Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 11 of 135
Found at i:3063131 original size:20 final size:18
Alignment explanation
Indices: 3063087--3063133 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
3063077 AATAAAATTA
3063087 TTTAAAA-ATTTTATATT
1 TTTAAAATATTTTATATT
*
3063104 TTAAAAAATATTTTTAATATT
1 TT-TAAAATA-TTTT-ATATT
3063125 TTTAAAATA
1 TTTAAAATA
3063134 ATTTGCTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 4 0.17
19 1 0.04
20 10 0.42
21 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAAATATTTTATATT
Found at i:3064958 original size:25 final size:25
Alignment explanation
Indices: 3064922--3064972 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3064912 TAAATCTAAG
**
3064922 AAAAATAATATATTAAATAATATTA
1 AAAAATAATATAACAAATAATATTA
*
3064947 AAAAATATTATAACAAATAATATTA
1 AAAAATAATATAACAAATAATATTA
3064972 A
1 A
3064973 TTGAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAATAATATAACAAATAATATTA
Found at i:3065005 original size:17 final size:18
Alignment explanation
Indices: 3064961--3065005 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
3064951 ATATTATAAC
*
3064961 AAATAATATTAATTGAAA
1 AAATAATATTTATTGAAA
*
3064979 AATTAA-ATTTATT-AAA
1 AAATAATATTTATTGAAA
3064995 AAATAATATTT
1 AAATAATATTT
3065006 TCAATAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 10 0.43
18 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATAATATTTATTGAAA
Found at i:3078603 original size:2 final size:2
Alignment explanation
Indices: 3078596--3078629 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3078586 TTGTCTAGTG
3078596 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
3078630 TAATCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3084784 original size:13 final size:13
Alignment explanation
Indices: 3084766--3084796 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3084756 CCCACAAATA
3084766 TTTTATTTTATTT
1 TTTTATTTTATTT
3084779 TTTTATTTTATTT
1 TTTTATTTTATTT
3084792 TTTTA
1 TTTTA
3084797 ACAAGTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:3091100 original size:29 final size:30
Alignment explanation
Indices: 3091059--3091125 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
3091049 AACAATATAG
* * *
3091059 TGATT-AATTGTAACTTTTTAA-AATTAAT
1 TGATTAAATTGTAAATTATTAATAATTAAA
3091087 TGATTAAATTGTAAATTATTAATAATTAAA
1 TGATTAAATTGTAAATTATTAATAATTAAA
3091117 T-ATTAAATT
1 TGATTAAATT
3091126 TATCGATCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.15
29 22 0.65
30 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (30 bp):
TGATTAAATTGTAAATTATTAATAATTAAA
Found at i:3091336 original size:2 final size:2
Alignment explanation
Indices: 3091324--3091371 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3091314 TATAATTTGA
*
3091324 AT AT GT 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
3091366 AT AT AT
1 AT AT AT
3091372 TTTGAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3091549 original size:2 final size:2
Alignment explanation
Indices: 3091542--3091597 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3091532 CTAAGACTCA
3091542 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
3091584 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3091598 GTGTGTGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3107530 original size:51 final size:51
Alignment explanation
Indices: 3107475--3107577 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
3107465 AATTGTTTGG
* *
3107475 TTACCAGAATAGACCAAACCAGCAGAACCCATTCAGCTAGGAATGACAAGT
1 TTACCAGAATAGACCAAACCAGCAGAACCCATCCAGCTAGGAATAACAAGT
* * *
3107526 TTACCGGAATAGACCAATCCAGCAGAACCCATCCAGCTTGGAATAACAAGT
1 TTACCAGAATAGACCAAACCAGCAGAACCCATCCAGCTAGGAATAACAAGT
3107577 T
1 T
3107578 CATGTTCCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (51 bp):
TTACCAGAATAGACCAAACCAGCAGAACCCATCCAGCTAGGAATAACAAGT
Found at i:3111189 original size:8 final size:9
Alignment explanation
Indices: 3111094--3111188 Score: 80
Period size: 9 Copynumber: 11.2 Consensus size: 9
3111084 TGTGGCAAAC
3111094 AAATTATAA
1 AAATTATAA
3111103 AAA--ACTAA
1 AAATTA-TAA
* *
3111111 AAGTAATAA
1 AAATTATAA
3111120 AAATTATAA
1 AAATTATAA
3111129 AAATTAT--
1 AAATTATAA
*
3111136 --ATAATAA
1 AAATTATAA
3111143 AAA-TATAA
1 AAATTATAA
3111151 AAATTATAA
1 AAATTATAA
3111160 AAATCT-TAA
1 AAAT-TATAA
*
3111169 AAAATATAA
1 AAATTATAA
3111178 AAATTATAA
1 AAATTATAA
3111187 AA
1 AA
3111189 TATAAATTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
5 4 0.06
7 1 0.01
8 13 0.19
9 49 0.71
10 2 0.03
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (9 bp):
AAATTATAA
Found at i:3112483 original size:3 final size:3
Alignment explanation
Indices: 3112475--3112521 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3112465 TTTAGGGCAT
3112475 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3112522 AATGAAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3113500 original size:12 final size:12
Alignment explanation
Indices: 3113483--3113507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3113473 AGGAAACTTT
3113483 ACAAAAAGTTCA
1 ACAAAAAGTTCA
3113495 ACAAAAAGTTCA
1 ACAAAAAGTTCA
3113507 A
1 A
3113508 AAACAGCTCA
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
ACAAAAAGTTCA
Found at i:3113698 original size:21 final size:21
Alignment explanation
Indices: 3113674--3113721 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3113664 CATTTGCAAT
3113674 TGAGTTATGCTGCTCACTTGC
1 TGAGTTATGCTGCTCACTTGC
* *
3113695 TGAGATGTGCTGCTCACTTGC
1 TGAGTTATGCTGCTCACTTGC
3113716 TGAGTT
1 TGAGTT
3113722 GGGGTCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (21 bp):
TGAGTTATGCTGCTCACTTGC
Found at i:3113731 original size:21 final size:21
Alignment explanation
Indices: 3113686--3113732 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3113676 AGTTATGCTG
* *
3113686 CTCACTTGCTGAGATGTGCTG
1 CTCACTTGCTGAGATGGGCTC
* *
3113707 CTCACTTGCTGAGTTGGGGTC
1 CTCACTTGCTGAGATGGGCTC
3113728 CTCAC
1 CTCAC
3113733 ATGAAAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.32
Consensus pattern (21 bp):
CTCACTTGCTGAGATGGGCTC
Found at i:3118344 original size:24 final size:23
Alignment explanation
Indices: 3118317--3118383 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
3118307 TTTCAATAAA
3118317 TAAAAAAATAAAATTATTAAATA-T
1 TAAAAAAATAAAA-TA-TAAATATT
* *
3118341 TAAAATAATATAATATAAATATT
1 TAAAAAAATAAAATATAAATATT
*
3118364 TAAAAAAAATAAAAAATAAA
1 T-AAAAAAATAAAATATAAA
3118384 ATGAGTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.17
23 4 0.11
24 26 0.72
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAAATAAAATATAAATATT
Found at i:3118375 original size:22 final size:21
Alignment explanation
Indices: 3118321--3118375 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3118311 AATAAATAAA
*
3118321 AAAATAAAATTATTAAATATT
1 AAAATAAAATAATTAAATATT
*
3118342 AAAATAATATAATATAAATATTT
1 AAAATAAAATAAT-TAAATA-TT
3118365 AAAA-AAAATAA
1 AAAATAAAATAA
3118376 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.38
22 12 0.41
23 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAAATAATTAAATATT
Found at i:3120295 original size:47 final size:47
Alignment explanation
Indices: 3120165--3120306 Score: 250
Period size: 47 Copynumber: 3.0 Consensus size: 47
3120155 AGTTTTTTTT
*
3120165 TATATTATACAATTAAAAAATTAGTATTCACACGTAACCTACGAACA
1 TATATTATACAATTAAAAAATTAGTATTCACACGTAACCTACCAACA
3120212 TATATTATACAATT-AAAAATTAGTATTCACACGTAACCTACCAACA
1 TATATTATACAATTAAAAAATTAGTATTCACACGTAACCTACCAACA
* *
3120258 TATATTATACAATTAAAAAATTAGTACTGACACGTAACCTACCAACA
1 TATATTATACAATTAAAAAATTAGTATTCACACGTAACCTACCAACA
3120305 TA
1 TA
3120307 CTCGTTCAAA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
46 45 0.49
47 46 0.51
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (47 bp):
TATATTATACAATTAAAAAATTAGTATTCACACGTAACCTACCAACA
Found at i:3126235 original size:24 final size:24
Alignment explanation
Indices: 3126192--3126252 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
3126182 TAAAAATCTA
3126192 ATTAAATAAAA-AATTATATTAAT
1 ATTAAATAAAATAATTATATTAAT
3126215 ATTAAATAAAATAATTATATTAAT
1 ATTAAATAAAATAATTATATTAAT
3126239 ATTAAATAAAATAA
1 ATTAAATAAAATAA
3126253 ATAAAAGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTAAATAAAATAATTATATTAAT
Found at i:3129216 original size:12 final size:12
Alignment explanation
Indices: 3129196--3129226 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3129186 GGAAAACAGG
3129196 AAAGAAGATGAA
1 AAAGAAGATGAA
*
3129208 AAAGGAGATGAA
1 AAAGAAGATGAA
3129220 AAAGAAG
1 AAAGAAG
3129227 CGAAAAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (12 bp):
AAAGAAGATGAA
Found at i:3137269 original size:13 final size:13
Alignment explanation
Indices: 3137251--3137275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3137241 TGATATATAT
3137251 TTTCTTTTTCTTG
1 TTTCTTTTTCTTG
3137264 TTTCTTTTTCTT
1 TTTCTTTTTCTT
3137276 TATCTTTGGA
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:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTCTTG
Found at i:3142495 original size:45 final size:45
Alignment explanation
Indices: 3142437--3142548 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 45
3142427 CAAGAACAAG
* *
3142437 GATGATAGTAAAGAAAGTAAAAATAAGGAGTCTTTGCATAAGAAA
1 GATGATCGCAAAGAAAGTAAAAATAAGGAGTCTTTGCATAAGAAA
3142482 GATGATCGCAAAGAAAGTAAAAATAAGGAGTCTTTGCATAAGAAA
1 GATGATCGCAAAGAAAGTAAAAATAAGGAGTCTTTGCATAAGAAA
*
3142527 GATGATC-CAAAAGAAAGCAAAA
1 GATGATCGC-AAAGAAAGTAAAA
3142549 GGCTCGAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 1 0.02
45 62 0.98
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.19
Consensus pattern (45 bp):
GATGATCGCAAAGAAAGTAAAAATAAGGAGTCTTTGCATAAGAAA
Found at i:3156484 original size:91 final size:91
Alignment explanation
Indices: 3156329--3156511 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
3156319 AACCCACGGG
3156329 GAGAATGGTGGCTTTCGGAGGTCACCTACGGCGCGTATGGATGATAGGACGACGCGTACTTGAGG
1 GAGAATGGTGGCTTTCGGAGGTCACCTACGGCGCGTATGGATGATAGGACGACGCGTACTTGAGG
3156394 GTACCGGAGGCCGGGATGATCTATGT
66 GTACCGGAGGCCGGGATGATCTATGT
3156420 GAGAATGGTGGCTTTCGGAGGTCACCTACGGCGCGTATGGATGATAGGACGACGCGTACTTGAGG
1 GAGAATGGTGGCTTTCGGAGGTCACCTACGGCGCGTATGGATGATAGGACGACGCGTACTTGAGG
3156485 GTACCGGAGGCCGGGATGATCTATGT
66 GTACCGGAGGCCGGGATGATCTATGT
3156511 G
1 G
3156512 GAGATTATGC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.22
Consensus pattern (91 bp):
GAGAATGGTGGCTTTCGGAGGTCACCTACGGCGCGTATGGATGATAGGACGACGCGTACTTGAGG
GTACCGGAGGCCGGGATGATCTATGT
Found at i:3158983 original size:9 final size:9
Alignment explanation
Indices: 3158953--3158996 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
3158943 TGTATTAGTT
3158953 GAATATATG
1 GAATATATG
3158962 CTGAATGATATG
1 --GAAT-ATATG
3158974 GAATATATG
1 GAATATATG
3158983 GAATATATG
1 GAATATATG
*
3158992 AAATA
1 GAATA
3158997 AATTGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 18 0.58
10 4 0.13
11 4 0.13
12 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.32
Consensus pattern (9 bp):
GAATATATG
Found at i:3159010 original size:16 final size:18
Alignment explanation
Indices: 3158989--3159021 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3158979 TATGGAATAT
3158989 ATGAAA-TAAAT-TGATG
1 ATGAAATTAAATGTGATG
3159005 ATGAAATTAAATGTGAT
1 ATGAAATTAAATGTGAT
3159022 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (18 bp):
ATGAAATTAAATGTGATG
Found at i:3159027 original size:2 final size:2
Alignment explanation
Indices: 3159020--3159045 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3159010 ATTAAATGTG
3159020 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
3159046 TGATTTGATG
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:3163399 original size:2 final size:2
Alignment explanation
Indices: 3163392--3163437 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3163382 TATAACAACA
3163392 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
3163434 AT AT
1 AT AT
3163438 TTAGAAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3165404 original size:24 final size:24
Alignment explanation
Indices: 3165318--3165392 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
3165308 AGAAATAATC
*
3165318 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
**
3165342 TTTCAATTAAACTCCGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
3165366 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
3165390 TTT
1 TTT
3165393 GAGTCAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:3167346 original size:24 final size:24
Alignment explanation
Indices: 3167318--3167368 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3167308 AGAAATAATC
* * *
3167318 TTTCAGTTAAATTCTATTTATTTG
1 TTTCAATTAAACTATATTTATTTG
*
3167342 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTATATTTATTTG
3167366 TTT
1 TTT
3167369 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTATATTTATTTG
Found at i:3168132 original size:10 final size:11
Alignment explanation
Indices: 3168106--3168132 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3168096 TTAACTCAAT
3168106 TAAAAAATTAC
1 TAAAAAATTAC
3168117 TAAAAAATTAC
1 TAAAAAATTAC
3168128 TAAAA
1 TAAAA
3168133 GAAAACTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAAAATTAC
Found at i:3176048 original size:20 final size:20
Alignment explanation
Indices: 3176007--3176059 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
3175997 TATTTAAATA
*
3176007 TAAATATTTTATAATTATATT
1 TAAATA-TTTAAAATTATATT
3176028 TAAATATTTAAAA-TATAATT
1 TAAATATTTAAAATTAT-ATT
*
3176048 TATATAATTTAA
1 TAAAT-ATTTAA
3176060 TTAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATATTTAAAATTATATT
Found at i:3179831 original size:15 final size:14
Alignment explanation
Indices: 3179808--3179852 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
3179798 AAAATTATAT
3179808 TATTTTTAATTTTA
1 TATTTTTAATTTTA
3179822 TATTTATTAATTTTA
1 TATTT-TTAATTTTA
*
3179837 TATGTTTTTATTTTA
1 TAT-TTTTAATTTTA
3179852 T
1 T
3179853 TAAAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.18
15 21 0.75
16 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (14 bp):
TATTTTTAATTTTA
Found at i:3189787 original size:6 final size:6
Alignment explanation
Indices: 3189778--3189823 Score: 65
Period size: 6 Copynumber: 7.2 Consensus size: 6
3189768 ACTAATAAAA
3189778 ATATTT ATATTT ATATTT AATGTATTT ATATTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT -A--TATTT ATATTT ATATTT ATATTT A
3189824 ATTATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 30 0.81
7 1 0.03
8 1 0.03
9 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:3189835 original size:27 final size:28
Alignment explanation
Indices: 3189775--3189835 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
3189765 AAAACTAATA
3189775 AAAATATTTATATTTATATTTAATGTAT
1 AAAATATTTATATTTATATTTAATGTAT
**
3189803 -TTATATTTATATTTATATTTAAT-TAT
1 AAAATATTTATATTTATATTTAATGTAT
3189829 AAAATAT
1 AAAATAT
3189836 ATAAATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AAAATATTTATATTTATATTTAATGTAT
Found at i:3190649 original size:6 final size:6
Alignment explanation
Indices: 3190638--3190674 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
3190628 CAGGTTCTCC
3190638 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
3190675 CGTATAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:3198531 original size:22 final size:22
Alignment explanation
Indices: 3198506--3198570 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
3198496 GAATTAAAAT
3198506 TAAATTATAATTTTTATTATAA
1 TAAATTATAATTTTTATTATAA
* ** * *
3198528 TAAAAATATAATTTTTAAAAGAT
1 T-AAATTATAATTTTTATTATAA
*
3198551 TAAATTAAAATTTTTATTAT
1 TAAATTATAATTTTTATTAT
3198571 TTTTAAAGAG
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAATTATAATTTTTATTATAA
Found at i:3200279 original size:21 final size:24
Alignment explanation
Indices: 3200258--3200301 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3200248 ACATATGTTA
3200258 TGTT-GTTAAATTTT-ATTATTAT
1 TGTTAGTTAAATTTTGATTATTAT
*
3200280 TTTTAGTTAAATTTTGATTATT
1 TGTTAGTTAAATTTTGATTATT
3200302 TAAAAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 10 0.53
24 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (24 bp):
TGTTAGTTAAATTTTGATTATTAT
Found at i:3200495 original size:21 final size:21
Alignment explanation
Indices: 3200465--3200532 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
3200455 AACTCAAAGA
*
3200465 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTGACTTAGAC
** *
3200485 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTGACTTAGAC
3200506 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTGACTTAGAC
3200530 AAA
1 AAA
3200533 TCTTTTTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.16
21 16 0.43
23 1 0.03
24 14 0.38
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTGACTTAGAC
Found at i:3204863 original size:17 final size:17
Alignment explanation
Indices: 3204800--3204857 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
3204790 TTTTAAAATA
* *
3204800 TTAA-AAATAATTATAT
1 TTAATAAATAAATATTT
*
3204816 TT-ATAAATTAA-ATTT
1 TTAATAAATAAATATTT
*
3204831 TTAATATATAAATATTT
1 TTAATAAATAAATATTT
3204848 TTAATAAATA
1 TTAATAAATA
3204858 TTTATTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 6 0.18
16 14 0.42
17 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATAAATAAATATTT
Found at i:3204879 original size:20 final size:20
Alignment explanation
Indices: 3204856--3204893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3204846 TTTTAATAAA
3204856 TATTTA-TTGTTTTAGATAGT
1 TATTTATTTG-TTTAGATAGT
3204876 TATTTATTTGTTTAGATA
1 TATTTATTTGTTTAGATA
3204894 AAAGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (20 bp):
TATTTATTTGTTTAGATAGT
Found at i:3206089 original size:19 final size:20
Alignment explanation
Indices: 3206065--3206102 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3206055 TCTTATAAAA
3206065 AAATCTA-TTATTAATTTGC
1 AAATCTATTTATTAATTTGC
*
3206084 AAATCTATTTATTAGTTTG
1 AAATCTATTTATTAATTTG
3206103 TCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (20 bp):
AAATCTATTTATTAATTTGC
Found at i:3213532 original size:125 final size:125
Alignment explanation
Indices: 3213310--3213565 Score: 458
Period size: 125 Copynumber: 2.0 Consensus size: 125
3213300 GAGAGATAAT
* *
3213310 AGGAGAACAATCCAGGTAATGGTTTAGTCATTTATCAGAATATCCGAAATCACTTCTCTCTAGTA
1 AGGAGAACAATCCAGGAAATGGTTTAGTCATTTATCAGAATATCCAAAATCACTTCTCTCTAGTA
* *
3213375 ATGCAGATAAAAGAGGAAGACAGTGAACAACATAATATCTTAAATTTAACATCTGCCGCA
66 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
* *
3213435 AGGAGAACAATCCGGGAAATGGTTTAGTGATTTATCAGAATATCCAAAATCACTTCTCTCTAGTA
1 AGGAGAACAATCCAGGAAATGGTTTAGTCATTTATCAGAATATCCAAAATCACTTCTCTCTAGTA
3213500 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
66 ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
3213560 AGGAGA
1 AGGAGA
3213566 TGCAGTTAAG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (125 bp):
AGGAGAACAATCCAGGAAATGGTTTAGTCATTTATCAGAATATCCAAAATCACTTCTCTCTAGTA
ATGCAGATAAAAGAGCAAGACAGTGAACAACATAATATCTTAAATCTAACATCTGCCGCA
Found at i:3215656 original size:14 final size:15
Alignment explanation
Indices: 3215631--3215663 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3215621 TCGCTAAAGC
3215631 TCTGAGCTATTTATT
1 TCTGAGCTATTTATT
*
3215646 TCTGA-CTATTTTTT
1 TCTGAGCTATTTATT
3215660 TCTG
1 TCTG
3215664 TTGTTTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (15 bp):
TCTGAGCTATTTATT
Found at i:3216078 original size:14 final size:14
Alignment explanation
Indices: 3216061--3216094 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3216051 TACAACATCC
3216061 AAATAATAACAATA
1 AAATAATAACAATA
*
3216075 AAATAGTAACAATA
1 AAATAATAACAATA
*
3216089 TAATAA
1 AAATAA
3216095 CGAAACGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:3218957 original size:38 final size:38
Alignment explanation
Indices: 3218906--3218984 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
3218896 TTTTTCTTCT
3218906 CCATTGTATTGAAGACCTCCATTGCACTCAAAGGGTCA
1 CCATTGTATTGAAGACCTCCATTGCACTCAAAGGGTCA
*
3218944 CCATTGTATTGAAGACCTCCGTTGCACTCAAAGGGTCA
1 CCATTGTATTGAAGACCTCCATTGCACTCAAAGGGTCA
3218982 CCA
1 CCA
3218985 CATCTGATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (38 bp):
CCATTGTATTGAAGACCTCCATTGCACTCAAAGGGTCA
Found at i:3228097 original size:26 final size:25
Alignment explanation
Indices: 3228049--3228123 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
3228039 ATTAAATTGT
* *
3228049 AATTATAATAATTTATATATTTATAA
1 AATTAAAATAATTTATAT-TTTAAAA
* *
3228075 ATTTTAAATAATTTATCATTTTAAAAA
1 AATTAAAATAATTTAT-ATTTT-AAAA
3228102 AATTAAAATAATTT-TAATTTTA
1 AATTAAAATAATTTAT-ATTTTA
3228124 CTCATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.03
26 22 0.55
27 17 0.43
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTAAAATAATTTATATTTTAAAA
Found at i:3228454 original size:13 final size:13
Alignment explanation
Indices: 3228420--3228455 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3228410 GTTTTAAAAA
*
3228420 AATTTAAATTTTG
1 AATTTAAGTTTTG
3228433 AATTTTAAGTTTTG
1 AA-TTTAAGTTTTG
3228447 AATTTAAGT
1 AATTTAAGT
3228456 CGAGTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (13 bp):
AATTTAAGTTTTG
Found at i:3230911 original size:17 final size:16
Alignment explanation
Indices: 3230889--3230929 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
3230879 TTTTTTAAAA
*
3230889 AATATTTATATTATTTT
1 AATATTTA-ATAATTTT
3230906 AATATTTAATAATTTT
1 AATATTTAATAATTTT
3230922 ATATATTT
1 A-ATATTT
3230930 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTAATAATTTT
Found at i:3230931 original size:26 final size:27
Alignment explanation
Indices: 3230887--3230954 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
3230877 TTTTTTTTAA
3230887 AAAATATTTATAT-TATTTTAATAT-TT
1 AAAAT-TTTATATATATTTTAATATATT
* *
3230913 AATAATTTTATATAT-TTTTTATTTATT
1 AA-AATTTTATATATATTTTAATATATT
*
3230940 AAAATTTTTTATATA
1 AAAATTTTATATATA
3230955 ATCATCTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
AAAATTTTATATATATTTTAATATATT
Found at i:3230939 original size:28 final size:26
Alignment explanation
Indices: 3230887--3230953 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
3230877 TTTTTTTTAA
*
3230887 AAAATATT-TATATTATTTTAATATTT
1 AAAATTTTATATATTATTTTAATA-TT
*
3230913 AATAATTTTATATATT-TTTTATTTATT
1 AA-AATTTTATATATTATTTTA-ATATT
*
3230940 AAAATTTTTTATAT
1 AAAATTTTATATAT
3230954 AATCATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 13 0.37
27 14 0.40
28 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AAAATTTTATATATTATTTTAATATT
Found at i:3232907 original size:17 final size:18
Alignment explanation
Indices: 3232885--3232920 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3232875 GGTTTTGAAT
*
3232885 GGAGGAGATTAAT-AAAA
1 GGAGGAAATTAATCAAAA
3232902 GGAGGAAATTAATCAAAA
1 GGAGGAAATTAATCAAAA
3232920 G
1 G
3232921 CAGTAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (18 bp):
GGAGGAAATTAATCAAAA
Found at i:3238337 original size:29 final size:29
Alignment explanation
Indices: 3238295--3238352 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3238285 CCAACTCATA
3238295 AATAGGAGGATAATGCGTTTCAGCGCACT
1 AATAGGAGGATAATGCGTTTCAGCGCACT
*
3238324 AATAGGAGGATAATGCGTTTCAGTGCACT
1 AATAGGAGGATAATGCGTTTCAGCGCACT
3238353 TGAACCCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (29 bp):
AATAGGAGGATAATGCGTTTCAGCGCACT
Found at i:3251497 original size:107 final size:107
Alignment explanation
Indices: 3251330--3251729 Score: 637
Period size: 107 Copynumber: 3.8 Consensus size: 107
3251320 ATTTTTTGTA
*
3251330 TATTGGCCCTTTTGACGCTAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
1 TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
* *
3251395 CATACTCTAAATTTATTATCATCATTTTTTTACTTAAGAATG
66 CACACTCTCAATTTATTATCATCATTTTTTTACTTAAGAATG
3251437 TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
1 TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
* *
3251502 CGCACTCTCAATTTATT-TGCATTATTTTTTTACTTAAGAATG
66 CACACTCTCAATTTATTAT-CATCATTTTTTTACTTAAGAATG
* * **
3251544 TATTGGCCCTTTTGACGCGAAATGAAATGACAACCCAAGCACTCCATCCCGGTTACTCAGTTCAA
1 TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
* *
3251609 TACA--CTCAATTTATTATCATCA-TTTTTTACTTAAGAACG
66 CACACTCTCAATTTATTATCATCATTTTTTTACTTAAGAATG
* *
3251648 TATTGGCCATTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCTGCCCAA
1 TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
*
3251713 CACACTCTTAATTTATT
66 CACACTCTCAATTTATT
3251730 TTTTTCCATA
Statistics
Matches: 268, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
104 78 0.29
105 15 0.06
106 12 0.04
107 163 0.61
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (107 bp):
TATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
CACACTCTCAATTTATTATCATCATTTTTTTACTTAAGAATG
Found at i:3251691 original size:211 final size:214
Alignment explanation
Indices: 3251330--3251730 Score: 673
Period size: 211 Copynumber: 1.9 Consensus size: 214
3251320 ATTTTTTGTA
* *
3251330 TATTGGCCCTTTTGACGCTAAATGGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
1 TATTGGCCCTTTTGACGCGAAATGAAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
* * *
3251395 CATACTCTAAATTTATTATCATCATTTTTTTACTTAAGAATGTATTGGCCCTTTTGACGCGAAAT
66 CATACACTAAATTTATTATCATCATTTTTTTACTTAAGAACGTATTGGCCATTTTGACGCGAAAT
*
3251460 GGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAACGCACTCTCAATTTATTTGCATT
131 GGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAACACACTCTCAATTTATTTGCATT
3251525 ATTTTTTTACTTAAGAATG
196 ATTTTTTTACTTAAGAATG
* **
3251544 TATTGGCCCTTTTGACGCGAAATGAAATGACAACCCAAGCACTCCATCCCGGTTACTCAGTTC-A
1 TATTGGCCCTTTTGACGCGAAATGAAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
*
3251608 -ATACACTCAATTTATTATCATCA-TTTTTTACTTAAGAACGTATTGGCCATTTTGACGCGAAAT
66 CATACACTAAATTTATTATCATCATTTTTTTACTTAAGAACGTATTGGCCATTTTGACGCGAAAT
* *
3251671 GGAATGACAACCCAAGCACCCCATCCCGGTTACTCTGCCCAACACACTCTTAATTTATTT
131 GGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAACACACTCTCAATTTATTT
3251731 TTTTCCATAA
Statistics
Matches: 175, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
211 95 0.54
212 21 0.12
213 1 0.01
214 58 0.33
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (214 bp):
TATTGGCCCTTTTGACGCGAAATGAAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAA
CATACACTAAATTTATTATCATCATTTTTTTACTTAAGAACGTATTGGCCATTTTGACGCGAAAT
GGAATGACAACCCAAGCACCCCATCCCGGTTACTCAGCCCAACACACTCTCAATTTATTTGCATT
ATTTTTTTACTTAAGAATG
Found at i:3263383 original size:10 final size:8
Alignment explanation
Indices: 3263360--3263385 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3263350 TTGTATTTGT
3263360 ATTCTCTC
1 ATTCTCTC
3263368 ATTCTCTC
1 ATTCTCTC
3263376 ATTCTCTC
1 ATTCTCTC
3263384 AT
1 AT
3263386 CAATATCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTCTCTC
Found at i:3266027 original size:10 final size:11
Alignment explanation
Indices: 3266001--3266025 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3265991 TTCAATATAT
3266001 AAAATGTTTAA
1 AAAATGTTTAA
3266012 AAAATGTTTAA
1 AAAATGTTTAA
3266023 AAA
1 AAA
3266026 TGGGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (11 bp):
AAAATGTTTAA
Found at i:3272674 original size:30 final size:31
Alignment explanation
Indices: 3272625--3272682 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3272615 TCAAATTTTA
*
3272625 AAAAGTACAGAGACTTAAAAT-GATTAATTG
1 AAAAGTACAGAGACCTAAAATCGATTAATTG
3272655 AAAAGATACAGAG-CCTAAAATCGATTAA
1 AAAAG-TACAGAGACCTAAAATCGATTAA
3272683 GTATAGGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (31 bp):
AAAAGTACAGAGACCTAAAATCGATTAATTG
Found at i:3273383 original size:9 final size:8
Alignment explanation
Indices: 3273358--3273391 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3273348 AAAAATAAAA
3273358 AAAATTAT
1 AAAATTAT
3273366 AAAATTAT
1 AAAATTAT
3273374 AAAA-TAT
1 AAAATTAT
*
3273381 ATAATTAT
1 AAAATTAT
3273389 AAA
1 AAA
3273392 TTTTAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:3273386 original size:15 final size:16
Alignment explanation
Indices: 3273358--3273391 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3273348 AAAAATAAAA
3273358 AAAATTATAAAATTAT
1 AAAATTATAAAATTAT
*
3273374 AAAA-TATATAATTAT
1 AAAATTATAAAATTAT
3273389 AAA
1 AAA
3273392 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATAAAATTAT
Found at i:3273417 original size:19 final size:18
Alignment explanation
Indices: 3273395--3273462 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
3273385 TTATAAATTT
3273395 TAAAAGTCAAAATAATATA
1 TAAAAGTCAAAA-AATATA
* **
3273414 TAAAAATTGAAAAATATTA
1 TAAAAGTCAAAAAATA-TA
*
3273433 TAAAAGTTCAAAAAAATATT
1 TAAAAG-TC-AAAAAATATA
*
3273453 TAAAATTCAA
1 TAAAAGTCAA
3273463 GTAATTGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.16
19 18 0.47
20 7 0.18
21 7 0.18
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (18 bp):
TAAAAGTCAAAAAATATA
Found at i:3273429 original size:21 final size:21
Alignment explanation
Indices: 3273403--3273462 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
3273393 TTTAAAAGTC
*
3273403 AAAATAATATATAAAAATTGA
1 AAAATAATATATAAAAATTCA
*
3273424 AAAAT-AT-TATAAAAGTTCA
1 AAAATAATATATAAAAATTCA
*
3273443 AAAA-AATAT-TTAAAATTCA
1 AAAATAATATATAAAAATTCA
3273462 A
1 A
3273463 GTAATTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 25 0.76
20 3 0.09
21 5 0.15
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATAATATATAAAAATTCA
Found at i:3273585 original size:20 final size:21
Alignment explanation
Indices: 3273562--3273602 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3273552 TTTTAAATTG
3273562 TTTTACAAGTTTT-TAATAAT
1 TTTTACAAGTTTTGTAATAAT
**
3273582 TTTTACATTTTTTGTAATAAT
1 TTTTACAAGTTTTGTAATAAT
3273603 ATTATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTACAAGTTTTGTAATAAT
Found at i:3278124 original size:29 final size:29
Alignment explanation
Indices: 3278085--3278163 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
3278075 AAAATACTAA
3278085 CATAAGTGACTAAAACGTAACATTTCAAT
1 CATAAGTGACTAAAACGTAACATTTCAAT
3278114 CATAAGTGACTAAAACGTAACATTTCAAT
1 CATAAGTGACTAAAACGTAACATTTCAAT
*
3278143 CATAAGTGACTAAAATGTAAC
1 CATAAGTGACTAAAACGTAAC
3278164 CTGAGGCAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (29 bp):
CATAAGTGACTAAAACGTAACATTTCAAT
Found at i:3280236 original size:29 final size:31
Alignment explanation
Indices: 3280204--3280261 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3280194 GAATTAAATT
*
3280204 TTTAATA-AAAAA-ATTAATTTATTTTTTAA
1 TTTAATATAAAAATATTAATTTATCTTTTAA
3280233 TTTAATATAAAAATATTAATTTATCTTTT
1 TTTAATATAAAAATATTAATTTATCTTTT
3280262 CTTAAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 5 0.19
31 14 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATATAAAAATATTAATTTATCTTTTAA
Found at i:3282838 original size:6 final size:6
Alignment explanation
Indices: 3282827--3282851 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3282817 ATGAAATGTA
3282827 ATTTTG ATTTTG ATTTTG ATTTTG A
1 ATTTTG ATTTTG ATTTTG ATTTTG A
3282852 CATCTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (6 bp):
ATTTTG
Found at i:3284726 original size:28 final size:28
Alignment explanation
Indices: 3284673--3284725 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
3284663 ACTCATCACA
*
3284673 TTTCCTTCTCTCACAAAAAAGAAAAACC
1 TTTCCTTCTCCCACAAAAAAGAAAAACC
3284701 TTTCCTTC-CCCA-AAAGAAAGAAAAA
1 TTTCCTTCTCCCACAAA-AAAGAAAAA
3284726 AAAATGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 12 0.52
28 8 0.35
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (28 bp):
TTTCCTTCTCCCACAAAAAAGAAAAACC
Found at i:3286383 original size:14 final size:14
Alignment explanation
Indices: 3286364--3286390 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3286354 AGCAACAGGT
3286364 ATACATATATATAC
1 ATACATATATATAC
3286378 ATACATATATATA
1 ATACATATATATA
3286391 ATTCGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
ATACATATATATAC
Found at i:3290069 original size:125 final size:125
Alignment explanation
Indices: 3289847--3290239 Score: 573
Period size: 125 Copynumber: 3.2 Consensus size: 125
3289837 TTGCTCAAGG
*
3289847 TATCATCCATGGTTCAATCATG-TTTT-TCAAGCTAAGCTGCATTAGTTGAAATCAA-CCTGGAA
1 TATCATCCATGGTTGAATCATGTTTTTATC-AGCTAAGCTGCATTAGTTGAAATCAACCCT-GAA
*
3289909 AAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTCACTTATTCA
64 AAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATT-ACTTATTCA
* * **
3289972 TATCATCCATGGCTGAATCATGTTTTTATCA-CTAAGCTGCATTAGTTGAAATTAACCCTGAAGG
1 TATCATCCATGGTTGAATCATGTTTTTATCAGCTAAGCTGCATTAGTTGAAATCAACCCTGAAAA
* **
3290036 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTTTCTTATTTG
66 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCA-TTACTTATTCA
* * *
3290097 TATCATCCATGGTTGAATCTTGTTTTTA-AAGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAA
1 TATCATCCATGGTTGAATCATGTTTTTATCAGCTAAGCTGCATTAGTTGAAATCAACCCTGAAAA
*
3290161 ACTTTTCTTTTACATGTTTCTATTCTAGTG-CATATTGCTTGAGCACCATTATCTTATTCA
66 ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTA-CTTATTCA
*
3290221 TATCATCCATGGTCGAATC
1 TATCATCCATGGTTGAATC
3290240 TTATTTTCAA
Statistics
Matches: 241, Mismatches: 21, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
123 2 0.01
124 42 0.17
125 185 0.77
126 10 0.04
127 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (125 bp):
TATCATCCATGGTTGAATCATGTTTTTATCAGCTAAGCTGCATTAGTTGAAATCAACCCTGAAAA
ACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTACTTATTCA
Found at i:3290282 original size:98 final size:99
Alignment explanation
Indices: 3290148--3290338 Score: 312
Period size: 99 Copynumber: 1.9 Consensus size: 99
3290138 TTAGTTGAAA
** *
3290148 TCAACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTG-CATATTGCTTGAGCACCATTA
1 TCAACCCAAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGACATATTGCTTGACCACCATTA
*
3290212 TCTTATTCATATCATCCATGGTCGAATCTTATTT
66 TCTTATTCATATCATCCATGATCGAATCTTATTT
*
3290246 TCAACCCAAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTA
1 TCAACCCAAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGACATATTGCTTGACCACCATTA
* *
3290311 TCTTATTCGTGTCATCCATGATCGAATC
66 TCTTATTCATATCATCCATGATCGAATC
3290339 ATGTTTTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 41 0.48
99 44 0.52
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (99 bp):
TCAACCCAAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGACATATTGCTTGACCACCATTA
TCTTATTCATATCATCCATGATCGAATCTTATTT
Found at i:3290473 original size:350 final size:350
Alignment explanation
Indices: 3289907--3290970 Score: 1069
Period size: 350 Copynumber: 3.0 Consensus size: 350
3289897 ATCAACCTGG
*
3289907 AAAAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTCACTTATTCA
1 AAAAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTCACTTATTCA
* **
3289972 TATCATCCATGGCTGAATCATGTTTTTATCACTAAGCTGCATTAGTTGAAATTAACCCTGAAGGA
66 TATCATCCATGGCTGAATCATGTTTTTATCACTAAGCTGCATTAGCTGAAATTAACCCTGAAAAA
* **
3290037 CTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTTTCTTATTTGTATCA
131 CTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTTTCTTATTCCTATCA
* * *
3290102 TCCATGGTTGAATCTTGTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTTTT
196 TCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCCGAAAAAACTTTT
*
3290167 CTTTTACATGTTTCTATTCTAGTG-CATATTGCTTGAGCACCATTATC-TTATTCATATCATCCA
261 CTTTTACATGTTTCTATTCTAGTGACATATTGCTTGAACACCATTATCTTTATTCATATCATCCA
3290230 TGGTCGAATCTTATTTTCAACCCAA
326 TGGTCGAATCTTATTTTCAACCCAA
*
3290255 AAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATT-ATCTTATTC
1 AAAAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTCA-CTTATTC
* * * *
3290319 GTGTCATCCAT-GATCGAATCATGTTTTTTTAT-AGCTAAGCTGCATTGGCTGAAATCT-A-CCT
65 ATATCATCCATGGCT-GAATCATG--TTTTTATCA-CTAAGCTGCATTAGCTGAAAT-TAACCCT
* *
3290380 GGAAAAACTTTTCTTTTACATGTTTGTATTCTAGTGATATATTTCTTGAGAACCATTATT-TTAT
125 -GAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATT-TTCTTAT
* * *
3290444 TCCTATCATCCATGGTTGAGTCATGTTTTTAAAGCTAAGCTGCATTAATTGCAATCAACCTGAAA
188 TCCTATCATCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCCGAAA
* * *
3290509 AAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCATTTTCTTTATTCGT
253 AAACTTTTCTTTTACATGTTTCTATTCTAGTGACATATTGCTTGAACACCATTATCTTTATTCAT
** *
3290574 ATCATCCATAATTGAATCATGT-TTTTCTATAGCTAAGCTGCATTAGTTGAAATTGA
318 ATCATCCATGGTCGAATC-T-TATTTTC-A-A-C----C--C----------A---A
*
3290630 CCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCA-CATT-ATCT
1 -----AAAAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTCA-CT
* * * * * * * *
3290693 TATTCGTATCATCTATGG-TCAAATCATGTTTTTTATATAGC-AAGCTGCATTGGTTTAAATTGA
60 TATTCATATCATCCATGGCT-GAATCATG-TTTTTAT-CA-CTAAGCTGCATTAGCTGAAATTAA
* * * * ***
3290756 CCCAGAAATACTTTTCTCTTTTACATGTTTCTATTCTAGTGATAGATTGCTTGAGCACCATTCAA
121 CCCTGAAAAAC-TTT-TCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTTTC
* * * * * *
3290821 TTATTCATATCATCCATGGTAGGATCATGTTTTTAAAGCTAAGCTGCATTAGTTGAAATCGATCC
184 TTATTCCTATCATCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCC
** * * * * * * **
3290886 GGTAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATATATTGCTCGAGCACCGGTATC-TTA
249 GAAAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGACATATTGCTTGAACACCATTATCTTTA
* *
3290949 TTCATGTCATCCATGGTTGAAT
313 TTCATATCATCCATGGTCGAAT
3290971 AAGGTTTTTA
Statistics
Matches: 605, Mismatches: 63, Indels: 64
0.83 0.09 0.09
Matches are distributed among these distances:
347 3 0.00
348 77 0.13
349 4 0.01
350 171 0.28
351 23 0.04
352 22 0.04
353 6 0.01
354 2 0.00
355 1 0.00
356 1 0.00
360 1 0.00
362 1 0.00
372 1 0.00
375 1 0.00
378 9 0.01
379 55 0.09
380 80 0.13
381 145 0.24
382 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (350 bp):
AAAAACATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTCACTTATTCA
TATCATCCATGGCTGAATCATGTTTTTATCACTAAGCTGCATTAGCTGAAATTAACCCTGAAAAA
CTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGAACCATTTTCTTATTCCTATCA
TCCATGGTTGAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAATCAACCCGAAAAAACTTTT
CTTTTACATGTTTCTATTCTAGTGACATATTGCTTGAACACCATTATCTTTATTCATATCATCCA
TGGTCGAATCTTATTTTCAACCCAA
Found at i:3290537 original size:125 final size:125
Alignment explanation
Indices: 3290254--3290995 Score: 814
Period size: 125 Copynumber: 5.9 Consensus size: 125
3290244 TTTCAACCCA
*
3290254 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATTATCTTATTC
1 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
* * * * * * *
3290319 GTGTCATCCATGATCGAATCATGTTTTTTTATAGCTAAGCTGCATTGGCTGAAATCTACCTG
66 GTATCATCCATGGTTGAATCATG-TTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACC-G
* * * * *
3290381 GAAAAACTTTTCTTTTACATGTTTGTATTCTAGTGATATATTTCTTGAGAACCATTATTTTATTC
1 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
* * * *
3290446 CTATCATCCATGGTTGAGTCATG-TTTTTAAAGCTAAGCTGCATTAATTGCAATCAACCTG
66 GTATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACC-G
* *
3290506 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCATTTTCTTTATT
1 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATC-TTATT
** * * *
3290571 CGTATCATCCATAATTGAATCATGTTTTTCTATAGCTAAGCTGCATTAGTTGAAATTGACCCG
65 CGTATCATCCATGGTTGAATCATGTTTTT-TAAAGCTAAGCTGCATTAGTTGAAA-TCAACCG
* *
3290634 GAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCA-CATTATCTTATTC
1 AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
* ** * * ** *
3290698 GTATCATCTATGGTCAAATCATGTTTTTTATATAGC-AAGCTGCATTGGTTTAAATTGACCC
66 GTATCATCCATGGTTGAATCATGTTTTTTA-A-AGCTAAGCTGCATTAGTTGAAATCAACCG
* * *
3290759 AGAAATACTTTTCTCTTTTACATGTTTCTATTCTAGTGATAGATTGCTTGAGCACCATTCA-ATT
1 A-AAAAAC-TTT-TCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATT-ATCTT
* * * *
3290823 ATTCATATCATCCATGGTAGGATCATG-TTTTTAAAGCTAAGCTGCATTAGTTGAAATCGATCCG
62 ATTCGTATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATC-AACCG
** * * * * **
3290887 GTAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATATATTGCTCGAGCACCGGTATCTTATT
1 AAAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGATATATTGCTTGAGCACCATTATCTTATT
* * * * * *
3290951 CATGTCATCCATGGTTGAAT-AAGGTTTTTATAGCTAGGCTGCATT
65 CGTATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATT
3290996 TACTAGGATG
Statistics
Matches: 518, Mismatches: 81, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
124 3 0.01
125 167 0.32
126 82 0.16
127 114 0.22
128 119 0.23
129 32 0.06
130 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (125 bp):
AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTATCTTATTC
GTATCATCCATGGTTGAATCATGTTTTTTAAAGCTAAGCTGCATTAGTTGAAATCAACCG
Found at i:3290863 original size:253 final size:251
Alignment explanation
Indices: 3290246--3290995 Score: 836
Period size: 253 Copynumber: 3.0 Consensus size: 251
3290236 AATCTTATTT
*
3290246 TCAACCCA-AAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCACCATT
1 TCAA-CCAGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCATT
* * * * *
3290310 -ATCTTATTCGTGTCATCCATGATCGAATCATGTTTTTTTATAGCTAAGCTGCATTGGCTGAAAT
65 CA-ATTATTCGTATCATCCATGATAGAATCATG-TTTTTTATAGCTAAGCTGCATTAGTTGAAAT
* * * *
3290374 CT-ACCTGGAAAAACTTTTCTTTTACATGTTTGTATTCTAGTGATATATTTCTTGAGAACCATTA
128 -TGACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACAACCATTA
* ** * *
3290438 TTTTATTCCTATCATCCATGGTTGAGTCATGTTTTTAAAGCTAAGCTGCATTAATTGCAA
192 TCTTATTCCTATCATCCATGGTCAAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAA
*
3290498 TCAACCTGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCATTT
1 TCAACCAGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCA--T
* * *
3290563 TC-TTTATTCGTATCATCCATAATTGAATCATGTTTTTCTATAGCTAAGCTGCATTAGTTGAAAT
64 TCAATTATTCGTATCATCCATGATAGAATCATGTTTTT-TATAGCTAAGCTGCATTAGTTGAAAT
*
3290627 TGACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACCA-CATTAT
128 TGACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACAACCATTAT
* * ** *
3290691 CTTATTCGTATCATCTATGGTCAAATCATGTTTTTTATATAGC-AAGCTGCATTGGTTTAAA
193 CTTATTCCTATCATCCATGGTCAAATCATG-TTTTTA-A-AGCTAAGCTGCATTAATTGAAA
* * * * *
3290752 TTGACCCAG-AAATACTTTTCTCTTTTACATGTTTCTATTCTAGTGATAGATTGCTTGAGCACCA
1 -TCAACCAGAAAAAAC-TTT-TCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCA
* * * *
3290816 TTCAATTATTCATATCATCCATGGTAGGATCATG-TTTTTAAAGCTAAGCTGCATTAGTTGAAAT
63 TTCAATTATTCGTATCATCCATGATAGAATCATGTTTTTTATAGCTAAGCTGCATTAGTTGAAAT
* * * * * * * **
3290880 CGATCCGGTAAAGCTTATCTTTTACATGTTCCTATTCCT-GTGATATATTGCTCGAGC-ACCGGT
128 TGACCCGGAAAAACTTTTCTTTTACATGTTTCTATT-CTAGTGATATATTGCTTGA-CAACCATT
* * ** * * * *
3290943 ATCTTATTCATGTCATCCATGGTTGAATAAGGTTTTTATAGCTAGGCTGCATT
191 ATCTTATTCCTATCATCCATGGTCAAATCATGTTTTTAAAGCTAAGCTGCATT
3290996 TACTAGGATG
Statistics
Matches: 427, Mismatches: 54, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
251 5 0.01
252 102 0.24
253 184 0.43
254 59 0.14
255 35 0.08
256 42 0.10
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (251 bp):
TCAACCAGAAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAACACCATTC
AATTATTCGTATCATCCATGATAGAATCATGTTTTTTATAGCTAAGCTGCATTAGTTGAAATTGA
CCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGACAACCATTATCTT
ATTCCTATCATCCATGGTCAAATCATGTTTTTAAAGCTAAGCTGCATTAATTGAAA
Found at i:3295980 original size:19 final size:19
Alignment explanation
Indices: 3295938--3295986 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
3295928 CCTTATTTTT
3295938 ATTTTTTCTTTTCTGCAAA
1 ATTTTTTCTTTTCTGCAAA
* * * *
3295957 CTTTTTTTTTTTTTGTAAA
1 ATTTTTTCTTTTCTGCAAA
*
3295976 ATTTTTACTTT
1 ATTTTTTCTTT
3295987 AATGGGGTAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTCTTTTCTGCAAA
Found at i:3299643 original size:25 final size:26
Alignment explanation
Indices: 3299593--3299644 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
3299583 TTTCAATAAA
*
3299593 TAAAAATATATAAAATTATTAAATAT
1 TAAAAATATATAAAATTATAAAATAT
*
3299619 TAAAAA-ATATACAA-TATAAATATAT
1 TAAAAATATATAAAATTATAAA-ATAT
3299644 T
1 T
3299645 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 12 0.52
26 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAAATATATAAAATTATAAAATAT
Found at i:3309832 original size:14 final size:14
Alignment explanation
Indices: 3309796--3309825 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3309786 AAAGTGAAGA
*
3309796 AAATATATAATAAT
1 AAATATTTAATAAT
3309810 AAATATTTAATAAT
1 AAATATTTAATAAT
3309824 AA
1 AA
3309826 GATTTTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATTTAATAAT
Found at i:3310491 original size:364 final size:362
Alignment explanation
Indices: 3309661--3310388 Score: 901
Period size: 374 Copynumber: 2.0 Consensus size: 362
3309651 GATGAAACTT
* *** * * ** *
3309661 AAATAGATCATAAAATATTGAGAAAATTTATACATAATTTACACAACCAGTTACTCAAATTTGAA
1 AAATAGATCATAAAATATTCAGAAAATCCGTACATAATTGACGCAACCAACTACTC-AGTTT-AA
* *
3309726 ATATCTAAT--TTTACGATTATCTTTAAAAACAAATTATTTAAGGATAAGTGATTTAGCATAAAA
64 ATAGCTAATCATGTA--ATTATCTTTAAAAACAAATTATTTAAGGATAAGTGATTTAGCATAAAA
*
3309789 GTGAAGAAAATATATAATAATAAATATTTAATAATAAGATTTTAGGAGTTTGGTCATTTGAAGAA
127 GTGAAGAAAATATATAATAATAAAAATTTAATAATAAGATTTTAGGAGTTTGGTC--------AA
*
3309854 ACATTAATTTTTTTTACAAATTTTATAATTATAATTAATTAGCATCACTATCACAAGATTTGGAA
184 ACATTAATTTTTTTAACAAATTTTATAATTATAATTAATTAGCATCACTATCACAAGATTTGGAA
*
3309919 AAATCAAATTTTATTAATATAATATATTAAAGAAAACAACAATAATGGTTTTTTCGAAAATGATC
249 AAATCAAATTTTATTAATATAATATATTAAAGAAAACAACAATAATGGTTTTTTCAAAAATGATC
* * * ** * **
3309984 CAAAAGAATTATTAATTACGAAAATCTTCGAGTTCACTCTCGATGGAACTT
314 CAAAAGAATTATTAATTACAAAAATATTAGAGTAAAATCT--ATGGAACGA
* ** * * *
3310035 AAATAGATCATAAAATATTGAGAAAATTTGTACATAATTTACGCAATCAATTACTCAAGTTTGAA
1 AAATAGATCATAAAATATTCAGAAAATCCGTACATAATTGACGCAACCAACTACTC-AGTTT-AA
* ** * * *
3310100 ATATCTAATTTTGTGATTATCTTTAAAAACAAGTTATTTAAGGATAAGTGGTTTAGCATAAAAGT
64 ATAGCTAATCATGTAATTATCTTTAAAAACAAATTATTTAAGGATAAGTGATTTAGCATAAAAGT
*
3310165 GAAGAAAATATATAATAGTAAAAATTTAATAATAAGATTTTAGGAGTTTGGTC-AACATTAA-TT
129 GAAGAAAATATATAATAATAAAAATTTAATAATAAGATTTTAGGAGTTTGGTCAAACATTAATTT
3310228 TTTTAACAAATTTTATAATTATAATTAATTAGCATCACTATCACAAGATTTGGAAAAATCAAATT
194 TTTTAACAAATTTTATAATTATAATTAATTAGCATCACTATCACAAGATTTGGAAAAATCAAATT
3310293 TTATTAATATAATATA-TAATAGAAAACAACAATAATGGTTTTTTCAAAAATGATCCCAAAA-AA
259 TTATTAATATAATATATTAA-AGAAAACAACAATAATGGTTTTTTCAAAAATGAT-CCAAAAGAA
*
3310356 TTATTCATTACAAAAATGATCTAGATGTAAAAT
322 TTATTAATTACAAAAAT-AT-TAGA-GTAAAAT
3310389 TTTGTACGAA
Statistics
Matches: 327, Mismatches: 20, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
363 3 0.01
364 132 0.40
365 15 0.05
366 3 0.01
367 4 0.01
374 168 0.51
376 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (362 bp):
AAATAGATCATAAAATATTCAGAAAATCCGTACATAATTGACGCAACCAACTACTCAGTTTAAAT
AGCTAATCATGTAATTATCTTTAAAAACAAATTATTTAAGGATAAGTGATTTAGCATAAAAGTGA
AGAAAATATATAATAATAAAAATTTAATAATAAGATTTTAGGAGTTTGGTCAAACATTAATTTTT
TTAACAAATTTTATAATTATAATTAATTAGCATCACTATCACAAGATTTGGAAAAATCAAATTTT
ATTAATATAATATATTAAAGAAAACAACAATAATGGTTTTTTCAAAAATGATCCAAAAGAATTAT
TAATTACAAAAATATTAGAGTAAAATCTATGGAACGA
Found at i:3313604 original size:17 final size:18
Alignment explanation
Indices: 3313569--3313618 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
3313559 TTTTCTTAGT
*
3313569 ATTTTTTAGAAAATTTTAA
1 ATTTTTTAGAAAATATT-A
3313588 ATTTTTTA-AAAA-ATTA
1 ATTTTTTAGAAAATATTA
* *
3313604 ATTTTATATAAAATA
1 ATTTTTTAGAAAATA
3313619 AGTGTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 5 0.19
19 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTTTTAGAAAATATTA
Found at i:3320218 original size:3 final size:3
Alignment explanation
Indices: 3320210--3320242 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3320200 CCATATATGG
*
3320210 TGA TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3320243 CTGGTGTAGA
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:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3325005 original size:29 final size:31
Alignment explanation
Indices: 3324959--3325017 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
3324949 GTAATGTTAT
*
3324959 ATATGAAATTTGATTTTG-TTC-AATTTTAA
1 ATATAAAATTTGATTTTGATTCAAATTTTAA
3324988 ATATAAAATTTTGA-TTTGATTCAAATTTTA
1 ATATAAAA-TTTGATTTTGATTCAAATTTTA
3325018 CAAATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 11 0.42
30 8 0.31
31 7 0.27
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (31 bp):
ATATAAAATTTGATTTTGATTCAAATTTTAA
Found at i:3325555 original size:17 final size:17
Alignment explanation
Indices: 3325523--3325556 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3325513 ACTTAATGTT
**
3325523 TTAAAATTTTTCATTTA
1 TTAAAATTTTAAATTTA
3325540 TTAAAATTTTAAATTTA
1 TTAAAATTTTAAATTTA
3325557 GAGAACTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAATTTTAAATTTA
Found at i:3328293 original size:6 final size:6
Alignment explanation
Indices: 3328282--3328312 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3328272 TTGGTTGCCT
3328282 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
3328313 TATTCTCGAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:3332304 original size:22 final size:22
Alignment explanation
Indices: 3332269--3332321 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3332259 CTAAATAATA
* *
3332269 ACAACAATATAATAACGAAATG
1 ACAACAAAACAATAACGAAATG
* * *
3332291 ACCACAAAACAATAATGAGATG
1 ACAACAAAACAATAACGAAATG
3332313 ACAACAAAA
1 ACAACAAAA
3332322 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.13
Consensus pattern (22 bp):
ACAACAAAACAATAACGAAATG
Found at i:3338226 original size:57 final size:57
Alignment explanation
Indices: 3338146--3338489 Score: 208
Period size: 58 Copynumber: 5.9 Consensus size: 57
3338136 GACACCCTAT
*** *
3338146 TTTTCGAAAAAAAA-TTACATTTTTGGGTGTT-ACCATTGCATGGTCGATA-CCCCC
1 TTTTCGAAAAAAAATTTACATTTTTGGGTGTTGACCATCAAATGGTCGACACCCCCC
* *
3338200 TGTTTCAGAAAAAAAATTTA-ATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCC
1 T-TTTC-GAAAAAAAATTTACA-TTTTTGGGTGTTGACCATCAAATGGTCGACACCCCCC
* *** * *
3338259 TTTTCTCGAAAAAAAATTTCAAAATTTTTTCATGTTGGCCATCAAATGG-CTGACACCCCCT
1 -TTT-TCGAAAAAAAATTT--ACATTTTTGGGTGTTGACCATCAAATGGTC-GACACCCCCC
* * * *
3338320 TTTCTCG-GAAAAAA-TTACATTTTTGGGTGTTGGCCGTCAAATGGCCGACA-CCCCC
1 TTT-TCGAAAAAAAATTTACATTTTTGGGTGTTGACCATCAAATGGTCGACACCCCCC
* * * * * * *
3338375 TATTCTCAAAAAAAAATTCA-ACTTTTTTGGTGTTGGCTATCAAATGGCCGACA-CCCTC
1 T-TT-TCGAAAAAAAATTTACA-TTTTTGGGTGTTGACCATCAAATGGTCGACACCCCCC
* **
3338433 TATTCTC-AAGAAAAAATTTTAAATTTTTTTCGTGTT-AGCCATCAAATGGTCGACACC
1 T-TT-TCGAA-AAAAAA-TTTACA-TTTTTGGGTGTTGA-CCATCAAATGGTCGACACC
3338490 AACTTCTCCT
Statistics
Matches: 239, Mismatches: 29, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
54 1 0.00
55 9 0.04
56 42 0.18
57 24 0.10
58 62 0.26
59 28 0.12
60 38 0.16
61 34 0.14
62 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (57 bp):
TTTTCGAAAAAAAATTTACATTTTTGGGTGTTGACCATCAAATGGTCGACACCCCCC
Found at i:3338320 original size:60 final size:58
Alignment explanation
Indices: 3338194--3338489 Score: 298
Period size: 58 Copynumber: 5.1 Consensus size: 58
3338184 CATGGTCGAT
* *
3338194 ACCCCCTGTTTC-AGAAAAAAAATTTAATTTTTTTGGTGTTGGCCATCAAATGG-TCGAC
1 ACCCCCT-TTTCTCGAAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCT-GAC
**
3338252 ACCCCCCTTTTCTCGAAAAAAAATTTCAAAATTTTTTCATGTTGGCCATCAAATGGCTGAC
1 A-CCCCCTTTTCTCGAAAAAAAATTT--AAATTTTTTGGTGTTGGCCATCAAATGGCTGAC
* * * * *
3338313 ACCCCCTTTTCTCG-GAAAAAA-TTACATTTTTGGGTGTTGGCCGTCAAATGGCCGAC
1 ACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGAC
* * * * * *
3338369 ACCCCCTATTCTCAAAAAAAAATTCAACTTTTTTGGTGTTGGCTATCAAATGGCCGAC
1 ACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGAC
* * * *
3338427 ACCCTCTATTCTC-AAGAAAAAATTTTAAATTTTTTTCGTGTTAGCCATCAAATGG-TCGAC
1 ACCCCCTTTTCTCGAA-AAAAAA-TTTAAA-TTTTTTGGTGTTGGCCATCAAATGGCT-GAC
3338487 ACC
1 ACC
3338490 AACTTCTCCT
Statistics
Matches: 200, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
56 39 0.19
57 8 0.04
58 54 0.27
59 28 0.14
60 41 0.20
61 29 0.14
62 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (58 bp):
ACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTGGTGTTGGCCATCAAATGGCTGAC
Found at i:3338463 original size:174 final size:174
Alignment explanation
Indices: 3338154--3338489 Score: 446
Period size: 174 Copynumber: 1.9 Consensus size: 174
3338144 ATTTTTCGAA
*** * * * *
3338154 AAAAAATTACATTTTTGGGTGTTACCATTGCATGGTCGATACCCCCTGTTTCAGAAAAAAAATTT
1 AAAAAATTACATTTTTGGGTGTTACCATCAAATGGCCGACACCCCCTATTTCAGAAAAAAAATTC
* * *
3338219 AATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCCTTTTCTCGAAAAAAAATTTCAAAAT
66 AACTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTATTCTCGAAAAAAAATTTCAAAAT
*
3338284 TTTTTCATGTTGGCCATCAAATGG-CTGACACCCCCTTTTCTCGG
131 TTTTTCATGTTAGCCATCAAATGGTC-GACACCCCCTTTTCTCGG
* *
3338328 AAAAAATTACATTTTTGGGTGTTGGCCGTCAAATGGCCGACACCCCCTATTCTCA-AAAAAAAAT
1 AAAAAATTACATTTTTGGGTGTT-ACCATCAAATGGCCGACACCCCCTATT-TCAGAAAAAAAAT
* * *
3338392 TCAACTTTTTTGGTGTTGGCTATCAAATGGCCGACA-CCCTCTATTCTC-AAGAAAAAATTTTAA
64 TCAACTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTATTCTCGAA-AAAAAATTTCAA
* *
3338455 ATTTTTTTCGTGTTAGCCATCAAATGGTCGACACC
128 AATTTTTTCATGTTAGCCATCAAATGGTCGACACC
3338490 AACTTCTCCT
Statistics
Matches: 140, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
173 2 0.01
174 74 0.53
175 61 0.44
176 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (174 bp):
AAAAAATTACATTTTTGGGTGTTACCATCAAATGGCCGACACCCCCTATTTCAGAAAAAAAATTC
AACTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCCTATTCTCGAAAAAAAATTTCAAAAT
TTTTTCATGTTAGCCATCAAATGGTCGACACCCCCTTTTCTCGG
Found at i:3338497 original size:58 final size:57
Alignment explanation
Indices: 3338208--3338489 Score: 300
Period size: 60 Copynumber: 4.8 Consensus size: 57
3338198 CCTGTTTCAG
*
3338208 AAAAAAAATTT-AATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCCTTTTCTC
1 AAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCC-TTTCTC
* ** *
3338266 GAAAAAAAATTTCAAAATTTTTTCATGTTGGCCATCAAATGGCTGACACCCCCTTTTCTC
1 -AAAAAAAATTT-AAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC-TTTCTC
** * * *
3338326 GGAAAAAA-TTACA-TTTTTGGGTGTTGGCCGTCAAATGGCCGACACCCCCTATTCTC
1 AAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTCTC
* * * * *
3338382 AAAAAAAAATTCAACTTTTTTGGTGTTGGCTATCAAATGGCCGACACCCTCTATTCTC
1 AAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-TTCTC
* * *
3338440 AAGAAAAAATTTTAAATTTTTTTCGTGTTAGCCATCAAATGGTCGACACC
1 AA-AAAAAA-TTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
3338490 AACTTCTCCT
Statistics
Matches: 188, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
55 1 0.01
56 42 0.22
57 5 0.03
58 43 0.23
59 23 0.12
60 45 0.24
61 29 0.15
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (57 bp):
AAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTCTC
Found at i:3339224 original size:19 final size:20
Alignment explanation
Indices: 3339187--3339226 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3339177 GTTAAGGAAT
3339187 AAATATTATCTACAAATTAA
1 AAATATTATCTACAAATTAA
3339207 AAATATTAAT-TA-AAATTAA
1 AAATATT-ATCTACAAATTAA
3339226 A
1 A
3339227 TTTACGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTATCTACAAATTAA
Found at i:3341054 original size:23 final size:23
Alignment explanation
Indices: 3341006--3341054 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3340996 TGATCTAAGG
* *
3341006 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
3341029 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
3341053 AA
1 AA
3341055 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:3341891 original size:19 final size:19
Alignment explanation
Indices: 3341867--3341909 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3341857 AAATATAAAT
3341867 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
3341886 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
3341905 TAAAT
1 TAAAT
3341910 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:3341948 original size:8 final size:9
Alignment explanation
Indices: 3341930--3341957 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3341920 AATATTTTTT
3341930 AAAAATAAA
1 AAAAATAAA
3341939 AAAAATAAA
1 AAAAATAAA
3341948 AAAAATAAA
1 AAAAATAAA
3341957 A
1 A
3341958 CCAAGTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:3342822 original size:105 final size:105
Alignment explanation
Indices: 3342487--3342782 Score: 506
Period size: 105 Copynumber: 2.8 Consensus size: 105
3342477 ATTTTGTGGA
* * * *
3342487 TTTT-TTC-CTTTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCA
1 TTTTCTTCTCTTTTTTTT-TTT-AGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACACCCA
3342550 AGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
64 AGCACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
3342592 TTTTCTTCTCTTTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACACCCAAG
1 TTTTCTTCTCTTTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACACCCAAG
3342657 CACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
66 CACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
*
3342697 TTTTCTTCTCTTTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCAAG
1 TTTTCTTCTCTTTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACACCCAAG
*
3342762 CACTCCACCCCGGTTACTCAG
66 CACTCCATCCCGGTTACTCAG
3342783 TCTAACACAT
Statistics
Matches: 183, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
105 168 0.92
106 6 0.03
107 9 0.05
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (105 bp):
TTTTCTTCTCTTTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACACCCAAG
CACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
Found at i:3343481 original size:4 final size:4
Alignment explanation
Indices: 3343472--3343526 Score: 62
Period size: 4 Copynumber: 13.8 Consensus size: 4
3343462 TCTTGGACAA
3343472 AAAT AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAA- AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
3343520 AAAT AAA
1 AAAT AAA
3343527 AATAATTGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 8 0.18
4 28 0.62
5 8 0.18
6 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:3343521 original size:13 final size:13
Alignment explanation
Indices: 3343470--3343531 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
3343460 TTTCTTGGAC
3343470 AAAAATAAATAAAT
1 AAAAATAAA-AAAT
*
3343484 AAATAA-ATAAAAT
1 AAA-AATAAAAAAT
*
3343497 -AAGATAGAAAAAT
1 AAAAATA-AAAAAT
3343510 AAAAAATAAAAAAT
1 -AAAAATAAAAAAT
3343524 AAAAATAA
1 AAAAATAA
3343532 TTGGGTTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 1 0.03
12 3 0.08
13 17 0.44
14 11 0.28
15 7 0.18
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:3343531 original size:6 final size:7
Alignment explanation
Indices: 3343470--3343528 Score: 64
Period size: 7 Copynumber: 7.6 Consensus size: 7
3343460 TTTCTTGGAC
3343470 AAAAATA
1 AAAAATA
3343477 AATAAATA
1 AA-AAATA
3343485 AATAAATAA
1 AA-AAAT-A
3343494 AATAAGATA
1 AA-AA-ATA
3343503 GAAAAATA
1 -AAAAATA
3343511 AAAAATA
1 AAAAATA
3343518 AAAAATA
1 AAAAATA
3343525 AAAA
1 AAAA
3343529 TAATTGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
7 20 0.42
8 15 0.31
9 9 0.19
10 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:3347698 original size:30 final size:30
Alignment explanation
Indices: 3347664--3347755 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
3347654 TCCCTTTACT
*
3347664 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
3347694 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
3347724 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
3347754 TT
1 TT
3347756 CTAATTATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.04
30 51 0.94
31 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:3348691 original size:60 final size:60
Alignment explanation
Indices: 3348577--3348798 Score: 275
Period size: 60 Copynumber: 3.7 Consensus size: 60
3348567 AGGAGAAGTT
* *
3348577 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTATTCGAGAAAATGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-AAATTTTTTT-CTCGAGAAAACGG
** * * *
3348639 GGTGTCGTTCATTTGATGGCCAACACGAAAAAAATTTGAATTTTTTTCTCGAGAATACGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAACGG
* * * ** *
3348699 AGTGTCGGTCATTTGATGGCCAACACC-CAAAAATGCAAATTTTTTTCTCGAGAAAAGGAG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAACG-G
* *
3348759 GGTGTCGGCCATTTGATGGCCTACACCAAAAAATTTTAAA
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAA
3348799 AAAAAATTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
59 25 0.19
60 59 0.44
61 17 0.13
62 34 0.25
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (60 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAACGG
Found at i:3353102 original size:14 final size:14
Alignment explanation
Indices: 3353082--3353120 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3353072 GAATGAAATT
3353082 AAAATTTT-GACAAA
1 AAAATTTTAGA-AAA
*
3353096 CAAATTTTAGAAAA
1 AAAATTTTAGAAAA
3353110 AAAATTTTAGA
1 AAAATTTTAGA
3353121 TTTGATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (14 bp):
AAAATTTTAGAAAA
Found at i:3354312 original size:29 final size:30
Alignment explanation
Indices: 3354249--3354312 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
3354239 TCAAAACTAT
* * *
3354249 ACATGAACTATGATTTAATGTGTAATTTTAT
1 ACATGAACTATGATTT-ATGTGAAACTTTAA
*
3354280 ACATGAACTTTGATTT-TGTGAAACTTTAA
1 ACATGAACTATGATTTATGTGAAACTTTAA
3354309 ACAT
1 ACAT
3354313 AAAATTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.48
31 15 0.52
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (30 bp):
ACATGAACTATGATTTATGTGAAACTTTAA
Found at i:3354504 original size:31 final size:30
Alignment explanation
Indices: 3354468--3354540 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
3354458 GATTAAATCA
3354468 AAATTAAAATTTCAAGTATACAATTA-AGCC
1 AAATTAAAATTTCAAGTATACAATTACA-CC
* * *
3354498 ACAATTAGAATTTCACGTGTACAATTACACC
1 A-AATTAAAATTTCAAGTATACAATTACACC
3354529 AAATTAAAATTT
1 AAATTAAAATTT
3354541 ATATACATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.30
31 25 0.68
32 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTATACAATTACACC
Found at i:3357023 original size:22 final size:22
Alignment explanation
Indices: 3356981--3357023 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3356971 ATATTAACAA
*
3356981 ATATATTTTTAATTAATATTTT
1 ATATATTTTCAATTAATATTTT
3357003 ATATATTTTACAATTAA-ATTT
1 ATATATTTT-CAATTAATATTT
3357024 AAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATTTTCAATTAATATTTT
Found at i:3358509 original size:10 final size:10
Alignment explanation
Indices: 3358494--3358532 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3358484 AAAATATAAG
3358494 TTATTTTAAA
1 TTATTTTAAA
3358504 TTATTTTAAAA
1 TTATTTT-AAA
*
3358515 TTAATTTAAAA
1 TT-ATTTTAAA
3358526 TTATTTT
1 TTATTTT
3358533 TTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 11 0.44
11 10 0.40
12 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:3358517 original size:11 final size:11
Alignment explanation
Indices: 3358494--3358532 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3358484 AAAATATAAG
3358494 TTATTTT-AAA
1 TTATTTTAAAA
3358504 TTATTTTAAAA
1 TTATTTTAAAA
*
3358515 TTAATTTAAAA
1 TTATTTTAAAA
3358526 TTATTTT
1 TTATTTT
3358533 TTAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:3358600 original size:6 final size:6
Alignment explanation
Indices: 3358589--3358618 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3358579 AGTTTTTTTT
3358589 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
3358619 TTATTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:3360473 original size:31 final size:31
Alignment explanation
Indices: 3360435--3360501 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3360425 ATGAAGTCAG
3360435 AATTTTTGTTAGGGAATCGAAATTAAATTGT
1 AATTTTTGTTAGGGAATCGAAATTAAATTGT
** * *
3360466 AATTTTTGTTAGGGGGTTGAAATTAAATTTT
1 AATTTTTGTTAGGGAATCGAAATTAAATTGT
3360497 AATTT
1 AATTT
3360502 CACCATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (31 bp):
AATTTTTGTTAGGGAATCGAAATTAAATTGT
Found at i:3362526 original size:24 final size:25
Alignment explanation
Indices: 3362482--3362528 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
3362472 GTTGGATCCA
3362482 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATTCTAAAAAGATAATTAG
3362507 AATTAAA-TCTAAACAA-ATAATT
1 AATTAAATTCTAAA-AAGATAATT
3362529 TCCTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTAG
Found at i:3362620 original size:13 final size:13
Alignment explanation
Indices: 3362599--3362632 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3362589 ACAATATAAC
3362599 AATAATAATCCTA
1 AATAATAATCCTA
*
3362612 AATATTAATCCTA
1 AATAATAATCCTA
*
3362625 AAAAATAA
1 AATAATAA
3362633 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:3370232 original size:13 final size:14
Alignment explanation
Indices: 3370209--3370237 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3370199 ACTGATATAC
3370209 AATGCTTATACTAT
1 AATGCTTATACTAT
3370223 AATG-TTATACTAT
1 AATGCTTATACTAT
3370236 AA
1 AA
3370238 GTTGATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (14 bp):
AATGCTTATACTAT
Found at i:3374948 original size:21 final size:22
Alignment explanation
Indices: 3374891--3374974 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
3374881 TTTAGTTTTA
* *
3374891 AATTTTTAAATTTATTTTGACA-
1 AATTTTAAAATTTATTTT-ATAG
*
3374913 AA--TTAAATTTTATTTTAT-G
1 AATTTTAAAATTTATTTTATAG
* *
3374932 AATTTCTAATA-TTATTTGATAG
1 AATTT-TAAAATTTATTTTATAG
3374954 AATTTTAAAATTTATTTTATA
1 AATTTTAAAATTTATTTTATA
3374975 AATATTTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
19 3 0.06
20 12 0.25
21 13 0.27
22 20 0.42
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTTAAAATTTATTTTATAG
Found at i:3374958 original size:22 final size:23
Alignment explanation
Indices: 3374916--3374987 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 23
3374906 TTTGACAAAT
*
3374916 TAAATTTTATTTTAT-GAATTTC
1 TAAAATTTATTTTATAGAATTTC
* *
3374938 TAATA-TTATTTGATAGAATTT-
1 TAAAATTTATTTTATAGAATTTC
*
3374959 TAAAATTTATTTTATAAATATTTC
1 TAAAATTTATTTTATAGA-ATTTC
3374983 TAAAA
1 TAAAA
3374988 AATTAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 12 0.30
22 19 0.47
23 4 0.10
24 5 0.12
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (23 bp):
TAAAATTTATTTTATAGAATTTC
Found at i:3375996 original size:27 final size:28
Alignment explanation
Indices: 3375929--3375996 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
3375919 TTCACCTACA
*
3375929 TAATTTAATTTATATAAATTTTATATAT
1 TAATTTAATTTATATAAATTATATATAT
*
3375957 TAATTTACA-TTATATAAA-TATCTATAT
1 TAATTTA-ATTTATATAAATTATATATAT
* *
3375984 TATTTTATTTTAT
1 TAATTTAATTTAT
3375997 TTTAGGCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 17 0.50
28 16 0.47
29 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TAATTTAATTTATATAAATTATATATAT
Found at i:3379665 original size:15 final size:15
Alignment explanation
Indices: 3379619--3379670 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3379609 AGAAAACGAT
*
3379619 AATATAAATGACTAA
1 AATATAAATGATTAA
* *
3379634 AATGTAACAT--TTTA
1 AATATAA-ATGATTAA
3379648 AATATAAATGATTAA
1 AATATAAATGATTAA
3379663 AATATAAA
1 AATATAAA
3379671 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.28
15 17 0.59
16 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (15 bp):
AATATAAATGATTAA
Found at i:3381584 original size:16 final size:16
Alignment explanation
Indices: 3381554--3381591 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3381544 TTGGAATTGA
3381554 ATTTTTT-ATAAAAAT
1 ATTTTTTGATAAAAAT
*
3381569 ATTTTTTGATAGAAAT
1 ATTTTTTGATAAAAAT
3381585 -TTTTTTG
1 ATTTTTTG
3381592 GATTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
ATTTTTTGATAAAAAT
Found at i:3383247 original size:32 final size:32
Alignment explanation
Indices: 3383204--3383266 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3383194 TTGTATTGTT
3383204 ATTTTTCAACATTAATGAATTTCTCCCCTTTC
1 ATTTTTCAACATTAATGAATTTCTCCCCTTTC
* *
3383236 ATTTTTTAACATTAATGAATTTCTCCTCTTT
1 ATTTTTCAACATTAATGAATTTCTCCCCTTT
3383267 TGCCCATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTTTTCAACATTAATGAATTTCTCCCCTTTC
Found at i:3391497 original size:16 final size:16
Alignment explanation
Indices: 3391460--3391497 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3391450 TGTAATAAAC
3391460 TATTAA-AATATTTTA
1 TATTAATAATATTTTA
3391475 TATTAATAAT-TTTTA
1 TATTAATAATATTTTA
3391490 TAATTAAT
1 T-ATTAAT
3391498 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATAATATTTTA
Found at i:3392431 original size:24 final size:24
Alignment explanation
Indices: 3392380--3392460 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
3392370 AAATATTCTT
* * *
3392380 AAAATAATTAAAATTTAATTGAGAA
1 AAAATAA-TAGAATTTAACTGAAAA
3392405 AAAATAATAGAATTTAACT-AAATA
1 AAAATAATAGAATTTAACTGAAA-A
*
3392429 AAAATAACAGAATTTAACTGAAAA
1 AAAATAATAGAATTTAACTGAAAA
3392453 AAAA-AATA
1 AAAATAATA
3392461 TGAAACCCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 5 0.10
24 34 0.69
25 10 0.20
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (24 bp):
AAAATAATAGAATTTAACTGAAAA
Found at i:3393392 original size:18 final size:18
Alignment explanation
Indices: 3393371--3393405 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3393361 CTTTAATAAA
3393371 ATTTACAAATATAATTAT
1 ATTTACAAATATAATTAT
**
3393389 ATTTATTAATATAATTA
1 ATTTACAAATATAATTA
3393406 CAAATTAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTACAAATATAATTAT
Found at i:3394911 original size:2 final size:2
Alignment explanation
Indices: 3394900--3394930 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3394890 TATGTTTCAC
3394900 AT AT AT -T 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
3394931 GTATGCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3395667 original size:3 final size:3
Alignment explanation
Indices: 3395659--3395683 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3395649 TATATATTAA
3395659 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
3395684 TTTGGGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3404112 original size:17 final size:17
Alignment explanation
Indices: 3404090--3404128 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3404080 AGGTCGTTCT
3404090 ATATTTTT-TCACTTACC
1 ATATTTTTATCACTTA-C
*
3404107 ATATTTTTATCATTTAC
1 ATATTTTTATCACTTAC
3404124 ATATT
1 ATATT
3404129 GATCATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTTATCACTTAC
Found at i:3404317 original size:14 final size:14
Alignment explanation
Indices: 3404298--3404325 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3404288 TTCAGGACCT
3404298 GTAAGGTTGTCATA
1 GTAAGGTTGTCATA
3404312 GTAAGGTTGTCATA
1 GTAAGGTTGTCATA
3404326 CTTAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
GTAAGGTTGTCATA
Found at i:3413552 original size:14 final size:14
Alignment explanation
Indices: 3413533--3413559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3413523 ACAGGGATGT
3413533 GTTCTCTCTGGATA
1 GTTCTCTCTGGATA
3413547 GTTCTCTCTGGAT
1 GTTCTCTCTGGAT
3413560 GTGTCCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
GTTCTCTCTGGATA
Done.