833 AACCCTA
1 AACCCTA
*
78367840 AACCATA
1 AACCCTA
*
78367847 AACCTTA
1 AACCCTA
*
78367854 AATCCTA
1 AACCCTA
*
78367861 AACGCTA
1 AACCCTA
*
78367868 AATCCTTAA
1 AA-CCCT-A
*
78367877 AACCATAA
1 AACCCT-A
*
78367885 AACCTTA
1 AACCCTA
78367892 AACCCTA
1 AACCCTA
* *
78367899 AATCTTA
1 AACCCTA
78367906 AACCC
1 AACCC
78367911 CAACTATGAA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
7 46 0.75
8 12 0.20
9 3 0.05
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:78367848 original size:14 final size:14
Alignment explanation
Indices: 78367826--78367910 Score: 73
Period size: 14 Copynumber: 5.9 Consensus size: 14
78367816 TTATGCATAG
*
78367826 AACCCTAAACCCTA
1 AACCTTAAACCCTA
* *
78367840 AACCATAAACCTTA
1 AACCTTAAACCCTA
*
78367854 AATCC-TAAACGCTA
1 AA-CCTTAAACCCTA
*
78367868 AATCCTTAAAACCATAA
1 AA-CCTT-AAACCCT-A
78367885 AACCTTAAACCCTA
1 AACCTTAAACCCTA
*
78367899 AATCTTAAACCC
1 AACCTTAAACCC
78367911 CAACTATGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
14 38 0.64
15 9 0.15
16 9 0.15
17 3 0.05
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:78368183 original size:27 final size:26
Alignment explanation
Indices: 78368145--78368223 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 26
78368135 TACACTTGGC
*
78368145 GAGCTGTGCTCATAGATGTGATTTAGT
1 GAGCTGTGCTCATAGATGTG-TTTAGA
* * *
78368172 GAGCTGTACTCACAGATATGGTTTAGA
1 GAGCTGTGCTCATAGATGT-GTTTAGA
* * *
78368199 GAACTATGTTCATAGATGTGTTTAG
1 GAGCTGTGCTCATAGATGTGTTTAG
78368224 GTGAAGTATG
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
26 6 0.15
27 34 0.83
28 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (26 bp):
GAGCTGTGCTCATAGATGTGTTTAGA
Found at i:78368624 original size:33 final size:33
Alignment explanation
Indices: 78368587--78368654 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
78368577 ATAATATGTG
78368587 TTAAATAAAATTATAACATAAAATGGTATTCAT
1 TTAAATAAAATTATAACATAAAATGGTATTCAT
78368620 TTAAATAAAATTATAACATAAAATGGTATTCAT
1 TTAAATAAAATTATAACATAAAATGGTATTCAT
78368653 TT
1 TT
78368655 TACCATGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (33 bp):
TTAAATAAAATTATAACATAAAATGGTATTCAT
Found at i:78369990 original size:15 final size:16
Alignment explanation
Indices: 78369965--78369994 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
78369955 AGTTTTGGTG
78369965 TATGTTTCTAATGTGC
1 TATGTTTCTAATGTGC
78369981 TATG-TTCTAATGTG
1 TATGTTTCTAATGTG
78369995 ATTTGGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (16 bp):
TATGTTTCTAATGTGC
Found at i:78380189 original size:231 final size:231
Alignment explanation
Indices: 78379781--78380243 Score: 881
Period size: 231 Copynumber: 2.0 Consensus size: 231
78379771 CACAATTGCT
78379781 ACATTCTTATAGTTGTTGATTCGGATATTTTCCTACTATGGTAAGACTAAAGATTGAAGTTCAAG
1 ACATTCTTATAGTTGTTGATTCGGATATTTTCCTACTATGGTAAGACTAAAGATTGAAGTTCAAG
78379846 TATAGGGTTGTTTGTTCACCCGAGGTAAGTGTTATGAGTTTCTCCTGCGAAAGTGATATTGCTTG
66 TATAGGGTTGTTTGTTCACCCGAGGTAAGTGTTATGAGTTTCTCCTGCGAAAGTGATATTGCTTG
* * *
78379911 AGTGTAAATAGAAAGATGTATAAGTAAGGTCTTGCATAGAGTTTGTTTAGGTTTTAGATGAAAAT
131 AGTGTAAATAGAAAGATGTATAAGTAAGGCCTTCCATAGAATTTGTTTAGGTTTTAGATGAAAAT
78379976 AAGAGTTAAGTTTTGACAGGATTCCTATGTCTTACG
196 AAGAGTTAAGTTTTGACAGGATTCCTATGTCTTACG
78380012 ACATTCTTATAGTTGTTGATTCGGATATTTTCCTACTATGGTAAGACTAAAGATTGAAGTTCAAG
1 ACATTCTTATAGTTGTTGATTCGGATATTTTCCTACTATGGTAAGACTAAAGATTGAAGTTCAAG
*
78380077 TATAGGGTTGTTTGTTCACCCGGGGTAAGTGTTATGAGTTTCTCCTGCGAAAGTGATATTGCTTG
66 TATAGGGTTGTTTGTTCACCCGAGGTAAGTGTTATGAGTTTCTCCTGCGAAAGTGATATTGCTTG
78380142 AGTGTAAATAGAAAGATGTATAAGTAAGGCCTTCCATAGAATTTGTTTAGGTTTTAGATGAAAAT
131 AGTGTAAATAGAAAGATGTATAAGTAAGGCCTTCCATAGAATTTGTTTAGGTTTTAGATGAAAAT
*
78380207 AAGAGTTAGGTTTTGACAGGATTCCTATGTCTTACG
196 AAGAGTTAAGTTTTGACAGGATTCCTATGTCTTACG
78380243 A
1 A
78380244 ATAGTGACCT
Statistics
Matches: 227, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 227 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (231 bp):
ACATTCTTATAGTTGTTGATTCGGATATTTTCCTACTATGGTAAGACTAAAGATTGAAGTTCAAG
TATAGGGTTGTTTGTTCACCCGAGGTAAGTGTTATGAGTTTCTCCTGCGAAAGTGATATTGCTTG
AGTGTAAATAGAAAGATGTATAAGTAAGGCCTTCCATAGAATTTGTTTAGGTTTTAGATGAAAAT
AAGAGTTAAGTTTTGACAGGATTCCTATGTCTTACG
Found at i:78387318 original size:12 final size:12
Alignment explanation
Indices: 78387301--78387331 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
78387291 CTTGTACAAG
78387301 CATTTACAGATA
1 CATTTACAGATA
*
78387313 CATTTACAGTTA
1 CATTTACAGATA
78387325 CATTTAC
1 CATTTAC
78387332 GGGCACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (12 bp):
CATTTACAGATA
Found at i:78387435 original size:13 final size:13
Alignment explanation
Indices: 78387419--78387593 Score: 129
Period size: 13 Copynumber: 13.5 Consensus size: 13
78387409 ATGAAAATAA
78387419 TATATGAAATGGT
1 TATATGAAATGGT
* *
78387432 TATATGTAATGGC
1 TATATGAAATGGT
* *
78387445 TATACGAAATGAT
1 TATATGAAATGGT
78387458 TATATGAAATGGT
1 TATATGAAATGGT
* ** *
78387471 TACACAAAATAGT
1 TATATGAAATGGT
* *
78387484 AATATGATATGGT
1 TATATGAAATGGT
* *
78387497 TATACGAAATAGT
1 TATATGAAATGGT
*
78387510 TATAT-AAATAAG-
1 TATATGAAAT-GGT
*
78387522 TATATGAAATGAT
1 TATATGAAATGGT
* *
78387535 TATATGAACTGAT
1 TATATGAAATGGT
* *
78387548 TAAATGGAAATAGT
1 TATAT-GAAATGGT
*
78387562 TATATGAAATGAT
1 TATATGAAATGGT
* *
78387575 TATACGAAATGTT
1 TATATGAAATGGT
78387588 TATATG
1 TATATG
78387594 GATAGATATG
Statistics
Matches: 122, Mismatches: 36, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
12 9 0.07
13 104 0.85
14 9 0.07
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:78404119 original size:30 final size:29
Alignment explanation
Indices: 78404025--78404126 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
78404015 TATAGTGAAT
* * *
78404025 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
78404054 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
78404082 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
78404112 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
78404127 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:78406950 original size:13 final size:13
Alignment explanation
Indices: 78406932--78406956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78406922 AGGCCGTGTG
78406932 AAGGACACGGGCC
1 AAGGACACGGGCC
78406945 AAGGACACGGGC
1 AAGGACACGGGC
78406957 GTGTGCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.40, T:0.00
Consensus pattern (13 bp):
AAGGACACGGGCC
Found at i:78406975 original size:42 final size:40
Alignment explanation
Indices: 78406894--78406975 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 40
78406884 CTGAGGTTTT
*
78406894 GGACACGGGCAATGACACAGACGTGTCTAGGCCGTGTGAA
1 GGACACGGGCAAGGACACAGACGTGTCTAGGCCGTGTGAA
* * **
78406934 GGACACGGGCCAAGGACACGGGCGTGTGCTTTGCCGTGTGAA
1 GGACACGGG-CAAGGACACAGACGTGT-CTAGGCCGTGTGAA
78406976 AACCTCTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 9 0.26
41 14 0.40
42 12 0.34
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.16
Consensus pattern (40 bp):
GGACACGGGCAAGGACACAGACGTGTCTAGGCCGTGTGAA
Found at i:78413292 original size:25 final size:25
Alignment explanation
Indices: 78413258--78413307 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
78413248 CGACGAGTGA
78413258 ATCCATAAATATTATTAATTAATAT
1 ATCCATAAATATTATTAATTAATAT
*
78413283 ATCCGTAAATATTATTAATTAATAT
1 ATCCATAAATATTATTAATTAATAT
78413308 TTATGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (25 bp):
ATCCATAAATATTATTAATTAATAT
Found at i:78415742 original size:10 final size:10
Alignment explanation
Indices: 78415729--78415757 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
78415719 TTATGTGCAT
78415729 GTATTTAATA
1 GTATTTAATA
78415739 GTATTTAATA
1 GTATTTAATA
78415749 GTATTTAAT
1 GTATTTAAT
78415758 GAATGGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
GTATTTAATA
Found at i:78430391 original size:13 final size:11
Alignment explanation
Indices: 78430360--78430384 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
78430350 TGGCTATGCC
78430360 ATTACAAGTCT
1 ATTACAAGTCT
78430371 ATTACAAGTCT
1 ATTACAAGTCT
78430382 ATT
1 ATT
78430385 CTACAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTACAAGTCT
Found at i:78439107 original size:12 final size:12
Alignment explanation
Indices: 78439090--78439125 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
78439080 GCCCTAGTAG
*
78439090 ACCGGAGTCGTT
1 ACCGGAGTCATT
78439102 ACCGGAGTCATT
1 ACCGGAGTCATT
78439114 ACCGGAGTCATT
1 ACCGGAGTCATT
78439126 CCGTAACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (12 bp):
ACCGGAGTCATT
Found at i:78441387 original size:29 final size:29
Alignment explanation
Indices: 78441354--78441484 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
78441344 TGACGAGATC
*
78441354 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
78441383 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
78441412 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
78441441 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
78441470 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
78441485 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:78448121 original size:23 final size:21
Alignment explanation
Indices: 78448089--78448131 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
78448079 TTTATGTAAA
*
78448089 AGAAAGGAAATAATAAAAGAAAT
1 AGAAAAGAAA-AA-AAAAGAAAT
78448112 AGAAAAGAAAAAAAAAGAAA
1 AGAAAAGAAAAAAAAAGAAA
78448132 AAAAAAGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (21 bp):
AGAAAAGAAAAAAAAAGAAAT
Found at i:78448129 original size:10 final size:10
Alignment explanation
Indices: 78448103--78448138 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
78448093 AGGAAATAAT
*
78448103 AAAAGAAATAG
1 AAAAGAAA-AA
78448114 AAAAGAAAAA
1 AAAAGAAAAA
78448124 AAAAGAAAAA
1 AAAAGAAAAA
78448134 AAAAG
1 AAAAG
78448139 GCTTCATTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:78449377 original size:29 final size:29
Alignment explanation
Indices: 78449344--78449474 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
78449334 TGACGAGATC
*
78449344 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
78449373 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
78449402 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
78449431 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
78449460 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
78449475 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:78452200 original size:27 final size:27
Alignment explanation
Indices: 78452170--78452462 Score: 354
Period size: 27 Copynumber: 10.9 Consensus size: 27
78452160 ATTACCAAAG
* *
78452170 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
78452197 TACCCTCGATTTATAGAAGTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * **
78452224 TACCCTTGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
78452251 TACCTTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
78452278 TACCCTCGATTTTTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
78452305 TACCCTCCATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
78452332 TACCCTC-AGTTTACAGAATTACCATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
78452359 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
78452386 TACCCTCAATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
78452413 TACCCTCAATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
78452440 TACCCTCGATTTGCAAAATTACC
1 TACCCTCGATTTACAGAATTACC
78452463 AAAATACCCC
Statistics
Matches: 234, Mismatches: 30, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
26 1 0.00
27 232 0.99
28 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:78452470 original size:27 final size:27
Alignment explanation
Indices: 78452440--78452525 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
78452430 ATTACCATTT
*
78452440 TACCCTCGATTTGCAAAATTACCAAAA
1 TACCCTCGGTTTGCAAAATTACCAAAA
* *
78452467 TACCC-CTGGTTTGTAAAATTACCAAAG
1 TACCCTC-GGTTTGCAAAATTACCAAAA
*
78452494 TACCCAT-GGTTTGCAAAATTACTAAAA
1 TACCC-TCGGTTTGCAAAATTACCAAAA
78452521 TACCC
1 TACCC
78452526 CTGTAAGGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.02
27 49 0.98
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (27 bp):
TACCCTCGGTTTGCAAAATTACCAAAA
Found at i:78452537 original size:54 final size:54
Alignment explanation
Indices: 78452449--78452552 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
78452439 TTACCCTCGA
**
78452449 TTTGCAAAATTACCAAAATACCCCTGGTTTGTAAAATTACC-AAAGTACCCATGG
1 TTTGCAAAATTACCAAAATACCCCTGGTAGGTAAAATTACCGAAA-TACCCATGG
*
78452503 TTTGCAAAATTACTAAAATACCCCT-GTAAGGTAAAATTACCGAAATACCC
1 TTTGCAAAATTACCAAAATACCCCTGGT-AGGTAAAATTACCGAAATACCC
78452553 CTGTAGGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
53 2 0.04
54 40 0.89
55 3 0.07
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (54 bp):
TTTGCAAAATTACCAAAATACCCCTGGTAGGTAAAATTACCGAAATACCCATGG
Found at i:78452538 original size:27 final size:27
Alignment explanation
Indices: 78452454--78452571 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 27
78452444 CTCGATTTGC
**
78452454 AAAATTACCAAAATACCCCTGGT-TTGT
1 AAAATTACCAAAATACCCCT-GTAAGGT
* * ** *
78452481 AAAATTACCAAAGTACCCATGGT-TTGC
1 AAAATTACCAAAATACCCCT-GTAAGGT
*
78452508 AAAATTACTAAAATACCCCTGTAAGGT
1 AAAATTACCAAAATACCCCTGTAAGGT
* *
78452535 AAAATTACCGAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTGTAAGGT
*
78452562 AGAATTACCA
1 AAAATTACCA
78452572 TTTTGCCCCT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.03
27 74 0.97
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGTAAGGT
Found at i:78456551 original size:27 final size:27
Alignment explanation
Indices: 78456259--78456540 Score: 359
Period size: 27 Copynumber: 10.4 Consensus size: 27
78456249 ATTACCAAAG
* * *
78456259 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
78456286 TACCCTCGATTTATAGAAGTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
78456313 TACCCTCGATTTATAGAAGTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* ** *
78456340 TGCCCTCGATTTACGGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
78456367 TACCCTCGATTTTTAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
78456394 TACCCTCTATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
78456421 TACCCTC-AGTTTACAGAATTACCATTT
1 TACCCTCGA-TTTATAGAATTACCGTTT
*
78456448 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * **
78456475 TACCCTCAATTTATAAAATTACTATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
78456502 TACCCTCAATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
78456529 TACCCTCGATTT
1 TACCCTCGATTT
78456541 GCAAAATTAC
Statistics
Matches: 225, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
26 1 0.00
27 223 0.99
28 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:78456559 original size:27 final size:27
Alignment explanation
Indices: 78456529--78456614 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
78456519 ATTACCGTTT
78456529 TACCCTCGATTTGCAAAATTACCAAAA
1 TACCCTCGATTTGCAAAATTACCAAAA
* *
78456556 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTGCAAAATTACCAAAA
* *
78456583 TACCCAT-GGTTTGCAAAATTACTAAAA
1 TACCC-TCGATTTGCAAAATTACCAAAA
78456610 TACCC
1 TACCC
78456615 CTGTAAGGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 2 0.04
27 48 0.96
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (27 bp):
TACCCTCGATTTGCAAAATTACCAAAA
Found at i:78456573 original size:81 final size:80
Alignment explanation
Indices: 78456267--78456579 Score: 329
Period size: 81 Copynumber: 3.9 Consensus size: 80
78456257 AGTACCCCCG
* * * * * * *
78456267 ATTTACATAATTACCGTTTTACCCTCGATTTATAGAAGTACCGTTTTACCCTCGATTTATAGAAG
1 ATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCC-CTATTTATAAAAT
* * *
78456332 TACCGTTTTGCCCTCG
65 TACCATTTTACCCTCA
* * * * * *
78456348 ATTTACGGAATTATCGTTTTACCCTCGATTTTTAAAATTACCGTTTTACCCTCTATTTACAGAAT
1 ATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCC-CTATTTATAAAAT
*
78456413 TACCGTTTTACCCTCA
65 TACCATTTTACCCTCA
* * * *
78456429 GTTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAAAAT
1 ATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCC-CTATTTATAAAAT
*
78456494 TACTATTTTACCCTCA
65 TACCATTTTACCCTCA
* ** *** *
78456510 ATTTATAGAATTACCGTTTTACCCTCGATTTGCAAAATTACCAAAATACCCCTAGTTTGTAAAAT
1 ATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCCTA-TTTATAAAAT
78456575 TACCA
65 TACCA
78456580 AAATACCCAT
Statistics
Matches: 196, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
80 2 0.01
81 194 0.99
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (80 bp):
ATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCCTATTTATAAAATT
ACCATTTTACCCTCA
Found at i:78456587 original size:81 final size:81
Alignment explanation
Indices: 78456229--78456587 Score: 207
Period size: 81 Copynumber: 4.4 Consensus size: 81
78456219 CCAATTATTG
* * * * * * * *
78456229 AAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACATAATTACCGTTTTACCCTCG
1 AAATACCCTCAATTTATAAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCG
* * * *
78456294 ATTTATAGAAGTACCG
66 ATTTACAAAATTACCA
*** * * * **** * * * * *
78456310 TTTTACCCTCGATTTATAGAAGTACCGTTTTGCCCTCGATTTACGGAATTATCGTTTTACCCTCG
1 AAATACCCTCAATTTATAAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCG
** *
78456375 ATTTTTAAAATTACCG
66 ATTTACAAAATTACCA
*** * * * **** *
78456391 TTTTACCCTCTATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACCATTTTACCCTCG
1 AAATACCCTCAATTTATAAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCG
* *
78456456 ATTTATAGAATTACCA
66 ATTTACAAAATTACCA
*** * *** * *
78456472 TTTTACCCTCAATTTATAAAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCG
1 AAATACCCTCAATTTATAAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCG
*
78456537 ATTTGCAAAATTACCA
66 ATTTACAAAATTACCA
* *
78456553 AAATACCC-CTAGTTTGTAAAATTACCAAAATACCC
1 AAATACCCTC-AATTTATAAAATTACCAAAATACCC
78456588 ATGGTTTGCA
Statistics
Matches: 226, Mismatches: 51, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
80 1 0.00
81 225 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (81 bp):
AAATACCCTCAATTTATAAAATTACCAAAATACCCTCAATTTACAGAATTACCATTTTACCCTCG
ATTTACAAAATTACCA
Found at i:78456626 original size:54 final size:54
Alignment explanation
Indices: 78456538--78456641 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
78456528 TTACCCTCGA
**
78456538 TTTGCAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCATGG
1 TTTGCAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCCATGG
* * *
78456592 TTTGCAAAATTACTAAAATACCCCT-GTAAGGTAAAATTATCGAAATACCC
1 TTTGCAAAATTACCAAAATACCCCTAGT-AGGTAAAATTACCAAAATACCC
78456642 CTGTAGGGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (54 bp):
TTTGCAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCCATGG
Found at i:78456627 original size:27 final size:27
Alignment explanation
Indices: 78456543--78456660 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 27
78456533 CTCGATTTGC
*
78456543 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTGGT
* * * *
78456570 AAAATTACCAAAATACCCATGGTTTGC
1 AAAATTACCAAAATACCCCTAGTTGGT
* *
78456597 AAAATTACTAAAATACCCCT-GTAAGGT
1 AAAATTACCAAAATACCCCTAGT-TGGT
* * *
78456624 AAAATTATCGAAATACCCCT-GTAGGGT
1 AAAATTACCAAAATACCCCTAGT-TGGT
*
78456651 AGAATTACCA
1 AAAATTACCA
78456661 TTTTGCCCCT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 2 0.03
27 73 0.97
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTGGT
Found at i:78460281 original size:26 final size:23
Alignment explanation
Indices: 78460272--78460327 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
78460262 AGCATACTGA
*
78460272 TGTTTCAGCTCGTCAGAGCTTAC
1 TGTTTCAGCTCGTCAGAGCATAC
*
78460295 TGTTTCAGCTCGTC-GAGCTTAC
1 TGTTTCAGCTCGTCAGAGCATAC
*
78460317 TATTTCAGCTC
1 TGTTTCAGCTC
78460328 AATAGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (23 bp):
TGTTTCAGCTCGTCAGAGCATAC
Found at i:78460302 original size:23 final size:23
Alignment explanation
Indices: 78460272--78460342 Score: 101
Period size: 23 Copynumber: 3.1 Consensus size: 23
78460262 AGCATACTGA
78460272 TGTTTCAGCTCGTCAGAGCTTAC
1 TGTTTCAGCTCGTCAGAGCTTAC
78460295 TGTTTCAGCTCGTC-GAGCTTAC
1 TGTTTCAGCTCGTCAGAGCTTAC
* *
78460317 TATTTCAGCTCAAT-AGAGCTTAC
1 TGTTTCAGCTC-GTCAGAGCTTAC
78460340 TGT
1 TGT
78460343 CCATCAGCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 18 0.42
23 25 0.58
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (23 bp):
TGTTTCAGCTCGTCAGAGCTTAC
Found at i:78461470 original size:65 final size:64
Alignment explanation
Indices: 78461370--78461517 Score: 165
Period size: 65 Copynumber: 2.3 Consensus size: 64
78461360 TGACCGATCG
* *
78461370 TGTGATACAAGTCAGTATACCCTCTAAATGGCACACAGCCTAGCACACGGGCGTGTGAC-TTGGC
1 TGTGAT-CAAGTCAGTATACCCTCCAAATGCCACACAGCCTAGCACAC-GG-GTGTGACTTTGGC
78461434 CA
63 CA
** * * * *
78461436 TGTTGAT-AAGTCAGTATACCCTCCAGTTTCCACACGGCCTGGCACACGGGTGTGTCTTTGGCCA
1 TG-TGATCAAGTCAGTATACCCTCCAAATGCCACACAGCCTAGCACACGGGTGTGACTTTGGCCA
78461500 TGTGATGCAAGTCAGTAT
1 TGTGAT-CAAGTCAGTAT
78461518 GTACGCCCCG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
63 10 0.14
64 11 0.16
65 43 0.61
66 2 0.03
67 4 0.06
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.26
Consensus pattern (64 bp):
TGTGATCAAGTCAGTATACCCTCCAAATGCCACACAGCCTAGCACACGGGTGTGACTTTGGCCA
Found at i:78463265 original size:46 final size:46
Alignment explanation
Indices: 78463198--78463326 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
78463188 TGTAACCCGC
* * *
78463198 CCATAAGCGAACTCGAACTCAACTCAACGAGCTT-GGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
78463244 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
78463290 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
78463327 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:78467313 original size:42 final size:42
Alignment explanation
Indices: 78467195--78467398 Score: 180
Period size: 42 Copynumber: 4.8 Consensus size: 42
78467185 TACCATACCA
* * **
78467195 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
* * * * * *
78467237 ACGCTAATAGCCTA-ACTATAGTCTTACATGAAATCTCACATCG
1 ATGC-CATATCCCAGA-TATGGTCTTACACGAAATCTCACATCG
*
78467280 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCACATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
* * * * * *
78467322 ATGCCATAACCTAGGTATGGTCTTACACGAAGTTTCATA-CAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATC-G
* *
78467364 ATGCCATAT-CCTGTATATGGTCTTACACGTAATCT
1 ATGCCATATCCCAG-ATATGGTCTTACACGAAATCT
78467399 TAGTAACCCT
Statistics
Matches: 128, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
41 3 0.02
42 92 0.72
43 33 0.26
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
Found at i:78467398 original size:84 final size:85
Alignment explanation
Indices: 78467195--78467398 Score: 225
Period size: 84 Copynumber: 2.4 Consensus size: 85
78467185 TACCATACCA
* ** *
78467195 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCGACGCTAATAGCCTAACTATAGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCACATCGACGCTAATAACCTAACTATAGTC
*
78467260 TTACATGAAATCTCACATCG
66 TTACACGAAATCTCACATCG
** * * ** *
78467280 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCACATCGATGC-CATAACCTAGGTATGGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCACATCGACGCTAATAACCTAACTATAGTC
* * *
78467344 TTACACGAAGTTTCATA-CAG
66 TTACACGAAATCTCACATC-G
*
78467364 ATGCCATAT-CCTGTATATGGTCTTACACGTAATCT
1 ATGCCATATCCCAG-ATATGGTCTTACACGTAATCT
78467399 TAGTAACCCT
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
83 4 0.04
84 55 0.56
85 40 0.40
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (85 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCACATCGACGCTAATAACCTAACTATAGTC
TTACACGAAATCTCACATCG
Found at i:78472652 original size:43 final size:43
Alignment explanation
Indices: 78472584--78472668 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
78472574 CATAAAAGGA
*
78472584 CCATAGCTTGGAAATTTTCTAACATTAAAGGGATCAGCCCTTT
1 CCATAGCTTGGAAAATTTCTAACATTAAAGGGATCAGCCCTTT
* *
78472627 CCATTGCTTGGAAAATTTCTGACATTAAAGGGATCAGCCCTT
1 CCATAGCTTGGAAAATTTCTAACATTAAAGGGATCAGCCCTT
78472669 CTTTTTGCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (43 bp):
CCATAGCTTGGAAAATTTCTAACATTAAAGGGATCAGCCCTTT
Found at i:78477501 original size:170 final size:170
Alignment explanation
Indices: 78477219--78477559 Score: 646
Period size: 170 Copynumber: 2.0 Consensus size: 170
78477209 AATAACTTTT
*
78477219 CATATTGACTAATGAGTACTTTTATTGATGTTCTTAAACACCTTGACTGATTTGAGTGAATCTTT
1 CATATTGACTAATGAGTACGTTTATTGATGTTCTTAAACACCTTGACTGATTTGAGTGAATCTTT
*
78477284 ACTGAGGATGTTGAACTATGTGATATTTTGATCAAAGGTAATCACTTAGATGAGGGGAGACACCT
66 ACTGAGGATGTTAAACTATGTGATATTTTGATCAAAGGTAATCACTTAGATGAGGGGAGACACCT
78477349 ATGTTTTCGTGATAAAATGCTCAACTTGGAATGTTTGAAA
131 ATGTTTTCGTGATAAAATGCTCAACTTGGAATGTTTGAAA
*
78477389 CATATTGACTAATGAGTGCGTTTATTGATGTTCTTAAACACCTTGACTGATTTGAGTGAATCTTT
1 CATATTGACTAATGAGTACGTTTATTGATGTTCTTAAACACCTTGACTGATTTGAGTGAATCTTT
*
78477454 ATTGAGGATGTTAAACTATGTGATATTTTGATCAAAGGTAATCACTTAGATGAGGGGAGACACCT
66 ACTGAGGATGTTAAACTATGTGATATTTTGATCAAAGGTAATCACTTAGATGAGGGGAGACACCT
78477519 ATGTTTTCGTGATAAAATGCTCAACTTGGAATGTTTGAAA
131 ATGTTTTCGTGATAAAATGCTCAACTTGGAATGTTTGAAA
78477559 C
1 C
78477560 TTTGATGTAC
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 167 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (170 bp):
CATATTGACTAATGAGTACGTTTATTGATGTTCTTAAACACCTTGACTGATTTGAGTGAATCTTT
ACTGAGGATGTTAAACTATGTGATATTTTGATCAAAGGTAATCACTTAGATGAGGGGAGACACCT
ATGTTTTCGTGATAAAATGCTCAACTTGGAATGTTTGAAA
Found at i:78481706 original size:47 final size:46
Alignment explanation
Indices: 78481637--78481764 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 46
78481627 TTATTTGTGT
78481637 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACATT-ATGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCT-CATTGA-GACGA
* *
78481683 GCTAGTGTAAAACCATGTTTGGGACATAGCATC-G-TCATTGAGACGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTCATTGAGACGA
78481729 GATCTAGTGTAAGACATGTCTGGGACATGCATCGGC
1 G--CTAGTGTAAGACATGTCTGGGACATGCATCGGC
78481765 CTCGAGATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
45 6 0.09
46 21 0.30
47 28 0.40
48 15 0.21
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTCATTGAGACGA
Found at i:78493189 original size:40 final size:40
Alignment explanation
Indices: 78493144--78493310 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
78493134 CGGAATATAA
78493144 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
78493184 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
78493224 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
78493264 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
78493303 CCGGATAT
1 CCGGATAT
78493311 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:78493294 original size:80 final size:79
Alignment explanation
Indices: 78493160--78493310 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
78493150 ATAATCACGT
*
78493160 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
78493225 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
78493240 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
78493303 CCGGATAT
64 CCGGATAT
78493311 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:78494569 original size:56 final size:55
Alignment explanation
Indices: 78494506--78494612 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 55
78494496 CCCCCTTTTC
78494506 CCTTAGTA-ATTTCGGCCAAGAAGAT-GAGAAAGGATGAACAAATTTTTCTTTTCTTT
1 CCTTAGTACA-TTCGGCCAAGAAGATGGAG-AAGGATGAAC-AATTTTTCTTTTCTTT
*** *
78494562 CCTTAGTACATTCGGCCAAGCCTATGGAGAAGGATGAACATTTTTTCTTTT
1 CCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACAATTTTTCTTTT
78494613 TTTTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 11 0.24
56 30 0.67
57 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (55 bp):
CCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACAATTTTTCTTTTCTTT
Found at i:78501025 original size:26 final size:23
Alignment explanation
Indices: 78500986--78501055 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
78500976 GGACTCACCA
78500986 CAGCTCAT-ATGAGCTTACTGATATT
1 CAGCTCATCA-GAGCTTACTG-T-TT
*
78501011 CTAGCTCATCAGAGCATACTGTTT
1 C-AGCTCATCAGAGCTTACTGTTT
*
78501035 CAGCTCGTCAGAGCTTACTGT
1 CAGCTCATCAGAGCTTACTGT
78501056 CCATCAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 18 0.45
24 3 0.08
25 2 0.05
26 16 0.40
27 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (23 bp):
CAGCTCATCAGAGCTTACTGTTT
Found at i:78503463 original size:27 final size:27
Alignment explanation
Indices: 78503431--78503486 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
78503421 GGGTCAGAAT
78503431 GTAAGCTACACGATGCTACTCACATGA
1 GTAAGCTACACGATGCTACTCACATGA
78503458 GTAAGCTACACGATGCTACTCACATGA
1 GTAAGCTACACGATGCTACTCACATGA
78503485 GT
1 GT
78503487 TGTGGAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (27 bp):
GTAAGCTACACGATGCTACTCACATGA
Found at i:78506435 original size:46 final size:44
Alignment explanation
Indices: 78506350--78506502 Score: 166
Period size: 46 Copynumber: 3.3 Consensus size: 44
78506340 CATATCTGTA
78506350 CCGATGTCATGTCCCAGACATGGTCTTACACT-GAC-ACATCTCATAG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTACATCTCA-AG
* * *
78506396 CCGATGCATGTCTCAAACATGTCTTACACTAGCTTACATCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC-TACATCTC-AAG
* *
78506442 TCGATGCATGTCCCAGACATGTCTTACACTAGCTCCTATCTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTAC-ATCTCAA-G
78506488 CCGATGCAATGTCCC
1 CCGATGC-ATGTCCC
78506503 GGTGGTCTTA
Statistics
Matches: 91, Mismatches: 9, Indels: 13
0.81 0.08 0.12
Matches are distributed among these distances:
44 11 0.12
45 16 0.18
46 56 0.62
47 8 0.09
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (44 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTACATCTCAAG
Found at i:78510580 original size:40 final size:40
Alignment explanation
Indices: 78510521--78510781 Score: 400
Period size: 40 Copynumber: 6.5 Consensus size: 40
78510511 CATTTGAATG
*
78510521 ATATCCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
78510561 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
78510601 ATATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
78510641 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* *
78510681 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * * *
78510721 ATGTTCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
78510761 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
78510782 AAACTTGGGT
Statistics
Matches: 205, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
38 1 0.00
39 12 0.06
40 192 0.94
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:78519348 original size:46 final size:47
Alignment explanation
Indices: 78519298--78519479 Score: 203
Period size: 46 Copynumber: 3.9 Consensus size: 47
78519288 TACGTTGACA
78519298 CATCTTGTA-GCCGATGCATGTCCCAGACATGTCTTACACTAGCT-T
1 CATCTTGTAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
* * *
78519343 GCATCTCG-AGGTCGATGCATGTCCCAGACATATCTTACACTAGCTCT
1 -CATCTTGTAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
* ** * *
78519390 CGTC-TCAATGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCT
1 CATCTTGTAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT
** *
78519438 CATAATGT-GGCCGATGCATGTCCCAAACATGTCTTACACTAG
1 CATCTTGTAGGCCGATGCATGTCCCAGACATGTCTTACACTAG
78519480 TACACAAATA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.01
46 60 0.53
47 28 0.25
48 23 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
CATCTTGTAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
Found at i:78524478 original size:58 final size:58
Alignment explanation
Indices: 78524416--78524550 Score: 164
Period size: 58 Copynumber: 2.3 Consensus size: 58
78524406 AATTCATATG
* * * *
78524416 ATAATAATTATATTAAGAATGTTATTAAATTATATATTA-TTTTATTAAATTGTATTTA
1 ATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
* * * *
78524474 ATAATAATTGTGTTAAAATATGATTAAATTATTTTTTATTTTTATTAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
* *
78524532 ACAATAATTTTATTAAAAT
1 ATAATAATTATATTAAAAT
78524551 TTAATAACAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 18 0.28
58 47 0.72
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (58 bp):
ATAATAATTATATTAAAATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
Found at i:78524543 original size:26 final size:25
Alignment explanation
Indices: 78524513--78524563 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
78524503 TATTTTTTAT
*
78524513 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATA-ATAACAATAA
*
78524539 TTTTATTAAAATTTAATAACAATAA
1 TTTTATTAAAATATAATAACAATAA
78524564 CAATAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTATTAAAATATAATAACAATAA
Found at i:78524744 original size:16 final size:16
Alignment explanation
Indices: 78524723--78524772 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
78524713 TACTGATTGC
*
78524723 AGCTCTATTCTATTAT
1 AGCTCTATTCAATTAT
* *
78524739 AGCTCTATCCAATTAC
1 AGCTCTATTCAATTAT
*
78524755 AGCTCTATTCCATTAT
1 AGCTCTATTCAATTAT
78524771 AG
1 AG
78524773 TGAACCAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (16 bp):
AGCTCTATTCAATTAT
Found at i:78526209 original size:53 final size:55
Alignment explanation
Indices: 78526127--78526276 Score: 178
Period size: 53 Copynumber: 2.7 Consensus size: 55
78526117 GGGGTGTTAG
* * * * * * *
78526127 GATATTATTATGGGATTTTTTTTTTAGCAATTTGATTCCTAGTGGGATGTTATAA
1 GATATTATTATGGAAGTTATATCTTAGCAATTTGATTCCTAATGGGATATTATAA
* *
78526182 GATATTATTAT-GAA-TTATCTCTTAGCAATTTAATTCCTAATGGGATATTATAA
1 GATATTATTATGGAAGTTATATCTTAGCAATTTGATTCCTAATGGGATATTATAA
* *
78526235 GATATTATTATGGAATGTTATATTTTAACAATTTGATTCCTA
1 GATATTATTATGGAA-GTTATATCTTAGCAATTTGATTCCTA
78526277 CATAACTGCT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
53 44 0.54
54 5 0.06
55 11 0.14
56 21 0.26
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (55 bp):
GATATTATTATGGAAGTTATATCTTAGCAATTTGATTCCTAATGGGATATTATAA
Found at i:78533953 original size:31 final size:31
Alignment explanation
Indices: 78533918--78533985 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
78533908 AATAAAATAG
*
78533918 TTATTCAACTATTTAAGA-ATTTTTATTTAAA
1 TTATTAAACTATTTAA-ATATTTTTATTTAAA
* * *
78533949 TTATTAAATTATTTAAATTTTTTTATTTAAG
1 TTATTAAACTATTTAAATATTTTTATTTAAA
78533980 TTATTA
1 TTATTA
78533986 GATTGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TTATTAAACTATTTAAATATTTTTATTTAAA
Found at i:78537750 original size:47 final size:47
Alignment explanation
Indices: 78537541--78537804 Score: 168
Period size: 47 Copynumber: 5.6 Consensus size: 47
78537531 TATAATGCCA
* * *
78537541 ATGCCATGTCCCAGACATGGTCTTACA-TTAGCTCATCCATCAAGT-CG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CACATCCAT-ACGTGCG
* * * * * * *
78537588 ATGCCACGTCCCAAACATTGTCTTACACTGAC-TATCAAAACTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCCATAC-G-TG-CG
* ** * **
78537637 ACGCCATGTCCCAGGTATGGTCTTACACTAGCTTTCACAT--ATTTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G---ACACATCCATACGTG-CG
* *
78537687 ATGCCATGTCCTAGACATGGTCTTACACTGACACCTCCATACGTGCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACATCCATACGTGCG
* * * *
78537734 ATGCCATGTCCCAGACATTGTCTTACACTAACATATCTCGTA-GT-CG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACATC-CATACGTGCG
78537780 ATG-CATGTCCCAGACAT-GTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
78537805 TTAGCTCTCG
Statistics
Matches: 169, Mismatches: 35, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
44 8 0.05
45 15 0.09
46 14 0.08
47 61 0.36
48 10 0.06
49 26 0.15
50 30 0.18
51 1 0.01
52 1 0.01
53 1 0.01
54 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACACATCCATACGTGCG
Found at i:78551323 original size:24 final size:24
Alignment explanation
Indices: 78551296--78551343 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
78551286 TAACCGTGTG
78551296 TCACACACGGTTGAGACACCGCCC
1 TCACACACGGTTGAGACACCGCCC
78551320 TCACACACGGTTGAGACACCGCCC
1 TCACACACGGTTGAGACACCGCCC
78551344 GTGTGGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.21, T:0.12
Consensus pattern (24 bp):
TCACACACGGTTGAGACACCGCCC
Found at i:78554365 original size:26 final size:26
Alignment explanation
Indices: 78554336--78554413 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
78554326 TTAGGTCGCG
78554336 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
** * *
78554362 TGTGTACCA-GATAGT-TAGG-TAGC-A
1 TGTGTAGTACTA-AGTGCAGGCTA-CTA
*
78554386 TGTGTAGTACTAAATGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
78554412 TG
1 TG
78554414 CGTACCTGAC
Statistics
Matches: 37, Mismatches: 9, Indels: 12
0.64 0.16 0.21
Matches are distributed among these distances:
24 12 0.32
25 10 0.27
26 15 0.41
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:78554404 original size:50 final size:50
Alignment explanation
Indices: 78554285--78554525 Score: 227
Period size: 50 Copynumber: 4.8 Consensus size: 50
78554275 GTGAGAACAC
* * *** * * *
78554285 GTGTAGTACTATGTGTAGGCTACTATGTGTTTAAGATGGTTTTAGGTCGCGT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG--TTAGGTAGCAT
78554337 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTAGCAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTAGCAT
* * * * * * * *
78554387 GTGTAGTACTAAATGCAGGCTACTATGCGTACCTGACAACTTCGATCA-CGT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA-TAGTTAGGT-AGCAT
* * *
78554438 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT-GGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTAGCAT
* *
78554487 GTGTAGTACTAAGTGCAGGTTACTAT-TCTTACCAGATAG
1 GTGTAGTACTAAGTGCAGGCTACTATGT-GTACCAGATAG
78554526 CTTCCGTTAC
Statistics
Matches: 155, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 44 0.28
51 39 0.25
52 34 0.22
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTAGCAT
Found at i:78554456 original size:51 final size:50
Alignment explanation
Indices: 78554333--78554522 Score: 177
Period size: 51 Copynumber: 3.8 Consensus size: 50
78554323 GTTTTAGGTC
* * * *
78554333 GCGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGTA
1 GCGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAACTTAGATA
* * * *
78554383 GCATGTGTAGTACTAAATGCAGGCTACTATGCGTACCTGACAACTTCGATCA
1 GCGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA-AACTTAGAT-A
* * *** * *
78554435 -CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT-GGTC
1 GCGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAACTTAGATA
* * * *
78554483 GCATGTGTAGTACTAAGTGCAGGTTACTATTCTTACCAGA
1 GCGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
78554523 TAGCTTCCGT
Statistics
Matches: 113, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 35 0.31
50 38 0.34
51 39 0.35
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
GCGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAAACTTAGATA
Found at i:78555009 original size:21 final size:21
Alignment explanation
Indices: 78554985--78555028 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
78554975 TCATTAAAAC
78554985 TTGTACAAATATAATTATGGG
1 TTGTACAAATATAATTATGGG
78555006 TTGTACAAATATAATTATGGG
1 TTGTACAAATATAATTATGGG
78555027 TT
1 TT
78555029 ATAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGTACAAATATAATTATGGG
Found at i:78558134 original size:22 final size:22
Alignment explanation
Indices: 78558109--78558150 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
78558099 CCATATTCAA
*
78558109 AAATATAAATCAAATTATACCG
1 AAATATAAATCAAACTATACCG
78558131 AAATATAAATCAAACTATAC
1 AAATATAAATCAAACTATAC
78558151 TGAATGCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATATAAATCAAACTATACCG
Found at i:78559307 original size:27 final size:27
Alignment explanation
Indices: 78559263--78559389 Score: 130
Period size: 27 Copynumber: 4.7 Consensus size: 27
78559253 TACAGAAATG
* * ***
78559263 CCCTCGACTTGTAAAATTACCAAAGTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
78559290 CCCTCGATTTATAGAATTACTATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * *
78559317 CCCTTGATTTATAGAATTACTATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
78559344 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
78559371 CCCTCGA-TTGTAAAATTAC
1 CCCTCGATTTATAAAATTAC
78559390 TGAAATACCC
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 10 0.12
27 75 0.88
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:78559401 original size:27 final size:27
Alignment explanation
Indices: 78559371--78559616 Score: 125
Period size: 27 Copynumber: 9.1 Consensus size: 27
78559361 TACCGTTTTA
* *
78559371 CCCTCGATTGTAAAATTACTGAAATAC
1 CCCTAGATTGTAAAATTACCGAAATAC
* ** * *
78559398 CCCTATAAGGTAGAATTACCAAAATA-
1 CCCTAGATTGTAAAATTACCGAAATAC
* *
78559424 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGATTGTAAAATTACCGAAATAC
* * * **
78559451 CACTAGTTTGTGAAATTATTGAAATA-
1 CCCTAGATTGTAAAATTACCGAAATAC
*
78559477 CCCTCA-ATTTGTAAAATTACCAAAATAC
1 CCCT-AGA-TTGTAAAATTACCGAAATAC
*
78559505 CCCT-GATT-TACAAAATTACAGAAATA-
1 CCCTAGATTGT--AAAATTACCGAAATAC
* * **
78559531 CCCTTGACTTTCTAAAAATTATTGAAATA-
1 CCCTAGA--TTGT-AAAATTACCGAAATAC
*
78559560 CCCTCA-ATTTGTAAAATTACCAAAATAC
1 CCCT-AGA-TTGTAAAATTACCGAAATAC
*
78559588 CCCT-GATT-TACAAAATTACAGAAATAC
1 CCCTAGATTGT--AAAATTACCGAAATAC
78559615 CC
1 CC
78559617 TTGACTTTCT
Statistics
Matches: 168, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
25 2 0.01
26 32 0.19
27 101 0.60
28 12 0.07
29 20 0.12
30 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
CCCTAGATTGTAAAATTACCGAAATAC
Found at i:78559521 original size:54 final size:53
Alignment explanation
Indices: 78559411--78559534 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 53
78559401 TATAAGGTAG
* ***
78559411 AATTACCA-AAATACCCTAGTTTGTAAAATTACCAAAATACCACTAGTTTGTGA
1 AATTA-CAGAAATACCCTAATTTGTAAAATTACCAAAATACCACTAGTTTACAA
** *
78559464 AATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAA
1 AATTACAGAAATACCCT-AATTTGTAAAATTACCAAAATACCACTAG-TTTACAA
78559518 AATTACAGAAATACCCT
1 AATTACAGAAATACCCT
78559535 TGACTTTCTA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 15 0.25
54 44 0.75
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (53 bp):
AATTACAGAAATACCCTAATTTGTAAAATTACCAAAATACCACTAGTTTACAA
Found at i:78559561 original size:83 final size:83
Alignment explanation
Indices: 78559463--78559644 Score: 364
Period size: 83 Copynumber: 2.2 Consensus size: 83
78559453 CTAGTTTGTG
78559463 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
1 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
78559528 ATACCCTTGACTTTCTAA
66 ATACCCTTGACTTTCTAA
78559546 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
1 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
78559611 ATACCCTTGACTTTCTAA
66 ATACCCTTGACTTTCTAA
78559629 AAATTATTGAAATACC
1 AAATTATTGAAATACC
78559645 ATTGGTTTAC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (83 bp):
AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
ATACCCTTGACTTTCTAA
Found at i:78559659 original size:83 final size:83
Alignment explanation
Indices: 78559463--78559672 Score: 321
Period size: 83 Copynumber: 2.5 Consensus size: 83
78559453 CTAGTTTGTG
* **
78559463 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
1 AAATTATTGAAATACCATCAATTTACAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
78559528 ATACCCTTGACTTTCTAA
66 ATACCCTTGACTTTCTAA
* **
78559546 AAATTATTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
1 AAATTATTGAAATACCATCAATTTACAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
78559611 ATACCCTTGACTTTCTAA
66 ATACCCTTGACTTTCTAA
*** **
78559629 AAATTATTGAAATACCATTGGTTTACAAAATTACTGAAATACCC
1 AAATTATTGAAATACCATCAATTTACAAAATTACCAAAATACCC
78559673 TTGGTTTGTA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 119 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (83 bp):
AAATTATTGAAATACCATCAATTTACAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAA
ATACCCTTGACTTTCTAA
Found at i:78559666 original size:27 final size:27
Alignment explanation
Indices: 78559489--78559679 Score: 134
Period size: 27 Copynumber: 6.9 Consensus size: 27
78559479 CTCAATTTGT
** * *
78559489 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
78559516 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *** **
78559543 TAAAAATTATTGAAATACCCTCAATTTGT
1 --AAAATTACTGAAATACCCTTGGTTTAC
** * *
78559572 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
78559599 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *
78559626 TAAAAATTATTGAAATACCATTGGTTTAC
1 --AAAATTACTGAAATACCCTTGGTTTAC
78559655 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
78559680 GTAGATTTAC
Statistics
Matches: 128, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
27 80 0.62
28 12 0.09
29 36 0.28
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.32
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:78559785 original size:27 final size:27
Alignment explanation
Indices: 78559708--78559785 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
78559698 CCTTGTAGAG
* *
78559708 AATACCCCT-AATAGGTAAAAAGACTGT
1 AATACCCCTGTAT-GGTAAAATGACTGT
* *
78559735 AA-AGCCCCTGTAGGGTAAAGTGACTGT
1 AATA-CCCCTGTATGGTAAAATGACTGT
78559762 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
78559786 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACTGT
Found at i:78560701 original size:24 final size:25
Alignment explanation
Indices: 78560594--78560688 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
78560584 AAGAAGTGCT
* * * *
78560594 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
78560619 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
78560644 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
78560669 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
78560689 ATTAAAAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:78560957 original size:31 final size:31
Alignment explanation
Indices: 78560908--78560990 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
78560898 TGCTTACAGT
78560908 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
78560938 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
78560969 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
78560991 TCGAGACTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.31
31 36 0.69
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:78561038 original size:29 final size:28
Alignment explanation
Indices: 78561004--78561058 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
78560994 AGACTGAATT
* *
78561004 AGGGCTTAGGCCCATACTGCTACTGTTTA
1 AGGGCTAAGGCCCAAACTG-TACTGTTTA
78561033 AGGGCTAAGGCCCAAACTGTACTGTT
1 AGGGCTAAGGCCCAAACTGTACTGTT
78561059 ACTGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (28 bp):
AGGGCTAAGGCCCAAACTGTACTGTTTA
Found at i:78561078 original size:33 final size:33
Alignment explanation
Indices: 78560996--78561089 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
78560986 ATATGTCGAG
*
78560996 ACTGAATTAGGGCTTAGGCCCATACTGCTACTGTT
1 ACTGAA-TAGGGCTTAGGCCCAAACTG-TACTGTT
*
78561031 --T--A-AGGGCTAAGGCCCAAACTGTACTGTT
1 ACTGAATAGGGCTTAGGCCCAAACTGTACTGTT
* * *
78561059 ACTGAATAGGGCTTTGGCCCAGATTGTACTG
1 ACTGAATAGGGCTTAGGCCCAAACTGTACTG
78561090 ACACAGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 7 0.15
29 17 0.35
30 1 0.02
31 1 0.02
32 1 0.02
33 21 0.44
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (33 bp):
ACTGAATAGGGCTTAGGCCCAAACTGTACTGTT
Found at i:78562187 original size:46 final size:45
Alignment explanation
Indices: 78562074--78562291 Score: 162
Period size: 46 Copynumber: 4.7 Consensus size: 45
78562064 GGGGTAAGGT
* **
78562074 GCCGATGCCATGTCCCAGACATGGTCATACACTGACACATC-T-TGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACT-ACAC-TCGTCTCAAG
* *
78562120 GCTGATGCATGTCCCAGACATGTCTTACACTA-ACTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTACAC-T-CGTCTCAAG
* *
78562166 GCCGATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTA-CACTCGTCTCAAG
* **
78562212 GCCAATGCCATGTCCCAGACATGGTCTTACACT-GGCTC-TCAT-AATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTACACTCGTC-TCAA---G
* *
78562260 GCTGATGAATGTCCCAGACATGTCTTACACTA
1 GCCGATGCATGTCCCAGACATGTCTTACACTA
78562292 GCTCACAATA
Statistics
Matches: 142, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
42 3 0.02
43 2 0.01
44 10 0.07
45 20 0.14
46 63 0.44
47 27 0.19
48 17 0.12
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTACACTCGTCTCAAG
Found at i:78564964 original size:12 final size:13
Alignment explanation
Indices: 78564928--78564965 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
78564918 AAATATTTGA
78564928 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
78564941 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
78564955 CTTG-TCTTAAT
1 CTTGTTCTTAAT
78564966 ATTCCAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:78573526 original size:60 final size:60
Alignment explanation
Indices: 78573428--78573560 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
78573418 CTGTGTTAAT
* *
78573428 ATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTGATACTGAC
1 ATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTGAC
* * * * * * *
78573488 ATGGGCTAGGCCCAGTATACTCTGGTAC-TGTAA-GGGGCTATGGCCCGGATTAATATTGAT
1 ATGGGCTAGGCCCAATATA-TCTCG-ACTTGTAATAGGGCTACGGCCCAGATTAATACTGAC
78573548 ATGGGCTAAGGCC
1 ATGGGCT-AGGCC
78573561 TAGTTAACTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 45 0.74
61 14 0.23
62 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (60 bp):
ATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTGAC
Found at i:78581464 original size:12 final size:12
Alignment explanation
Indices: 78581447--78581477 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
78581437 ATAATTTGAA
78581447 TATTATTGTTAT
1 TATTATTGTTAT
*
78581459 TATTATTTTTAT
1 TATTATTGTTAT
78581471 TATTATT
1 TATTATT
78581478 ACGTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
TATTATTGTTAT
Found at i:78582357 original size:15 final size:16
Alignment explanation
Indices: 78582339--78582371 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
78582329 TCTTTTCTCC
78582339 TCTCTTCATC-TATTT
1 TCTCTTCATCTTATTT
*
78582354 TCTCTTCTTCTTATTT
1 TCTCTTCATCTTATTT
78582370 TC
1 TC
78582372 CTCTATAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (16 bp):
TCTCTTCATCTTATTT
Found at i:78583170 original size:16 final size:16
Alignment explanation
Indices: 78583149--78583179 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
78583139 TTAGATCGAT
78583149 AAATGCCGAAAAGCTG
1 AAATGCCGAAAAGCTG
78583165 AAATGCCGAAAAGCT
1 AAATGCCGAAAAGCT
78583180 AGTATTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (16 bp):
AAATGCCGAAAAGCTG
Found at i:78583462 original size:27 final size:26
Alignment explanation
Indices: 78583432--78583489 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
78583422 TACCAAAATA
* *
78583432 CCCTAAGTATGAAAATTACCATTATGC
1 CCCTAAGTAT-AAAATGACCATTATAC
* *
78583459 CCCTAGGTGTAAAATGACCATTATAC
1 CCCTAAGTATAAAATGACCATTATAC
78583485 CCCTA
1 CCCTA
78583490 GGGTTGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (26 bp):
CCCTAAGTATAAAATGACCATTATAC
Found at i:78583636 original size:28 final size:28
Alignment explanation
Indices: 78583594--78583681 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
78583584 GGAGGAAGCG
* *
78583594 TTCTGGTGGCTCTGCCACAAATATTTGT
1 TTCTGGTGGCCCTGCCACAAATATCTGT
*
78583622 TTCTGGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCCCTGCCACAAATATCTGT
* * * *
78583650 ATCTGGTGACTCTGGCAC-AATATCTG-
1 TTCTGGTGGCCCTGCCACAAATATCTGT
78583676 TTCTGG
1 TTCTGG
78583682 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 5 0.10
27 7 0.14
28 39 0.76
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (28 bp):
TTCTGGTGGCCCTGCCACAAATATCTGT
Found at i:78585199 original size:49 final size:50
Alignment explanation
Indices: 78585004--78585224 Score: 237
Period size: 50 Copynumber: 4.4 Consensus size: 50
78584994 CACATGATCA
* * * *
78585004 GCTACTATGTGTACTAGATAGTTAGGTCGCATGTGTAGTACTAAGTGTAG
1 GCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGCAG
* * * * * * * *
78585054 GCTACTATGCGTACCCGACAACTTCGATCACGTGTGTAGTACTAAGTGCAG
1 GCTACTACGTGTACCAGA-TAGTTAGGTCACATGTGTAGTACTAAGTGCAG
* * * * *
78585105 GATACTACGTGTATCAGATGGTTTGGTCACGTGTGTAGTACTAAGTGCAG
1 GCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGCAG
*
78585155 GCTACTACGTGTACCAGATTGTT-GGTCACATGTGTAGTACTAAGTGCAG
1 GCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGCAG
* * *
78585204 GCTACTATGCGTAACAGATAG
1 GCTACTACGTGTACCAGATAG
78585225 CTTCGGTTAC
Statistics
Matches: 142, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 42 0.30
50 62 0.44
51 38 0.27
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
GCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGCAG
Found at i:78585443 original size:16 final size:15
Alignment explanation
Indices: 78585422--78585451 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
78585412 GAATGGAGTA
78585422 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
78585438 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
78585452 TAAAATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:78589398 original size:43 final size:43
Alignment explanation
Indices: 78589334--78589442 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
78589324 GCAGACACAT
* *
78589334 GGGCGTGTGTCTAGACCGTGTGTGACACACGGCCTGGTAACAC
1 GGGCGTGTGTTTAGACCGTGTGTGACACACGGCCAGGTAACAC
*
78589377 GGGCGTGTGTTTAGACTGTGTGTGACACACGGCCAGGTAACAC
1 GGGCGTGTGTTTAGACCGTGTGTGACACACGGCCAGGTAACAC
* * *
78589420 GGGCATGTGGTTAGGCCGTGTGT
1 GGGCGTGTGTTTAGACCGTGTGT
78589443 CCCCTGCACC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.24
Consensus pattern (43 bp):
GGGCGTGTGTTTAGACCGTGTGTGACACACGGCCAGGTAACAC
Found at i:78591607 original size:30 final size:29
Alignment explanation
Indices: 78591564--78591625 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
78591554 CAAGTAGCTG
78591564 AAGCTAGTTAAATCGCACA-CTTAGTGCCA
1 AAGCTAGTTAAATCGCACATC-TAGTGCCA
78591593 AAGCTAGTTTAAATCGCACATCTAGTGCCA
1 AAGCTAG-TTAAATCGCACATCTAGTGCCA
78591623 AAG
1 AAG
78591626 ATTCCGATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 7 0.23
30 23 0.74
31 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACATCTAGTGCCA
Found at i:78598837 original size:30 final size:29
Alignment explanation
Indices: 78598794--78598855 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
78598784 CAAGTAGCCG
78598794 AAGCTAGTTAAATCGCACA-CTTAGTGCCA
1 AAGCTAGTTAAATCGCACATC-TAGTGCCA
78598823 AAGCTAGTTTAAATCGCACATCTAGTGCCA
1 AAGCTAG-TTAAATCGCACATCTAGTGCCA
78598853 AAG
1 AAG
78598856 ATTCCGATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 7 0.23
30 23 0.74
31 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACATCTAGTGCCA
Found at i:78603165 original size:21 final size:21
Alignment explanation
Indices: 78603126--78603165 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
78603116 ACTTGTTTAG
*
78603126 CTATCAACAACCATTCAAAAC
1 CTATCAACAACCATCCAAAAC
* *
78603147 CTATCATCAATCATCCAAA
1 CTATCAACAACCATCCAAA
78603166 CTCATACATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
CTATCAACAACCATCCAAAAC
Found at i:78603412 original size:14 final size:13
Alignment explanation
Indices: 78603376--78603414 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
78603366 GATGATAGCC
*
78603376 TTTAATTATTTGT
1 TTTAATTATTTAT
78603389 TTTAATTATTTAT
1 TTTAATTATTTAT
78603402 TTTATATTATTTA
1 TTTA-ATTATTTA
78603415 CCAAATTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTAATTATTTAT
Found at i:78609808 original size:17 final size:17
Alignment explanation
Indices: 78609786--78609826 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
78609776 AAATAAACAA
78609786 AGTAAGCTATAAAGCTT
1 AGTAAGCTATAAAGCTT
*
78609803 AGTAAGCTCTAAAGCTT
1 AGTAAGCTATAAAGCTT
78609820 AGTAAGC
1 AGTAAGC
78609827 CCGTATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (17 bp):
AGTAAGCTATAAAGCTT
Found at i:78611176 original size:40 final size:40
Alignment explanation
Indices: 78610990--78611175 Score: 295
Period size: 40 Copynumber: 4.7 Consensus size: 40
78610980 GCAAGCCTAT
* * *
78610990 GGGTCTTTAA-CTCGGATACCATTCCAGCACGA-AGCCTGC
1 GGGTCTTTAAGCCCGGATACAATTCCAGCA-TATAGCCTGC
* *
78611029 GGATCTTTATGCCCGGATACAATTCCAGCATATAGCCTGC
1 GGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGC
78611069 GGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGC
1 GGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGC
*
78611109 GGGTCTTTAAGCCCGGATACAATTCCAACATATAGCCTGC
1 GGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGC
78611149 GGGTCTTTAAGCCCGGATACAATTCCA
1 GGGTCTTTAAGCCCGGATACAATTCCA
78611176 AATATCATAC
Statistics
Matches: 137, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 9 0.07
40 128 0.93
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
GGGTCTTTAAGCCCGGATACAATTCCAGCATATAGCCTGC
Found at i:78611442 original size:2 final size:2
Alignment explanation
Indices: 78611435--78611467 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
78611425 ATTCATCTAG
*
78611435 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78611468 CAAGGCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78618163 original size:46 final size:46
Alignment explanation
Indices: 78618096--78618265 Score: 156
Period size: 46 Copynumber: 3.7 Consensus size: 46
78618086 AACCCGCCCC
* *
78618096 TAAGTGAACTCGGACTTAACTCAACGAGCTCGGGAGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGAGTTCGCATCCA
* *
78618142 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G---AGTTCGCATCCA
* * * *
78618190 TCA-CGAACTTGGACTCAACTCAACGAGTTC-GGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGA-GTTCGCATCCA
*
78618235 TAAGT-AACTC-GACTCAACTCTACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
78618266 ATGCTCAACC
Statistics
Matches: 99, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 3 0.03
44 20 0.20
45 7 0.07
46 31 0.31
47 24 0.24
48 3 0.03
49 1 0.01
50 3 0.03
51 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGAGTTCGCATCCA
Found at i:78618213 original size:93 final size:91
Alignment explanation
Indices: 78618101--78618269 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 91
78618091 GCCCCTAAGT
* *
78618101 GAACTCGGACTTAACTCAACGAGCTCGGGA-GTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGT-AACTC-GACTCAACTCA
*
78618165 ATGAGTTCGGATGCCTAGTTACATCTCAC
63 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
78618194 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTAACTCGACTCAACTCTACG
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAACTCGACTCAACTCAACG
78618259 AGTTCGGATGC
66 AGTTCGGATGC
78618270 TCAACCATCC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
91 23 0.33
92 8 0.12
93 38 0.55
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAACTCGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:78621225 original size:40 final size:40
Alignment explanation
Indices: 78621032--78621224 Score: 302
Period size: 40 Copynumber: 4.8 Consensus size: 40
78621022 TTCTAGCGCA
* * *
78621032 AGCCTACGGGTCTTTAA--CCGGATACCATTCCAGCACGA-
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCA-TAT
*
78621070 AGCCTGCGGAGTCTTTATGCCCGGATACAATTCCAGCATAT
1 AGCCTGCGG-GTCTTTAAGCCCGGATACAATTCCAGCATAT
78621111 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
*
78621151 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAACATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
78621191 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
78621225 AATATCATAC
Statistics
Matches: 145, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
38 8 0.06
39 7 0.05
40 104 0.72
41 26 0.18
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
Found at i:78628215 original size:47 final size:49
Alignment explanation
Indices: 78628098--78628272 Score: 183
Period size: 45 Copynumber: 3.8 Consensus size: 49
78628088 TAACCCGCCC
* * * *
78628098 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G--GTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
78628143 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATCCA
* *
78628191 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
78628236 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
78628273 TCAACCATCC
Statistics
Matches: 109, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 34 0.31
46 29 0.27
47 30 0.28
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
Found at i:78628261 original size:93 final size:92
Alignment explanation
Indices: 78628103--78628272 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 92
78628093 CGCCCTAAGT
**
78628103 GAACTCGGACTCAACTCAACGAGCTCGGGGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
78628168 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
78628195 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
78628260 CGAGTTCGGATGC
65 CGAGTTCGGATGC
78628273 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 27 0.36
93 47 0.64
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:78628721 original size:30 final size:30
Alignment explanation
Indices: 78628687--78628746 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
78628677 ATTTAATACG
78628687 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
78628717 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
78628747 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:78635714 original size:47 final size:49
Alignment explanation
Indices: 78635597--78635771 Score: 183
Period size: 45 Copynumber: 3.8 Consensus size: 49
78635587 AACCCGCCCC
* * * *
78635597 TAAGTGAACTCGGACTCAACTCAACGAGCTC-G--G-CGTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
78635642 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATCCA
* *
78635690 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
78635735 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
78635772 TCAACCATCC
Statistics
Matches: 109, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 32 0.29
46 30 0.28
47 29 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
Found at i:78635760 original size:93 final size:92
Alignment explanation
Indices: 78635602--78635771 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 92
78635592 GCCCCTAAGT
*
78635602 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
78635667 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
78635694 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
78635759 CGAGTTCGGATGC
65 CGAGTTCGGATGC
78635772 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:78636225 original size:30 final size:30
Alignment explanation
Indices: 78636191--78636250 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
78636181 ATTTAATACG
78636191 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
78636221 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
78636251 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:78643719 original size:30 final size:30
Alignment explanation
Indices: 78643685--78643744 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
78643675 ATTTAATACG
78643685 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
78643715 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
78643745 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:78646240 original size:2 final size:2
Alignment explanation
Indices: 78646233--78646269 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
78646223 TATTAGCTGA
78646233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78646270 AATACACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78646745 original size:81 final size:81
Alignment explanation
Indices: 78646633--78646790 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 81
78646623 TTTAACCCGG
* * * *
78646633 ATACCATTCCAGCACGAAGCCTGCGGATCTTTATGCCCGGATACAATTCCAGCATATAGCCTGCC
1 ATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACAATTCCAACATATAGCCTGAC
78646698 GGTCTTTAAGCCAAAA
66 GGTCTTTAAGCCAAAA
* *
78646714 ATACAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAACATATAGCCTGA
1 ATACAATTCCAGCACGA-AGCCTGCGGATCTTTAAGCCCGGATACAATTCCAACATATAGCCTGA
*
78646778 GGGTCTTTAAGCC
65 CGGTCTTTAAGCC
78646791 CGGATACAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 68 0.99
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (81 bp):
ATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACAATTCCAACATATAGCCTGAC
GGTCTTTAAGCCAAAA
Found at i:78646805 original size:40 final size:40
Alignment explanation
Indices: 78646611--78646804 Score: 257
Period size: 40 Copynumber: 4.8 Consensus size: 40
78646601 TTCTAGTGCA
* * *
78646611 AGCCTACGGGTCTTTAA-CCCGGATACCATTCCAGCACGA-
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCA-TAT
* *
78646650 AGCCTGCGGATCTTTATGCCCGGATACAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
* ***
78646690 AGCCTGCCGGTCTTTAAGCCAAAAATACAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCC-CGGATACAATTCCAGCATAT
*
78646731 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAACATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
*
78646771 AGCCTGAGGGTCTTTAAGCCCGGATACAATTCCA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
78646805 AATATCATAC
Statistics
Matches: 135, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.11
40 84 0.62
41 36 0.27
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
Found at i:78647071 original size:2 final size:2
Alignment explanation
Indices: 78647064--78647116 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
78647054 ATTCATCTAG
* * *
78647064 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA CA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
78647106 TA TG TA TA TA T
1 TA TA TA TA TA T
78647117 CAAGGCATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:78648116 original size:21 final size:21
Alignment explanation
Indices: 78648091--78648131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
78648081 CGGCAATTTC
78648091 AATTCATACCT-TTCAACCATA
1 AATTCA-ACCTATTCAACCATA
*
78648112 AATTCAACTTATTCAACCAT
1 AATTCAACCTATTCAACCAT
78648132 CATTTAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTCAACCTATTCAACCATA
Found at i:78648141 original size:21 final size:21
Alignment explanation
Indices: 78648102--78648141 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
78648092 ATTCATACCT
*
78648102 TTCAACCATAAATTCAACTTA
1 TTCAACCATAAATTAAACTTA
* *
78648123 TTCAACCATCATTTAAACT
1 TTCAACCATAAATTAAACT
78648142 ACTTAACATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
TTCAACCATAAATTAAACTTA
Found at i:78650931 original size:40 final size:40
Alignment explanation
Indices: 78650887--78651034 Score: 215
Period size: 40 Copynumber: 3.7 Consensus size: 40
78650877 TACCGGCACT
* *
78650887 AAGCCTGTGAGATTTAACCCGGATATACTTTACCAGCATA
1 AAGCCTGCGAGATTTAACCCGGATATACTTTACCAGCATG
* *
78650927 AAGCCTACGGGATTTAACCCGGATATACTTTACCAGCATG
1 AAGCCTGCGAGATTTAACCCGGATATACTTTACCAGCATG
* *
78650967 AAGCCTGCGAGATTTAACCCGGATATACATTACCAGCACG
1 AAGCCTGCGAGATTTAACCCGGATATACTTTACCAGCATG
* * *
78651007 ATGCCTGCGGGATTTAACCTGGATATAC
1 AAGCCTGCGAGATTTAACCCGGATATAC
78651035 AATATATCGA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
AAGCCTGCGAGATTTAACCCGGATATACTTTACCAGCATG
Found at i:78650971 original size:80 final size:79
Alignment explanation
Indices: 78650836--78651034 Score: 240
Period size: 80 Copynumber: 2.5 Consensus size: 79
78650826 CCGAATCCAG
* * * * *
78650836 TTACTAGCACAAAGCCTACAGGACTTTAGGCCCGGATATA-GTACCGGCACTAAGCCTGTGAGAT
1 TTACCAGCACAAAGCCTACGGGA-TTTA-ACCCGGATATACGTACCAGCACTAAGCCTGCGAGAT
*
78650900 TTAACCCGGATATACT
64 TTAACCCGGATATACA
* *
78650916 TTACCAGCATAAAGCCTACGGGATTTAACCCGGATATACTTTACCAGCA-TGAAGCCTGCGAGAT
1 TTACCAGCACAAAGCCTACGGGATTTAACCCGGATATAC-GTACCAGCACT-AAGCCTGCGAGAT
78650980 TTAACCCGGATATACA
64 TTAACCCGGATATACA
* * * *
78650996 TTACCAGCACGATGCCTGCGGGATTTAACCTGGATATAC
1 TTACCAGCACAAAGCCTACGGGATTTAACCCGGATATAC
78651035 AATATATCGA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 10 0.10
79 5 0.05
80 88 0.85
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (79 bp):
TTACCAGCACAAAGCCTACGGGATTTAACCCGGATATACGTACCAGCACTAAGCCTGCGAGATTT
AACCCGGATATACA
Found at i:78656401 original size:46 final size:46
Alignment explanation
Indices: 78656341--78656474 Score: 153
Period size: 46 Copynumber: 2.9 Consensus size: 46
78656331 GGGATATTTG
* * *
78656341 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGA
1 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-ACGA
* *** * *
78656388 -GCGTCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGAACGA
*
78656434 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
78656475 GAAGGTTACA
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
46 35 0.50
47 35 0.50
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.30
Consensus pattern (46 bp):
GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAACGA
Found at i:78661730 original size:40 final size:40
Alignment explanation
Indices: 78661531--78661730 Score: 233
Period size: 40 Copynumber: 5.0 Consensus size: 40
78661521 CCGAATCCAG
* * * *
78661531 TTACTAGCACAAAGCCTACGGGACTTTAGGCCCGGATAT--A
1 TTACCAGCACGAAGCCTGCGGGA-TTTA-ACCCGGATATACA
* * * * *
78661571 GTACCAGCACTAAGCCTGCGAGACTTAACCCGGATATACT
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACA
* * *
78661611 TTACCAGCATGAAGCCTGCGGGATTTAACCCGAATATACT
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACA
*
78661651 TTACCAGCATGAAGCCTGCGGGATTTAACCCGGATATACA
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACA
* *
78661691 TTACCAGCACGATGCCTGCGGGATTTAACCTGGATATACA
1 TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACA
78661731 ATATATCGAG
Statistics
Matches: 139, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
38 9 0.06
39 3 0.02
40 127 0.91
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
TTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACA
Found at i:78664023 original size:8 final size:8
Alignment explanation
Indices: 78664012--78664059 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
78664002 TTTAAGAAAT
78664012 TAATATAA
1 TAATATAA
78664020 TAATATAA
1 TAATATAA
78664028 TAATATAA
1 TAATATAA
*
78664036 T--T-TAG
1 TAATATAA
*
78664041 TAATTTAA
1 TAATATAA
78664049 TAATATAA
1 TAATATAA
78664057 TAA
1 TAA
78664060 AACATACAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 3 0.09
6 1 0.03
7 1 0.03
8 29 0.85
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (8 bp):
TAATATAA
Found at i:78664108 original size:18 final size:18
Alignment explanation
Indices: 78664074--78664111 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
78664064 TACAAGAAAT
*
78664074 AAAAGAAATAAACAAAGA
1 AAAAGAAATAAAAAAAGA
78664092 AAAAGAAA-AAAGAAAAGA
1 AAAAGAAATAAA-AAAAGA
78664110 AA
1 AA
78664112 CGAAACAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAGAAATAAAAAAAGA
Found at i:78666454 original size:40 final size:40
Alignment explanation
Indices: 78666399--78666543 Score: 220
Period size: 40 Copynumber: 3.6 Consensus size: 40
78666389 CGGATGATAA
* *
78666399 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
78666439 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
** *
78666479 CCGGGCTAAGTCCAAAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
78666519 CCGGGCTAAGTCTCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
78666544 AGCAAGTAGT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 95 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:78666843 original size:22 final size:21
Alignment explanation
Indices: 78666802--78666845 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
78666792 GAATGTGCAT
78666802 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
78666824 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
78666846 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:78679470 original size:38 final size:38
Alignment explanation
Indices: 78679398--78679470 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
78679388 GAGGTATTAT
**
78679398 TCAAGCTCAGTGCCTAGCAGGCTCAATGTTGGTGTTAA
1 TCAAGCTCAGTGCCTAGCAGGCTCAATGCCGGTGTTAA
* *
78679436 TCAAGCTTAGTGCCTAGTAGGCTCAATGCCGGTGT
1 TCAAGCTCAGTGCCTAGCAGGCTCAATGCCGGTGT
78679471 AGTAAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (38 bp):
TCAAGCTCAGTGCCTAGCAGGCTCAATGCCGGTGTTAA
Found at i:78685114 original size:78 final size:80
Alignment explanation
Indices: 78684979--78685195 Score: 331
Period size: 78 Copynumber: 2.8 Consensus size: 80
78684969 ATTCGGATTG
78684979 ATAACCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
78685042 TTTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
*
78685057 ATAACCGGGC-AAGTCCCGAAGGCAATTGTGCGAGTTACTATA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
78685120 ATTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
* * *
78685135 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-AAGCTATATCC-GGCTAA-ACCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
78685196 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
77 3 0.02
78 64 0.50
79 59 0.46
80 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTTACT
Found at i:78685177 original size:40 final size:40
Alignment explanation
Indices: 78684979--78685169 Score: 318
Period size: 40 Copynumber: 4.9 Consensus size: 40
78684969 ATTCGGATTG
78684979 ATAACCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
78685017 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
78685057 ATAACCGGGC-AAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
78685096 AT-ACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
78685135 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
78685170 AAGCTATATC
Statistics
Matches: 144, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 20 0.14
39 61 0.42
40 63 0.44
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:78691458 original size:29 final size:29
Alignment explanation
Indices: 78691424--78691495 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 29
78691414 TAATCGATCA
* * *
78691424 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATATAATTTAAACT
* *
78691453 CGCACA--TAGTGCCGTATAATTTAAATT
1 CGCACACTTAGTGCCATATAATTTAAACT
78691480 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
78691496 ACTTTTCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 22 0.63
29 13 0.37
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATAATTTAAACT
Done.