Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold170
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: 1632119
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 57634 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:499601 original size:18 final size:18
Alignment explanation
Indices: 499578--499612 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
499568 AGATCACGAT
499578 TTTAAAT-TGAAATTTAAG
1 TTTAAATCT-AAATTTAAG
499596 TTTAAATCTAAATTTAA
1 TTTAAATCTAAATTTAA
499613 TTCGATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTAAATCTAAATTTAAG
Found at i:499700 original size:21 final size:21
Alignment explanation
Indices: 499674--499714 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
499664 ATATTAATAA
499674 ATATTTT-TAATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
499695 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
499715 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:501141 original size:30 final size:29
Alignment explanation
Indices: 501101--501157 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
501091 TATATTAATA
**
501101 TTTATAATTAATTTTAAATAAAATTATTT
1 TTTATAATTAAAATTAAATAAAATTATTT
*
501130 TTTATTAATTAAAATTAAATTAAATTAT
1 TTTA-TAATTAAAATTAAATAAAATTAT
501158 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTATAATTAAAATTAAATAAAATTATTT
Found at i:502602 original size:20 final size:19
Alignment explanation
Indices: 502564--502611 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
502554 TTACATACTT
* *
502564 TTTATATATTTATATTATA
1 TTTATATTTTTAAATTATA
502583 TTTATATTTTTAAAATTATA
1 TTTATATTTTT-AAATTATA
*
502603 ATTATATTT
1 TTTATATTT
502612 AAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTTTTAAATTATA
Found at i:502823 original size:2 final size:2
Alignment explanation
Indices: 502806--502844 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
502796 AGGGAAACAA
* *
502806 AT AT AT AC AT AC 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 AT A
502845 GCGAAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:503115 original size:19 final size:20
Alignment explanation
Indices: 503084--503126 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
503074 AAATTTATGG
503084 TTTTATATATTT-AAATAAAT
1 TTTTATATATTTAAAAT-AAT
503104 TTTTATAT-TTTAAAATAAT
1 TTTTATATATTTAAAATAAT
503123 TTTT
1 TTTT
503127 TTAAACTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTAAAATAAT
Found at i:503127 original size:20 final size:20
Alignment explanation
Indices: 503084--503126 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
503074 AAATTTATGG
503084 TTTTATATATTTAAATAAAT
1 TTTTATATATTTAAATAAAT
503104 TTTTATAT-TTTAAA-ATAAT
1 TTTTATATATTTAAATA-AAT
503123 TTTT
1 TTTT
503127 TTAAACTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTAAATAAAT
Found at i:503552 original size:30 final size:32
Alignment explanation
Indices: 503503--503571 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
503493 TTAATGGATT
* *
503503 ATTATAATATATAAAAATA-TAT-TTAAAAAA
1 ATTATAATAAATAAAAATATTATGTCAAAAAA
**
503533 ATTATAATAAATATTAATATTTATGTCAAAAAA
1 ATTATAATAAATAAAAATA-TTATGTCAAAAAA
503566 ATTATA
1 ATTATA
503572 TTTTATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 16 0.50
32 3 0.09
33 13 0.41
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (32 bp):
ATTATAATAAATAAAAATATTATGTCAAAAAA
Found at i:503963 original size:22 final size:22
Alignment explanation
Indices: 503933--503982 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
503923 AATAGTTAAA
503933 AAATATTTTTAT-ATTAATATTT
1 AAATATTTTTATAATTAA-ATTT
*
503955 ATATATTTTTATAATTAAATTT
1 AAATATTTTTATAATTAAATTT
503977 AAATAT
1 AAATAT
503983 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATTTTTATAATTAAATTT
Found at i:509985 original size:2 final size:2
Alignment explanation
Indices: 509978--510012 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
509968 TGCTAAAACA
509978 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 A
510013 CATACCGCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:511187 original size:19 final size:19
Alignment explanation
Indices: 511156--511192 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
511146 TTTTTATTTA
511156 TTTATAATTAATATTAAAT
1 TTTATAATTAATATTAAAT
511175 TTTA-AATTAAATATTAAA
1 TTTATAATT-AATATTAAA
511193 ATAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATAATTAATATTAAAT
Found at i:511213 original size:13 final size:13
Alignment explanation
Indices: 511159--511235 Score: 67
Period size: 13 Copynumber: 6.3 Consensus size: 13
511149 TTATTTATTT
511159 ATAATTAATATTAA
1 ATAATTAA-ATTAA
*
511173 AT-TTTAAATTAA
1 ATAATTAAATTAA
*
511185 AT-ATTAAAATAA
1 ATAATTAAATTAA
*
511197 ATAATTTAATTAA
1 ATAATTAAATTAA
*
511210 ATAAATAAATT--
1 ATAATTAAATTAA
511221 -TAATTAAA-TAA
1 ATAATTAAATTAA
511232 ATAA
1 ATAA
511236 AAATTATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 1 0.02
10 7 0.14
12 20 0.39
13 21 0.41
14 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATTAAATTAA
Found at i:511244 original size:18 final size:19
Alignment explanation
Indices: 511191--511247 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
511181 TTAAATATTA
511191 AAATAAATAATTTAATTAAAT
1 AAATAAA-AA-TTAATTAAAT
*
511212 AAAT-AAATTTAATTAAAT
1 AAATAAAAATTAATTAAAT
511230 AAATAAAAATT-ATTAAAT
1 AAATAAAAATTAATTAAAT
511248 TTTTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 21 0.64
19 6 0.18
20 2 0.06
21 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAAAAATTAATTAAAT
Found at i:511245 original size:22 final size:18
Alignment explanation
Indices: 511191--511236 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
511181 TTAAATATTA
511191 AAATAAAT-AATTTAATT
1 AAATAAATAAATTTAATT
511208 AAATAAATAAATTTAATT
1 AAATAAATAAATTTAATT
511226 AAATAAATAAA
1 AAATAAATAAA
511237 AATTATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAAATAAATTTAATT
Found at i:511286 original size:13 final size:13
Alignment explanation
Indices: 511263--511317 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
511253 CCATAAATTA
511263 AAAATTTTAAAAAT
1 AAAATTTT-AAAAT
511277 AAAA-TTTAAAAT
1 AAAATTTTAAAAT
**
511289 -AAATTCCAAACAT
1 AAAATTTTAAA-AT
*
511302 AAAATTTTAAATT
1 AAAATTTTAAAAT
511315 AAA
1 AAA
511318 GTCAGGTCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.09
12 9 0.27
13 9 0.27
14 12 0.36
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATTTTAAAAT
Found at i:514012 original size:21 final size:19
Alignment explanation
Indices: 513974--514013 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
513964 TTGACATGAT
*
513974 TTTTAATTAAATTTAATAA
1 TTTTAAATAAATTTAATAA
513993 TTTTAAATATAATATTAATAA
1 TTTTAAATA-AAT-TTAATAA
514014 AATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAAATAAATTTAATAA
Found at i:514018 original size:16 final size:15
Alignment explanation
Indices: 513997--514038 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
513987 TAATAATTTT
513997 AAATATAATATTAATA
1 AAATATAATA-TAATA
514013 AAATATAA-A-AATA
1 AAATATAATATAATA
*
514026 AAATATTATATAA
1 AAATATAATATAA
514039 AATAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 11 0.48
14 1 0.04
15 3 0.13
16 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAATATAATA
Found at i:514030 original size:18 final size:17
Alignment explanation
Indices: 514009--514048 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
513999 ATATAATATT
514009 AATAAAATATAAAAATAA
1 AATAAAATAT-AAAATAA
**
514027 AATATTATATAAAATAA
1 AATAAAATATAAAATAA
514044 AATAA
1 AATAA
514049 TTATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAATATAAAATAA
Found at i:514042 original size:17 final size:18
Alignment explanation
Indices: 514015--514055 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
514005 TATTAATAAA
514015 ATATAAAAATAAAAT-ATT
1 ATAT-AAAATAAAATAATT
514033 ATATAAAATAAAATAATT
1 ATATAAAATAAAATAATT
514051 ATATA
1 ATATA
514056 TTAAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAATAAAATAATT
Found at i:514056 original size:25 final size:24
Alignment explanation
Indices: 513997--514059 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
513987 TAATAATTTT
*
513997 AAATATAATATTAATAAAATATAA
1 AAATAAAATATTAATAAAATATAA
514021 AAATAAAATATTATATAAAATA-AA
1 AAATAAAATATTA-ATAAAATATAA
* *
514045 ATAATTATATATTAA
1 A-AATAAAATATTAA
514060 ATTAAGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAAATATTAATAAAATATAA
Found at i:514211 original size:21 final size:22
Alignment explanation
Indices: 514185--514226 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
514175 TTATGATTAA
514185 ATATTA-ATAAAAAATAATTTT
1 ATATTATATAAAAAATAATTTT
* *
514206 ATATTATTTAAATAATAATTT
1 ATATTATATAAAAAATAATTT
514227 AAATCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATATAAAAAATAATTTT
Found at i:514217 original size:32 final size:31
Alignment explanation
Indices: 514147--514224 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
514137 ATTTAAAATA
**
514147 ATATTAAA-AATTTTAAAAAATATTATATTT
1 ATATTAAATAATAATAAAAAATATTATATTT
* *
514177 ATGATTAAATATTAATAAAAAATAATTTTATATT
1 AT-ATTAAATAATAATAAAAAAT-ATTATAT-TT
514211 AT-TTAAATAATAAT
1 ATATTAAATAATAAT
514225 TTAAATCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 2 0.05
31 6 0.15
32 21 0.54
33 6 0.15
34 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATTAAATAATAATAAAAAATATTATATTT
Found at i:514384 original size:31 final size:31
Alignment explanation
Indices: 514332--514478 Score: 121
Period size: 31 Copynumber: 4.8 Consensus size: 31
514322 TAAAATTACC
* * * *
514332 ATAA-ATATTATATCAATTATTAAAATTTAT
1 ATAATATATGATATAAATTATTAATATTAAT
* *
514362 ATAATATATAATATAAATTATTATATATTAAA
1 ATAATATATGATATAAATTATTA-ATATTAAT
*
514394 AT-TTATATGATATAAATTATTAATA-TAAT
1 ATAATATATGATATAAATTATTAATATTAAT
*
514423 AAAATTTATATGATATAAATTATTAATA-TAAT
1 ATAA--TATATGATATAAATTATTAATATTAAT
514455 A-AA-ACT-T-ATATAAATATATTAATA
1 ATAATA-TATGATATAAAT-TATTAATA
514479 ATTTAAAACG
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
27 8 0.08
28 10 0.10
29 5 0.05
30 7 0.07
31 36 0.36
32 34 0.34
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
ATAATATATGATATAAATTATTAATATTAAT
Found at i:514388 original size:17 final size:17
Alignment explanation
Indices: 514366--514472 Score: 97
Period size: 18 Copynumber: 6.6 Consensus size: 17
514356 ATTTATATAA
514366 TATATAATATAAATTAT
1 TATATAATATAAATTAT
*
514383 TATAT-AT-TAAAAT-T
1 TATATAATATAAATTAT
*
514397 TATATGATATAAATTAT
1 TATATAATATAAATTAT
514414 TAATATAATA-AAA-T-T
1 T-ATATAATATAAATTAT
*
514429 TATATGATATAAATTAT
1 TATATAATATAAATTAT
514446 TAATATAATA-AAACTTA-
1 T-ATATAATATAAA-TTAT
514463 TATA-AATATA
1 TATATAATATA
514473 TTAATAATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.17
15 16 0.21
16 13 0.17
17 16 0.21
18 17 0.23
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (17 bp):
TATATAATATAAATTAT
Found at i:514392 original size:38 final size:32
Alignment explanation
Indices: 514366--514480 Score: 162
Period size: 32 Copynumber: 3.7 Consensus size: 32
514356 ATTTATATAA
*
514366 TATATAATATAAATTATT-ATATATTAAAATT
1 TATATAATATAAATTATTAATATAATAAAATT
*
514397 TATATGATATAAATTATTAATATAATAAAATT
1 TATATAATATAAATTATTAATATAATAAAATT
* *
514429 TATATGATATAAATTATTAATATAATAAAACT
1 TATATAATATAAATTATTAATATAATAAAATT
* *
514461 TATATAA-ATATATTAATAAT
1 TATATAATATAAATTATTAAT
514481 TTAAAACGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 28 0.36
32 49 0.64
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (32 bp):
TATATAATATAAATTATTAATATAATAAAATT
Found at i:514426 original size:32 final size:32
Alignment explanation
Indices: 514366--514465 Score: 166
Period size: 32 Copynumber: 3.2 Consensus size: 32
514356 ATTTATATAA
* *
514366 TATATAATATAAATTATT-ATATATTAAAATT
1 TATATGATATAAATTATTAATATAATAAAATT
514397 TATATGATATAAATTATTAATATAATAAAATT
1 TATATGATATAAATTATTAATATAATAAAATT
*
514429 TATATGATATAAATTATTAATATAATAAAACT
1 TATATGATATAAATTATTAATATAATAAAATT
514461 TATAT
1 TATAT
514466 AAATATATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
31 17 0.26
32 48 0.74
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (32 bp):
TATATGATATAAATTATTAATATAATAAAATT
Found at i:514456 original size:16 final size:16
Alignment explanation
Indices: 514374--514457 Score: 70
Period size: 16 Copynumber: 5.3 Consensus size: 16
514364 AATATATAAT
514374 ATAAATTATT-ATATA
1 ATAAATTATTAATATA
* *
514389 TTAAA--ATTTATATGA
1 ATAAATTATTAATAT-A
514404 TATAAATTATTAATATA
1 -ATAAATTATTAATATA
*
514421 ATAAA--ATTTATATGA
1 ATAAATTATTAATAT-A
514436 TATAAATTATTAATATA
1 -ATAAATTATTAATATA
514453 ATAAA
1 ATAAA
514458 ACTTATATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
13 3 0.05
14 11 0.20
15 6 0.11
16 19 0.35
17 2 0.04
18 14 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATAAATTATTAATATA
Found at i:514465 original size:27 final size:30
Alignment explanation
Indices: 514336--514478 Score: 132
Period size: 32 Copynumber: 4.7 Consensus size: 30
514326 ATTACCATAA
* * * * *
514336 ATATTATATCAATTATTAAAATTTATATAAT
1 ATATGATATAAATTATTAATA-TAATAAAAT
* *
514367 ATATAATATAAATTATT-ATATATTAAAATTT
1 ATATGATATAAATTATTAATATAATAAAA--T
514398 ATATGATATAAATTATTAATATAATAAAATTT
1 ATATGATATAAATTATTAATATAATAAAA--T
514430 ATATGATATAAATTATTAATATAATAAAA-
1 ATATGATATAAATTATTAATATAATAAAAT
*
514459 CT-T-ATATAAATATATTAATA
1 ATATGATATAAAT-TATTAATA
514479 ATTTAAAACG
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
27 8 0.08
28 9 0.09
29 6 0.06
30 2 0.02
31 32 0.32
32 42 0.42
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
ATATGATATAAATTATTAATATAATAAAAT
Found at i:514467 original size:14 final size:13
Alignment explanation
Indices: 514366--514467 Score: 51
Period size: 16 Copynumber: 6.5 Consensus size: 13
514356 ATTTATATAA
514366 TATATAATATAAAT
1 TATATAATA-AAAT
514380 TATTATATATTAAAATT
1 TA-TATA-A-TAAAA-T
514397 TATATGATATAAATTAT
1 TATAT-A-ATAAA--AT
514414 TAATATAATAAAATT
1 T-ATATAATAAAA-T
514429 TATATGATATAAATTAT
1 TATAT-A-ATAAA--AT
514446 TAATATAATAAAACT
1 T-ATATAATAAAA-T
514461 TATATAA
1 TATATAA
514468 ATATATTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 30
0.71 0.00 0.29
Matches are distributed among these distances:
14 14 0.19
15 9 0.12
16 26 0.36
17 14 0.19
18 10 0.14
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (13 bp):
TATATAATAAAAT
Found at i:515524 original size:38 final size:38
Alignment explanation
Indices: 515473--515550 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
515463 TTGATTTTTT
*
515473 TATGTATTTGAGTTTGGTTGTGTGTTGGGTATGGTAGA
1 TATGTATTTGAGTTTGGTTGTGTCTTGGGTATGGTAGA
*
515511 TATGTATTTGAGTTTGGTTGTGTCTTGGGTCTGGTAGA
1 TATGTATTTGAGTTTGGTTGTGTCTTGGGTATGGTAGA
515549 TA
1 TA
515551 ATCTGATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.15, C:0.03, G:0.35, T:0.47
Consensus pattern (38 bp):
TATGTATTTGAGTTTGGTTGTGTCTTGGGTATGGTAGA
Found at i:522726 original size:20 final size:20
Alignment explanation
Indices: 522701--522742 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
522691 CTTGGAAGAT
522701 CATATACTCACACTTATACC
1 CATATACTCACACTTATACC
522721 CATATACTCACACTTATACC
1 CATATACTCACACTTATACC
522741 CA
1 CA
522743 CATATGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (20 bp):
CATATACTCACACTTATACC
Found at i:524207 original size:2 final size:2
Alignment explanation
Indices: 524200--524226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
524190 GGCATTGTAT
524200 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
524227 TCTAAGGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:524578 original size:4 final size:4
Alignment explanation
Indices: 524569--524647 Score: 95
Period size: 4 Copynumber: 19.8 Consensus size: 4
524559 ATGTTTTAGT
* *
524569 TATA TATA TATA TATA TATA TATA TATA TATA TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
524617 TATA TGTA TGTA TGTA TATA TGTA TGTA TAT
1 TATA TATA TATA TATA TATA TATA TATA TAT
524648 CCTTGGTGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:527845 original size:28 final size:27
Alignment explanation
Indices: 527814--527868 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
527804 ATAATTTATT
*
527814 TATTTAAAATTTTATTAAAAATATTTTA
1 TATTTAAAATATTATT-AAAATATTTTA
* *
527842 TATTTATAATATTATTATAATATTTTA
1 TATTTAAAATATTATTAAAATATTTTA
527869 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TATTTAAAATATTATTAAAATATTTTA
Found at i:527874 original size:20 final size:20
Alignment explanation
Indices: 527841--527893 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
527831 AAAATATTTT
527841 ATATTTATAA-TATTATTAT-A
1 ATATTT-TAATTATT-TTATAA
*
527861 ATATTTTAATTATTTTTTAA
1 ATATTTTAATTATTTTATAA
*
527881 ATATTTTATTTAT
1 ATATTTTAATTAT
527894 ACCATGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTTAATTATTTTATAA
Found at i:528635 original size:22 final size:22
Alignment explanation
Indices: 528604--528657 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
528594 AAGCTCCTAT
528604 ATTTATATTTGT-AAATTATTTAA
1 ATTTA-ATTTGTAAAATTA-TTAA
*
528627 TTTTAATTT-TAAAATTATTAA
1 ATTTAATTTGTAAAATTATTAA
528648 ATTTAATTTG
1 ATTTAATTTG
528658 ATTATTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 13 0.48
22 10 0.37
23 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTTAATTTGTAAAATTATTAA
Found at i:529948 original size:21 final size:21
Alignment explanation
Indices: 529922--529961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
529912 TGTTAGAAGG
*
529922 ATAATTTAATTCTTTTACTGA
1 ATAATTTAATTCTTGTACTGA
*
529943 ATAATTTTATTCTTGTACT
1 ATAATTTAATTCTTGTACT
529962 TTTGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
ATAATTTAATTCTTGTACTGA
Found at i:530565 original size:11 final size:11
Alignment explanation
Indices: 530546--530584 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
530536 ATTGAATTCC
530546 AAAACAAAAAA-
1 AAAA-AAAAAAG
530557 AAAAAAAAAAG
1 AAAAAAAAAAG
*
530568 AAGAAAAAAAG
1 AAAAAAAAAAG
530579 AAAAAA
1 AAAAAA
530585 GTAAAGCCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.90, C:0.03, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:531460 original size:2 final size:2
Alignment explanation
Indices: 531453--531482 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
531443 ATTAGCCATT
531453 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
531483 AAATATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:532284 original size:5 final size:5
Alignment explanation
Indices: 532276--532328 Score: 70
Period size: 5 Copynumber: 10.6 Consensus size: 5
532266 ATTTCATGCA
* * * *
532276 AATAT AATAT AATAC AATAT GATAC AATAG AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
532326 AAT
1 AAT
532329 TTATTTTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:532869 original size:21 final size:21
Alignment explanation
Indices: 532843--532885 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
532833 AATATTAAAA
532843 ATATATTTCA-AATTAATATTT
1 ATATATTTCATAATTAA-ATTT
*
532864 ATATATTTTATAATTAAATTT
1 ATATATTTCATAATTAAATTT
532885 A
1 A
532886 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTCATAATTAAATTT
Found at i:533407 original size:12 final size:12
Alignment explanation
Indices: 533390--533421 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
533380 CATAAAATAA
533390 AATTTTTATATT
1 AATTTTTATATT
533402 AATTTTTATATT
1 AATTTTTATATT
533414 --TTTTTATA
1 AATTTTTATA
533422 AATAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
AATTTTTATATT
Found at i:534275 original size:15 final size:16
Alignment explanation
Indices: 534256--534297 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
534246 CTTCTTCTAC
534256 CTTGGGTTCTTCCTTT
1 CTTGGGTTCTTCCTTT
*
534272 -TTGGCTTCTT-CTTT
1 CTTGGGTTCTTCCTTT
*
534286 CTTTGGTTCTTC
1 CTTGGGTTCTTC
534298 ATCTGATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.00, C:0.24, G:0.17, T:0.60
Consensus pattern (16 bp):
CTTGGGTTCTTCCTTT
Found at i:534280 original size:30 final size:29
Alignment explanation
Indices: 534240--534297 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
534230 GGTGCCTCAG
534240 TTTTTGCTTCTTCTACCTTGGGTTCTTCC
1 TTTTTGCTTCTTCTACCTTGGGTTCTTCC
** *
534269 TTTTTGGCTTCTTCTTTCTTTGGTTCTTC
1 TTTTT-GCTTCTTCTACCTTGGGTTCTTC
534298 ATCTGATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.02, C:0.24, G:0.14, T:0.60
Consensus pattern (29 bp):
TTTTTGCTTCTTCTACCTTGGGTTCTTCC
Found at i:540395 original size:20 final size:20
Alignment explanation
Indices: 540366--540406 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
540356 TAATAACTTC
* *
540366 AATCAGGGATCCTTTATTTG
1 AATCACGGATCCTTTAATTG
540386 AATCACGGATCCTTTAATTG
1 AATCACGGATCCTTTAATTG
540406 A
1 A
540407 GAAAAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
AATCACGGATCCTTTAATTG
Found at i:546987 original size:14 final size:14
Alignment explanation
Indices: 546968--546996 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
546958 TTTACTTCTA
546968 TAATGGTCTTTGTC
1 TAATGGTCTTTGTC
546982 TAATGGTCTTTGTC
1 TAATGGTCTTTGTC
546996 T
1 T
546997 CATAATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (14 bp):
TAATGGTCTTTGTC
Found at i:548235 original size:10 final size:9
Alignment explanation
Indices: 548203--548239 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
548193 GAGCAAGTTC
*
548203 TTTCTTTCT
1 TTTCTTTTT
548212 TTTCTTTTT
1 TTTCTTTTT
548221 TTTCTTTTT
1 TTTCTTTTT
548230 TCTTCTTTTT
1 T-TTCTTTTT
548240 CCTGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:553173 original size:30 final size:28
Alignment explanation
Indices: 553116--553244 Score: 119
Period size: 25 Copynumber: 4.7 Consensus size: 28
553106 GGAAAACTTG
*
553116 TTATACATCTATAATATATTT-ATATATT
1 TTATA-ATATATAATATATTTAATATATT
553144 TTATAATATCATAATCATATTTAATATATT
1 TTATAATAT-ATAAT-ATATTTAATATATT
*
553174 TTATATTATATAA-AT-TTTAATATA-T
1 TTATAATATATAATATATTTAATATATT
* *
553199 TTATATTATATAA-AT-TTTAAAATATT
1 TTATAATATATAATATATTTAATATATT
* *
553225 TT-TATATTTATATTATATTT
1 TTATA-ATATATAATATATTT
553245 TAATTAATTT
Statistics
Matches: 88, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
25 26 0.30
26 17 0.19
27 7 0.08
28 13 0.15
29 10 0.11
30 15 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATAATATATAATATATTTAATATATT
Found at i:553190 original size:16 final size:15
Alignment explanation
Indices: 553173--553215 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
553163 TTTAATATAT
553173 TTTATATTATATAAA
1 TTTATATTATATAAA
553188 TTT-TA--ATAT--A
1 TTTATATTATATAAA
553198 TTTATATTATATAAA
1 TTTATATTATATAAA
553213 TTT
1 TTT
553216 TAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 4 0.17
11 2 0.09
12 4 0.17
13 4 0.17
14 2 0.09
15 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:553190 original size:25 final size:26
Alignment explanation
Indices: 553137--553266 Score: 136
Period size: 25 Copynumber: 4.7 Consensus size: 26
553127 TAATATATTT
*
553137 ATATATTTTATAATATCATAATCATATTTA
1 ATATATTTTATATTAT-ATAA--AT-TTTA
553167 ATATATTTTATATTATATAAATTTTA
1 ATATATTTTATATTATATAAATTTTA
553193 ATATA-TTTATATTATATAAATTTTA
1 ATATATTTTATATTATATAAATTTTA
* *
553218 AAATATTTTTATATTTATATTATATTTTA
1 ATATA-TTTTATA-TTATA-TAAATTTTA
*
553247 ATTAATTTTTTATATTATAT
1 A-T-ATATTTTATATTATAT
553267 TTATATAATC
Statistics
Matches: 89, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
25 24 0.27
26 9 0.10
27 8 0.09
28 6 0.07
29 18 0.20
30 22 0.25
31 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATTTTATATTATATAAATTTTA
Found at i:553240 original size:11 final size:11
Alignment explanation
Indices: 553226--553272 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
553216 TAAAATATTT
553226 TTATATTTATA
1 TTATATTTATA
553237 TTATATTT-TAA
1 TTATATTTAT-A
*
553248 TTAATTTTTTATA
1 TT-A-TATTTATA
553261 TTATATTTATA
1 TTATATTTATA
553272 T
1 T
553273 AATCGTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 19 0.63
12 2 0.07
13 7 0.23
14 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:553685 original size:2 final size:2
Alignment explanation
Indices: 553672--553712 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
553662 GGGGGTATTT
*
553672 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
553713 CTGTGTGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:558421 original size:23 final size:23
Alignment explanation
Indices: 558390--558439 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
558380 TCATAATTAT
* *
558390 TATTTATATTTA-TTATAAAAAA
1 TATTTATATGTACTAATAAAAAA
558412 TATTTGATATGTACTAATAAAAAA
1 TATTT-ATATGTACTAATAAAAAA
558436 TATT
1 TATT
558440 CGAGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 6 0.25
24 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTTATATGTACTAATAAAAAA
Found at i:559091 original size:34 final size:35
Alignment explanation
Indices: 559053--559119 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
559043 CCTTACAACA
*
559053 CTATC-TTTC-AAGGTTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
559087 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
559120 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:561960 original size:2 final size:2
Alignment explanation
Indices: 561953--562004 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
561943 AACAAAAATC
561953 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
561995 AT AT AT AT AT
1 AT AT AT AT AT
562005 TAAAAGATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:563189 original size:2 final size:2
Alignment explanation
Indices: 563182--563220 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
563172 TAGGACGCAA
563182 AT 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 AT A
563221 AAGGTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:563351 original size:17 final size:19
Alignment explanation
Indices: 563331--563365 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
563321 TATATTATTT
563331 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
563348 ATATAAATTATTAAATAT
1 ATATAAATTATTAAATAT
563366 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:563695 original size:17 final size:17
Alignment explanation
Indices: 563672--563711 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
563662 TTTATTTTAT
563672 TAAATATTTTTAAATAAA
1 TAAATATTTTTAAA-AAA
563690 -AAATA-TTTTAAAAAA
1 TAAATATTTTTAAAAAA
563705 TAAATAT
1 TAAATAT
563712 ATCTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.15
16 12 0.60
17 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATTTTTAAAAAA
Found at i:563748 original size:17 final size:17
Alignment explanation
Indices: 563708--563749 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
563698 TAAAAAATAA
*
563708 ATATATCTATATTAGAT
1 ATATATTTATATTAGAT
*
563725 ATATATTTATATTTGAT
1 ATATATTTATATTAGAT
*
563742 ATTTATTT
1 ATATATTT
563750 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
ATATATTTATATTAGAT
Found at i:572733 original size:2 final size:2
Alignment explanation
Indices: 572726--572767 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
572716 AGAAAAATCT
572726 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
572768 AAGTGCTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574329 original size:22 final size:23
Alignment explanation
Indices: 574291--574333 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
574281 AATTATTATT
574291 TAAAATTAATTATTAAAAATATA
1 TAAAATTAATTATTAAAAATATA
574314 TAAATATTAA-TA-TAAAAATA
1 TAAA-ATTAATTATTAAAAATA
574334 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAATTAATTATTAAAAATATA
Found at i:574840 original size:21 final size:22
Alignment explanation
Indices: 574811--574858 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
574801 ATATATAAAA
*
574811 AATTAAATATT-TTAATTATAT
1 AATTTAATATTATTAATTATAT
* *
574832 AATTTAATATTATTATTTATTT
1 AATTTAATATTATTAATTATAT
574854 AATTT
1 AATTT
574859 TTAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTAATATTATTAATTATAT
Found at i:574861 original size:24 final size:23
Alignment explanation
Indices: 574813--574881 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
574803 ATATAAAAAA
574813 TTAAATATTTTAATT-ATATAA--T
1 TTAAATATTTT-ATTAAT-TAATTT
*
574835 TT-AATATTATTATTTATTTAATTT
1 TTAAATATT-TTA-TTAATTAATTT
574859 TTAAATATTTTATTAATTAATTT
1 TTAAATATTTTATTAATTAATTT
574882 GATATGAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 7 0.18
22 9 0.23
23 11 0.28
24 6 0.15
25 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAAATATTTTATTAATTAATTT
Found at i:578786 original size:39 final size:39
Alignment explanation
Indices: 578719--578800 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
578709 AGATATATAT
** *
578719 ATTTATCATTAATTCAAATATTTTAATATAAATAGTTAA
1 ATTTATCATTAATTCAAATATTCAAATATAAATAATTAA
* * * * *
578758 ATTTATTATTAATTTAATTATTCAAATATTAATAATTTA
1 ATTTATCATTAATTCAAATATTCAAATATAAATAATTAA
578797 ATTT
1 ATTT
578801 TTTTGAATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (39 bp):
ATTTATCATTAATTCAAATATTCAAATATAAATAATTAA
Found at i:579264 original size:13 final size:13
Alignment explanation
Indices: 579246--579270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579236 GCTGCCAAGT
579246 TAAAATAAATAAA
1 TAAAATAAATAAA
579259 TAAAATAAATAA
1 TAAAATAAATAA
579271 TCTTCAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:584264 original size:24 final size:25
Alignment explanation
Indices: 584221--584267 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
584211 TATGTTATTA
*
584221 AAATTATACTTTTATAATTAAATTT
1 AAATAATACTTTTATAATTAAATTT
*
584246 AAATAATA-TTTTATTATTAAAT
1 AAATAATACTTTTATAATTAAAT
584268 AATAATTCAG
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:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATAATACTTTTATAATTAAATTT
Found at i:595319 original size:34 final size:33
Alignment explanation
Indices: 595271--595491 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 33
595261 TGGTAAAAAC
*
595271 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
595304 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
595338 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
595372 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
595406 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
595440 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
595474 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
595492 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 133 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:595387 original size:68 final size:67
Alignment explanation
Indices: 595273--595491 Score: 296
Period size: 68 Copynumber: 3.2 Consensus size: 67
595263 GTAAAAACCA
* * *
595273 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
595338 CAC
65 CAC
* * * *
595341 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
595406 CTC
65 CAC
* * * *
595409 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
595474 CA-
65 CAC
595476 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
595492 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 17 0.13
68 114 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:595415 original size:102 final size:101
Alignment explanation
Indices: 595271--595491 Score: 352
Period size: 102 Copynumber: 2.2 Consensus size: 101
595261 TGGTAAAAAC
* *
595271 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
595336 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
595372 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
595437 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
595474 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
595492 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:599952 original size:34 final size:34
Alignment explanation
Indices: 599902--600083 Score: 183
Period size: 34 Copynumber: 5.4 Consensus size: 34
599892 TAAAAACCAT
* *
599902 CATTTAATCAATAATGGCAACCTACCAAATCTAC
1 CATTTAATCAACAATGGTAACCTACCAAATCTAC
*
599936 CATTTAGTCAACAATGGTAAGCC-ACCAAATC-AC
1 CATTTAATCAACAATGGTAA-CCTACCAAATCTAC
* * * **
599969 CTATTTAATCAATAATGGTAAGCTACCAAATTTTT
1 C-ATTTAATCAACAATGGTAACCTACCAAATCTAC
* * *
600004 CATTTAATCAACAATGGTAAGCTACTAAATCTCC
1 CATTTAATCAACAATGGTAACCTACCAAATCTAC
**
600038 CATTTAATCAACAATGACAAACC-ACCAAATC-AC
1 CATTTAATCAACAATG-GTAACCTACCAAATCTAC
600071 CTATTTAATCAAC
1 C-ATTTAATCAAC
600084 GCATATTGAA
Statistics
Matches: 123, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
33 6 0.05
34 111 0.90
35 6 0.05
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAACCTACCAAATCTAC
Found at i:600015 original size:68 final size:68
Alignment explanation
Indices: 599902--600083 Score: 224
Period size: 68 Copynumber: 2.7 Consensus size: 68
599892 TAAAAACCAT
*
599902 CATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGTAAGCCACCAAATC
599967 ACC
66 ACC
* * * * ** * *
599970 TATTTAATCAATAATGGTAAGCTACCAAATTTTTCATTTAATCAACAATGGTAAGCTACTAAATC
1 CATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGTAAGCCACCAAATC
*
600035 TCC
66 ACC
* *
600038 CATTTAATCAACAATGACAAACC-ACCAAATC-ACCTATTTAATCAAC
1 CATTTAATCAATAATGGC-AACCTACCAAATCTACC-ATTTAATCAAC
600084 GCATATTGAA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
67 1 0.01
68 90 0.96
69 3 0.03
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (68 bp):
CATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGTAAGCCACCAAATC
ACC
Found at i:601472 original size:17 final size:17
Alignment explanation
Indices: 601450--601484 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
601440 ACCTGTATTC
601450 ATTTATTATATATGAGT
1 ATTTATTATATATGAGT
601467 ATTTATTATATATGAGT
1 ATTTATTATATATGAGT
601484 A
1 A
601485 AATGAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTTATTATATATGAGT
Found at i:604565 original size:2 final size:2
Alignment explanation
Indices: 604558--604583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
604548 TTGTGGCTTA
604558 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
604584 TTAATTGTAA
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:609932 original size:11 final size:11
Alignment explanation
Indices: 609925--609955 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
609915 TAGATTATTA
609925 TAAAATTAATT
1 TAAAATTAATT
*
609936 TAAATTTAATT
1 TAAAATTAATT
609947 TAAAATTAA
1 TAAAATTAA
609956 AATTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAAATTAATT
Found at i:609932 original size:22 final size:23
Alignment explanation
Indices: 609905--609956 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
609895 AAAAAAAATT
*
609905 AAATTAAATTTAGA-TT-ATTATA
1 AAATTAAATTTAAATTTAATT-TA
609927 AAATT-AATTTAAATTTAATTTA
1 AAATTAAATTTAAATTTAATTTA
609949 AAATTAAA
1 AAATTAAA
609957 ATTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATTAAATTTAAATTTAATTTA
Found at i:610127 original size:12 final size:12
Alignment explanation
Indices: 610094--610133 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
610084 ATTCAAATAA
610094 AAATAATATAAAT
1 AAATAAT-TAAAT
*
610107 CAA-AATTAAAT
1 AAATAATTAAAT
610118 AAATAATTAAAT
1 AAATAATTAAAT
610130 AAAT
1 AAAT
610134 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.29
12 15 0.62
13 2 0.08
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATTAAAT
Found at i:610131 original size:27 final size:27
Alignment explanation
Indices: 610082--610133 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
610072 AATTTAATTT
610082 AAATTCAAATAAAAATAATATAAATCA
1 AAATTCAAATAAAAATAATATAAATCA
610109 AAATT-AAATAAATAATTAA-ATAAAT
1 AAATTCAAATAAA-AA-TAATATAAAT
610134 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.30
27 13 0.57
28 3 0.13
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAATTCAAATAAAAATAATATAAATCA
Found at i:610141 original size:27 final size:29
Alignment explanation
Indices: 610111--610164 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
610101 ATAAATCAAA
610111 ATTAAATAAAT-AA-TTAAATAAATTTTT
1 ATTAAATAAATAAATTTAAATAAATTTTT
* *
610138 ATTAATTAAATAAATTTAATTAAATTT
1 ATTAAATAAATAAATTTAAATAAATTT
610165 AATAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 2 0.09
29 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTAAATAAATAAATTTAAATAAATTTTT
Found at i:610167 original size:24 final size:21
Alignment explanation
Indices: 610121--610159 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
610111 ATTAAATAAA
610121 TAATTAAATAAATTT--TTAT
1 TAATTAAATAAATTTAATTAT
610140 TAATTAAATAAATTTAATTA
1 TAATTAAATAAATTTAATTA
610160 AATTTAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
21 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTAAATAAATTTAATTAT
Found at i:610473 original size:6 final size:6
Alignment explanation
Indices: 610456--610487 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
610446 AACGCCATTT
610456 CTTTTG CTTTTTG CTTTTG CTTTTG CTTTTG C
1 CTTTTG C-TTTTG CTTTTG CTTTTG CTTTTG C
610488 ACACAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.00, C:0.19, G:0.16, T:0.66
Consensus pattern (6 bp):
CTTTTG
Found at i:622433 original size:13 final size:13
Alignment explanation
Indices: 622421--622484 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
622411 ATTTTTTATT
622421 ATTTTTAAATATTA
1 ATTTTTAAATA-TA
*
622435 ATATTT-AATA-A
1 ATTTTTAAATATA
*
622446 ATATTTAAATATA
1 ATTTTTAAATATA
* * *
622459 AGTATAAAATATA
1 ATTTTTAAATATA
622472 ATTTTTAAATATA
1 ATTTTTAAATATA
622485 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
11 7 0.17
12 4 0.10
13 24 0.60
14 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
ATTTTTAAATATA
Found at i:622456 original size:25 final size:27
Alignment explanation
Indices: 622424--622483 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
622414 TTTTATTATT
**
622424 TTTAAATATTAA-TATTTAATA-AATA
1 TTTAAATATTAAGTATAAAATATAATA
*
622449 TTTAAATA-TAAGTATAAAATATAATT
1 TTTAAATATTAAGTATAAAATATAATA
622475 TTTAAATAT
1 TTTAAATAT
622484 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 15 0.52
26 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTAAATATTAAGTATAAAATATAATA
Found at i:622497 original size:21 final size:21
Alignment explanation
Indices: 622435--622497 Score: 54
Period size: 26 Copynumber: 2.8 Consensus size: 21
622425 TTAAATATTA
* * *
622435 ATATTTAATAAATATTTAAAT
1 ATATTAAAAAAATTTTTAAAT
622456 ATAAGTATAAAATATAATTTTTAAAT
1 AT-A-T-TAAAA-A-AATTTTTAAAT
622482 ATATTAAAAAAATTTT
1 ATATTAAAAAAATTTT
622498 AAAAATTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
21 8 0.24
22 2 0.06
23 6 0.18
24 4 0.12
25 2 0.06
26 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTAAAAAAATTTTTAAAT
Found at i:622771 original size:24 final size:24
Alignment explanation
Indices: 622714--622771 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
622704 TTAAAGATAA
*
622714 AAAAATAA-AAAATATTTAAATTT
1 AAAAATAATTAAATATTTAAATTT
* * **
622737 AAAATTTATTAAATATTTTTATTT
1 AAAAATAATTAAATATTTAAATTT
622761 AAAAATAATTA
1 AAAAATAATTA
622772 TATAAATTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATAATTAAATATTTAAATTT
Found at i:626505 original size:21 final size:24
Alignment explanation
Indices: 626461--626508 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
626451 AATCATATAA
626461 ATTGAATTAATTTAAAATAAATTTT
1 ATTGAATTAATTTAAAAT-AATTTT
626486 ATTGAATTAA-TT-AAAT-ATTTT
1 ATTGAATTAATTTAAAATAATTTT
626507 AT
1 AT
626509 CTGTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
23 4 0.17
24 2 0.09
25 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTGAATTAATTTAAAATAATTTT
Found at i:626560 original size:9 final size:11
Alignment explanation
Indices: 626531--626562 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
626521 ATTAATAAAC
626531 AATATTTTTAT
1 AATATTTTTAT
626542 AATATTTTTA-
1 AATATTTTTAT
626552 AAT-TTTTTAT
1 AATATTTTTAT
626562 A
1 A
626563 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 4 0.20
11 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATATTTTTAT
Found at i:626731 original size:15 final size:15
Alignment explanation
Indices: 626711--626742 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
626701 TCTGAACCAA
*
626711 AATAAAATCAAATTT
1 AATAAAATCAAAATT
626726 AATAAAATCAAAATT
1 AATAAAATCAAAATT
626741 AA
1 AA
626743 AACCGAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAAATCAAAATT
Found at i:627368 original size:4 final size:4
Alignment explanation
Indices: 627359--627387 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
627349 TTATTCTTAG
627359 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
627388 AAATCTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:627440 original size:26 final size:25
Alignment explanation
Indices: 627406--627457 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
627396 AAATCTATTT
*
627406 AAATAAATATACATAAAAATAATTA
1 AAATAAATATAAATAAAAATAATTA
* *
627431 AAATATAATATAAATACAAATTATTA
1 AAATA-AATATAAATAAAAATAATTA
627457 A
1 A
627458 TTTTATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAAATATAAATAAAAATAATTA
Found at i:628419 original size:24 final size:23
Alignment explanation
Indices: 628388--628436 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
628378 TTTTTATTTT
628388 TATTATATTTA-ATCATATTATAA
1 TATTATATTTATAT-ATATTATAA
*
628411 TATTAATATTTATATATTTTATAA
1 TATT-ATATTTATATATATTATAA
628435 TA
1 TA
628437 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATATTTATATATATTATAA
Found at i:628688 original size:17 final size:18
Alignment explanation
Indices: 628652--628698 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
628642 AGTTAGTCCG
628652 ATTTAAAAATTTATTTTTT
1 ATTT-AAAATTTATTTTTT
628671 ATTTAAAATTTA-TTTTT
1 ATTTAAAATTTATTTTTT
*
628688 ATCTAAAATTT
1 ATTTAAAATTT
628699 TATATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 15 0.56
18 8 0.30
19 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAAAATTTATTTTTT
Found at i:629404 original size:23 final size:22
Alignment explanation
Indices: 629365--629408 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
629355 CTTTAAAGTT
**
629365 AATATATATTATTTATAATTAA
1 AATATATATTAAATATAATTAA
629387 AATATTATATTAAATATAATTA
1 AATA-TATATTAAATATAATTA
629409 TTAATGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATATATTAAATATAATTAA
Found at i:629844 original size:6 final size:5
Alignment explanation
Indices: 629797--629853 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
629787 AATCAAATTA
* * * * * *
629797 TTAAT TTAAT TTAAT TGAAA TTATAT TTAAA TTAAA ATATT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTA-AT TTAAT TTAAT TTAAT TTAAT TTAAT
629848 TTAAT T
1 TTAAT T
629854 AATATTATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:630294 original size:2 final size:2
Alignment explanation
Indices: 630287--630312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
630277 GATGTGGCTT
630287 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
630313 TACCCTTTTA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:630714 original size:6 final size:6
Alignment explanation
Indices: 630705--630735 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
630695 TTAGTTTGAG
630705 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
630736 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:630848 original size:8 final size:8
Alignment explanation
Indices: 630837--630939 Score: 75
Period size: 8 Copynumber: 12.2 Consensus size: 8
630827 AAAAAATATG
630837 TATAAATA
1 TATAAATA
630845 TATAAATA
1 TATAAATA
*
630853 TATTAATACA
1 TA-TAA-ATA
630863 TATAAATA
1 TATAAATA
*
630871 TATAAATG
1 TATAAATA
*
630879 TATTAATA
1 TATAAATA
*
630887 TATAAAAA
1 TATAAATA
630895 TTATAAATA
1 -TATAAATA
*
630904 AATTAAATTTTA
1 TA-TAAA---TA
630916 TATAAATA
1 TATAAATA
630924 TA-AAATA
1 TATAAATA
*
630931 -ATAATTA
1 TATAAATA
630938 TA
1 TA
630940 CAAAAAAAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
6 1 0.01
7 9 0.12
8 37 0.49
9 17 0.23
10 4 0.05
11 4 0.05
12 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (8 bp):
TATAAATA
Found at i:630851 original size:18 final size:18
Alignment explanation
Indices: 630816--630930 Score: 80
Period size: 18 Copynumber: 6.6 Consensus size: 18
630806 AATATAATAT
* *
630816 TATATAAA-ATAAAAAAA
1 TATATAAATATATATAAA
*
630833 TATGTATAA-ATATATAAA
1 TATATA-AATATATATAAA
* *
630851 TATATTAATACATATAAA
1 TATATAAATATATATAAA
*
630869 TATATAAATGTAT-T-AA
1 TATATAAATATATATAAA
*
630885 TATATAAAAAT-TATAAA
1 TATATAAATATATATAAA
* *
630902 TAAATTAAATTTTATATAAA
1 TATA-TAAA-TATATATAAA
630922 TATA-AAATA
1 TATATAAATA
630931 ATAATTATAC
Statistics
Matches: 75, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
15 1 0.01
16 12 0.16
17 14 0.19
18 38 0.51
19 1 0.01
20 9 0.12
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (18 bp):
TATATAAATATATATAAA
Found at i:630851 original size:26 final size:26
Alignment explanation
Indices: 630807--630877 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
630797 AATAATTAAA
*
630807 ATATAATATTATATAAAATAAAAAAATAT
1 ATATAA-A-TATAT-AAATAAAAAAATAC
* * **
630836 GTATAAATATATAAATATATTAATAC
1 ATATAAATATATAAATAAAAAAATAC
630862 ATATAAATATATAAAT
1 ATATAAATATATAAAT
630878 GTATTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 25 0.69
27 5 0.14
28 1 0.03
29 5 0.14
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
ATATAAATATATAAATAAAAAAATAC
Found at i:630882 original size:26 final size:26
Alignment explanation
Indices: 630837--630909 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
630827 AAAAAATATG
630837 TATAAATATATAAATATATTAATACA
1 TATAAATATATAAATATATTAATACA
* *
630863 TATAAATATATAAATGTATTAATATA
1 TATAAATATATAAATATATTAATACA
* *
630889 TAAAAAT-TATAAATAAATTAA
1 TATAAATATATAAATATATTAA
630910 ATTTTATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 12 0.29
26 30 0.71
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
TATAAATATATAAATATATTAATACA
Found at i:639819 original size:2 final size:2
Alignment explanation
Indices: 639814--639850 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
639804 TCTCTCTCTC
639814 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
639851 GTTGATTGGC
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:640186 original size:31 final size:30
Alignment explanation
Indices: 640140--640208 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 30
640130 ATATTATGAT
640140 TTTATTTGTTATAAATTAAAAAATTAAAAA
1 TTTATTTGTTATAAATTAAAAAATTAAAAA
640170 TTTATTTGATTATAAATTAAAAAATTAAAAA
1 TTTATTTG-TTATAAATTAAAAAATTAAAAA
640201 TTTCATTT
1 TTT-ATTT
640209 AAGTGTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 8 0.22
31 25 0.68
32 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (30 bp):
TTTATTTGTTATAAATTAAAAAATTAAAAA
Found at i:640221 original size:30 final size:31
Alignment explanation
Indices: 640149--640239 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
640139 TTTTATTTGT
* *
640149 TATAAATTAAAAAATTAAAAATTTATTTGAT
1 TATAAATTAAAAAATTAAAAATTTATTTAAG
640180 TATAAATTAAAAAATTAAAAATTTCATTTAAG
1 TATAAATTAAAAAATTAAAAATTT-ATTTAAG
* * * *
640212 TGT-AA-TAAAAATTTAAGAATTAATTTAA
1 TATAAATTAAAAAATTAAAAATTTATTTAA
640240 ATTAGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.11
30 14 0.26
31 26 0.49
32 7 0.13
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (31 bp):
TATAAATTAAAAAATTAAAAATTTATTTAAG
Found at i:640310 original size:16 final size:14
Alignment explanation
Indices: 640269--640312 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
640259 ACAAAGTGAG
640269 TAAAATAAAAAAAA
1 TAAAATAAAAAAAA
*
640283 TAAAATATAAAAAA
1 TAAAATAAAAAAAA
*
640297 TATAAATGAAAAAAA
1 TA-AAATAAAAAAAA
640312 T
1 T
640313 TTATGTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:640855 original size:11 final size:10
Alignment explanation
Indices: 640835--640874 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
640825 TTTTTTTATT
640835 AAAAGAAAAA
1 AAAAGAAAAA
*
640845 AAAAGGAAAA
1 AAAAGAAAAA
*
640855 AATAGAAAAA
1 AAAAGAAAAA
640865 TAAAAGAAAA
1 -AAAAGAAAA
640875 GGATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:642803 original size:2 final size:2
Alignment explanation
Indices: 642796--642833 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
642786 ACATCTGCCT
642796 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
642834 CCCCCCCCCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:644178 original size:9 final size:9
Alignment explanation
Indices: 644166--644223 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
644156 ACATCAATGA
644166 TGATGATGG
1 TGATGATGG
644175 TGATGATGG
1 TGATGATGG
*
644184 TGATGATGA
1 TGATGATGG
*
644193 TGATGATGT
1 TGATGATGG
* *
644202 TGACGGTGG
1 TGATGATGG
*
644211 TGATGATAG
1 TGATGATGG
644220 TGAT
1 TGAT
644224 TGCAAAGATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.24, C:0.02, G:0.40, T:0.34
Consensus pattern (9 bp):
TGATGATGG
Found at i:644217 original size:3 final size:3
Alignment explanation
Indices: 644162--644200 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
644152 GATGACATCA
* *
644162 ATG ATG ATG ATG GTG ATG ATG GTG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
644201 TTGACGGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:655990 original size:11 final size:12
Alignment explanation
Indices: 655965--656011 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
655955 TTAAAGAAAC
655965 ATAA-ATAAAAT
1 ATAATATAAAAT
655976 ATAATATAAAA-
1 ATAATATAAAAT
655987 ATAAT-TAAAAT
1 ATAATATAAAAT
*
655998 ATAAAATAAAAT
1 ATAATATAAAAT
656010 AT
1 AT
656012 TACAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 5 0.16
11 13 0.41
12 14 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:656018 original size:20 final size:22
Alignment explanation
Indices: 655965--656021 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
655955 TTAAAGAAAC
* *
655965 ATAAATAAAATATAATATAAAA
1 ATAATTAAAATATAAAATAAAA
655987 ATAATTAAAATATAAAAT-AAA
1 ATAATTAAAATATAAAATAAAA
*
656008 AT-ATTACAATATAA
1 ATAATTAAAATATAA
656022 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 16 0.50
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAATTAAAATATAAAATAAAA
Found at i:656074 original size:11 final size:12
Alignment explanation
Indices: 656061--656121 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
656051 CATTAAATAT
656061 AAAATAATTATA
1 AAAATAATTATA
* *
656073 AAAATATAATATG
1 AAAATA-ATTATA
* * *
656086 TAAATAATAATT
1 AAAATAATTATA
656098 AAAAT-ATTATA
1 AAAATAATTATA
*
656109 AAAATAAATATA
1 AAAATAATTATA
656121 A
1 A
656122 TATAAAAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 9 0.24
12 19 0.51
13 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AAAATAATTATA
Found at i:656098 original size:28 final size:27
Alignment explanation
Indices: 656055--656133 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
656045 TGATAACATT
656055 AAATATAA-AATAATTATAAAAATATAA
1 AAATA-AATAATAATTATAAAAATATAA
** *
656082 TATGTAAATAATAATTA-AAATATTATAA
1 -AAATAAATAATAATTATAAA-AATATAA
656110 AAATAAAT-ATAA-TATAAAAATATA
1 AAATAAATAATAATTATAAAAATATA
656134 TATTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
25 7 0.17
26 7 0.17
27 11 0.26
28 17 0.40
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (27 bp):
AAATAAATAATAATTATAAAAATATAA
Found at i:656123 original size:20 final size:20
Alignment explanation
Indices: 656074--656124 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
656064 ATAATTATAA
*
656074 AAATATAATATGTAAATAAT
1 AAATATAATATGTAAAAAAT
* *
656094 AATTAAAATAT-TATAAAAAT
1 AAATATAATATGTA-AAAAAT
656114 AAATATAATAT
1 AAATATAATAT
656125 AAAAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATATAATATGTAAAAAAT
Found at i:656131 original size:40 final size:40
Alignment explanation
Indices: 656074--656166 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 40
656064 ATAATTATAA
**
656074 AAATATAATATGTAAATA-ATAATTAAAATATTA-TAAAAAT
1 AAATATAATATAAAAATATAT-ATTAAAAT-TTATTAAAAAT
* * *
656114 AAATATAATATAAAAATATATATTCAAATTTATTTAATAT
1 AAATATAATATAAAAATATATATTAAAATTTATTAAAAAT
656154 AAATATTAATATA
1 AAATA-TAATATA
656167 TCAAATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 33 0.73
41 9 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (40 bp):
AAATATAATATAAAAATATATATTAAAATTTATTAAAAAT
Found at i:657032 original size:21 final size:21
Alignment explanation
Indices: 657008--657051 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
656998 TATTATTTGA
657008 AATTATCAAAAATT-AAATTTT
1 AATTAT-AAAAATTAAAATTTT
**
657029 AATTATTTAAATTAAAATTTT
1 AATTATAAAAATTAAAATTTT
657050 AA
1 AA
657052 CATATTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATAAAAATTAAAATTTT
Found at i:658496 original size:4 final size:4
Alignment explanation
Indices: 658487--658513 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
658477 CTTCTTTGAC
658487 AAGG AAGG AAGG AAGG AAGG AAGG AAG
1 AAGG AAGG AAGG AAGG AAGG AAGG AAG
658514 ATCGAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:658559 original size:3 final size:3
Alignment explanation
Indices: 658553--658597 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
658543 CTACTACCAC
658553 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
658598 CAGAATATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:658804 original size:9 final size:11
Alignment explanation
Indices: 658775--658815 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
658765 AGAATTCGTG
*
658775 TATTCATATTA
1 TATTTATATTA
658786 TATTTATATTA
1 TATTTATATTA
658797 T-TTT-TATTA
1 TATTTATATTA
*
658806 TAATTATATT
1 TATTTATATT
658816 TAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 6 0.23
10 5 0.19
11 15 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATATTA
Found at i:659384 original size:3 final size:3
Alignment explanation
Indices: 659376--659418 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
659366 AATTAATTAG
659376 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
659419 AAAGAGGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:659547 original size:2 final size:2
Alignment explanation
Indices: 659540--659569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
659530 TCGATTTGGA
659540 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
659570 GTATGTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:660864 original size:48 final size:46
Alignment explanation
Indices: 660762--660864 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 46
660752 CATTAATCTT
* *
660762 AAATATAATACTAAAAATGAATAAAATATGATTTAACAAATAATAA
1 AAATATAACACTAAAAATGAATAAAATATAATTTAACAAATAATAA
* * *
660808 AATCATATAACATTAAAAATTATATAAAATTTAATTTAA-AAATAAATATA
1 AA--ATATAACACTAAAAATGA-ATAAAATATAATTTAACAAAT-AATA-A
660858 AAATATA
1 AAATATA
660865 TATTCGATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
46 2 0.04
48 24 0.51
49 18 0.38
50 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (46 bp):
AAATATAACACTAAAAATGAATAAAATATAATTTAACAAATAATAA
Done.