Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold484
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: 1030986
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 6
Found at i:444280 original size:22 final size:22
Alignment explanation
Indices: 444255--444298 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
444245 TAAGAATTGT
444255 CGCTCTAATTGAAACAATTTGC
1 CGCTCTAATTGAAACAATTTGC
444277 CGCTCTAATTGAAACAATTTGC
1 CGCTCTAATTGAAACAATTTGC
444299 TATTAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
CGCTCTAATTGAAACAATTTGC
Found at i:447300 original size:19 final size:18
Alignment explanation
Indices: 447263--447301 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
447253 TTTTTTTGGG
447263 GGGGGGGGGGTTGGGGTT
1 GGGGGGGGGGTTGGGGTT
* *
447281 GGGGTGGGGGTGTGGTGTT
1 GGGGGGGGGGT-TGGGGTT
447300 GG
1 GG
447302 ATGCTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (18 bp):
GGGGGGGGGGTTGGGGTT
Found at i:456051 original size:22 final size:19
Alignment explanation
Indices: 456018--456057 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
456008 ATAAAAAAAA
456018 ATATTTTTATTAATATTTAC
1 ATATTTTTATTAA-ATTTAC
456038 ATATTTTATAATTAAATTTA
1 ATATTTT-T-ATTAAATTTA
456058 AATTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTATTAAATTTAC
Found at i:456871 original size:2 final size:2
Alignment explanation
Indices: 456866--456890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
456856 GTGTGTGTGT
456866 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
456891 CGTCTGGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:463059 original size:16 final size:16
Alignment explanation
Indices: 463038--463068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
463028 ATTTGATTTG
*
463038 ATAAATTTAATTTAAT
1 ATAAATTAAATTTAAT
463054 ATAAATTAAATTTAA
1 ATAAATTAAATTTAA
463069 GTAAGTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATTAAATTTAAT
Found at i:463134 original size:22 final size:23
Alignment explanation
Indices: 463104--463156 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
463094 ATTTGATTCG
* *
463104 AATTATTATTTTAATAAAATAAT
1 AATTTTTATTTAAATAAAATAAT
* *
463127 -ATTTTTATTTAAATATAATTAT
1 AATTTTTATTTAAATAAAATAAT
463149 AATTTTTA
1 AATTTTTA
463157 ATATAACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTTATTTAAATAAAATAAT
Found at i:464113 original size:13 final size:13
Alignment explanation
Indices: 464097--464130 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
464087 ATAAAACCAA
464097 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
464110 AAAATACAAAAAT
1 AAAATAAAAAAAT
464123 AACAATAA
1 AA-AATAA
464131 CTTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:464290 original size:103 final size:103
Alignment explanation
Indices: 464173--464579 Score: 640
Period size: 103 Copynumber: 4.0 Consensus size: 103
464163 TCAAATCAAA
* *
464173 GCCATGACTTAATATAATTAAAGATAAAAGCCTTTTATTTTATAGGTGAAAAAATTGAAATTTTT
1 GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGAAAAAATTGAAATTTTT
* * * *
464238 TGGGTTGAATTAAAGTAAAAATAACATTAATATATGGG
66 TGGGTTGAATTAAAGTGAAAATAACATTGATATTTGGT
* *
464276 GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGGAAAAATTAAAATTTTT
1 GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGAAAAAATTGAAATTTTT
* *
464341 TAGGTTGAATTAAAGTGAAAATAACATTGATATTTGAT
66 TGGGTTGAATTAAAGTGAAAATAACATTGATATTTGGT
* *
464379 GCC--GACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTAAAAAAATT-AAAGATTT
1 GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGAAAAAATTGAAA-TTTT
464441 TTGGGTTGAATTAAAGTGAAAATAACATTGATATTTGGT
65 TTGGGTTGAATTAAAGTGAAAATAACATTGATATTTGGT
* * * *
464480 GCCATGACTGAATATAATTAAAGACAAAAGCTTTTTGTTTTATAGGTGGAAAAATTGAAGTTTTT
1 GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGAAAAAATTGAAATTTTT
464545 TGGGTTGAATTAAAGTGAAAATAACATTGATATTT
66 TGGGTTGAATTAAAGTGAAAATAACATTGATATTT
464580 AGTGGAGAAT
Statistics
Matches: 279, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
100 3 0.01
101 92 0.33
103 182 0.65
104 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (103 bp):
GCCATGACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTGAAAAAATTGAAATTTTT
TGGGTTGAATTAAAGTGAAAATAACATTGATATTTGGT
Found at i:464533 original size:204 final size:204
Alignment explanation
Indices: 464178--464579 Score: 671
Period size: 204 Copynumber: 2.0 Consensus size: 204
464168 TCAAAGCCAT
* * *
464178 GACTTAATATAATTAAAGATAAAAGCCTTTTATTTTATAGGTGAAAAAATTGAAATTTTTTGGGT
1 GACTGAATATAATTAAAGATAAAAGCCTTTTATTTTATAGGTAAAAAAATTGAAAATTTTTGGGT
*
464243 TGAATTAAAGTAAAAATAACATTAATATATGGGGCCATGACTGAATATAATTAAAGATAAAAGCC
66 TGAATTAAAGTAAAAATAACATTAATATATGGGGCCATGACTGAATATAATTAAAGACAAAAGCC
464308 TTTTGTTTTATAGGTGGAAAAATTAAAATTTTTTAGGTTGAATTAAAGTGAAAATAACATTGATA
131 TTTTGTTTTATAGGTGGAAAAATTAAAATTTTTTAGGTTGAATTAAAGTGAAAATAACATTGATA
464373 TTTGATGCC
196 TTTGATGCC
*
464382 GACTGAATATAATTAAAGATAAAAGCCTTTTGTTTTATAGGTAAAAAAATT-AAAGATTTTTGGG
1 GACTGAATATAATTAAAGATAAAAGCCTTTTATTTTATAGGTAAAAAAATTGAAA-ATTTTTGGG
* * * *
464446 TTGAATTAAAGTGAAAATAACATTGATATTTGGTGCCATGACTGAATATAATTAAAGACAAAAGC
65 TTGAATTAAAGTAAAAATAACATTAATATATGGGGCCATGACTGAATATAATTAAAGACAAAAGC
* * * *
464511 TTTTTGTTTTATAGGTGGAAAAATTGAAGTTTTTTGGGTTGAATTAAAGTGAAAATAACATTGAT
130 CTTTTGTTTTATAGGTGGAAAAATTAAAATTTTTTAGGTTGAATTAAAGTGAAAATAACATTGAT
464576 ATTT
195 ATTT
464580 AGTGGAGAAT
Statistics
Matches: 184, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
203 3 0.02
204 181 0.98
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (204 bp):
GACTGAATATAATTAAAGATAAAAGCCTTTTATTTTATAGGTAAAAAAATTGAAAATTTTTGGGT
TGAATTAAAGTAAAAATAACATTAATATATGGGGCCATGACTGAATATAATTAAAGACAAAAGCC
TTTTGTTTTATAGGTGGAAAAATTAAAATTTTTTAGGTTGAATTAAAGTGAAAATAACATTGATA
TTTGATGCC
Found at i:468129 original size:2 final size:2
Alignment explanation
Indices: 468122--468166 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
468112 TGCTCTGCTT
468122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
468164 TA T
1 TA T
468167 TTATTGTCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:468861 original size:22 final size:22
Alignment explanation
Indices: 468835--468879 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
468825 ATTTTTTATT
*
468835 TAAAT-TTAATTTATAAAATATA
1 TAAATATTAATATA-AAAATATA
468857 TAAATATTAATATAAAAATATA
1 TAAATATTAATATAAAAATATA
468879 T
1 T
468880 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:469233 original size:2 final size:2
Alignment explanation
Indices: 469226--469257 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
469216 AGTAGAAGAA
469226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469258 TGCACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470155 original size:18 final size:18
Alignment explanation
Indices: 470134--470186 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 18
470124 TAAATTTTAA
470134 TATATAATATTTTTATAT
1 TATATAATATTTTTATAT
*
470152 TATATAA-ATTTTAATAT
1 TATATAATATTTTTATAT
*
470169 T-TATATTATTTTTATAT
1 TATATAATATTTTTATAT
470186 T
1 T
470187 TTTTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.13
17 20 0.65
18 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATAATATTTTTATAT
Found at i:470161 original size:32 final size:33
Alignment explanation
Indices: 470114--470186 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
470104 TAAGGTATTA
*
470114 TATATTTATTTAAATTTTAATA-TATAATATTTT
1 TATA-TTATATAAATTTTAATATTATAATATTTT
*
470147 TATATTATATAAATTTTAATATTTATATTATTTT
1 TATATTATATAAATTTTAATA-TTATAATATTTT
470181 TATATT
1 TATATT
470187 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 16 0.44
33 4 0.11
34 16 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TATATTATATAAATTTTAATATTATAATATTTT
Found at i:470179 original size:17 final size:16
Alignment explanation
Indices: 470127--470186 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
470117 ATTTATTTAA
*
470127 ATTTTAATA-TATAAT
1 ATTTTAATATTATATT
* *
470142 ATTTTTATATTATATAA
1 ATTTTAATATTATAT-T
470159 ATTTTAATATTTATATT
1 ATTTTAATA-TTATATT
*
470176 ATTTTTATATT
1 ATTTTAATATT
470187 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 8 0.22
16 6 0.17
17 16 0.44
18 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATATTATATT
Found at i:470325 original size:2 final size:2
Alignment explanation
Indices: 470318--470355 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
470308 TCACATCTTC
470318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
470356 ATAATTTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:470557 original size:3 final size:3
Alignment explanation
Indices: 470549--470576 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
470539 TATTTAGATG
470549 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
470577 ACATAATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:470861 original size:12 final size:12
Alignment explanation
Indices: 470836--470897 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
470826 ATATTTTATT
470836 TAAAT-TTAATTA
1 TAAATATTAA-TA
470848 TAAATATTAATA
1 TAAATATTAATA
*
470860 TAAAT-TT-TTA
1 TAAATATTAATA
* *
470870 T-AATATTATTT
1 TAAATATTAATA
*
470881 TAAATAATAATA
1 TAAATATTAATA
470893 TAAAT
1 TAAAT
470898 TTTTTCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 3 0.07
10 5 0.12
11 5 0.12
12 24 0.59
13 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTAATA
Found at i:470910 original size:22 final size:23
Alignment explanation
Indices: 470868--470910 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
470858 TATAAATTTT
470868 TATAATATTATTTTAAATAATAA
1 TATAATATTATTTTAAATAATAA
470891 TATAA-ATT-TTTTCAAATAAT
1 TATAATATTATTTT-AAATAAT
470911 TAAATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAATATTATTTTAAATAATAA
Found at i:471438 original size:21 final size:21
Alignment explanation
Indices: 471409--471449 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
471399 ATCTCTATCA
*
471409 ATTTATTTATATATATTTTTT
1 ATTTATTTATAAATATTTTTT
*
471430 ATTTTTTTATAAATATTTTT
1 ATTTATTTATAAATATTTTT
471450 ATCCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTATTTATAAATATTTTTT
Found at i:473903 original size:29 final size:30
Alignment explanation
Indices: 473855--473912 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
473845 ATATTATTTT
473855 ATTTATATAAATAATAATTTTAAT-CAAATA
1 ATTTATATAAATAATAA-TTTAATACAAATA
* *
473885 ATTTATTTAAA-ATTAATTTAATACAAAT
1 ATTTATATAAATAATAATTTAATACAAAT
473913 TAAATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTTATATAAATAATAATTTAATACAAATA
Found at i:474690 original size:18 final size:17
Alignment explanation
Indices: 474669--474726 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
474659 AAATTAATTG
*
474669 ATAAAATTTAATTTAAAT
1 ATAAAATTTAATAT-AAT
474687 ATAAAATTATAA-ATAAT
1 ATAAAATT-TAATATAAT
* *
474704 TTAAAATTTAAT-CAAT
1 ATAAAATTTAATATAAT
474720 ATAAAAT
1 ATAAAAT
474727 AATATCATCG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 12 0.35
17 10 0.29
18 9 0.26
19 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAATTTAATATAAT
Found at i:477088 original size:20 final size:21
Alignment explanation
Indices: 477063--477119 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
477053 AATTAGATTG
477063 AATTATTATTTAAATAAAA-A
1 AATTATTATTTAAATAAAATA
**
477083 AATTATT-TTTATTTAAAATA
1 AATTATTATTTAAATAAAATA
*
477103 AATTATTA-ATAAATAAA
1 AATTATTATTTAAATAAA
477120 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATTATTTAAATAAAATA
Found at i:477631 original size:53 final size:51
Alignment explanation
Indices: 477537--477651 Score: 121
Period size: 52 Copynumber: 2.2 Consensus size: 51
477527 TTAAGTTTAA
* * *
477537 ATTTTATTTAATTTGAATCTATTATTTAAATATATTAAAATATTAAAAA-CTT
1 ATTTTATTTAATTTGAATATATTATTTAAATAAATTAAAATA--AAAAATATT
477589 ATTTTATATTAATATT-AATATATT-TTTATAATTAAATT-AAATAAAAAATATT
1 ATTTTAT-TTAAT-TTGAATATATTATTTA-AA-TAAATTAAAATAAAAAATATT
477641 ATTTTATTTAA
1 ATTTTATTTAA
477652 AAAAAATTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
51 9 0.16
52 20 0.36
53 19 0.35
54 7 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (51 bp):
ATTTTATTTAATTTGAATATATTATTTAAATAAATTAAAATAAAAAATATT
Found at i:478245 original size:25 final size:25
Alignment explanation
Indices: 478217--478264 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
478207 ATATTATTAA
478217 TATT-TATTATATCATATAATATTTT
1 TATTATATTATAT-ATATAATATTTT
*
478242 TATTATTTTATATATATAATATT
1 TATTATATTATATATATAATATT
478265 CATGTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTATATTATATATATAATATTTT
Found at i:478248 original size:28 final size:25
Alignment explanation
Indices: 478206--478264 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 25
478196 ATTTACTTTG
478206 AATATTATTAATATTTATTATATCATAT
1 AATATTATTAATA-TT-TTATAT-ATAT
* *
478234 AATATTTTTATTATTTTATATATAT
1 AATATTATTAATATTTTATATATAT
478259 AATATT
1 AATATT
478265 CATGTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
26 6 0.21
27 2 0.07
28 11 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
AATATTATTAATATTTTATATATAT
Found at i:482042 original size:38 final size:37
Alignment explanation
Indices: 481997--482087 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
481987 CGATTAATTT
*
481997 AAAATTTTATTTTATTTTTTAAAAATAATATTTAAA-AA
1 AAAATTTTATTTTATTATTT-AAAATAA-ATTTAAATAA
* * * *
482035 ATAATTTTATATTAATATTTATAATAAATTTAAATAA
1 AAAATTTTATTTTATTATTTAAAATAAATTTAAATAA
*
482072 AAAATATT-TTTTATTA
1 AAAATTTTATTTTATTA
482088 CGTAAATAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
36 13 0.30
37 14 0.33
38 16 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
AAAATTTTATTTTATTATTTAAAATAAATTTAAATAA
Found at i:482764 original size:2 final size:2
Alignment explanation
Indices: 482757--482794 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
482747 AAAGTTAATA
482757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
482795 TCTTTTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490060 original size:2 final size:2
Alignment explanation
Indices: 490053--490081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
490043 GGAATAAATC
490053 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
490082 TTGACCTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:490262 original size:7 final size:7
Alignment explanation
Indices: 490250--490276 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
490240 ATACAAAGTA
490250 GAAACCT
1 GAAACCT
490257 GAAACCT
1 GAAACCT
490264 GAAACCT
1 GAAACCT
490271 GAAACC
1 GAAACC
490277 CTAAACCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.15, T:0.11
Consensus pattern (7 bp):
GAAACCT
Found at i:494864 original size:2 final size:2
Alignment explanation
Indices: 494851--494899 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
494841 AGAAGAATAC
*
494851 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494893 AT AT AT A
1 AT AT AT A
494900 ACTCTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:496316 original size:2 final size:2
Alignment explanation
Indices: 496309--496345 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
496299 TAAGCTTAAG
496309 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
496346 AAAATAAATA
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:499244 original size:17 final size:17
Alignment explanation
Indices: 499211--499245 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
499201 TTCTCAAAAG
*
499211 AATCTAAATAACCACCA
1 AATCTAAATAACAACCA
*
499228 AATCTAAATAGCAACCA
1 AATCTAAATAACAACCA
499245 A
1 A
499246 GCAATTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (17 bp):
AATCTAAATAACAACCA
Found at i:506895 original size:2 final size:2
Alignment explanation
Indices: 506888--506926 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
506878 GCTTCATGAA
506888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506927 CTTCTGCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:509957 original size:2 final size:2
Alignment explanation
Indices: 509945--510022 Score: 57
Period size: 2 Copynumber: 39.0 Consensus size: 2
509935 TGCGTGCATC
* * * * * * *
509945 TA TA CA TA TA TA TA TA TA TA CA CA TA TA TA TA TA CA CA CA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
509987 TA TA TA TA TG TA TG TA TA CA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
510023 GCAAAAATAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (2 bp):
TA
Found at i:509966 original size:16 final size:16
Alignment explanation
Indices: 509945--509995 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
509935 TGCGTGCATC
*
509945 TATACATATATATATA
1 TATACACATATATATA
509961 TATACACATATATATA
1 TATACACATATATATA
* *
509977 TACACACACATATATA
1 TATACACATATATATA
509993 TAT
1 TAT
509996 GTATGTATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TATACACATATATATA
Found at i:509971 original size:12 final size:12
Alignment explanation
Indices: 509945--510022 Score: 66
Period size: 12 Copynumber: 6.3 Consensus size: 12
509935 TGCGTGCATC
* *
509945 TATACATATATA
1 TATATATATACA
*
509957 TATATATACACA
1 TATATATATACA
509969 TATATATATACACA
1 TATATATAT--ACA
* * *
509983 CACATATATATA
1 TATATATATACA
* *
509995 TGTATGTATACA
1 TATATATATACA
510007 TATATATATACA
1 TATATATATACA
510019 TATA
1 TATA
510023 GCAAAAATAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
12 40 0.80
14 10 0.20
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (12 bp):
TATATATATACA
Found at i:509971 original size:18 final size:18
Alignment explanation
Indices: 509948--510016 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
509938 GTGCATCTAT
509948 ACATATATATATATATAC
1 ACATATATATATATATAC
* *
509966 ACATATATATATACACAC
1 ACATATATATATATATAC
* *
509984 ACATATATATATGTATGTAT
1 ACATATATATA--TATATAC
510004 ACATATATATATA
1 ACATATATATATA
510017 CATATAGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 29 0.67
20 14 0.33
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.38
Consensus pattern (18 bp):
ACATATATATATATATAC
Found at i:515146 original size:2 final size:2
Alignment explanation
Indices: 515139--515164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
515129 TCTGCAGCAA
515139 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
515165 ATGCGCGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:516834 original size:10 final size:10
Alignment explanation
Indices: 516819--516843 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
516809 TTTTAAGGAG
516819 AAAAAAATTT
1 AAAAAAATTT
516829 AAAAAAATTT
1 AAAAAAATTT
516839 AAAAA
1 AAAAA
516844 GAAAAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:517262 original size:12 final size:12
Alignment explanation
Indices: 517247--517271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
517237 TGGCCGTGTT
517247 CATGAATTGGGC
1 CATGAATTGGGC
517259 CATGAATTGGGC
1 CATGAATTGGGC
517271 C
1 C
517272 TGATTAGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (12 bp):
CATGAATTGGGC
Found at i:532143 original size:8 final size:8
Alignment explanation
Indices: 532130--532167 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
532120 TTAATTAATA
532130 TTAAAAAT
1 TTAAAAAT
532138 TT-AAAAT
1 TTAAAAAT
532145 TTAAAATAT
1 TTAAAA-AT
*
532154 TTATAAAT
1 TTAAAAAT
532162 TTAAAA
1 TTAAAA
532168 TTAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAAAT
Found at i:532163 original size:17 final size:16
Alignment explanation
Indices: 532130--532168 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
532120 TTAATTAATA
532130 TTAAAA-ATTTAAAAT
1 TTAAAATATTTAAAAT
532145 TTAAAATATTTATAAAT
1 TTAAAATATTTA-AAAT
532162 TTAAAAT
1 TTAAAAT
532169 TAATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.27
16 5 0.23
17 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATTTAAAAT
Found at i:536551 original size:15 final size:16
Alignment explanation
Indices: 536525--536554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
536515 ATAAATTTTT
536525 TAATTAAATAAAATTA
1 TAATTAAATAAAATTA
536541 TAATT-AATAAAATT
1 TAATTAAATAAAATT
536555 TATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAATAAAATTA
Found at i:536557 original size:16 final size:17
Alignment explanation
Indices: 536515--536557 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
536505 TTTAATATTT
* *
536515 ATAAATTTTTTAATTAA
1 ATAAAATTTATAATTAA
536532 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
536547 ATAAAATTTAT
1 ATAAAATTTAT
536558 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:537103 original size:15 final size:16
Alignment explanation
Indices: 537078--537107 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
537068 ACATAAATTT
537078 TTTCTCTTTTTCTTTC
1 TTTCTCTTTTTCTTTC
537094 TTTC-CTTTTTCTTT
1 TTTCTCTTTTTCTTT
537108 TTTTATAAAA
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTCTTTTTCTTTC
Found at i:537547 original size:2 final size:2
Alignment explanation
Indices: 537542--537589 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
537532 CATAAAAATG
* * *
537542 AT AT AT AT AT GAC AT AA AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537585 AT AT A
1 AT AT A
537590 AAAAATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 38 0.97
3 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:537640 original size:20 final size:19
Alignment explanation
Indices: 537612--537650 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
537602 TATGTTAAAA
*
537612 TTTATATAAAAATATAATAT
1 TTTAAATAAAAA-ATAATAT
537632 TTTAAATAAAAAATAATAT
1 TTTAAATAAAAAATAATAT
537651 AAATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAATAAAAAATAATAT
Found at i:538124 original size:32 final size:36
Alignment explanation
Indices: 538047--538126 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 36
538037 TAAAATGTTC
538047 AATTATAAA-AAAAATTATTTTTATTAATATTTTATAAT
1 AATT-TAAATAAAAATTATTTTTATT-ATA-TTTATAAT
538085 AATTTTAAATAAAAA-TATTTTTATT-TA-TTA-AAT
1 AA-TTTAAATAAAAATTATTTTTATTATATTTATAAT
538118 AATTTAAAT
1 AATTTAAAT
538127 TTTATCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
32 7 0.17
33 5 0.12
34 3 0.08
36 2 0.05
38 16 0.40
39 7 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
AATTTAAATAAAAATTATTTTTATTATATTTATAAT
Found at i:538674 original size:23 final size:23
Alignment explanation
Indices: 538610--538667 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
538600 ATATAATAGA
* *
538610 ATAATAATAAAA-TAATTATTTT
1 ATAAAAATAAAATTAAATATTTT
538632 ATAAAAATAAAATTAAATATTTT
1 ATAAAAATAAAATTAAATATTTT
538655 A-ACAAAATAAAAT
1 ATA-AAAATAAAAT
538668 ATCATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
ATAAAAATAAAATTAAATATTTT
Found at i:544618 original size:13 final size:13
Alignment explanation
Indices: 544598--544635 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
544588 TTGTTATAAA
544598 ATTTAAATTTATT
1 ATTTAAATTTATT
544611 -TATTAAATATTATT
1 AT-TTAAAT-TTATT
544625 ATTTAAATTTA
1 ATTTAAATTTA
544636 AATTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.05
13 9 0.41
14 11 0.50
15 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTAAATTTATT
Found at i:544649 original size:25 final size:26
Alignment explanation
Indices: 544598--544654 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
544588 TTGTTATAAA
* *
544598 ATTTAAATTTATTTATTAAATATTATT
1 ATTTAAATTTA-TAATTAAATAATATT
544625 ATTTAAATTTA-AATTAAATAATATT
1 ATTTAAATTTATAATTAAATAATATT
544650 ATTTA
1 ATTTA
544655 TTAGATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 17 0.61
27 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAATTTATAATTAAATAATATT
Found at i:545046 original size:55 final size:55
Alignment explanation
Indices: 544931--545046 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 55
544921 CCATATATTC
** *
544931 ATATTTAAATTTATTATTTATAAAAAATAAAATGAATTTAAATAACATATTTAGA
1 ATATTTAAATTTATTATTTATAAAAAATAAAACAAATTTAAATAAAATATTTAGA
* * * * *
544986 TTATTTGAATTTATTATTTAT-ATAATTAATACAAATTTAAATTATAAATATTTA-A
1 ATATTTAAATTTATTATTTATAAAAAATAAAACAAATTTAAA-TA-AAATATTTAGA
545041 ATATTT
1 ATATTT
545047 TTAATTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
54 15 0.30
55 27 0.54
56 8 0.16
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (55 bp):
ATATTTAAATTTATTATTTATAAAAAATAAAACAAATTTAAATAAAATATTTAGA
Found at i:547938 original size:3 final size:3
Alignment explanation
Indices: 547930--547962 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
547920 GGAAACATGA
*
547930 GTG GTG GTG GTG GTG GTG GTG GTG GTG ATG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
547963 AATGGTGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.64, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:558856 original size:16 final size:16
Alignment explanation
Indices: 558837--558876 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
558827 TAAAGTGTAA
* *
558837 ATATATATATACATAT
1 ATATATATATACACAC
558853 ATATATATATACACAC
1 ATATATATATACACAC
558869 ATATATAT
1 ATATATAT
558877 TCACAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATATATACACAC
Found at i:559383 original size:2 final size:2
Alignment explanation
Indices: 559376--559401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
559366 TCATATTTGA
559376 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
559402 TTACACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:566972 original size:26 final size:27
Alignment explanation
Indices: 566920--566975 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
566910 AAATAAATAA
*
566920 ATTTTTTTAATTACCTACTCAATCATT
1 ATTTTTTTAATTACCTACTCAACCATT
** *
566947 ATTTTTTTAATTTTCTA-TTAACCATT
1 ATTTTTTTAATTACCTACTCAACCATT
566973 ATT
1 ATT
566976 GTGCATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTTTTTAATTACCTACTCAACCATT
Found at i:568496 original size:21 final size:21
Alignment explanation
Indices: 568446--568511 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
568436 GAATAATAAT
* *
568446 ATTTTATAATCAATAACATTTTA
1 ATTTTATAAACAA-AA-ATTATA
*
568469 ATATTATAAACAAAAATTATA
1 ATTTTATAAACAAAAATTATA
*
568490 ATTTTAT-AACTAAAATTTATA
1 ATTTTATAAAC-AAAAATTATA
568511 A
1 A
568512 ATATTAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 3 0.08
21 21 0.57
22 2 0.05
23 11 0.30
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTATAAACAAAAATTATA
Found at i:568524 original size:21 final size:21
Alignment explanation
Indices: 568467--568524 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
568457 AATAACATTT
*
568467 TAATATTATAAACAAAAATTA
1 TAATATTATAAATAAAAATTA
* * *
568488 TAATTTTATAACTAAAATTTA
1 TAATATTATAAATAAAAATTA
568509 TAAATATTA-AAATAAA
1 T-AATATTATAAATAAA
568525 TCTAAAAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATTATAAATAAAAATTA
Found at i:568837 original size:29 final size:31
Alignment explanation
Indices: 568800--568860 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
568790 CAAATCTTCG
*
568800 ATCGATAAA-T-GTTAAATATATATATTTAAA
1 ATCGATAAATTAGTTAAAAATATAT-TTTAAA
*
568830 ATCG-TAAATTATTTAAAAATATATTTTAAA
1 ATCGATAAATTAGTTAAAAATATATTTTAAA
568860 A
1 A
568861 AATTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 12 0.44
31 11 0.41
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
ATCGATAAATTAGTTAAAAATATATTTTAAA
Found at i:569470 original size:17 final size:17
Alignment explanation
Indices: 569439--569490 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
569429 TATTATAATC
*
569439 ATATTTA-AAAAATTTT
1 ATATTTATATAAATTTT
569455 ATATTTATATAAATTTT
1 ATATTTATATAAATTTT
**
569472 AATATTCGTATAAATTTT
1 -ATATTTATATAAATTTT
569490 A
1 A
569491 AAACATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
18 15 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATTTATATAAATTTT
Found at i:569483 original size:18 final size:18
Alignment explanation
Indices: 569448--569491 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
569438 CATATTTAAA
*
569448 AAATTTT-ATATTTATAT
1 AAATTTTAATATTCATAT
*
569465 AAATTTTAATATTCGTAT
1 AAATTTTAATATTCATAT
569483 AAATTTTAA
1 AAATTTTAA
569492 AACATACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTTTAATATTCATAT
Found at i:570985 original size:32 final size:32
Alignment explanation
Indices: 570914--571015 Score: 100
Period size: 32 Copynumber: 3.2 Consensus size: 32
570904 AACGACCATC
* * *
570914 AAATTTATGAATAATTATATCTAATATTTATA
1 AAATTTATGAGTAATTATATTTAATATTCATA
* * *
570946 AAATTTATGAGTAATTTTATTTAATATTCGTT
1 AAATTTATGAGTAATTATATTTAATATTCATA
* * * *
570978 AATTTTATAAGTAATTATGTTT-A-ATTCATC
1 AAATTTATGAGTAATTATATTTAATATTCATA
571008 AAATTTAT
1 AAATTTAT
571016 TTAATTTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 12 0.21
31 1 0.02
32 44 0.77
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (32 bp):
AAATTTATGAGTAATTATATTTAATATTCATA
Found at i:571258 original size:23 final size:24
Alignment explanation
Indices: 571231--571279 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
571221 TAAATTTAAG
571231 TTTAAATTTT-AATGTAT-ATAATT
1 TTTAAATTTTAAAT-TATGATAATT
*
571254 TTTAATTTTTAAATTATGATAATT
1 TTTAAATTTTAAATTATGATAATT
571278 TT
1 TT
571280 GTATCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTAAATTTTAAATTATGATAATT
Found at i:576161 original size:124 final size:124
Alignment explanation
Indices: 575962--576209 Score: 379
Period size: 124 Copynumber: 2.0 Consensus size: 124
575952 AATGTGTCAG
** * *
575962 ATAAGGGTGTCAAACACGAGTACTTCAAAAAAATGAAGAGCTGTTGCAACATAGGTTGCACTTAC
1 ATAAGGGTGTCAAACACGAGTACTTCAAAAAAACAAAGAGCCGTAGCAACATAGGTTGCACTTAC
** * * *
576027 ACCTTTACCTTTCAAAGGATGAGAAGGTTTGGTTTTTATCACTTTGATCTTCCTGACAT
66 ACCTACACCTTTCAAAGGATGAGAAAGTTTGGCTTTGATCACTTTGATCTTCCTGACAT
* * *
576086 ATAAGGGTGTCAAACACGATTACTTCAAAAAACCAAAGAGCCGTAGCGACATAGGTTGCACTTAC
1 ATAAGGGTGTCAAACACGAGTACTTCAAAAAAACAAAGAGCCGTAGCAACATAGGTTGCACTTAC
*
576151 ACCTACACCTTTCAAAGGATGGGAAAGTTTGGCTTTGATCACTTTGATCTTCCTGACAT
66 ACCTACACCTTTCAAAGGATGAGAAAGTTTGGCTTTGATCACTTTGATCTTCCTGACAT
576210 TTGGCTGCAT
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (124 bp):
ATAAGGGTGTCAAACACGAGTACTTCAAAAAAACAAAGAGCCGTAGCAACATAGGTTGCACTTAC
ACCTACACCTTTCAAAGGATGAGAAAGTTTGGCTTTGATCACTTTGATCTTCCTGACAT
Found at i:578891 original size:66 final size:66
Alignment explanation
Indices: 578782--578913 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
578772 TTTTTCAAGT
*
578782 TCTTCTATGTATTCGGAGGGTCTTTGGAGGTTCATATCCTGATACCTATGTCTATATATAAATCG
1 TCTTCTATGTATTCGGAGGGTCCTTGGAGGTTCATATCCTGATACCTATGTCTATATATAAATCG
578847 G
66 G
* *
578848 TCTTCTATGTATTTGGAGGGTCCTTGGAGGTTCATATCTTGATACCTATGTCTATATATAAATCG
1 TCTTCTATGTATTCGGAGGGTCCTTGGAGGTTCATATCCTGATACCTATGTCTATATATAAATCG
578913 G
66 G
578914 ACATGGGTGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (66 bp):
TCTTCTATGTATTCGGAGGGTCCTTGGAGGTTCATATCCTGATACCTATGTCTATATATAAATCG
G
Found at i:581429 original size:16 final size:16
Alignment explanation
Indices: 581410--581455 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
581400 TTTTAAATAT
*
581410 TTATATTTAATATTTA
1 TTATATTTAAAATTTA
* *
581426 TTATAATAAAAATTTA
1 TTATATTTAAAATTTA
*
581442 TTATATTTATAATT
1 TTATATTTAAAATT
581456 ATAATAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTAAAATTTA
Found at i:591092 original size:48 final size:48
Alignment explanation
Indices: 590775--591082 Score: 449
Period size: 48 Copynumber: 6.4 Consensus size: 48
590765 CAAGAAAGAA
* *
590775 TCGAGAG-TTGTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTAGGGTTT
1 TCGAGAGCTT-TCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
*
590823 TCGAAAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGTTGGCTGGGGTTG
1 TCGAGAGCTTTCTGCTTCCCCGGACTTCTTA---GTTGTTGGCTGGGGTTG
*
590874 TTGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
1 TCGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
590922 TCGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
1 TCGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
* * *
590970 TCGAGAGCTTTCCGCTTCCCTGGACTTCTTAATTGTTGGCTGGGGTTG
1 TCGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
* **
591018 TTGAGAG-TTTCTTGCTTCCCCGGACTTCTTAGTTGTTGGCTGCAGTTG
1 TCGAGAGCTTTC-TGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
**
591066 TCGAGATTTTTCTGCTT
1 TCGAGAGCTTTCTGCTT
591083 TGTCGGACTT
Statistics
Matches: 237, Mismatches: 17, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
47 4 0.02
48 183 0.77
49 6 0.03
51 44 0.19
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (48 bp):
TCGAGAGCTTTCTGCTTCCCCGGACTTCTTAGTTGTTGGCTGGGGTTG
Found at i:598555 original size:36 final size:36
Alignment explanation
Indices: 598508--598579 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
598498 TTTGGCGCAG
* * * *
598508 TTGATGAAGGCAATGTTCTGGACGACGCTTCAGCCT
1 TTGATGAAGGCAACGTTCTAGACAAAGCTTCAGCCT
598544 TTGATGAAGGCAACGTTCTAGACAAAGCTTCAGCCT
1 TTGATGAAGGCAACGTTCTAGACAAAGCTTCAGCCT
598580 GAGTCATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (36 bp):
TTGATGAAGGCAACGTTCTAGACAAAGCTTCAGCCT
Found at i:599207 original size:16 final size:16
Alignment explanation
Indices: 599186--599267 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 16
599176 AAGTTGAATT
599186 AATTTAAATTTTTTTA
1 AATTTAAATTTTTTTA
*
599202 AATTT-AATTTTAATTTT
1 AATTTAAATTTT--TTTA
* *
599219 AATTTTAATTTATGTTA
1 AATTTAAATTT-TTTTA
* *
599236 AATATAATTATTTTTATA
1 AATTTAA--ATTTTTTTA
599254 TAATTTAAATTTTT
1 -AATTTAAATTTTT
599268 AAAAATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 6 0.12
16 5 0.10
17 21 0.41
18 8 0.16
19 11 0.22
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (16 bp):
AATTTAAATTTTTTTA
Found at i:599214 original size:12 final size:12
Alignment explanation
Indices: 599184--599244 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
599174 TGAAGTTGAA
599184 TTAA-TTTAAAT
1 TTAATTTTAAAT
599195 TT--TTTTAAAT
1 TTAATTTTAAAT
*
599205 TTAATTTTAATT
1 TTAATTTTAAAT
599217 TTAATTTT-AAT
1 TTAATTTTAAAT
*
599228 TT-ATGTTAAAT
1 TTAATTTTAAAT
*
599239 ATAATT
1 TTAATT
599245 ATTTTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 13 0.32
11 10 0.25
12 17 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TTAATTTTAAAT
Found at i:600169 original size:32 final size:36
Alignment explanation
Indices: 600121--600191 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 36
600111 ATTTATAAAA
600121 AAAATAAATAAATTTTTATTTA-TAAAAA-AA-TAT
1 AAAATAAATAAATTTTTATTTATTAAAAATAATTAT
*
600154 AAAA-AAATAATTTTTTATTTATTAAAAATAATTAT
1 AAAATAAATAAATTTTTATTTATTAAAAATAATTAT
600189 AAA
1 AAA
600192 GAAAGATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 16 0.47
33 10 0.29
34 2 0.06
35 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
AAAATAAATAAATTTTTATTTATTAAAAATAATTAT
Found at i:600170 original size:28 final size:27
Alignment explanation
Indices: 600111--600171 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
600101 TTCATATTAA
* *
600111 ATTTATAAAAAAAATAAATAAATTTTT
1 ATTTATAAAAAAAATAAAAAAATATTT
600138 ATTTATAAAAAAATATAAAAAAATAATTT
1 ATTTATAAAAAAA-ATAAAAAAAT-ATTT
600167 -TTTAT
1 ATTTAT
600172 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 13 0.43
28 14 0.47
29 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTATAAAAAAAATAAAAAAATATTT
Found at i:600398 original size:12 final size:12
Alignment explanation
Indices: 600381--600430 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
600371 ATTAATTAAC
*
600381 TTAATTTTATAA
1 TTAATTTTATTA
600393 TTAA-TTTATTA
1 TTAATTTTATTA
*
600404 TTCAATTTTTTTA
1 TT-AATTTTATTA
600417 TTATATTTTATTA
1 TTA-ATTTTATTA
600430 T
1 T
600431 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 8 0.25
12 7 0.22
13 17 0.53
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTAATTTTATTA
Found at i:600605 original size:15 final size:15
Alignment explanation
Indices: 600585--600614 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
600575 ATAATATTCA
*
600585 ATAATTTATTTAAAT
1 ATAATTTAATTAAAT
600600 ATAATTTAATTAAAT
1 ATAATTTAATTAAAT
600615 TTTAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATTTAATTAAAT
Found at i:612272 original size:2 final size:2
Alignment explanation
Indices: 612265--612333 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
612255 GATCCTCCAA
612265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
612307 AT AT CT 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 A
612334 AACTTTAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:612435 original size:15 final size:15
Alignment explanation
Indices: 612415--612461 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
612405 CACCTTCTGT
612415 TCATTTGCTATTGCA
1 TCATTTGCTATTGCA
612430 TCATTTG-TA-TG-A
1 TCATTTGCTATTGCA
612442 TC--TTGCTATTGCA
1 TCATTTGCTATTGCA
612455 TCATTTG
1 TCATTTG
612462 TATGATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
10 3 0.11
11 2 0.07
12 5 0.19
13 5 0.19
14 2 0.07
15 10 0.37
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (15 bp):
TCATTTGCTATTGCA
Found at i:612448 original size:25 final size:25
Alignment explanation
Indices: 612419--612468 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
612409 TTCTGTTCAT
612419 TTGCTATTGCATCATTTGTATGATC
1 TTGCTATTGCATCATTTGTATGATC
612444 TTGCTATTGCATCATTTGTATGATC
1 TTGCTATTGCATCATTTGTATGATC
612469 ATCTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (25 bp):
TTGCTATTGCATCATTTGTATGATC
Found at i:613791 original size:22 final size:20
Alignment explanation
Indices: 613743--613792 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
613733 GCTGCTTTAG
*
613743 AAAATTGATAATATAAAATAA
1 AAAATT-ATAATAAAAAATAA
*
613764 ATAATTATAGATAAAAATATAA
1 AAAATTATA-ATAAAAA-ATAA
613786 AAAATTA
1 AAAATTA
613793 ATAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAATTATAATAAAAAATAA
Found at i:618687 original size:120 final size:121
Alignment explanation
Indices: 618468--618708 Score: 412
Period size: 120 Copynumber: 2.0 Consensus size: 121
618458 GTCAAGTATT
* *
618468 ACGAGACACAGTCCAAACCAGCCACGCTACCAGATCAGTATCTTTAGCCTCATGAAGATCATCAC
1 ACGAGACACAGTCCAAACCAGCCACGCTAACAGATCAGTATCTTTAGCCTCATGAAGACCATCAC
618533 CGATGAGGCTTATAAATTATTCATTTTAACCATGGAATGGTAATGCAGAAGAATGA
66 CGATGAGGCTTATAAATTATTCATTTTAACCATGGAATGGTAATGCAGAAGAATGA
* * *
618589 ACGATACACAGTCCAAGCCAGCCATGC-AACAGATCAGTATCTTTAGCCTCATGAAGACCATCAC
1 ACGAGACACAGTCCAAACCAGCCACGCTAACAGATCAGTATCTTTAGCCTCATGAAGACCATCAC
* *
618653 CGATGAGGCTTATGAATTATTCATTTTAACCATGGAATGGTAATGCAGAAGGATGA
66 CGATGAGGCTTATAAATTATTCATTTTAACCATGGAATGGTAATGCAGAAGAATGA
618709 TGATTTGCCC
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 89 0.79
121 24 0.21
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (121 bp):
ACGAGACACAGTCCAAACCAGCCACGCTAACAGATCAGTATCTTTAGCCTCATGAAGACCATCAC
CGATGAGGCTTATAAATTATTCATTTTAACCATGGAATGGTAATGCAGAAGAATGA
Found at i:619058 original size:11 final size:11
Alignment explanation
Indices: 619042--619067 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
619032 TATGAATCAT
619042 AAGGTCATGAG
1 AAGGTCATGAG
619053 AAGGTCATGAG
1 AAGGTCATGAG
619064 AAGG
1 AAGG
619068 AGCCAAGAAT
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:0.38, T:0.15
Consensus pattern (11 bp):
AAGGTCATGAG
Found at i:624561 original size:18 final size:16
Alignment explanation
Indices: 624532--624582 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
624522 GTTAAAAGGA
624532 TATTTTATATTTAATT
1 TATTTTATATTTAATT
*
624548 TATTATTAATATTT-ATA
1 TATT-TT-ATATTTAATT
*
624565 TATTTTATAATTAATT
1 TATTTTATATTTAATT
624581 TA
1 TA
624583 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.17
16 10 0.34
17 8 0.28
18 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTATATTTAATT
Found at i:625441 original size:23 final size:22
Alignment explanation
Indices: 625414--625478 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
625404 TAACTATTTA
*
625414 AATTTTTTATTTTAAAAATTACT
1 AATTTTTTATTTTAAAAA-AACT
* * *
625437 AATTTCCTTATTTGAAAAAAATT
1 AATTT-TTTATTTTAAAAAAACT
*
625460 ACTTTTTTATTTTAAAAAA
1 AATTTTTTATTTTAAAAAA
625479 TCAATCTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 12 0.35
23 11 0.32
24 11 0.32
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTTTTATTTTAAAAAAACT
Found at i:625944 original size:12 final size:12
Alignment explanation
Indices: 625927--625951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
625917 TTATTATTTG
625927 TTAAAATAAATT
1 TTAAAATAAATT
625939 TTAAAATAAATT
1 TTAAAATAAATT
625951 T
1 T
625952 AAGTATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAATAAATT
Found at i:626008 original size:24 final size:21
Alignment explanation
Indices: 625967--626012 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 21
625957 TTTGATGTTA
625967 TTTAAATTAAAATTTAAAAAT
1 TTTAAATTAAAATTTAAAAAT
625988 TTTAAATAATAAATATTTAAAAAT
1 TTTAAAT--TAAA-ATTTAAAAAT
626012 T
1 T
626013 AATATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAATTAAAATTTAAAAAT
Found at i:626682 original size:22 final size:22
Alignment explanation
Indices: 626656--626697 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
626646 TCATATAAAA
626656 TTTTAAAATTAAATAAAAATAT
1 TTTTAAAATTAAATAAAAATAT
**
626678 TTTTATTATTAAATAAAAAT
1 TTTTAAAATTAAATAAAAAT
626698 TTAAATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTAAAATTAAATAAAAATAT
Found at i:632101 original size:51 final size:51
Alignment explanation
Indices: 632044--632145 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
632034 CTAGCATTCG
*
632044 TATCTGAACATGAATATAAAGATATATTTTTTTAAGAATTTTTCGAATACA
1 TATCTGAACATGAATATAAAGATATATTTTTTTAAGAACTTTTCGAATACA
* *
632095 TATCTGAATATGAATATAAAGATATGTTTTTTTAAGAACTTTTCGAATACA
1 TATCTGAACATGAATATAAAGATATATTTTTTTAAGAACTTTTCGAATACA
632146 CGCAAAACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (51 bp):
TATCTGAACATGAATATAAAGATATATTTTTTTAAGAACTTTTCGAATACA
Found at i:633583 original size:12 final size:12
Alignment explanation
Indices: 633551--633607 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
633541 TTTTTAAATC
633551 AATTTAAATTCAAT
1 AATTTAAA-T-AAT
633565 AATTTAAATAAT
1 AATTTAAATAAT
*
633577 AAATTAAAATAAT
1 -AATTTAAATAAT
*
633590 -TTTTAAATAAT
1 AATTTAAATAAT
633601 AATTTAA
1 AATTTAA
633608 TCTGAATGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 9 0.24
12 8 0.22
13 12 0.32
14 8 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
AATTTAAATAAT
Found at i:633594 original size:24 final size:24
Alignment explanation
Indices: 633532--633607 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
633522 TTTTAATTAA
633532 TAAAATAATTTTTTAAATCAATTTAAAT
1 TAAAATAA-TTTTTAAAT-AA--TAAAT
*
633560 T-CAATAA--TTTAAATAATAAAT
1 TAAAATAATTTTTAAATAATAAAT
*
633581 TAAAATAATTTTTAAATAATAATT
1 TAAAATAATTTTTAAATAATAAAT
633605 TAA
1 TAA
633608 TCTGAATGCG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
21 6 0.14
22 5 0.12
23 2 0.05
24 23 0.55
27 5 0.12
28 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATAATTTTTAAATAATAAAT
Found at i:634060 original size:76 final size:76
Alignment explanation
Indices: 633963--634112 Score: 246
Period size: 76 Copynumber: 2.0 Consensus size: 76
633953 TGCTAGGAAT
* * *
633963 TTGAGTGCACTACAAGTGTCACTTACGCCTGTTTTCTTCTAACATTATAATGGCAGCATTACTCG
1 TTGAGTGCACTACAAGTGTCACTTACGCCTGTTGTCTTCCAACATTATAATGGCAACATTACTCG
634028 CTCAAGCATGG
66 CTCAAGCATGG
* * *
634039 TTGAGTGCAGTCCAAGTGTCACTTATGCCTGTTGTCTTCCAACATTATAATGGCAACATTACTCG
1 TTGAGTGCACTACAAGTGTCACTTACGCCTGTTGTCTTCCAACATTATAATGGCAACATTACTCG
634104 CTCAAGCAT
66 CTCAAGCAT
634113 CGTCAAGTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (76 bp):
TTGAGTGCACTACAAGTGTCACTTACGCCTGTTGTCTTCCAACATTATAATGGCAACATTACTCG
CTCAAGCATGG
Found at i:634685 original size:21 final size:21
Alignment explanation
Indices: 634643--634715 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 21
634633 TGATTGATTT
* *
634643 AATTTATTTAATTTAAAAATTA
1 AATTAATTAAATTT-AAAATTA
* *
634665 ATTTAATTAAATTTAATATTAA
1 AATTAATTAAATTTAAAATT-A
*
634687 AATTGATTAAATTTAAAATTA
1 AATTAATTAAATTTAAAATTA
634708 AATTAATT
1 AATTAATT
634716 GAATGGATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 13 0.31
22 29 0.69
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
AATTAATTAAATTTAAAATTA
Found at i:634688 original size:27 final size:27
Alignment explanation
Indices: 634639--634713 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
634629 AGTTTGATTG
*
634639 ATTTAATT-TATTTAAT-TTAAAAATTA
1 ATTTAATTAAATTTAATATT-AAAATTA
*
634665 ATTTAATTAAATTTAATATTAAAATTG
1 ATTTAATTAAATTTAATATTAAAATTA
* *
634692 ATTAAATTTAAAATTAA-ATTAA
1 ATTTAA-TTAAATTTAATATTAA
634714 TTGAATGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.19
27 23 0.55
28 11 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
ATTTAATTAAATTTAATATTAAAATTA
Found at i:634823 original size:11 final size:11
Alignment explanation
Indices: 634781--634839 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
634771 AATTTTAATT
*
634781 TTAAATTTTAA
1 TTAAGTTTTAA
*
634792 TTGAGTTTT-A
1 TTAAGTTTTAA
*
634802 TTATTATTTTTAA
1 TTA--AGTTTTAA
634815 TTAAGTTTTAA
1 TTAAGTTTTAA
634826 TTAAGTTTTTAA
1 TTAAG-TTTTAA
634838 TT
1 TT
634840 TTTACATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.08
11 19 0.49
12 13 0.33
13 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (11 bp):
TTAAGTTTTAA
Found at i:634834 original size:23 final size:22
Alignment explanation
Indices: 634786--634839 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
634776 TAATTTTAAA
*
634786 TTTTAATTGAGTTTTATTATTAT
1 TTTTAATTAAGTTTTATTA-TAT
634809 TTTTAATTAAGTTTTAATTA-AGT
1 TTTTAATTAAGTTTT-ATTATA-T
634832 TTTTAATT
1 TTTTAATT
634840 TTTACATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.82
24 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTAATTAAGTTTTATTATAT
Found at i:635581 original size:12 final size:12
Alignment explanation
Indices: 635552--635597 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
635542 TTTTATTTGC
635552 TAATTTTTATGAT
1 TAATTTTTAT-AT
635565 TAATTTTTAT-T
1 TAATTTTTATAT
635576 TAAATTTTTAATAT
1 T-AATTTTT-ATAT
635590 TAATTTTT
1 TAATTTTT
635598 TGAATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.07
12 7 0.23
13 19 0.63
14 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TAATTTTTATAT
Found at i:638507 original size:23 final size:23
Alignment explanation
Indices: 638479--638531 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
638469 TTTAAAAAAT
*
638479 ATTAAATTTAAAAAATAATTTTAA
1 ATTAAATAT-AAAAATAATTTTAA
* *
638503 A-TAAAAATAAAAATTATTTTAA
1 ATTAAATATAAAAATAATTTTAA
638525 ATTAAAT
1 ATTAAAT
638532 CAAGTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 14 0.58
23 9 0.38
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTAAATATAAAAATAATTTTAA
Found at i:638517 original size:19 final size:19
Alignment explanation
Indices: 638472--638530 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
638462 AAAAAAATTT
* *
638472 AAAAAATATTAAATTTAAA
1 AAAAAATTTTAAATTAAAA
* *
638491 AAATAATTTTAAATAAAAA
1 AAAAAATTTTAAATTAAAA
638510 TAAAAATTATTTTAAATTAAA
1 -AAAAA--ATTTTAAATTAAA
638531 TCAAGTCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.48
20 4 0.13
22 12 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATTTTAAATTAAAA
Found at i:638602 original size:20 final size:20
Alignment explanation
Indices: 638579--638622 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
638569 ATGATTAATT
*
638579 ATTAAAATA-TATCATTTATA
1 ATTAAAATAGTA-AATTTATA
*
638599 ATTATAATAGTAAATTTATA
1 ATTAAAATAGTAAATTTATA
638619 ATTA
1 ATTA
638623 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTAAAATAGTAAATTTATA
Found at i:638950 original size:30 final size:30
Alignment explanation
Indices: 638896--638955 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
638886 TATATATAAA
** *
638896 TATTAATATAAAAATAATTTTATAATTTTT
1 TATTAATATAAAAATAATAATATAAATTTT
*
638926 TATTAATATATAAATAATAATATAAATTTT
1 TATTAATATAAAAATAATAATATAAATTTT
638956 AATTCGGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTAATATAAAAATAATAATATAAATTTT
Found at i:639327 original size:29 final size:28
Alignment explanation
Indices: 639268--639343 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
639258 TTGGTTAATT
* *
639268 TTTAAATTAGTTTT-TAATTTTTATTATA
1 TTTAAATTAATTTTAT-TTTTTTATTATA
639296 TTTAAATTAATTTTATTTTTTTATTTATA
1 TTTAAATTAATTTTATTTTTTTA-TTATA
*
639325 TTTAAATAAATTTTTATTT
1 TTTAAATTAA-TTTTATTT
639344 CAAATAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 19 0.45
29 15 0.36
30 8 0.19
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTAAATTAATTTTATTTTTTTATTATA
Found at i:639342 original size:16 final size:17
Alignment explanation
Indices: 639318--639351 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
639308 TTATTTTTTT
639318 ATTTATATTT-AAATAA
1 ATTTATATTTCAAATAA
*
639334 ATTTTTATTTCAAATAA
1 ATTTATATTTCAAATAA
639351 A
1 A
639352 AAGTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTATATTTCAAATAA
Found at i:639440 original size:26 final size:27
Alignment explanation
Indices: 639411--639467 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
639401 TTTATAAGCT
*
639411 AAAATTTGAGA-TTTATTTAAATA-TA
1 AAAAATTGAGATTTTATTTAAATATTA
639436 AAAAATTGAGATTTTATTTAAATATTA
1 AAAAATTGAGATTTTATTTAAATATTA
639463 AAAAA
1 AAAAA
639468 ATTAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 10 0.34
26 12 0.41
27 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (27 bp):
AAAAATTGAGATTTTATTTAAATATTA
Found at i:639478 original size:27 final size:26
Alignment explanation
Indices: 639421--639479 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
639411 AAAATTTGAG
*
639421 ATTTATTTAAATATAAAAAATTGAGA
1 ATTTATTTAAATATAAAAAATTGAAA
*
639447 TTTTATTTAAATATTAAAAAAATT-AAA
1 ATTTATTTAAATA-T-AAAAAATTGAAA
639474 ATTTAT
1 ATTTAT
639480 AAATAAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.43
27 8 0.29
28 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTTATTTAAATATAAAAAATTGAAA
Found at i:642491 original size:6 final size:6
Alignment explanation
Indices: 642480--642528 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
642470 AGTATTTGCA
* * * * *
642480 TCTCTC TCTCTC TGTCTC TGTCTC TCTCTT TCTCTT TCTCTC TTTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
642528 T
1 T
642529 TCTGACACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.57
Consensus pattern (6 bp):
TCTCTC
Found at i:642497 original size:8 final size:8
Alignment explanation
Indices: 642480--642528 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
642470 AGTATTTGCA
642480 TCTCTCTC
1 TCTCTCTC
*
642488 TCTCTGTC
1 TCTCTCTC
*
642496 TCTGTCTC
1 TCTCTCTC
*
642504 TCTCTTTC
1 TCTCTCTC
*
642512 TCTTTCTC
1 TCTCTCTC
*
642520 TCTTTCTC
1 TCTCTCTC
642528 T
1 T
642529 TCTGACACTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.57
Consensus pattern (8 bp):
TCTCTCTC
Found at i:642505 original size:16 final size:16
Alignment explanation
Indices: 642484--642522 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
642474 TTTGCATCTC
642484 TCTCTCTCTGTCTCTG
1 TCTCTCTCTGTCTCTG
* *
642500 TCTCTCTCTTTCTCTT
1 TCTCTCTCTGTCTCTG
642516 TCTCTCT
1 TCTCTCT
642523 TTCTCTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.05, T:0.56
Consensus pattern (16 bp):
TCTCTCTCTGTCTCTG
Found at i:642519 original size:14 final size:14
Alignment explanation
Indices: 642480--642529 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
642470 AGTATTTGCA
* *
642480 TCTCTCTCTCTCTG
1 TCTCTTTCTCTCTT
642494 TCTCTGTCTCTCTCTT
1 TCTCT-T-TCTCTCTT
642510 TCTCTTTCTCTCTT
1 TCTCTTTCTCTCTT
642524 TCTCTT
1 TCTCTT
642530 CTGACACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 19 0.59
15 1 0.03
16 12 0.38
ACGTcount: A:0.00, C:0.38, G:0.04, T:0.58
Consensus pattern (14 bp):
TCTCTTTCTCTCTT
Found at i:644083 original size:15 final size:15
Alignment explanation
Indices: 644055--644088 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
644045 AAGAACAAAG
*
644055 GTTTTATCTTTATTT
1 GTTTTATCTCTATTT
*
644070 GTTTTCTCTCTATTT
1 GTTTTATCTCTATTT
644085 GTTT
1 GTTT
644089 CTACGGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.71
Consensus pattern (15 bp):
GTTTTATCTCTATTT
Found at i:644843 original size:10 final size:11
Alignment explanation
Indices: 644826--644857 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
644816 CACAAGCATC
644826 TAATATGTATA
1 TAATATGTATA
644837 T-ATATGTATA
1 TAATATGTATA
644847 TAATAT-TATA
1 TAATATGTATA
644857 T
1 T
644858 GATCGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (11 bp):
TAATATGTATA
Found at i:645676 original size:23 final size:22
Alignment explanation
Indices: 645642--645686 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
645632 AAAATCAATT
* * *
645642 AAAAATTAATTTTTATAATTAA
1 AAAAATAAATTTTCAGAATTAA
645664 AAAAATAACATTTTCAGAATTAA
1 AAAAATAA-ATTTTCAGAATTAA
645687 TCTATTAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAATAAATTTTCAGAATTAA
Found at i:649628 original size:3 final size:3
Alignment explanation
Indices: 649620--649655 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
649610 TTGAGATGAG
* *
649620 TAT TAT TAT TAT TAT CAT TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
649656 GAAGCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:651505 original size:2 final size:2
Alignment explanation
Indices: 651498--651526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
651488 CAGACCACAA
651498 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 A
651527 CACACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:661244 original size:30 final size:28
Alignment explanation
Indices: 661210--661292 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 28
661200 AAAAAAAAAA
*
661210 TTATTATTTTATTTAAATTTAAAAATAATT
1 TTATTATTTT-TTAAAATTTAAAAAT-ATT
*
661240 TTATTTATTTTTTAAAAATTTGAATAATATT
1 TTA-TTATTTTTT-AAAATTT-AAAAATATT
661271 TTATT-TTTCTCTTAAAATTTAA
1 TTATTATTT-T-TTAAAATTTAA
661293 TATAAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
29 5 0.11
30 15 0.33
31 21 0.46
32 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (28 bp):
TTATTATTTTTTAAAATTTAAAAATATT
Found at i:661294 original size:29 final size:31
Alignment explanation
Indices: 661224--661294 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
661214 TATTTTATTT
* *
661224 AAATTTAAAAATAATTTTATTTATTTTTTAA
1 AAATTTAATAATAATTTTATTTATTTCTTAA
661255 AAATTTGAATAAT-ATTTTATTT-TTCTCTT-A
1 AAATTT-AATAATAATTTTATTTATT-TCTTAA
661285 AAATTTAATA
1 AAATTTAATA
661295 TAAAATATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 4 0.11
30 9 0.25
31 18 0.50
32 5 0.14
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (31 bp):
AAATTTAATAATAATTTTATTTATTTCTTAA
Found at i:662337 original size:22 final size:24
Alignment explanation
Indices: 662285--662337 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 24
662275 ATTTTATGTT
* *
662285 AAATTAATTATAATATAATTATAA
1 AAATTTATTATAATATAATTAAAA
662309 AAA--TATTAT-AT-TAATTAAAA
1 AAATTTATTATAATATAATTAAAA
662329 AAATTTATT
1 AAATTTATT
662338 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.44
21 2 0.08
22 9 0.36
24 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATTTATTATAATATAATTAAAA
Found at i:662537 original size:9 final size:9
Alignment explanation
Indices: 662505--662589 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
662495 TGAAAAATAC
662505 TATATAAAA
1 TATATAAAA
* *
662514 TAAAAAAAA
1 TATATAAAA
662523 TAATATAAAA
1 T-ATATAAAA
662533 TATATTAAAA
1 TATA-TAAAA
* *
662543 -AT-TATAT
1 TATATAAAA
* *
662550 TATTTATAA
1 TATATAAAA
*
662559 TATATTAAA
1 TATATAAAA
*
662568 TATGTTAAAA
1 TAT-ATAAAA
662578 TATAT-AAA
1 TATATAAAA
662586 TATA
1 TATA
662590 ATATTAATAT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.05
8 9 0.16
9 27 0.47
10 19 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (9 bp):
TATATAAAA
Found at i:662549 original size:21 final size:19
Alignment explanation
Indices: 662505--662549 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
662495 TGAAAAATAC
662505 TATATAAAATAAAAAAAAT
1 TATATAAAATAAAAAAAAT
* *
662524 AATATAAAATATATTAAAAAT
1 TATATAAAATA-A-AAAAAAT
662545 TATAT
1 TATAT
662550 TATTTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATATAAAATAAAAAAAAT
Found at i:664350 original size:15 final size:15
Alignment explanation
Indices: 664330--664360 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
664320 ATATAATCTT
664330 TTAAATATAAAATAA
1 TTAAATATAAAATAA
*
664345 TTAAATATTAAATAA
1 TTAAATATAAAATAA
664360 T
1 T
664361 ATTCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAATATAAAATAA
Found at i:665947 original size:7 final size:7
Alignment explanation
Indices: 665932--665997 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
665922 TTAGAATAAA
665932 AAATA-T
1 AAATATT
665938 AAATATT
1 AAATATT
665945 AAATA-T
1 AAATATT
665951 ATAATATT
1 A-AATATT
*
665959 -AATAAT
1 AAATATT
665965 AAA-A-T
1 AAATATT
*
665970 ACATATT
1 AAATATT
665977 AAATATAAT
1 AAATAT--T
665986 AAATATT
1 AAATATT
665993 AAATA
1 AAATA
665998 ATAATAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
5 3 0.06
6 14 0.29
7 24 0.49
8 1 0.02
9 7 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (7 bp):
AAATATT
Found at i:665967 original size:20 final size:20
Alignment explanation
Indices: 665933--666010 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
665923 TAGAATAAAA
* *
665933 AATATAAATATTAAATATAT
1 AATATTAATAATAAATATAT
665953 AATATTAATAATAAA-ATA-
1 AATATTAATAATAAATATAT
*
665971 CATATTAAATATAATAAATAT-T
1 AATATT--A-ATAATAAATATAT
665993 AA-A-TAATAAT-AATATAT
1 AATATTAATAATAAATATAT
666010 A
1 A
666011 TTTGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
16 5 0.10
17 7 0.15
18 6 0.12
19 3 0.06
20 15 0.31
21 9 0.19
22 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTAATAATAAATATAT
Done.