Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 24 of 141
Found at i:7495423 original size:16 final size:16
Alignment explanation
Indices: 7495402--7495433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7495392 TCAATTAATC
*
7495402 TAATTAACCTAAAAAT
1 TAATTAAACTAAAAAT
7495418 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
7495434 CAACCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATTAAACTAAAAAT
Found at i:7501298 original size:22 final size:23
Alignment explanation
Indices: 7501252--7501303 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
7501242 ACCACACCAA
*
7501252 TAGGCACTGAAGTGCTTTAATAG
1 TAGGCACTGAAGTGCTTGAATAG
7501275 TAGGCA-TCGAAGTG-TTGAATAG
1 TAGGCACT-GAAGTGCTTGAATAG
7501297 TAGGCAC
1 TAGGCAC
7501304 CAAGGTGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
TAGGCACTGAAGTGCTTGAATAG
Found at i:7501321 original size:22 final size:22
Alignment explanation
Indices: 7501294--7501390 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
7501284 AAGTGTTGAA
*
7501294 TAGTAGGCACCA-AGGTGCAAAT
1 TAGTAGGCACCATA-GTGCAAAG
* *
7501316 TTGTAGGCACTGA-AGTGCAAAG
1 TAGTAGGCAC-CATAGTGCAAAG
* * *
7501338 CAGTAAGCACCATAGTGCAAAT
1 TAGTAGGCACCATAGTGCAAAG
*
7501360 TATTAGGCACCATAGTGCAAAG
1 TAGTAGGCACCATAGTGCAAAG
7501382 TAGTAGGCA
1 TAGTAGGCA
7501391 TAGAAGTGCA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 1 0.02
22 57 0.95
23 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (22 bp):
TAGTAGGCACCATAGTGCAAAG
Found at i:7501348 original size:44 final size:44
Alignment explanation
Indices: 7501295--7501386 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
7501285 AGTGTTGAAT
* *
7501295 AGTAGGCACCA-AGGTGCAAATT-TGTAGGCACTGA-AGTGCAAAGC
1 AGTAAGCACCATA-GTGCAAATTAT-TAGGCAC-CATAGTGCAAAGC
*
7501339 AGTAAGCACCATAGTGCAAATTATTAGGCACCATAGTGCAAAGT
1 AGTAAGCACCATAGTGCAAATTATTAGGCACCATAGTGCAAAGC
7501383 AGTA
1 AGTA
7501387 GGCATAGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 39 0.93
45 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (44 bp):
AGTAAGCACCATAGTGCAAATTATTAGGCACCATAGTGCAAAGC
Found at i:7505444 original size:13 final size:13
Alignment explanation
Indices: 7505426--7505450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7505416 GGGCTCACAC
7505426 GCCCATGTGGTCT
1 GCCCATGTGGTCT
7505439 GCCCATGTGGTC
1 GCCCATGTGGTC
7505451 CCACACACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (13 bp):
GCCCATGTGGTCT
Found at i:7513194 original size:19 final size:19
Alignment explanation
Indices: 7513170--7513209 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
7513160 ATTAATTTTG
7513170 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
7513189 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
7513208 AT
1 AT
7513210 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:7513612 original size:22 final size:21
Alignment explanation
Indices: 7513571--7513711 Score: 77
Period size: 22 Copynumber: 6.8 Consensus size: 21
7513561 ATTCCAAAAA
*
7513571 TAATA-TTATTTTAATAAATT
1 TAATATTTAATTTAATAAATT
*
7513591 TAATATTTAATTTAATTTAATT
1 TAATATTTAATTTAA-TAAATT
* *
7513613 TAATGTTTATCTTGTAAATAAATAT
1 TAATATTTA-ATT-T-AATAAAT-T
*
7513638 T-CTA-TTAATTTAATAAATTT
1 TAATATTTAATTTAATAAA-TT
*
7513658 TAATATTAAATTT--T--ATT
1 TAATATTTAATTTAATAAATT
*
7513675 TAATATTT-ATCTTTATAAATAT
1 TAATATTTAAT-TTAATAAAT-T
7513697 T-ATA-TTAATTTAATA
1 TAATATTTAATTTAATA
7513712 TTAAAGTGAT
Statistics
Matches: 93, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
16 2 0.02
17 11 0.12
18 1 0.01
19 1 0.01
20 21 0.23
21 19 0.20
22 23 0.25
23 5 0.05
24 6 0.06
25 4 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (21 bp):
TAATATTTAATTTAATAAATT
Found at i:7513678 original size:17 final size:17
Alignment explanation
Indices: 7513656--7513716 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 17
7513646 TTTAATAAAT
7513656 TTTAATATTAAATTTTA
1 TTTAATATTAAATTTTA
*
7513673 TTTAATATT-TATCTTTA
1 TTTAATATTAAAT-TTTA
* * *
7513690 -TAAATATTATA-TTAA
1 TTTAATATTAAATTTTA
7513705 TTTAATATTAAA
1 TTTAATATTAAA
7513717 GTGATTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.08
16 18 0.50
17 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATATTAAATTTTA
Found at i:7513709 original size:59 final size:59
Alignment explanation
Indices: 7513596--7513711 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 59
7513586 AAATTTAATA
* *
7513596 TTTAATTTAATTTAATTTAATGTTTATCTTGTAAATAAATATTCTATTAATTTAATAAAT
1 TTTAATTTAATTTAATTTAATATTTATCTTGT-AATAAATATTATATTAATTTAATAAAT
*
7513656 TTTAATATTAAATTTTATTTAATATTTATCTT-T-ATAAATATTATATTAATTTAATA
1 TTTAAT-TT-AATTTAATTTAATATTTATCTTGTAATAAATATTATATTAATTTAATA
7513712 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 22 0.43
60 6 0.12
61 3 0.06
62 20 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (59 bp):
TTTAATTTAATTTAATTTAATATTTATCTTGTAATAAATATTATATTAATTTAATAAAT
Found at i:7516048 original size:3 final size:3
Alignment explanation
Indices: 7516040--7516071 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
7516030 AATTGGTTTC
*
7516040 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
7516072 CACCCAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:7517292 original size:19 final size:20
Alignment explanation
Indices: 7517268--7517318 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
7517258 ATATTAATAA
*
7517268 TATTATTAAAATTCAAA-TT
1 TATTATTAAAATTAAAATTT
7517287 TATTATTAAAA-TAAAATTT
1 TATTATTAAAATTAAAATTT
*
7517306 TAATATTAAAATT
1 TATTATTAAAATT
7517319 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATTAAAATTAAAATTT
Found at i:7518820 original size:21 final size:21
Alignment explanation
Indices: 7518794--7518838 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
7518784 TCTGTTTGGT
7518794 TGGTGAGAAAACTAAAGAAAA
1 TGGTGAGAAAACTAAAGAAAA
*
7518815 TGGTGAGAAAACTGAAGAAAA
1 TGGTGAGAAAACTAAAGAAAA
7518836 TGG
1 TGG
7518839 ATTTCATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (21 bp):
TGGTGAGAAAACTAAAGAAAA
Found at i:7519556 original size:16 final size:16
Alignment explanation
Indices: 7519519--7519560 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
7519509 TTAATCATAT
*
7519519 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
7519535 TT-AAATATATTATAA
1 TTAAAATATATTATAA
7519550 TTAAAATATAT
1 TTAAAATATAT
7519561 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:7519567 original size:14 final size:15
Alignment explanation
Indices: 7519528--7519569 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
7519518 TTTAAACATA
*
7519528 ATTATTATTAAATAT
1 ATTATAATTAAATAT
7519543 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
7519557 A-TATAATTTAATA
1 ATTATAATTAAATA
7519570 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:7519798 original size:16 final size:16
Alignment explanation
Indices: 7519755--7519800 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
7519745 ACTATAAAAG
*
7519755 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
7519771 ATTATT-AAATATATT
1 ATAATTAAAATATATT
7519786 ATAATTAAAATATAT
1 ATAATTAAAATATAT
7519801 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:7519807 original size:14 final size:15
Alignment explanation
Indices: 7519755--7519809 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
7519745 ACTATAAAAG
7519755 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
7519771 ATTATTAAATATATT
1 ATAATTAAATATATT
7519786 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
7519799 ATAATTTAATA
1 ATAATTAAATA
7519810 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:7519932 original size:59 final size:58
Alignment explanation
Indices: 7519735--7519923 Score: 172
Period size: 59 Copynumber: 3.2 Consensus size: 58
7519725 CTCAAATCAT
* *
7519735 AATATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTATAATTAA
1 AATATATGATACTATAAAAGATAATTTAA-ATAATTAATATTAAATATATTTTAATTAA
* * * ** *
7519794 AATATAT-A-A-TTTAATA-A-AATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCA
1 AATATATGATACTATAAAAGATAATT-TAAATAATTAATATT-AAATAT--ATTT--T--AATTA
*
7519854 T
58 A
7519855 AATATATGATACTATAAAAGATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAGATAATTT-AAATAATTAATATTAAATATATTTTAATTAA
7519914 AATATATGAT
1 AATATATGAT
7519924 TTAATAAAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 28
0.69 0.11 0.19
Matches are distributed among these distances:
54 15 0.15
55 7 0.07
56 5 0.05
57 4 0.04
58 1 0.01
59 22 0.22
61 12 0.12
62 1 0.01
63 5 0.05
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAAGATAATTTAAATAATTAATATTAAATATATTTTAATTAA
Found at i:7519945 original size:120 final size:120
Alignment explanation
Indices: 7519517--7519934 Score: 723
Period size: 120 Copynumber: 3.5 Consensus size: 120
7519507 ATTTAATCAT
*
7519517 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
7519582 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
7519638 AATTAACATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAACATAATTAA-TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
7519702 ATTAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
7519758 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
7519823 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
7519878 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
7519935 TAAAATAATT
Statistics
Matches: 283, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
119 2 0.01
120 274 0.97
121 7 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
ATTTAACATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:7519981 original size:101 final size:93
Alignment explanation
Indices: 7519875--7520157 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
7519865 ACTATAAAAG
* * * *
7519875 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
7519939 ATAATTATAACTAATAAATTATCTTATATGAATTTGT
62 -T--CT-TAA-TAATAAATTATCTTATATGAATTTAT
* *
7519976 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
7520039 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* *
7520067 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
7520130 AATAATAAAATGT-TCTTATATGAATTTA
66 AATAAT-AAAT-TATCTTATATGAATTTA
7520158 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
91 88 0.54
92 21 0.13
93 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTATCTTATATGAATTTAT
Found at i:7520004 original size:26 final size:28
Alignment explanation
Indices: 7519975--7520035 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
7519965 TATGAATTTG
*
7519975 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
7520001 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
7520029 TAAAATT
1 TATAATT
7520036 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:7520033 original size:47 final size:46
Alignment explanation
Indices: 7519982--7520125 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
7519972 TTGTATAATT
7519982 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
7520029 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
7520073 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
7520120 TAAAAT
1 TAAAAT
7520126 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:7520045 original size:91 final size:90
Alignment explanation
Indices: 7519950--7520157 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
7519940 TAATTATAAC
* * * *
7519950 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
7520015 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
7520041 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
7520106 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
7520132 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
7520158 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:7520117 original size:44 final size:43
Alignment explanation
Indices: 7519975--7520117 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
7519965 TATGAATTTG
* *
7519975 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
7520019 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
7520066 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
7520110 TATAATTT
1 TATAATTT
7520118 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:7520132 original size:47 final size:47
Alignment explanation
Indices: 7520000--7520138 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
7519990 TTATTATTAC
* *
7520000 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
7520047 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
7520091 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
7520138 A
1 A
7520139 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:7521577 original size:11 final size:11
Alignment explanation
Indices: 7521563--7521589 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7521553 AAAAATCAAT
7521563 ACAAAAGTTTC
1 ACAAAAGTTTC
7521574 ACAAAAGTTTC
1 ACAAAAGTTTC
7521585 ACAAA
1 ACAAA
7521590 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:7532167 original size:70 final size:71
Alignment explanation
Indices: 7532051--7532184 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 71
7532041 AATTTCATTT
* * * *
7532051 ATGTTTATTAGATAATCAACTCTGTTACAAAACATATTTTGTTATAGGCAACCCTCAGATTTTTT
1 ATGTTTATTAGACAATAAACTCTG-TACAAAACATAATTTATTATAGGCAACCCTCAGATTTTTT
7532116 TTCCTCC
65 TTCCTCC
*
7532123 ATGTTTATTTGACAATAAACTCTG-ACAAAACATAATTTATTATAGGCAACCCTCAGATTTTT
1 ATGTTTATTAGACAATAAACTCTGTACAAAACATAATTTATTATAGGCAACCCTCAGATTTTT
7532185 CTTGTTTCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 36 0.63
72 21 0.37
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (71 bp):
ATGTTTATTAGACAATAAACTCTGTACAAAACATAATTTATTATAGGCAACCCTCAGATTTTTTT
TCCTCC
Found at i:7539277 original size:29 final size:28
Alignment explanation
Indices: 7539240--7539305 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
7539230 ACCAGAAAAA
7539240 ACCATTTTTTTCAAAATTTACCGAAATGG
1 ACCA-TTTTTTCAAAATTTACCGAAATGG
* * ** *
7539269 GCCGATTTTTTGATTATTTACCGGAATGG
1 ACC-ATTTTTTCAAAATTTACCGAAATGG
7539298 ACCATTTT
1 ACCATTTT
7539306 CCGAGAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.17
29 24 0.80
30 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (28 bp):
ACCATTTTTTCAAAATTTACCGAAATGG
Found at i:7539525 original size:21 final size:22
Alignment explanation
Indices: 7539496--7539545 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
7539486 CTCTCTAATC
7539496 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
7539518 CTCT-AATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
7539539 CTCTCAA
1 CTCTCAA
7539546 ATCCATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:7539584 original size:11 final size:11
Alignment explanation
Indices: 7539564--7539614 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
7539554 TTTAAAATAA
7539564 TTATAATTTTT
1 TTATAATTTTT
7539575 TTAT-ATTTTT
1 TTATAATTTTT
* **
7539585 TTAAAATAATT
1 TTATAATTTTT
7539596 TTA-AATTTTT
1 TTATAATTTTT
7539606 TTAT-ATTTT
1 TTATAATTTT
7539615 CATCAATGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 22 0.67
11 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:7539587 original size:30 final size:31
Alignment explanation
Indices: 7539551--7539614 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
7539541 CTCAAATCCA
7539551 TTTTTTAAAATAATTAT-AATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
7539581 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
7539612 TTT
1 TTT
7539615 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:7539734 original size:21 final size:22
Alignment explanation
Indices: 7539705--7539754 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
7539695 CTCTCTAATC
7539705 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
7539727 CTCT-AATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
7539748 CTCTCAA
1 CTCTCAA
7539755 ATCCATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:7539790 original size:209 final size:209
Alignment explanation
Indices: 7539430--7539849 Score: 840
Period size: 209 Copynumber: 2.0 Consensus size: 209
7539420 AAATATATAT
7539430 ATATAAATACCCCCACCCCTTTATTTTTTTCACAAACAAATCCTATCTAATTTTTCCTCTCTAAT
1 ATATAAATACCCCCACCCCTTTATTTTTTTCACAAACAAATCCTATCTAATTTTTCCTCTCTAAT
7539495 CCTCTCAATTTCCTTCCAAAATTCTCTAATTTCCTTCCAAAATTCTCTCAAATCCATTTTTTAAA
66 CCTCTCAATTTCCTTCCAAAATTCTCTAATTTCCTTCCAAAATTCTCTCAAATCCATTTTTTAAA
7539560 ATAATTATAATTTTTTTATATTTTTTTAAAATAATTTTAAATTTTTTTATATTTTCATCAATGGC
131 ATAATTATAATTTTTTTATATTTTTTTAAAATAATTTTAAATTTTTTTATATTTTCATCAATGGC
7539625 CGGATCATTGACTC
196 CGGATCATTGACTC
7539639 ATATAAATACCCCCACCCCTTTATTTTTTTCACAAACAAATCCTATCTAATTTTTCCTCTCTAAT
1 ATATAAATACCCCCACCCCTTTATTTTTTTCACAAACAAATCCTATCTAATTTTTCCTCTCTAAT
7539704 CCTCTCAATTTCCTTCCAAAATTCTCTAATTTCCTTCCAAAATTCTCTCAAATCCATTTTTTAAA
66 CCTCTCAATTTCCTTCCAAAATTCTCTAATTTCCTTCCAAAATTCTCTCAAATCCATTTTTTAAA
7539769 ATAATTATAATTTTTTTATATTTTTTTAAAATAATTTTAAATTTTTTTATATTTTCATCAATGGC
131 ATAATTATAATTTTTTTATATTTTTTTAAAATAATTTTAAATTTTTTTATATTTTCATCAATGGC
7539834 CGGATCATTGACTC
196 CGGATCATTGACTC
7539848 AT
1 AT
7539850 NNNNNNNNNN
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.45
Consensus pattern (209 bp):
ATATAAATACCCCCACCCCTTTATTTTTTTCACAAACAAATCCTATCTAATTTTTCCTCTCTAAT
CCTCTCAATTTCCTTCCAAAATTCTCTAATTTCCTTCCAAAATTCTCTCAAATCCATTTTTTAAA
ATAATTATAATTTTTTTATATTTTTTTAAAATAATTTTAAATTTTTTTATATTTTCATCAATGGC
CGGATCATTGACTC
Found at i:7539793 original size:11 final size:11
Alignment explanation
Indices: 7539773--7539823 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
7539763 TTTAAAATAA
7539773 TTATAATTTTT
1 TTATAATTTTT
7539784 TTAT-ATTTTT
1 TTATAATTTTT
* **
7539794 TTAAAATAATT
1 TTATAATTTTT
7539805 TTA-AATTTTT
1 TTATAATTTTT
7539815 TTAT-ATTTT
1 TTATAATTTT
7539824 CATCAATGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 22 0.67
11 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:7539796 original size:30 final size:31
Alignment explanation
Indices: 7539760--7539823 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
7539750 CTCAAATCCA
7539760 TTTTTTAAAATAATTAT-AATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
7539790 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
7539821 TTT
1 TTT
7539824 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:7540682 original size:7 final size:7
Alignment explanation
Indices: 7540670--7540694 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7540660 AGTTGATTGA
7540670 TATTTAG
1 TATTTAG
7540677 TATTTAG
1 TATTTAG
7540684 TATTTAG
1 TATTTAG
7540691 TATT
1 TATT
7540695 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:7541354 original size:18 final size:18
Alignment explanation
Indices: 7541333--7541367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7541323 AGGTATGTTT
* *
7541333 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
7541351 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
7541368 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:7541659 original size:24 final size:24
Alignment explanation
Indices: 7541627--7541681 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
7541617 TGCGGAACCA
7541627 GAAGAACCACAACCACCACCAGAG
1 GAAGAACCACAACCACCACCAGAG
* *
7541651 GAAGGACCACAATCACCACCAGAG
1 GAAGAACCACAACCACCACCAGAG
7541675 GAAGAAC
1 GAAGAAC
7541682 AACCGCCGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.33, G:0.20, T:0.02
Consensus pattern (24 bp):
GAAGAACCACAACCACCACCAGAG
Found at i:7543211 original size:28 final size:29
Alignment explanation
Indices: 7543152--7543231 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
7543142 NNNNNNNNNN
*
7543152 AAAACCCT-AATCTAACCTAAATTAATTA
1 AAAACCCTAAAACTAACCTAAATTAATTA
*
7543180 AAAACCCTAAACCTAACCTAAATTAATTA
1 AAAACCCTAAAACTAACCTAAATTAATTA
7543209 AAAACCC-AAAACTAACCTAAATT
1 AAAACCCTAAAACTAACCTAAATT
7543232 TTTTTGGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 23 0.47
29 26 0.53
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (29 bp):
AAAACCCTAAAACTAACCTAAATTAATTA
Found at i:7543265 original size:26 final size:26
Alignment explanation
Indices: 7543229--7543285 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
7543219 ACTAACCTAA
7543229 ATTTTTTTGGCTTAATAATTTTACAT
1 ATTTTTTTGGCTTAATAATTTTACAT
7543255 ATTTTTTTGGCTTAATAATTTTACAT
1 ATTTTTTTGGCTTAATAATTTTACAT
7543281 ATTTT
1 ATTTT
7543286 GAACACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (26 bp):
ATTTTTTTGGCTTAATAATTTTACAT
Found at i:7547558 original size:43 final size:43
Alignment explanation
Indices: 7547503--7547695 Score: 201
Period size: 43 Copynumber: 4.5 Consensus size: 43
7547493 TTTACAATGT
* * *
7547503 CGCTTATTCCACAAACGCCGCTAAAGCTCATGTTCTTTAGCGA
1 CGCTTATCCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* * *
7547546 CGCTTATCCCACAAACGCCACTAAAGG--ATGCTCTTTAGTGG
1 CGCTTATCCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* ** * * * * *
7547587 CGCTTATTCCACAAACTTCGGTATAGGTCATATACTTTGGCGG
1 CGCTTATCCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* * *
7547630 CGCTTATCTCAAAAACGCCTCTAAAGGTCATGTTCTTTAGCGG
1 CGCTTATCCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* *
7547673 TGCTTATCCCACAATCGCCGCTA
1 CGCTTATCCCACAAACGCCGCTA
7547696 TAGATCTTAA
Statistics
Matches: 115, Mismatches: 33, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
41 32 0.28
43 83 0.72
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (43 bp):
CGCTTATCCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
Found at i:7547593 original size:41 final size:42
Alignment explanation
Indices: 7547503--7547602 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 42
7547493 TTTACAATGT
* *
7547503 CGCTTATTCCACAAACGCCGCTAAAGCTCATGTTCTTTAGCGA
1 CGCTTATTCCACAAACGCCACTAAAGC-CATGCTCTTTAGCGA
* * * *
7547546 CGCTTATCCCACAAACGCCACTAAAG-GATGCTCTTTAGTGG
1 CGCTTATTCCACAAACGCCACTAAAGCCATGCTCTTTAGCGA
7547587 CGCTTATTCCACAAAC
1 CGCTTATTCCACAAAC
7547603 TTCGGTATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 26 0.52
43 24 0.48
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (42 bp):
CGCTTATTCCACAAACGCCACTAAAGCCATGCTCTTTAGCGA
Found at i:7547646 original size:84 final size:85
Alignment explanation
Indices: 7547503--7547695 Score: 217
Period size: 84 Copynumber: 2.3 Consensus size: 85
7547493 TTTACAATGT
* * *
7547503 CGCTTATTCCACAAACGCCGCTAAAGCTCATGTTCTTTAGCGACGCTTATCCCACAAACGCCACT
1 CGCTTATTCCACAAACGCCGCTAAAGCTCATATACTTTAGCGACGCTTATCCCAAAAACGCCACT
*
7547568 AAAGG-ATGCTCTTTAGTGG
66 AAAGGCATGCTCTTTAGCGG
** * * * * * * *
7547587 CGCTTATTCCACAAACTTCGGTATAGGTCATATACTTTGGCGGCGCTTATCTCAAAAACGCCTCT
1 CGCTTATTCCACAAACGCCGCTAAAGCTCATATACTTTAGCGACGCTTATCCCAAAAACGCCACT
*
7547652 AAAGGTCATGTTCTTTAGCGG
66 AAAGG-CATGCTCTTTAGCGG
* * *
7547673 TGCTTATCCCACAATCGCCGCTA
1 CGCTTATTCCACAAACGCCGCTA
7547696 TAGATCTTAA
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
84 58 0.67
86 29 0.33
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (85 bp):
CGCTTATTCCACAAACGCCGCTAAAGCTCATATACTTTAGCGACGCTTATCCCAAAAACGCCACT
AAAGGCATGCTCTTTAGCGG
Found at i:7548413 original size:21 final size:21
Alignment explanation
Indices: 7548387--7548432 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
7548377 GCTCTGCTCT
*
7548387 GCTTCCCTCGCTTCAGCCTCC
1 GCTTCCCTCGCTTCAGCCTCA
7548408 GCTTCCCTCGCTTCAGCCTCA
1 GCTTCCCTCGCTTCAGCCTCA
7548429 GCTT
1 GCTT
7548433 TAAATTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.07, C:0.48, G:0.15, T:0.30
Consensus pattern (21 bp):
GCTTCCCTCGCTTCAGCCTCA
Found at i:7550807 original size:25 final size:25
Alignment explanation
Indices: 7550773--7550854 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
7550763 TAATAAGACC
** * *
7550773 AAGTTATGTATTATGTATGTTATGT
1 AAGTTATGTAGAATGTAAGCTATGT
*
7550798 AAGTTGTGTAGAATGTAAGCTATGT
1 AAGTTATGTAGAATGTAAGCTATGT
*
7550823 AAGTTATGT-GAGT-TATA--TATGT
1 AAGTTATGTAGAATGTA-AGCTATGT
7550845 AAGTTATGTA
1 AAGTTATGTA
7550855 TAATATTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 14 0.29
23 2 0.04
24 4 0.08
25 28 0.58
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (25 bp):
AAGTTATGTAGAATGTAAGCTATGT
Found at i:7550836 original size:9 final size:9
Alignment explanation
Indices: 7550773--7550970 Score: 81
Period size: 9 Copynumber: 23.1 Consensus size: 9
7550763 TAATAAGACC
7550773 AAGTTATGT
1 AAGTTATGT
7550782 -A-TTATGT
1 AAGTTATGT
*
7550789 ATGTTATGT
1 AAGTTATGT
*
7550798 AAGTTGTGT
1 AAGTTATGT
*
7550807 -AG-AATGT
1 AAGTTATGT
*
7550814 AAGCTATGT
1 AAGTTATGT
7550823 AAGTTATGT
1 AAGTTATGT
*
7550832 GAGTTA--T
1 AAGTTATGT
7550839 -A--TATGT
1 AAGTTATGT
7550845 AAGTTATGT
1 AAGTTATGT
*
7550854 ATA-ATAT-T
1 A-AGTTATGT
*
7550862 AA-TTAATCGGCC
1 AAGTT-AT--G-T
*
7550874 AAGTTGTG-
1 AAGTTATGT
*
7550882 AA-TAATGT
1 AAGTTATGT
*
7550890 AAGTTATGA
1 AAGTTATGT
7550899 AAGTTATGT
1 AAGTTATGT
7550908 -A-TTATGT
1 AAGTTATGT
*
7550915 AAGTTATTT
1 AAGTTATGT
7550924 AAGTTATGTAAT
1 AAGTTATG---T
*
7550936 AAGTTGTGT
1 AAGTTATGT
7550945 -A-TTATGT
1 AAGTTATGT
*
7550952 AAGTTATTT
1 AAGTTATGT
7550961 AAGTTATGT
1 AAGTTATGT
7550970 A
1 A
7550971 TTACGAAATT
Statistics
Matches: 141, Mismatches: 23, Indels: 50
0.66 0.11 0.23
Matches are distributed among these distances:
4 2 0.01
6 2 0.01
7 27 0.19
8 17 0.12
9 78 0.55
10 2 0.01
12 11 0.08
13 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
AAGTTATGT
Found at i:7550902 original size:25 final size:25
Alignment explanation
Indices: 7550874--7550937 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
7550864 TTAATCGGCC
*
7550874 AAGTTGTGAATAATGTAAGTTATGA
1 AAGTTATGAATAATGTAAGTTATGA
* * **
7550899 AAGTTATGTATTATGTAAGTTATTT
1 AAGTTATGAATAATGTAAGTTATGA
7550924 AAGTTATGTAATAA
1 AAGTTATG-AATAA
7550938 GTTGTGTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (25 bp):
AAGTTATGAATAATGTAAGTTATGA
Found at i:7550912 original size:16 final size:16
Alignment explanation
Indices: 7550893--7550958 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
7550883 ATAATGTAAG
7550893 TTATGAAAGTTATGTA
1 TTATGAAAGTTATGTA
* *
7550909 TTATGTAAGTTATTTAA
1 TTATGAAAGTTATGT-A
*
7550926 GTTATGTAATAAGTTGTGTA
1 -TTATG--A-AAGTTATGTA
*
7550946 TTATGTAAGTTAT
1 TTATGAAAGTTAT
7550959 TTAAGTTATG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
16 19 0.50
17 1 0.03
18 5 0.13
19 5 0.13
20 1 0.03
21 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (16 bp):
TTATGAAAGTTATGTA
Found at i:7550946 original size:37 final size:37
Alignment explanation
Indices: 7550899--7550970 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
7550889 TAAGTTATGA
7550899 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
1 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
*
7550936 AAGTTGTGTATTATGTAAGTTATTTAAGTTATGTA
1 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTA
7550971 TTACGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (37 bp):
AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
Found at i:7551042 original size:57 final size:57
Alignment explanation
Indices: 7550970--7551198 Score: 221
Period size: 57 Copynumber: 3.9 Consensus size: 57
7550960 TAAGTTATGT
7550970 ATTACGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATTGATGTGTA
1 ATTA-GAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATTGATGTGTA
* *
7551028 ATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAGAAATTA-ATATTATATAAGTTAT
1 ATTAGAAATTTTATCTTAATATTATATAAGTTAT-C--T-A-AAATTAGA-A--AT-T--GATGT
7551092 GTA
55 GTA
* * * *
7551095 ATTCGAAATTTTATTTTAATATTGTATAAGTTATATAAAATTAGAAATTGATGTGTA
1 ATTAGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATTGATGTGTA
* ** ** *
7551152 CTTAGAAATTAGAAATTAATATTATATAAGTTATGT--AATTAGAAATT
1 ATTAGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATT
7551199 TTATCTTAAT
Statistics
Matches: 143, Mismatches: 16, Indels: 27
0.77 0.09 0.15
Matches are distributed among these distances:
55 11 0.08
57 64 0.45
58 5 0.03
59 1 0.01
60 3 0.02
61 2 0.01
62 14 0.10
63 2 0.01
64 3 0.02
65 1 0.01
67 37 0.26
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (57 bp):
ATTAGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATTGATGTGTA
Found at i:7551072 original size:37 final size:36
Alignment explanation
Indices: 7551031--7551128 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 36
7551021 ATGTGTAATT
7551031 AGAAATTTTATCTTAATATTATATAAGTTATGCAATG
1 AGAAATTTTAT-TTAATATTATATAAGTTATGCAATG
* *
7551068 AG-AA----A-TTAATATTATATAAGTTATGTAATT
1 AGAAATTTTATTTAATATTATATAAGTTATGCAATG
* *
7551098 CGAAATTTTATTTTAATATTGTATAAGTTAT
1 AGAAATTTTA-TTTAATATTATATAAGTTAT
7551129 ATAAAATTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
30 24 0.48
31 2 0.04
32 1 0.02
35 1 0.02
36 2 0.04
37 20 0.40
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
AGAAATTTTATTTAATATTATATAAGTTATGCAATG
Found at i:7551114 original size:124 final size:127
Alignment explanation
Indices: 7550955--7551326 Score: 464
Period size: 124 Copynumber: 2.9 Consensus size: 127
7550945 ATTATGTAAG
*
7550955 TTATTTAAGTTATGT-ATTACGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAAT
1 TTATATAAGTTATGTAATT-CGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAAT
7551019 TGATGTGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAG-AA-A-TTAATA
65 TGATGTGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAGAAATACTTAATA
* * *
7551079 TTATATAAGTTATGTAATTCGAAATTTTATTTTAATATTGTATAAGTTATATAAAATTAGAAATT
1 TTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATT
* ** ** * *
7551144 GATGTGTACTTAGAAATTAGAAATTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAAT
66 GATGTGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAGAAA---TA-CTTAAT
7551209 A
127 A
* *
7551210 TTATATAAGTTATGTAATTAGAAATTTGATCTTAATATTATATAAGTTATCTTAATTTTATGTAA
1 TTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATC-T-A----A---AA
*
7551275 TTAGAAATTGATGTGTGATTAGAAATTTTATCTTAATATTATATAAGTTATG
57 TTAGAAATTGATGTGTAATTAGAAATTTTATCTTAATATTATATAAGTTATG
7551327 AAGTGTCCTG
Statistics
Matches: 209, Mismatches: 22, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
124 100 0.48
125 5 0.02
129 1 0.00
131 52 0.25
132 1 0.00
133 1 0.00
137 1 0.00
140 48 0.23
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (127 bp):
TTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTAAAATTAGAAATT
GATGTGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAGAAATACTTAATA
Found at i:7551208 original size:37 final size:37
Alignment explanation
Indices: 7551148--7551259 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
7551138 GAAATTGATG
* * **
7551148 TGTACTTAGAAATTAGAAATTAATATTATATAAGTTA
1 TGTAATTAGAAATTTGATCTTAATATTATATAAGTTA
*
7551185 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTA
1 TGTAATTAGAAATTTGATCTTAATATTATATAAGTTA
7551222 TGTAATTAGAAATTTGATCTTAATATTATATAAGTTA
1 TGTAATTAGAAATTTGATCTTAATATTATATAAGTTA
7551259 T
1 T
7551260 CTTAATTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (37 bp):
TGTAATTAGAAATTTGATCTTAATATTATATAAGTTA
Found at i:7551222 original size:20 final size:20
Alignment explanation
Indices: 7551199--7551270 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
7551189 ATTAGAAATT
7551199 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* * *
7551219 TTAT-GT-A-ATTAGA-AAT
1 TTATCTTAATATTATATAAG
7551235 TTGATCTTAATATTATATAAG
1 TT-ATCTTAATATTATATAAG
*
7551256 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
7551271 GTAATTAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
18 2 0.05
19 2 0.05
20 21 0.52
21 4 0.10
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:7551265 original size:94 final size:92
Alignment explanation
Indices: 7551070--7551245 Score: 257
Period size: 94 Copynumber: 1.9 Consensus size: 92
7551060 ATGCAATGAG
* * * *
7551070 AAATTAATATTATATAAGTTATGTAATTCGAAATTTTATTTTAATATTGTATAAGTTATATAAAA
1 AAATTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGT-AAA
* *
7551135 TTAGAAATTGATGTGTACTTAGAAATTA
65 TTAGAAATTGATCTGTAATTAGAAATTA
7551163 GAAATTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGT-AA
1 -AAATTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGTAAA
7551227 TTAGAAATTTGATCT-TAAT
65 TTAGAAA-TTGATCTGTAAT
7551246 ATTATATAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 12 0.16
93 6 0.08
94 57 0.76
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (92 bp):
AAATTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGTAAAT
TAGAAATTGATCTGTAATTAGAAATTA
Found at i:7553779 original size:19 final size:19
Alignment explanation
Indices: 7553755--7553796 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
7553745 CGTCGGGTTG
*
7553755 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
7553774 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
7553793 GGGG
1 GGGG
7553797 GAGATGACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:7554741 original size:14 final size:14
Alignment explanation
Indices: 7554719--7554783 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
7554709 TGTAAGCCTT
*
7554719 AACCGTAAATCTTA
1 AACCCTAAATCTTA
7554733 AACCCTAAA-CTATA
1 AACCCTAAATCT-TA
* **
7554747 AACCCTAAACCCCA
1 AACCCTAAATCTTA
* *
7554761 AATCATAAATCTTA
1 AACCCTAAATCTTA
7554775 AACCCTAAA
1 AACCCTAAA
7554784 CTCGTCAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
13 2 0.05
14 36 0.92
15 1 0.03
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.22
Consensus pattern (14 bp):
AACCCTAAATCTTA
Found at i:7554755 original size:21 final size:22
Alignment explanation
Indices: 7554731--7554786 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
7554721 CCGTAAATCT
7554731 TAAACCCTAAACT-ATAAACCC
1 TAAACCCTAAACTCATAAACCC
* * *
7554752 TAAACCCCAAA-TCATAAATCT
1 TAAACCCTAAACTCATAAACCC
7554773 TAAACCCTAAACTC
1 TAAACCCTAAACTC
7554787 GTCAATTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAACTCATAAACCC
Found at i:7554901 original size:22 final size:21
Alignment explanation
Indices: 7554864--7554907 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
7554854 AACCGAAAAT
*
7554864 ATTAAACCCTAAACCATAAAC
1 ATTAAACCCTAAACCACAAAC
7554885 ATTAAACCCGTAAACCACAAAC
1 ATTAAACCC-TAAACCACAAAC
7554907 A
1 A
7554908 ACAACCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.52, C:0.30, G:0.02, T:0.16
Consensus pattern (21 bp):
ATTAAACCCTAAACCACAAAC
Found at i:7555537 original size:114 final size:112
Alignment explanation
Indices: 7555362--7555697 Score: 321
Period size: 114 Copynumber: 3.0 Consensus size: 112
7555352 GCTTTCCTTA
* * ** *
7555362 AAGCGCCACTAAAAGTTGTTCTATAGCGGCGTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGT
1 AAGCGCCACTAAAAG-TGATATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCTCTATAGGT
7555427 CAAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGTGGCGCTTCAGTAG
65 CAAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGTGGCGCTTCAGT-G
* * * * * * *
7555476 AAGTGCCACTAAAAGCTGATATATAGCGGCTTTTTCGGGTAAGCGCCACTAACGACGCTATAGCT
1 AAGCGCCACTAAAAG-TGATATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCTCTATAGGT
* * * * * ** * ** * *
7555541 CAAGACGAAACGTTTCGTTTCGGTTTAAATTTTTTTGGCATTTTTTAGTT
65 CAAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGTGGC--GCTTCAGTG
* ** * ** ** *
7555591 AAGCGCCGCTAATTGAGGGATATAGCGGCGTTTTCAGGTAAGCGTTGCTAACGCCTTTATAGGTC
1 AAGCGCCACTAAAAGTGATATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCTCTATAGGTC
*
7555656 AAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGCGGCGCTT
66 AAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGTGGCGCTT
7555698 AGCTGATATA
Statistics
Matches: 168, Mismatches: 52, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
112 2 0.01
114 150 0.89
115 11 0.07
116 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (112 bp):
AAGCGCCACTAAAAGTGATATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCTCTATAGGTC
AAGCCGGAACGATGCGTTTTGGTCAAAATTTTTGTGGCGCTTCAGTG
Found at i:7557265 original size:11 final size:11
Alignment explanation
Indices: 7557249--7557274 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7557239 ATTTTTTTAA
7557249 TTTTAAAATAC
1 TTTTAAAATAC
7557260 TTTTAAAATAC
1 TTTTAAAATAC
7557271 TTTT
1 TTTT
7557275 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:7557286 original size:9 final size:9
Alignment explanation
Indices: 7557272--7557338 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
7557262 TTAAAATACT
7557272 TTTTTTTAA
1 TTTTTTTAA
7557281 TTTTTTTAA
1 TTTTTTTAA
7557290 TTTTAAATTTAAA
1 TTTT---TTT-AA
7557303 TTTTTTTAAAATA
1 TTTTTTT---A-A
7557316 CTTTTTTTAA
1 -TTTTTTTAA
7557326 TTTTTTTAA
1 TTTTTTTAA
7557335 TTTT
1 TTTT
7557339 AAAATATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
9 26 0.52
10 4 0.08
11 1 0.02
12 5 0.10
13 7 0.14
14 7 0.14
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:7557331 original size:46 final size:43
Alignment explanation
Indices: 7557234--7557395 Score: 167
Period size: 40 Copynumber: 3.7 Consensus size: 43
7557224 ATAATAAATA
**
7557234 TTTTT-ATTTTTTTAATTTT--A-AAATACTTTTAAAATACTTT
1 TTTTTAATTTTTTTAATTTTAAATAAATTTTTTTAAAATAC-TT
7557274 TTTTTAATTTTTTTAATTTTAAATTTAAATTTTTTTAAAATACTT
1 TTTTTAATTTTTTTAATTTTAAA--TAAATTTTTTTAAAATACTT
* *
7557319 TTTTTAATTTTTTTAATTTT--A-AAATATTTTTAGAATACTT
1 TTTTTAATTTTTTTAATTTTAAATAAATTTTTTTAAAATACTT
7557359 TTTTTAATTTTTATTTTAATTTTTAAAATAAATTTTT
1 TTTTTAA--TTT-TTTTAA-TTTT-AAATAAATTTTT
7557396 GGTATTTATT
Statistics
Matches: 103, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
40 29 0.28
41 14 0.14
42 3 0.03
43 8 0.08
44 4 0.04
45 22 0.21
46 15 0.15
47 1 0.01
48 7 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (43 bp):
TTTTTAATTTTTTTAATTTTAAATAAATTTTTTTAAAATACTT
Found at i:7557360 original size:29 final size:29
Alignment explanation
Indices: 7557306--7557361 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
7557296 ATTTAAATTT
** *
7557306 TTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAGAATCTTTTTAA
7557335 TTTTAAAATA-TTTTTAGAATACTTTTT
1 TTTTAAAATACTTTTTAGAAT-CTTTTT
7557362 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAGAATCTTTTTAA
Found at i:7557395 original size:86 final size:84
Alignment explanation
Indices: 7557234--7557395 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 84
7557224 ATAATAAATA
*
7557234 TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAATT
1 TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAATA
7557299 TAAATTTTTTTAAAATACTT
66 TAAA-TTTTTTAAAATACTT
* *
7557319 TTTTTAATTTTTTTAATTTTAAAATATTTTTAGAATAC-TTTTTTTAATTTTTATTTTAATTTTT
1 TTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAA--TTT-TTTTAA-TTTT
7557383 AAA-ATAAATTTTT
61 AAATATAAATTTTT
7557396 GGTATTTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
85 14 0.20
86 30 0.43
87 8 0.12
88 10 0.14
89 7 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (84 bp):
TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAATA
TAAATTTTTTAAAATACTT
Found at i:7558265 original size:13 final size:13
Alignment explanation
Indices: 7558247--7558321 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
7558237 TTCTTCATTA
7558247 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
7558260 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
* **
7558273 -TTGTGGAAAAGCA
1 CTT-TTGAAAAGTG
*
7558286 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
*
7558299 CTTTT-AAGAAGTA
1 CTTTTGAA-AAGTG
*
7558312 TTTTTGAAAA
1 CTTTTGAAAA
7558322 ATTTGAGTGC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
12 3 0.07
13 39 0.85
14 4 0.09
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:7569227 original size:40 final size:40
Alignment explanation
Indices: 7569172--7569259 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
7569162 GAGAATTGAG
*
7569172 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAGGAGCATTCGTGCT
7569212 AGTGATATATCCGGGCTAAATCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAGGAGCATTCGTGCT
7569252 AGTGATAT
1 AGTGATAT
7569260 GTATAATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAATCCCGAGGAGCATTCGTGCT
Found at i:7570972 original size:24 final size:24
Alignment explanation
Indices: 7570944--7570992 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
7570934 GAATTTAGGA
*
7570944 TCCACTTGGACGTAAGTTTAGAGC
1 TCCACTTGGAAGTAAGTTTAGAGC
*
7570968 TCCACTTGGAATTAAGTTTAGAGC
1 TCCACTTGGAAGTAAGTTTAGAGC
7570992 T
1 T
7570993 TTTGCTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
TCCACTTGGAAGTAAGTTTAGAGC
Found at i:7572713 original size:11 final size:11
Alignment explanation
Indices: 7572697--7572722 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7572687 TACAAGAAAT
7572697 AAATTACTAAG
1 AAATTACTAAG
7572708 AAATTACTAAG
1 AAATTACTAAG
7572719 AAAT
1 AAAT
7572723 AAATTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (11 bp):
AAATTACTAAG
Found at i:7575954 original size:44 final size:42
Alignment explanation
Indices: 7575846--7575959 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 42
7575836 AGCTCGTACA
* * *
7575846 ATGCCAACGTCCCAGATAG-GGTCTTACATGTAATCATATACG
1 ATGCCAATGTCCCAGAT-GTGGTCTTACACGTAATCAAATACG
* * * **
7575888 ACGGCAATGTCCTAGACATGGTCTTACACGTAAATCTCAAAT-CG
1 ATGCCAATGTCCCAGATGTGGTCTTACACGT-AA--TCAAATACG
7575932 ATGCCAATGTCCCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGATGTGGTCTTACA
7575960 AGATATCACA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
42 23 0.42
43 2 0.04
44 25 0.45
45 5 0.09
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGATGTGGTCTTACACGTAATCAAATACG
Found at i:7582164 original size:37 final size:37
Alignment explanation
Indices: 7582114--7582192 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
7582104 TTATTACGAA
* * *
7582114 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
7582151 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
7582188 GTCTT
1 GTCTT
7582193 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:7582389 original size:47 final size:47
Alignment explanation
Indices: 7582311--7582723 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
7582301 CCCTTCGGGA
* * * * * *
7582311 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7582358 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7582405 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582454 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582501 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582548 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582595 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582642 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7582689 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
7582724 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 308 0.87
49 46 0.13
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7588249 original size:40 final size:40
Alignment explanation
Indices: 7588194--7588343 Score: 282
Period size: 40 Copynumber: 3.8 Consensus size: 40
7588184 NNNNNNNNNN
*
7588194 CCGGATATATCACTAGCATGAATGCTCTTCGGGACTTAGC
1 CCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC
*
7588234 CCGGATATATCACTAGCATGAATGCTCTTCGGGACTTAGC
1 CCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC
7588274 CCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC
1 CCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC
7588314 CCGGATATATCACTAGCACGAATGCTCTTC
1 CCGGATATATCACTAGCACGAATGCTCTTC
7588344 TAAAAATGCA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGC
Found at i:7588550 original size:114 final size:114
Alignment explanation
Indices: 7588346--7588610 Score: 368
Period size: 114 Copynumber: 2.3 Consensus size: 114
7588336 TGCTCTTCTA
* * *
7588346 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGGCGCTTATGCAAAAACGCCGCTAGA
1 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAACGACACTTATGCAAAAACGCCGCTAGA
* *
7588411 GGTCGAGAATTAGCGGAGCTCTTCTAAAAATGCCACAAAAATGTTAATC
66 GGTCGAGAATTAGCAGAGCTCTTCTAAAAATACCACAAAAATGTTAATC
* * *
7588460 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAACGACACTTATTCAAAAATGCCGCTATA
1 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAACGACACTTATGCAAAAACGCCGCTAGA
* * * **
7588525 TGTCGAGAATTAGCAGTGCTTTTCTAAAAATACCGTAAAAATGTTAATC
66 GGTCGAGAATTAGCAGAGCTCTTCTAAAAATACCACAAAAATGTTAATC
* * * * *
7588574 AAAACGCATCATTCTAGCTTAAGATTTAGTGGCATTA
1 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTA
7588611 GCCGCGCTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 133 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (114 bp):
AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAACGACACTTATGCAAAAACGCCGCTAGA
GGTCGAGAATTAGCAGAGCTCTTCTAAAAATACCACAAAAATGTTAATC
Found at i:7589048 original size:14 final size:14
Alignment explanation
Indices: 7589013--7589097 Score: 77
Period size: 14 Copynumber: 6.1 Consensus size: 14
7589003 TTCCCAAAGA
*
7589013 TATGGTTTA-GGAT
1 TATGGTTTAGGGTT
7589026 TATGGTTTAGGGTT
1 TATGGTTTAGGGTT
* *
7589040 TACGGTTTAGAGTT
1 TATGGTTTAGGGTT
*
7589054 TAAGG-TT-GGTGTTT
1 TATGGTTTAGG-G-TT
*
7589068 TATGGTTTAGGATT
1 TATGGTTTAGGGTT
7589082 TATGGTTTAAGGGTT
1 TATGGTTT-AGGGTT
7589097 T
1 T
7589098 TGGGTATATT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
12 1 0.02
13 12 0.21
14 35 0.60
15 8 0.14
16 2 0.03
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:7589170 original size:7 final size:7
Alignment explanation
Indices: 7589160--7589203 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
7589150 CGGGTTTAAT
7589160 GTTTATG
1 GTTTATG
*
7589167 GTTTAGG
1 GTTTATG
7589174 GTTTA-G
1 GTTTATG
7589180 GATTTATG
1 G-TTTATG
*
7589188 GTTTAAG
1 GTTTATG
7589195 GTTTATG
1 GTTTATG
7589202 GT
1 GT
7589204 ATATTGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:7589175 original size:21 final size:22
Alignment explanation
Indices: 7589146--7589199 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
7589136 GGTTTTGTGA
*
7589146 TTTACGGGTTTAATG-TTTATGG
1 TTTA-GGGTTTAAGGATTTATGG
7589168 TTTAGGGTTT-AGGATTTATGG
1 TTTAGGGTTTAAGGATTTATGG
*
7589189 TTTAAGGTTTA
1 TTTAGGGTTTA
7589200 TGGTATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 22 0.79
22 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTTAAGGATTTATGG
Found at i:7589177 original size:14 final size:14
Alignment explanation
Indices: 7589146--7589203 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
7589136 GGTTTTGTGA
7589146 TTTACGGGTTTAAT-G
1 TTTA-GGGTTT-ATGG
* *
7589161 TTTATGGTTTAGGG
1 TTTAGGGTTTATGG
*
7589175 TTTAGGATTTATGG
1 TTTAGGGTTTATGG
*
7589189 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
7589203 T
1 T
7589204 ATATTGGGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
13 1 0.03
14 30 0.86
15 4 0.11
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:7589228 original size:102 final size:102
Alignment explanation
Indices: 7589066--7589280 Score: 312
Period size: 102 Copynumber: 2.1 Consensus size: 102
7589056 AGGTTGGTGT
*
7589066 TTTATGGTTTAGGATTTATGGTTTAAGGGTTTTGGGTATATTGGGGATTGAATTTTGGGTTTTGG
1 TTTAGGGTTTAGGATTTATGGTTTAAGGGTTTTGGGTATATTGGGGATTGAATTTTGGG-TTTGG
* *
7589131 TGGTT-G-GTTTTGTGATTTACGGGTTTAATGTTTATGG
65 TGGTTGGTGTTTTGTGATTTA-GGGTTTAAGGTTTAAGG
*
7589168 TTTAGGGTTTAGGATTTATGGTTTAA-GGTTTAT-GGTATATTGGGGATTGGATTTTAGGGTTTG
1 TTTAGGGTTTAGGATTTATGGTTTAAGGGTTT-TGGGTATATTGGGGATTGAATTTT-GGGTTTG
*
7589231 GTGGTTGGTGTTTTGTGGTTTAGGGTTTAAGGTTTAAGG
64 GTGGTTGGTGTTTTGTGATTTAGGGTTTAAGGTTTAAGG
*
7589270 TTTAGGATTTA
1 TTTAGGGTTTA
7589281 ATCTTTGAGT
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
101 36 0.35
102 55 0.53
103 12 0.12
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (102 bp):
TTTAGGGTTTAGGATTTATGGTTTAAGGGTTTTGGGTATATTGGGGATTGAATTTTGGGTTTGGT
GGTTGGTGTTTTGTGATTTAGGGTTTAAGGTTTAAGG
Found at i:7589563 original size:20 final size:21
Alignment explanation
Indices: 7589538--7589578 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7589528 AATATATTGA
7589538 TGTATTTA-TTTTTTAAAATG
1 TGTATTTATTTTTTTAAAATG
7589558 TGTATTTATTTTTTTAAAATG
1 TGTATTTATTTTTTTAAAATG
7589579 CATTATCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TGTATTTATTTTTTTAAAATG
Found at i:7590520 original size:27 final size:27
Alignment explanation
Indices: 7590490--7590560 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
7590480 TTTGGTACTG
7590490 GCATACTATTTTATGTATTTCCCATAT
1 GCATACTATTTTATGTATTTCCCATAT
**
7590517 GCATACGGTTTTAAT-TATTTCCCATAT
1 GCATACTATTTT-ATGTATTTCCCATAT
*
7590544 GCATACTGTTTTTATGT
1 GCATACT-ATTTTATGT
7590561 TTAAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (27 bp):
GCATACTATTTTATGTATTTCCCATAT
Found at i:7594048 original size:13 final size:14
Alignment explanation
Indices: 7594032--7594060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7594022 TTATAAATAT
7594032 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
7594045 TTATAATGGTTTAA
1 TTATAATGGTTTAA
7594059 TT
1 TT
7594061 TGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:7594790 original size:44 final size:43
Alignment explanation
Indices: 7594728--7594974 Score: 230
Period size: 43 Copynumber: 5.7 Consensus size: 43
7594718 TTGCCCAAAT
* *
7594728 TAGCGGCGTTTGTA-AAAAAAGCACCGCTAAAGACCACGAATTA
1 TAGCGGCGTTT-TATAAAAAAGCACCGCTAAAGGCCACGACTTA
* ** *
7594771 TAACGGCGTTTTATAAAAAAAGTGCTGCTAAAGGCCACGACTTA
1 TAGCGGCGTTTTAT-AAAAAAGCACCGCTAAAGGCCACGACTTA
* * * *
7594815 TAGCAGCGTTTTATAAAAAAACGCCGCTAAAGGCCATGACTTA
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGACTTA
* * * * *
7594858 TAGTGGAGTTTTATAAAAAAGCGCTGTTAAAGGCCACGACATT-
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGAC-TTA
* * ** * *
7594901 TAGCGGCATTTTCTATGATAGCACCGCTAAAGACCACGACCTT-
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGA-CTTA
* *
7594944 TAGCGGCGTTTTCTATAAAAGCACCGCTAAA
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAA
7594975 AGTCAAGATC
Statistics
Matches: 167, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
42 2 0.01
43 126 0.75
44 39 0.23
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGACTTA
Found at i:7595034 original size:35 final size:35
Alignment explanation
Indices: 7594984--7595066 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
7594974 AAGTCAAGAT
* *
7594984 CTTTAGCGGCATTTTTTTCAAAGAAACGCCGCAAG
1 CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
* *
7595019 CTTTAGCGGCCTTTTTTTCAAATAAACACTGCAAG
1 CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
*
7595054 TTTTAGCGGCCTT
1 CTTTAGCGGCCTT
7595067 GTCTATAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (35 bp):
CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
Found at i:7596165 original size:13 final size:14
Alignment explanation
Indices: 7596149--7596177 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7596139 TTATAAATAT
7596149 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
7596162 TTATAATGGTTTAA
1 TTATAATGGTTTAA
7596176 TT
1 TT
7596178 TGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:7596907 original size:44 final size:43
Alignment explanation
Indices: 7596845--7597091 Score: 230
Period size: 43 Copynumber: 5.7 Consensus size: 43
7596835 TTGCCCAAAT
* *
7596845 TAGCGGCGTTTGTA-AAAAAAGCACCGCTAAAGACCACGAATTA
1 TAGCGGCGTTT-TATAAAAAAGCACCGCTAAAGGCCACGACTTA
* ** *
7596888 TAACGGCGTTTTATAAAAAAAGTGCTGCTAAAGGCCACGACTTA
1 TAGCGGCGTTTTAT-AAAAAAGCACCGCTAAAGGCCACGACTTA
* * * *
7596932 TAGCAGCGTTTTATAAAAAAACGCCGCTAAAGGCCATGACTTA
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGACTTA
* * * * *
7596975 TAGTGGAGTTTTATAAAAAAGCGCTGTTAAAGGCCACGACATT-
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGAC-TTA
* * ** * *
7597018 TAGCGGCATTTTCTATGATAGCACCGCTAAAGACCACGACCTT-
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGA-CTTA
* *
7597061 TAGCGGCGTTTTCTATAAAAGCACCGCTAAA
1 TAGCGGCGTTTTATAAAAAAGCACCGCTAAA
7597092 AGTCAAGATC
Statistics
Matches: 167, Mismatches: 33, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
42 2 0.01
43 126 0.75
44 39 0.23
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTTATAAAAAAGCACCGCTAAAGGCCACGACTTA
Found at i:7597151 original size:35 final size:35
Alignment explanation
Indices: 7597101--7597183 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
7597091 AAGTCAAGAT
* *
7597101 CTTTAGCGGCATTTTTTTCAAAGAAACGCCGCAAG
1 CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
* *
7597136 CTTTAGCGGCCTTTTTTTCAAATAAACACTGCAAG
1 CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
*
7597171 TTTTAGCGGCCTT
1 CTTTAGCGGCCTT
7597184 GTCTATAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (35 bp):
CTTTAGCGGCCTTTTTTTCAAAGAAACACCGCAAG
Found at i:7601486 original size:47 final size:47
Alignment explanation
Indices: 7601408--7601820 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
7601398 CCCTTCGGGA
* * * * * *
7601408 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7601455 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601502 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601549 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601596 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601643 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7601690 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601737 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7601786 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
7601821 AGAATCCTAA
Statistics
Matches: 352, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 306 0.87
49 46 0.13
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7602982 original size:18 final size:18
Alignment explanation
Indices: 7602959--7603000 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
7602949 CATATGCATT
7602959 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
7602977 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
7602995 TTTAAT
1 TTTAAT
7603001 ACAATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
TTTAATCACATCAAGCAA
Found at i:7619833 original size:11 final size:11
Alignment explanation
Indices: 7619819--7619843 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7619809 AATTTTTCGA
7619819 AATATTTTATG
1 AATATTTTATG
7619830 AATATTTTATG
1 AATATTTTATG
7619841 AAT
1 AAT
7619844 TTATATTATT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
AATATTTTATG
Found at i:7624875 original size:27 final size:27
Alignment explanation
Indices: 7624840--7624905 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
7624830 TAGAACATAT
7624840 AGTCATTTTATAACAT-AGGGGCATAAC
1 AGTCATTTTATAACATGA-GGGCATAAC
***
7624867 AGTCATTTTACCGCATGAGGGCATAAC
1 AGTCATTTTATAACATGAGGGCATAAC
7624894 AGTCATTTTATA
1 AGTCATTTTATA
7624906 TAAGTTTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (27 bp):
AGTCATTTTATAACATGAGGGCATAAC
Found at i:7631886 original size:27 final size:27
Alignment explanation
Indices: 7631852--7631917 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
7631842 TACATCATAT
7631852 AGTCATTTTATAACATAGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
** * *
7631879 AGTCATTTTACCACGTGGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
7631906 AGTCATTTTATA
1 AGTCATTTTATA
7631918 TCTACTTGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (27 bp):
AGTCATTTTATAACATAGGGGCATAAC
Found at i:7634126 original size:17 final size:14
Alignment explanation
Indices: 7634079--7634117 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 14
7634069 CATTTGCTTT
7634079 TTTTGTTTTAATTTC
1 TTTT-TTTTAATTTC
7634094 TTTTTTTTAATTTC
1 TTTTTTTTAATTTC
7634108 TTTCTTTTTA
1 TTT-TTTTTA
7634118 CACTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTTAATTTC
Found at i:7636220 original size:22 final size:22
Alignment explanation
Indices: 7636194--7636235 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7636184 TTTGAATAAT
*
7636194 TAAATAAATTGAAT-AATAAACC
1 TAAAT-AATTCAATAAATAAACC
7636216 TAAATAATTCAATAAATAAA
1 TAAATAATTCAATAAATAAA
7636236 AACTGAGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAATTCAATAAATAAACC
Found at i:7640883 original size:14 final size:13
Alignment explanation
Indices: 7640860--7640901 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
7640850 TAATCTTTGA
7640860 TTTATTATTTTAT
1 TTTATTATTTTAT
7640873 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
7640886 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
7640900 TT
1 TT
7640902 GACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:7641275 original size:17 final size:18
Alignment explanation
Indices: 7641255--7641294 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
7641245 AAAAACGTAC
*
7641255 AAAAAA-TAAAATACAAA
1 AAAAAACTAAAAAACAAA
*
7641272 AAAAAACTAAAAAATAAA
1 AAAAAACTAAAAAACAAA
7641290 AAAAA
1 AAAAA
7641295 TTTGTGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (18 bp):
AAAAAACTAAAAAACAAA
Found at i:7643860 original size:14 final size:13
Alignment explanation
Indices: 7643843--7643876 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7643833 ATTTTAAAAA
7643843 TTAAAACAAAAATT
1 TTAAAA-AAAAATT
*
7643857 TTAAAAAAATATT
1 TTAAAAAAAAATT
7643870 TTAAAAA
1 TTAAAAA
7643877 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAAAAATT
Found at i:7643864 original size:11 final size:11
Alignment explanation
Indices: 7643861--7643985 Score: 96
Period size: 11 Copynumber: 12.4 Consensus size: 11
7643851 AAAATTTTAA
7643861 AAAAATATTTT
1 AAAAATATTTT
7643872 AAAAATATTTT
1 AAAAATATTTT
7643883 --AAA-A--TT
1 AAAAATATTTT
*
7643889 AAAAA-A-ATT
1 AAAAATATTTT
*
7643898 AAAAGTATTTT
1 AAAAATATTTT
*
7643909 AACAATATTTT
1 AAAAATATTTT
7643920 AAAAATATTTT
1 AAAAATATTTT
7643931 AAAAATATTTT
1 AAAAATATTTT
7643942 --AAA-A--TT
1 AAAAATATTTT
*
7643948 AAAAA-ATTTAA
1 AAAAATATTT-T
7643959 AAAAAGTATTTT
1 AAAAA-TATTTT
*
7643971 AAAAGTATTTT
1 AAAAATATTTT
7643982 AAAA
1 AAAA
7643986 TTAAAAAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
6 4 0.04
8 10 0.11
9 12 0.13
10 2 0.02
11 58 0.62
12 4 0.04
13 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:7643935 original size:59 final size:60
Alignment explanation
Indices: 7643861--7643985 Score: 200
Period size: 59 Copynumber: 2.1 Consensus size: 60
7643851 AAAATTTTAA
7643861 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATT-AAAAGTATTTTAACAA-TATTTT
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAGTATTTTAA-AAGTATTTT
*
7643920 AAAAATATTTTAAAAATATTTTAAAATTAAAAAATTTAAAAAAAGTATTTTAAAAGTATTTT
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATT--AAAAAGTATTTTAAAAGTATTTT
7643982 AAAA
1 AAAA
7643986 TTAAAAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
59 36 0.59
61 2 0.03
62 23 0.38
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (60 bp):
AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAGTATTTTAAAAGTATTTT
Found at i:7643962 original size:17 final size:17
Alignment explanation
Indices: 7643870--7643961 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 17
7643860 AAAAAATATT
*
7643870 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
7643887 TTAAAAA-AATTAAAAGTA
1 TTAAAAATATTTAAAA--A
*
7643905 TTTTAACAATATTTTAAAAATA
1 --TTAAAAATA-TTT-AAAA-A
*
7643927 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTAAAAA
7643946 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
7643962 AAGTATTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
16 14 0.23
17 14 0.23
18 1 0.02
19 1 0.02
20 9 0.15
21 4 0.07
22 14 0.23
23 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:7643969 original size:40 final size:40
Alignment explanation
Indices: 7643920--7643998 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
7643910 ACAATATTTT
7643920 AAAAATATTTTAAAAATATTTTAAAATT-AAAAAATTTAA
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTTAA
*
7643959 AAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAATTTA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAAAAAAATTTA
7643999 GAAATAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 5 0.14
40 22 0.59
41 10 0.27
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (40 bp):
AAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTTAA
Found at i:7644489 original size:72 final size:72
Alignment explanation
Indices: 7644403--7644547 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 72
7644393 TCAAGGAGAG
* *
7644403 ATACTTGGTCCATACTGATTCGAGATATCAAAATAATATCTTTGATCCTGGAGATACTTTTGGCG
1 ATACTTGATCCATACTGATTCGAGATATCAAAATAATATCTTTGATCCTAGAGATACTTTTGGCG
*
7644468 CAGAAGA
66 CACAAGA
* * * * * *
7644475 ATACTTGATCCATACTGATTTGGGATATCAAAATCATATCTTTGATCTTAGAGATAGTTTTGGTG
1 ATACTTGATCCATACTGATTCGAGATATCAAAATAATATCTTTGATCCTAGAGATACTTTTGGCG
7644540 CACAAGA
66 CACAAGA
7644547 A
1 A
7644548 AGCATAGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (72 bp):
ATACTTGATCCATACTGATTCGAGATATCAAAATAATATCTTTGATCCTAGAGATACTTTTGGCG
CACAAGA
Found at i:7648648 original size:27 final size:27
Alignment explanation
Indices: 7648617--7649485 Score: 944
Period size: 27 Copynumber: 32.4 Consensus size: 27
7648607 CCCCAAAATA
*
7648617 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
7648644 GGTAAAATGACCAAAATATCCCCAGAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648671 GATAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648698 GGTAAAATAACCGAAATAGCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648725 GGTAGAATGACCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648752 TGT--AATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
7648777 GGTAAAATCACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648804 GGTAGAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
7648831 GGTAGAATGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648858 GGTAAAATGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648885 GGTAAACTGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648912 GGTAGAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * **
7648939 GATAAAATGACCAAAATACCCGTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7648966 GGTAAAATAACCGAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* **
7648993 GGTAAAATAACTAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
7649020 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
7649047 GGTAGAACGACTGAAATA-CCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
7649073 GGTAAACTGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
7649100 GATAGAATGACCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* **
7649127 GGTAAAATGACCAAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** * *
7649154 GGTAAAATGACTAAAATACCCCTATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* ** * **
7649181 TGTAAAATGATTGAAATACACTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7649208 GATAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7649235 GGTAAAATGACTGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
7649262 GGTAGAACGACTGAAATA-CCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
**
7649288 GGTAAAATGATTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
7649315 GGTAAAATGACC-AAATTACCCCTATAG
1 GGTAAAATGACCGAAA-TACCCCCATAG
* * * *
7649342 GGTAGAATGATCGAAGTACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
7649369 GGTAAAATGACC-AAGATGCCCCCATAG
1 GGTAAAATGACCGAA-ATACCCCCATAG
* * *
7649396 GGAAAAATGATCGAATTACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7649423 GGTAAAATGACCAAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
7649450 GGTAAAATAACC-AAGAT-GCCCCATAG
1 GGTAAAATGACCGAA-ATACCCCCATAG
7649476 GGTAAAATGA
1 GGTAAAATGA
7649486 TTGTTATACC
Statistics
Matches: 714, Mismatches: 119, Indels: 19
0.84 0.14 0.02
Matches are distributed among these distances:
25 22 0.03
26 66 0.09
27 622 0.87
28 4 0.01
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:7663275 original size:7 final size:7
Alignment explanation
Indices: 7663249--7663321 Score: 60
Period size: 7 Copynumber: 10.1 Consensus size: 7
7663239 TGAGTGATAA
*
7663249 GAGAGTT
1 GAGAGAT
7663256 GAGAGA-
1 GAGAGAT
7663262 GAG-GAT
1 GAGAGAT
7663268 GAGAGAT
1 GAGAGAT
7663275 GAGCAGGAT
1 GAG-A-GAT
7663284 GAGAGAT
1 GAGAGAT
7663291 GAGATAGAT
1 GAG--AGAT
*
7663300 GAGGGAT
1 GAGAGAT
*
7663307 GAGGGAT
1 GAGAGAT
*
7663314 GAGGGAT
1 GAGAGAT
7663321 G
1 G
7663322 CTTGAAAAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
5 2 0.03
6 6 0.10
7 35 0.60
8 2 0.03
9 13 0.22
ACGTcount: A:0.36, C:0.01, G:0.48, T:0.15
Consensus pattern (7 bp):
GAGAGAT
Found at i:7663284 original size:16 final size:16
Alignment explanation
Indices: 7663263--7663293 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
7663253 GTTGAGAGAG
7663263 AGGATGAGAGATGAGC
1 AGGATGAGAGATGAGC
7663279 AGGATGAGAGATGAG
1 AGGATGAGAGATGAG
7663294 ATAGATGAGG
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:0.39, C:0.03, G:0.45, T:0.13
Consensus pattern (16 bp):
AGGATGAGAGATGAGC
Found at i:7663286 original size:9 final size:8
Alignment explanation
Indices: 7663260--7663321 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 8
7663250 AGAGTTGAGA
7663260 GAGAGGAT
1 GAGAGGAT
7663268 GAGA-GAT
1 GAGAGGAT
7663275 GAGCAGGAT
1 GAG-AGGAT
7663284 GAGA-GAT
1 GAGAGGAT
*
7663291 GAGATAGAT
1 GAGA-GGAT
7663300 GAG-GGAT
1 GAGAGGAT
7663307 GAG-GGAT
1 GAGAGGAT
7663314 GAG-GGAT
1 GAGAGGAT
7663321 G
1 G
7663322 CTTGAAAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
7 31 0.63
8 6 0.12
9 12 0.24
ACGTcount: A:0.35, C:0.02, G:0.48, T:0.15
Consensus pattern (8 bp):
GAGAGGAT
Found at i:7663293 original size:23 final size:21
Alignment explanation
Indices: 7663260--7663321 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 21
7663250 AGAGTTGAGA
7663260 GAGAGGATGAGAGATGAGCAGGAT
1 GAGA-GATGAGAGATGAG--GGAT
7663284 GAGAGATGAGATAGATGAGGGAT
1 GAGAGATGAG--AGATGAGGGAT
* *
7663307 GAGGGATGAGGGATG
1 GAGAGATGAGAGATG
7663322 CTTGAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.12
23 19 0.56
24 4 0.12
25 7 0.21
ACGTcount: A:0.35, C:0.02, G:0.48, T:0.15
Consensus pattern (21 bp):
GAGAGATGAGAGATGAGGGAT
Found at i:7663300 original size:16 final size:16
Alignment explanation
Indices: 7663265--7663309 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
7663255 TGAGAGAGAG
*
7663265 GATGAGAGATGAGCAG
1 GATGAGAGATGAGCAA
7663281 GATGAGAGATGAG-ATA
1 GATGAGAGATGAGCA-A
*
7663297 GATGAGGGATGAG
1 GATGAGAGATGAG
7663310 GGATGAGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.38, C:0.02, G:0.44, T:0.16
Consensus pattern (16 bp):
GATGAGAGATGAGCAA
Found at i:7682242 original size:6 final size:6
Alignment explanation
Indices: 7682231--7682262 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
7682221 GAGTAACTTG
7682231 TGGACC TGGACC TGGACC TGGACC TGGACC TG
1 TGGACC TGGACC TGGACC TGGACC TGGACC TG
7682263 AACTGGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (6 bp):
TGGACC
Found at i:7682654 original size:20 final size:21
Alignment explanation
Indices: 7682614--7682656 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7682604 ATTTAATTAT
7682614 TTTGTTATTTACTTATATAAA
1 TTTGTTATTTACTTATATAAA
* *
7682635 TTTGTTTTTTTCTT-TATAAA
1 TTTGTTATTTACTTATATAAA
7682655 TT
1 TT
7682657 AGCATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTGTTATTTACTTATATAAA
Found at i:7684444 original size:23 final size:23
Alignment explanation
Indices: 7684417--7684488 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
7684407 TTGCCCCTCT
* *
7684417 TGGTTAAATGATTGTTTTGTCTG
1 TGGTTAAATGACTGATTTGTCTG
*
7684440 TGGTTGAATGACTGATTTGTCTG
1 TGGTTAAATGACTGATTTGTCTG
* **
7684463 TGTTTGGTATGACTGATTTGTCTG
1 TGGTT-AAATGACTGATTTGTCTG
7684487 TG
1 TG
7684489 ATTTGAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 24 0.56
24 19 0.44
ACGTcount: A:0.15, C:0.07, G:0.29, T:0.49
Consensus pattern (23 bp):
TGGTTAAATGACTGATTTGTCTG
Found at i:7684479 original size:24 final size:24
Alignment explanation
Indices: 7684423--7684500 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
7684413 CTCTTGGTTA
* * *
7684423 AATGATTGTTTTGTCTGTGGTT-G
1 AATGACTGATTTGTCTGTGTTTGG
7684446 AATGACTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
*
7684470 TATGACTGATTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
7684494 AATGACT
1 AATGACT
7684501 AATTCTGAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 19 0.40
24 26 0.54
25 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.27, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:7684707 original size:32 final size:32
Alignment explanation
Indices: 7684664--7684781 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 32
7684654 GCGATGCTAC
**
7684664 TGATGGCTTTGTGCTAATCATAGTACCGTTAT
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAT
* * * *
7684696 TGATGGATTTGTCCCGATCATATTACCATTAT
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAT
* * *
7684728 CGATGG-TTGTGTGCCGGTAAT-GTTACCGTTAT
1 TGATGGCTT-TGTGCCGATCATAG-TACCGTTAT
7684760 TGATGGCTTTGTGCCGATCATA
1 TGATGGCTTTGTGCCGATCATA
7684782 TCACTGCTAC
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
31 2 0.03
32 63 0.94
33 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATAGTACCGTTAT
Found at i:7690910 original size:30 final size:28
Alignment explanation
Indices: 7690834--7690915 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
7690824 AACAGTATAG
7690834 TGTGGGCCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
7690862 TGTGGGCCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
7690890 TGTGAGCCTTAGCTCCCAATACAGTA
1 TGTGGGCCTTAG--CCCAATACAGTA
7690916 TCAGTACAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 39 0.76
30 12 0.24
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:7691299 original size:27 final size:27
Alignment explanation
Indices: 7691247--7691328 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 27
7691237 ACATAAGGCC
*
7691247 ATAACAGTCATTTCATCTCCTA--GGGGT
1 ATAACAGTCATTT--TATCCTATGGGGGT
7691274 ATAACAGTCATTTTATCCTATGGGGGT
1 ATAACAGTCATTTTATCCTATGGGGGT
* * * *
7691301 A-ATTCGGTCATTTTACCCTGTGGGGGT
1 ATA-ACAGTCATTTTATCCTATGGGGGT
7691328 A
1 A
7691329 ATTCGATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
25 6 0.13
26 1 0.02
27 40 0.85
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (27 bp):
ATAACAGTCATTTTATCCTATGGGGGT
Found at i:7691329 original size:27 final size:27
Alignment explanation
Indices: 7691281--7691502 Score: 320
Period size: 27 Copynumber: 8.2 Consensus size: 27
7691271 GGTATAACAG
* * *
7691281 TCATTTTATCCTATGGGGGTAATTCGG
1 TCATTTTACCCTGTGGGGGTAATTCGA
7691308 TCATTTTACCCTGTGGGGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
7691335 TTATTTTACCCTGTGGGGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
7691362 TCATTTTACCCTATGGGGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
7691389 TCATTTTACCCTGTGGGGTTAATTC-A
1 TCATTTTACCCTGTGGGGGTAATTCGA
* *
7691415 GTCATCTTACACTGTGGGGGTAATTCGA
1 -TCATTTTACCCTGTGGGGGTAATTCGA
* * *
7691443 TCATTTTACCCTATGAGGGTAATTCAA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
7691470 TCATTTTACCCTGTGGGGCTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
7691497 TCATTT
1 TCATTT
7691503 ATTAACCTCT
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 171 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCTGTGGGGGTAATTCGA
Found at i:7692108 original size:24 final size:24
Alignment explanation
Indices: 7692083--7692129 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
7692073 CCCAAATCCC
*
7692083 AATATTCTCTCCTCAAATCTCTCCA
1 AATATCCT-TCCTCAAATCTCTCCA
*
7692108 AATATCCTTCCTCAATTCTCTC
1 AATATCCTTCCTCAAATCTCTC
7692130 TATGATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATCCTTCCTCAAATCTCTCCA
Found at i:7694698 original size:27 final size:27
Alignment explanation
Indices: 7694666--7694899 Score: 208
Period size: 27 Copynumber: 8.7 Consensus size: 27
7694656 TACGCTATAG
*
7694666 GGGTATTTCAGTCATTTTACCCTTTC-A
1 GGGTATTTCAGTAATTTTACCC-TTCGA
* * * *
7694693 GAGTATTTCGGTAATTTTATCCTTCTA
1 GGGTATTTCAGTAATTTTACCCTTCGA
*
7694720 GGGTATTTC-GATAATTTTACCTTTC-A
1 GGGTATTTCAG-TAATTTTACCCTTCGA
* **
7694746 GGGGTATTT-TGATAATTTTACCCTTTAA
1 -GGGTATTTCAG-TAATTTTACCCTTCGA
* *
7694774 GGTTATTTCAGTAATTTTAACCTTCGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
** *
7694801 CAGTATTTAAGTAATTTTACCCTTCGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
7694828 GGGTATTTC-GATAATTTTACCCTTCGA
1 GGGTATTTCAG-TAATTTTACCCTTCGA
* *
7694855 GGGTAATTCGGTAATTTTACCCTTCGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
*** *
7694882 CAATATTTCAGTTATTTT
1 GGGTATTTCAGTAATTTT
7694900 TTGGCCCAAG
Statistics
Matches: 170, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
26 6 0.04
27 161 0.95
28 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACCCTTCGA
Found at i:7694781 original size:81 final size:80
Alignment explanation
Indices: 7694666--7694899 Score: 240
Period size: 81 Copynumber: 2.9 Consensus size: 80
7694656 TACGCTATAG
* * * * ** *
7694666 GGGTATTTC-AGTCATTTTACCCTTTCAGAGTATTTCGGTAATTTTATCCTTCTAGGGTATTT-C
1 GGGTATTTCGA-TAATTTTACCCTTTAAG-GTATTTCGGTAATTTTAACCTTCGACAGTATTTAA
*
7694729 GATAATTTTACCTTTC-A
64 G-TAATTTTACCCTTCGA
* *
7694746 GGGGTATTTTGATAATTTTACCCTTTAAGGTTATTTCAGTAATTTTAACCTTCGACAGTATTTAA
1 -GGGTATTTCGATAATTTTACCCTTTAAGG-TATTTCGGTAATTTTAACCTTCGACAGTATTTAA
7694811 GTAATTTTACCCTTCGA
64 GTAATTTTACCCTTCGA
* * * * * *
7694828 GGGTATTTCGATAATTTTACCCTTCGAGGGTAATTCGGTAATTTTACCCTTCGACAATATTTCAG
1 GGGTATTTCGATAATTTTACCCTT-TAAGGTATTTCGGTAATTTTAACCTTCGACAGTATTTAAG
*
7694893 TTATTTT
65 TAATTTT
7694900 TTGGCCCAAG
Statistics
Matches: 129, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
80 1 0.01
81 122 0.95
82 6 0.05
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (80 bp):
GGGTATTTCGATAATTTTACCCTTTAAGGTATTTCGGTAATTTTAACCTTCGACAGTATTTAAGT
AATTTTACCCTTCGA
Found at i:7699178 original size:26 final size:24
Alignment explanation
Indices: 7699125--7699183 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
7699115 ATTATTATAT
* *
7699125 TATTAAT-AAATTTTTATTTTTAA
1 TATTAATAAAATTTTAATTTTCAA
*
7699148 AATTAATAAAATATTATAATTTTCAA
1 TATTAATAAAAT-TT-TAATTTTCAA
*
7699174 TATTATTAAA
1 TATTAATAAA
7699184 CATACATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 2 0.07
26 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATAAAATTTTAATTTTCAA
Found at i:7705695 original size:27 final size:27
Alignment explanation
Indices: 7705663--7705870 Score: 247
Period size: 27 Copynumber: 7.7 Consensus size: 27
7705653 TCAACCCATA
* * *
7705663 AGGGTATTTCGGTCATTTTACTTTTCA
1 AGGGTATTTCGGTAATTTTACCTTTCG
* *
7705690 ACGGTATTTTGGTAATTTTATCCTTT-G
1 AGGGTATTTCGGTAATTTTA-CCTTTCG
*
7705717 AGGGTATTTCGATAATTTTACCTTTCG
1 AGGGTATTTCGGTAATTTTACCTTTCG
** *
7705744 AGGGTATTTCAATAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCTTTCG
* *
7705771 AGGGTATTTCAGTAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCTTTCG
* *
7705798 AGGGTATTTCAGTAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCTTTCG
* *
7705825 AGGGTATTTCAGTAATTTTACCCTTCG
1 AGGGTATTTCGGTAATTTTACCTTTCG
**
7705852 AGGGTATTTTAGTAATTTT
1 AGGGTATTTCGGTAATTTT
7705871 TCACCCCAAG
Statistics
Matches: 167, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
26 5 0.03
27 158 0.95
28 4 0.02
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACCTTTCG
Done.