Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 144 of 163
Found at i:39134169 original size:37 final size:37
Alignment explanation
Indices: 39134117--39134485 Score: 241
Period size: 37 Copynumber: 10.0 Consensus size: 37
39134107 CTGCAAAAAA
* * * *
39134117 AGGGAACAAAATAGAAAGCTTGAAGGATTGAAGGAAT
1 AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAAT
* * * *
39134154 CGGGAAGAAAGTAGAAAGCTTAAAGGGTTGAAGAAAGT
1 AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAA-T
* * * *
39134192 -GGGAAGAAGGTATG-GATCTTCAAGGGTTGAATGAAT
1 AGGGAAGAAAGTA-GAGAGCTTGAAGGGTTGAAGGAAT
* * * * *
39134228 CGGAAAGAAAGTAGGGAGCTTCAAGGGTTGAAGGAAG
1 AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAAT
* * * * *
39134265 AGGAAAGAAAGTAG-GAAGCTTAAATGGTTGAAGAAAA
1 AGGGAAGAAAGTAGAG-AGCTTGAAGGGTTGAAGGAAT
* * * *
39134302 AGGGAAGAACA-TATTA-ATCTTCAAGGGTTGAAGGAAG
1 AGGGAAGAA-AGTA-GAGAGCTTGAAGGGTTGAAGGAAT
* * * *
39134339 AGGGAAGAATGTA-AGGAGATTGAACGGTTGACGGAAT
1 AGGGAAGAAAGTAGA-GAGCTTGAAGGGTTGAAGGAAT
* * * * *
39134376 CGAGAAGAAACTAGAGAGCTTGAAGTGTTGAAGAAAT
1 AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAAT
* * * *
39134413 CA-AGAAGAAAGTAGGGAGATTGAAGGGTTGAAGGAAG
1 -AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAAT
* *
39134450 AGGGAAGAATGTA-AGGAGCTTGAAGGGTGGAAGGAA
1 AGGGAAGAAAGTAGA-GAGCTTGAAGGGTTGAAGGAA
39134486 AGCGTGTAAT
Statistics
Matches: 260, Mismatches: 57, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
35 1 0.00
36 4 0.02
37 251 0.97
38 4 0.02
ACGTcount: A:0.42, C:0.05, G:0.35, T:0.17
Consensus pattern (37 bp):
AGGGAAGAAAGTAGAGAGCTTGAAGGGTTGAAGGAAT
Found at i:39134294 original size:74 final size:73
Alignment explanation
Indices: 39134136--39134485 Score: 276
Period size: 74 Copynumber: 4.7 Consensus size: 73
39134126 AATAGAAAGC
* * * * * *
39134136 TTGAAGGATTGAAGGAATCGGGAAGAAAGTAGAAAGCTTAAAGGGTTGAAGAAAGTGGGAAGAAG
1 TTGAAGGGTTGAAGGAATCGGGAAGAAAGTAGAGAGCTTCAAGGGTTGAAGGAAGAGGGAAGAAA
**
39134201 GTATGGATC
66 GTA-GGAGA
* * * * *
39134210 TTCAAGGGTTGAATGAATCGGAAAGAAAGTAGGGAGCTTCAAGGGTTGAAGGAAGAGGAAAGAAA
1 TTGAAGGGTTGAAGGAATCGGGAAGAAAGTAGAGAGCTTCAAGGGTTGAAGGAAGAGGGAAGAAA
*
39134275 GTAGGAAGC
66 GTAGG-AGA
* * * ** * *
39134284 TTAAATGGTTGAAGAAAAAGGGAAGAACA-TATTA-ATCTTCAAGGGTTGAAGGAAGAGGGAAGA
1 TTGAAGGGTTGAAGGAATCGGGAAGAA-AGTA-GAGAGCTTCAAGGGTTGAAGGAAGAGGGAAGA
*
39134347 ATGTAAGGAGA
64 AAGT-AGGAGA
* * * * * * * * *
39134358 TTGAACGGTTGACGGAATCGAGAAGAAACTAGAGAGCTTGAAGTGTTGAAGAAATCA-AGAAGAA
1 TTGAAGGGTTGAAGGAATCGGGAAGAAAGTAGAGAGCTTCAAGGGTTGAAGGAA-GAGGGAAGAA
39134422 AGTAGGGAGA
65 AGTA-GGAGA
** * * *
39134432 TTGAAGGGTTGAAGGAAGAGGGAAGAATGTA-AGGAGCTTGAAGGGTGGAAGGAA
1 TTGAAGGGTTGAAGGAATCGGGAAGAAAGTAGA-GAGCTTCAAGGGTTGAAGGAA
39134486 AGCGTGTAAT
Statistics
Matches: 217, Mismatches: 50, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
73 6 0.03
74 206 0.95
75 5 0.02
ACGTcount: A:0.41, C:0.05, G:0.36, T:0.18
Consensus pattern (73 bp):
TTGAAGGGTTGAAGGAATCGGGAAGAAAGTAGAGAGCTTCAAGGGTTGAAGGAAGAGGGAAGAAA
GTAGGAGA
Found at i:39134347 original size:111 final size:108
Alignment explanation
Indices: 39134133--39134485 Score: 329
Period size: 111 Copynumber: 3.2 Consensus size: 108
39134123 CAAAATAGAA
* * **
39134133 AGCTTGAAGGATTGAAGGAATCG-GGAAGAAAGTAGAAAGCTTAAAGGGTTGAAGAAAGTGGGAA
1 AGCTTGAAGGGTTGAAGGAA--GAGGAAGAAAGTAGGAAGCTTAAA-GGTTGAAGAAAAAGGGAA
* * ** * * *
39134197 GAAGGTATGGATCTTCAAGGGTTGAATGAATCGGAAAGAAAGTAGGG
63 GAA-ATATGGATCTTCAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
*
39134244 AGCTTCAAGGGTTGAAGGAAGAGGAAAGAAAGTAGGAAGCTTAAATGGTTGAAGAAAAAGGGAAG
1 AGCTTGAAGGGTTGAAGGAAGAGG-AAGAAAGTAGGAAGCTTAAA-GGTTGAAGAAAAAGGGAAG
**
39134309 AACATATTAATCTTCAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
64 AA-ATATGGATCTTCAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
* * * * *
39134355 AGATTGAACGGTTGACGGAATCGA-GAAGAAACTA-GAGAGCTTGAAGTGTTGAAGAAATCAA--
1 AGCTTGAAGGGTTGAAGGAA--GAGGAAGAAAGTAGGA-AGCTTAAAG-GTTGAAGAAA--AAGG
* ** *
39134416 GAAGAAAGTAGGGAGATTGAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
60 GAAGAAA-TATGGATCTTCAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
*
39134466 AGCTTGAAGGGTGGAAGGAA
1 AGCTTGAAGGGTTGAAGGAA
39134486 AGCGTGTAAT
Statistics
Matches: 201, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
109 1 0.00
110 6 0.03
111 189 0.94
112 1 0.00
113 4 0.02
ACGTcount: A:0.41, C:0.05, G:0.36, T:0.18
Consensus pattern (108 bp):
AGCTTGAAGGGTTGAAGGAAGAGGAAGAAAGTAGGAAGCTTAAAGGTTGAAGAAAAAGGGAAGAA
ATATGGATCTTCAAGGGTTGAAGGAAGAGGGAAGAATGTAAGG
Found at i:39135590 original size:74 final size:73
Alignment explanation
Indices: 39135495--39135758 Score: 189
Period size: 74 Copynumber: 3.6 Consensus size: 73
39135485 TGGGATGAAG
* **
39135495 AGGGTTCAAGGAATAAAGAAGAAAGTAGGGAGCTTGAATGGTTGAAAGAAGAGGAAAGAACGTAG
1 AGGGTTGAAGGAATTGAGAAGAAAGTAGGGAGCTTGAATGGTT-AAAGAAGAGGAAAGAACGTAG
*
39135560 GGATCTTCA
65 GGAGCTTCA
* * * * * **
39135569 AGGGTTGGATGATTCTG-GAAGAAATTAGGGAGCTTTAA-GGATTAAAGGAAGAGTG-AAGATTG
1 AGGGTTGAAGGAAT-TGAGAAGAAAGTAGGGAGCTTGAATGG-TTAAA-GAAGAG-GAAAGAACG
*
39135631 TAGGGAGCTTGA
62 TAGGGAGCTTCA
* * * *
39135643 AGGGTTGAAGGAATTGAGAATAAAG-AAGGAGCTTGAATGGTTCAAGGAAG-TGAGAAGAACGTA
1 AGGGTTGAAGGAATTGAGAAGAAAGTAGGGAGCTTGAATGGTT-AAAGAAGAGGA-AAGAACGTA
* * *
39135706 GAGACCTTGA
64 GGGAGCTTCA
* * * * * *
39135716 AGTGTGGAATGAAGTAAGAAGAAAGT-GGGAAGCTTGAAGGGTT
1 AGGGTTGAAGGAATTGAGAAGAAAGTAGGG-AGCTTGAATGGTT
39135759 GAAGGAAGGC
Statistics
Matches: 146, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
71 1 0.01
73 59 0.40
74 85 0.58
75 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (73 bp):
AGGGTTGAAGGAATTGAGAAGAAAGTAGGGAGCTTGAATGGTTAAAGAAGAGGAAAGAACGTAGG
GAGCTTCA
Found at i:39135677 original size:36 final size:36
Alignment explanation
Indices: 39135511--39135766 Score: 156
Period size: 37 Copynumber: 6.9 Consensus size: 36
39135501 CAAGGAATAA
* * *
39135511 AGAAGAAAGTAGGGAGCTTGAATGGTTGAAAGAAGAG
1 AGAAGAAAGTA-GGAGCTTGAAGGGTTGAAGGAAGTG
* * * * * **
39135548 -GAAAGAACGTAGGGATCTTCAAGGGTTGGATGATTCTG
1 AG-AAGAAAGTA-GGAGCTTGAAGGGTTGAAGGA-AGTG
* * * * *
39135586 -GAAGAAATTAGGGAGCTTTAAGGATTAAAGGAAGAG
1 AGAAGAAAGTA-GGAGCTTGAAGGGTTGAAGGAAGTG
* ** *
39135622 TGAAGATTGTAGGGAGCTTGAAGGGTTGAAGGAATTG
1 AGAAGAAAGTA-GGAGCTTGAAGGGTTGAAGGAAGTG
* * * *
39135659 AGAATAAAGAAGGAGCTTGAATGGTTCAAGGAAGTG
1 AGAAGAAAGTAGGAGCTTGAAGGGTTGAAGGAAGTG
* * * * * *
39135695 AGAAGAACGTAGAGACCTTGAAGTGTGGAATGAAGTA
1 AGAAGAAAGTAG-GAGCTTGAAGGGTTGAAGGAAGTG
*
39135732 AGAAGAAAGTGGGAAGCTTGAAGGGTTGAAGGAAG
1 AGAAGAAAGTAGG-AGCTTGAAGGGTTGAAGGAAG
39135767 GCATGCGATT
Statistics
Matches: 162, Mismatches: 52, Indels: 10
0.72 0.23 0.04
Matches are distributed among these distances:
36 34 0.21
37 126 0.78
38 2 0.01
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.20
Consensus pattern (36 bp):
AGAAGAAAGTAGGAGCTTGAAGGGTTGAAGGAAGTG
Found at i:39142823 original size:95 final size:95
Alignment explanation
Indices: 39142660--39142850 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
39142650 GGAAGTGGAA
39142660 TTACAGCCGATAGAGCATTTAAATAAAGCTTCCAACATATGCCAGCTGAGTATACTAGTTCATAT
1 TTACAGCCGATAGAGCATTTAAATAAAGCTTCCAACATATGCCAGCTGAGTATACTAGTTCATAT
39142725 AGCAAACTCCTGCAGTTGCCAGTTCAAGAT
66 AGCAAACTCCTGCAGTTGCCAGTTCAAGAT
39142755 TTACAGCCGATAGAGCATTTAAATAAAGCTTCCAACATATGCCAGCTGAGTATACTAGTTCATAT
1 TTACAGCCGATAGAGCATTTAAATAAAGCTTCCAACATATGCCAGCTGAGTATACTAGTTCATAT
39142820 AGCAAACTCCTGCAGTTGCCAGTTCAAGAT
66 AGCAAACTCCTGCAGTTGCCAGTTCAAGAT
39142850 T
1 T
39142851 AGACGCATAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (95 bp):
TTACAGCCGATAGAGCATTTAAATAAAGCTTCCAACATATGCCAGCTGAGTATACTAGTTCATAT
AGCAAACTCCTGCAGTTGCCAGTTCAAGAT
Found at i:39145542 original size:16 final size:16
Alignment explanation
Indices: 39145517--39145552 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39145507 AATCAATAGA
*
39145517 AAATACAAAATATAAT
1 AAATAAAAAATATAAT
39145533 AAATAAAAAATATAAT
1 AAATAAAAAATATAAT
39145549 AAAT
1 AAAT
39145553 TTATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAAAAATATAAT
Found at i:39154323 original size:14 final size:14
Alignment explanation
Indices: 39154304--39154339 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39154294 TTGTTTGACT
*
39154304 GAAAATGGTTTCTA
1 GAAAATGATTTCTA
*
39154318 GAAAATGATTTCTG
1 GAAAATGATTTCTA
39154332 GAAAATGA
1 GAAAATGA
39154340 ATTATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:39154365 original size:20 final size:19
Alignment explanation
Indices: 39154326--39154371 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
39154316 TAGAAAATGA
39154326 TTTCTGGAAAATGAATTATT
1 TTTCTGGAAAATGAATTA-T
*
39154346 TTTCTGGAAAAGTTAA-TAT
1 TTTCTGGAAAA-TGAATTAT
39154365 TTTCTGG
1 TTTCTGG
39154372 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 13 0.54
21 3 0.12
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (19 bp):
TTTCTGGAAAATGAATTAT
Found at i:39154496 original size:22 final size:23
Alignment explanation
Indices: 39154471--39154530 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
39154461 TACATTTGAG
* *
39154471 AATTTATTATTTTTTAT-TATTT
1 AATTTATTATTTTATATCTATTA
*
39154493 AATTGAGTTTATTTTATATCTATTA
1 AATTTA--TTATTTTATATCTATTA
39154518 AATTTA-TATTTTA
1 AATTTATTATTTTA
39154531 CATTGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 12 0.39
24 10 0.32
25 9 0.29
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (23 bp):
AATTTATTATTTTATATCTATTA
Found at i:39154807 original size:46 final size:48
Alignment explanation
Indices: 39154707--39154813 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 48
39154697 TATTACAAAT
* * *
39154707 TAGTAGTACACCACATGATAACTACAATTAATATTATCCAAGTACATAAT
1 TAGTAGTACACAACATGATAACTA-AA-TAATATTATCAAAGTACATAAC
* * *
39154757 TAGTAGTACACAACATTATAACT-AA-AATATTGTCAAAGTGCATAAC
1 TAGTAGTACACAACATGATAACTAAATAATATTATCAAAGTACATAAC
*
39154803 TAGTATTACAC
1 TAGTAGTACAC
39154814 CATATAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 27 0.54
48 2 0.04
50 21 0.42
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (48 bp):
TAGTAGTACACAACATGATAACTAAATAATATTATCAAAGTACATAAC
Found at i:39167393 original size:15 final size:14
Alignment explanation
Indices: 39167360--39167393 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39167350 GTAAATTTAA
39167360 AATTAAAAACAAAT
1 AATTAAAAACAAAT
39167374 AATTAAAAACAAAT
1 AATTAAAAACAAAT
39167388 AGATTA
1 A-ATTA
39167394 CATAATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AATTAAAAACAAAT
Found at i:39171553 original size:24 final size:24
Alignment explanation
Indices: 39171508--39171553 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39171498 GACCACTCAA
*
39171508 TGTACAAAGGGCACCAGGTATTCT
1 TGTACAAAGGGCACCAGATATTCT
39171532 TGTACAAAAGGGCA-CAGATATT
1 TGTAC-AAAGGGCACCAGATATT
39171554 TGCTGCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (24 bp):
TGTACAAAGGGCACCAGATATTCT
Found at i:39186885 original size:2 final size:2
Alignment explanation
Indices: 39186872--39186901 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39186862 TTGTCTCTGC
*
39186872 AT AT AA 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
39186902 CATTGTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39194928 original size:15 final size:17
Alignment explanation
Indices: 39194910--39194952 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39194900 ATTTAATAAT
39194910 TATTAATT-T-TATACA
1 TATTAATTATATATACA
*
39194925 TATTTATTATATATACA
1 TATTAATTATATATACA
39194942 TATATAATTAT
1 TAT-TAATTAT
39194953 TGTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 9 0.39
18 6 0.26
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAATTATATATACA
Found at i:39195250 original size:22 final size:22
Alignment explanation
Indices: 39195209--39195250 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39195199 TTTTTGGACT
* *
39195209 TTGAGTCACATTTATTTCGAGC
1 TTGAGTCACATTGATCTCGAGC
*
39195231 TTGAGTCAGATTGATCTCGA
1 TTGAGTCACATTGATCTCGA
39195251 ACTCGAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (22 bp):
TTGAGTCACATTGATCTCGAGC
Found at i:39199231 original size:12 final size:12
Alignment explanation
Indices: 39199214--39199273 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
39199204 ATAACATCTA
39199214 AACAACCAAAAT
1 AACAACCAAAAT
*
39199226 AACAACCAAAAC
1 AACAACCAAAAT
* *
39199238 AACAGCAAAAAT
1 AACAACCAAAAT
** *
39199250 AACAATAAAAAC
1 AACAACCAAAAT
39199262 AAC-ACCAAAAT
1 AACAACCAAAAT
39199273 A
1 A
39199274 GTAAAAAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 6 0.16
12 32 0.84
ACGTcount: A:0.68, C:0.23, G:0.02, T:0.07
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:39199248 original size:24 final size:24
Alignment explanation
Indices: 39199221--39199271 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39199211 CTAAACAACC
* *
39199221 AAAATAACAACCAAAACAACAGCA
1 AAAATAACAACAAAAACAACACCA
*
39199245 AAAATAACAATAAAAACAACACCA
1 AAAATAACAACAAAAACAACACCA
39199269 AAA
1 AAA
39199272 TAGTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.71, C:0.22, G:0.02, T:0.06
Consensus pattern (24 bp):
AAAATAACAACAAAAACAACACCA
Found at i:39199314 original size:22 final size:22
Alignment explanation
Indices: 39199289--39199360 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
39199279 AAATAGCACC
*
39199289 AAAACAGCAATCAAAACAAT-A
1 AAAACAGCAACCAAAACAATAA
39199310 AAAA-A--AACCAAAACAATAA
1 AAAACAGCAACCAAAACAATAA
* *
39199329 AAATACAAC-ACCAAAACAGTAA
1 AAA-ACAGCAACCAAAACAATAA
*
39199351 AAAATAGCAA
1 AAAACAGCAA
39199361 ACCTAATCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.27
19 4 0.10
20 2 0.05
21 8 0.20
22 16 0.39
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.08
Consensus pattern (22 bp):
AAAACAGCAACCAAAACAATAA
Found at i:39199323 original size:18 final size:19
Alignment explanation
Indices: 39199300--39199354 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 19
39199290 AAACAGCAAT
39199300 CAAAACAATAAAAAAA-AC
1 CAAAACAATAAAAAAACAC
39199318 CAAAACAATAAAAATACAACAC
1 CAAAACAAT-AAAA-A-AACAC
*
39199340 CAAAACAGTAAAAAA
1 CAAAACAATAAAAAA
39199355 TAGCAAACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.28
19 5 0.16
20 2 0.06
21 6 0.19
22 10 0.31
ACGTcount: A:0.73, C:0.18, G:0.02, T:0.07
Consensus pattern (19 bp):
CAAAACAATAAAAAAACAC
Found at i:39201557 original size:14 final size:14
Alignment explanation
Indices: 39201538--39201588 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
39201528 GAAACTCAAT
39201538 TAAATAATAAAATA
1 TAAATAATAAAATA
*
39201552 TAAATAGTAATAATA
1 TAAATAATAA-AATA
*
39201567 TACTATAAATAAAATA
1 TA-AAT-AATAAAATA
39201583 -AAATAA
1 TAAATAA
39201589 ACAATAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.07
14 11 0.37
15 7 0.23
16 6 0.20
17 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAATAATAAAATA
Found at i:39201563 original size:20 final size:20
Alignment explanation
Indices: 39201540--39201577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39201530 AACTCAATTA
39201540 AATAATAAAATATAAATAGT
1 AATAATAAAATATAAATAGT
* *
39201560 AATAATATACTATAAATA
1 AATAATAAAATATAAATA
39201578 AAATAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
AATAATAAAATATAAATAGT
Found at i:39203884 original size:3 final size:3
Alignment explanation
Indices: 39203878--39203915 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
39203868 TATTTTTTTA
39203878 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39203916 GTTAGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39207618 original size:18 final size:18
Alignment explanation
Indices: 39207583--39207621 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39207573 ATTTTTTTAA
* * *
39207583 AATTTTTATTATTTTTTT
1 AATTTTTAATAATGTTTT
39207601 AATTTTTAATAATGTTTT
1 AATTTTTAATAATGTTTT
39207619 AAT
1 AAT
39207622 CAAACCAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
AATTTTTAATAATGTTTT
Found at i:39209859 original size:16 final size:16
Alignment explanation
Indices: 39209838--39209870 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39209828 TATCGGAAAA
39209838 TCAATTATAC-ACTATT
1 TCAATT-TACTACTATT
39209854 TCAATTTACTACTATT
1 TCAATTTACTACTATT
39209870 T
1 T
39209871 TTATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (16 bp):
TCAATTTACTACTATT
Found at i:39218621 original size:2 final size:2
Alignment explanation
Indices: 39218614--39218661 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
39218604 AACTCATGTT
39218614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39218655 TA T- TA TA
1 TA TA TA TA
39218662 AAATCATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39225661 original size:28 final size:29
Alignment explanation
Indices: 39225600--39225680 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
39225590 GAGTTTTATC
39225600 ATTTTTATACTTTTTAAAATAATTTTAATG
1 ATTTTTATA-TTTTTAAAATAATTTTAATG
*
39225630 ATTTTTAT-TTTTTAAAA-ATATTTT-TTG
1 ATTTTTATATTTTTAAAATA-ATTTTAATG
* * *
39225657 AATTTTTAAAATTTTAAAAAAATT
1 -ATTTTTATATTTTTAAAATAATT
39225681 AATTAAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 3 0.07
28 21 0.48
29 11 0.25
30 9 0.20
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTTTATATTTTTAAAATAATTTTAATG
Found at i:39231583 original size:73 final size:74
Alignment explanation
Indices: 39231492--39231635 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 74
39231482 GAAAAAAAAT
* * *
39231492 TTGTTTATGTTGTATTCTATTGTATTTTTACATCAATAATATACTTATTTACAATTTAC-CCAAA
1 TTGTTTATATTGTATTCTATTGTATTTTTACATCAATAATATAATTATTTACAATTTACTCAAAA
39231556 ATGAAAGTA
66 ATGAAAGTA
*
39231565 TTGTTTGTATTGTATTCTATTGTATTTTTACATCAATAATATAATTATTTACAATTTACTCAAAA
1 TTGTTTATATTGTATTCTATTGTATTTTTACATCAATAATATAATTATTTACAATTTACTCAAAA
39231630 ATGAAA
66 ATGAAA
39231636 AAATGAACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 56 0.85
74 10 0.15
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (74 bp):
TTGTTTATATTGTATTCTATTGTATTTTTACATCAATAATATAATTATTTACAATTTACTCAAAA
ATGAAAGTA
Found at i:39238066 original size:453 final size:453
Alignment explanation
Indices: 39237214--39238124 Score: 1453
Period size: 453 Copynumber: 2.0 Consensus size: 453
39237204 CCTTCCAAAA
* * * *
39237214 TATAAAGATTGTCAGTCCTTTTACCTTCTAACAAAACGAGAGCCCCACAAGACACTTTAATGTCG
1 TATAAAGATTCTCAATCCTTTTACCTTCTAACAAAACGAGAGCCCCACAAGACACTTTAAGGTCA
* * * * *
39237279 CTAAACTCAATGTTGATCTTGTAACCTTTCGAGTCTAAAATATTCAAAGAGATAAGATTTTTTCG
66 CTAAACTCAATGTTGATCCTGTAACCTTTCAAATCTAAAATACTCAAAGAGATAAGATTTTTTAG
*
39237344 TAAATCAGGTACATACCTGACATCTGAGACTGTCTTAAGCATCCTATCGTGCATCCTAATTTTAA
131 TAAATCAGGTACATACCTGACATCTGAGACTGTCCTAAGCATCCTATCGTGCATCCTAATTTTAA
* * * * *
39237409 TAGTACCAAAACCGATTACCTTACTGGATGAACCGTTTCCCATGTGCACAACTCCACCTTTAATC
196 CAGTACCAAAACCGATTACCTTACTGAATGAACCGTTTCCCATGTACACAACTCCACCTTCAACC
* *
39237474 GAACTGTATGTGAAGAACCATTCTCTGTTAGGACACATGTGGAAAGAACATCCCGAATTTAGGAT
261 GAACTGTATGTGAAGAACCATTCTCTGTTAGGACACATGTGAAAAGAACATCCCGAATCTAGGAT
* * * * * *
39237539 CCACTCAGACATAAGCTCGGAGCTTTCGCTCGTTGACACTAATAAGAAATCATCACCCTTTTCGT
326 CCACTCAGACATAAGCTCGAAGCTTTCACTCGTTGACACTAACAAGAAATAATCACCCCTTTCAT
* * * * *
39237604 CGGCCAAATTAGTACTAGCTACAGCTTCTTTGTTACTCTCAGCAGTCCTTTTATTTTGTAGTT
391 CGACCAAATTAGCACTAGCTACAGCTTCTTTGTTACTCTCAACAATCATTTTATTTTGTAGTT
* * *
39237667 TATAAAGATTCTCAATCCTTTTACCTTTTAACAAAATGAGAGCCCCACGAGACACTTTAAGGTCA
1 TATAAAGATTCTCAATCCTTTTACCTTCTAACAAAACGAGAGCCCCACAAGACACTTTAAGGTCA
39237732 CTAAACTCAATGTTGATCCTGTAACCTTTCAAATCTAAAATACTCAAAGAGATAAGATTTTTTAG
66 CTAAACTCAATGTTGATCCTGTAACCTTTCAAATCTAAAATACTCAAAGAGATAAGATTTTTTAG
* *
39237797 TAAATCAGGTACATACCTGACATCTGAGAGTGTCCTAAGCGTCCTATCGTGCATCCTAATTTTAA
131 TAAATCAGGTACATACCTGACATCTGAGACTGTCCTAAGCATCCTATCGTGCATCCTAATTTTAA
* *
39237862 CAGTACCAATATCGATTACCTTACTGAATGAACCGTTTCCCATGTACACAACTCCACCTTCAACC
196 CAGTACCAAAACCGATTACCTTACTGAATGAACCGTTTCCCATGTACACAACTCCACCTTCAACC
* * * *
39237927 GAACTGTATGTGGAGAACCATTCTCTGTTGGGACATATGTGAAAAGAACATCCTGAATCTAGGAT
261 GAACTGTATGTGAAGAACCATTCTCTGTTAGGACACATGTGAAAAGAACATCCCGAATCTAGGAT
* *
39237992 CCACTTAGACATAAGCTCGAAGCTTTCACTTGTTGACACTAACAAGAAATAATCACCCCTTTCAT
326 CCACTCAGACATAAGCTCGAAGCTTTCACTCGTTGACACTAACAAGAAATAATCACCCCTTTCAT
39238057 CGACCAAATTAGCACTAGCTACAGCTTCTTTGTTACTCTCAACAATCATTTTATTTTGTAGTT
391 CGACCAAATTAGCACTAGCTACAGCTTCTTTGTTACTCTCAACAATCATTTTATTTTGTAGTT
39238120 TATAA
1 TATAA
39238125 TAATCTGCTT
Statistics
Matches: 417, Mismatches: 41, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
453 417 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (453 bp):
TATAAAGATTCTCAATCCTTTTACCTTCTAACAAAACGAGAGCCCCACAAGACACTTTAAGGTCA
CTAAACTCAATGTTGATCCTGTAACCTTTCAAATCTAAAATACTCAAAGAGATAAGATTTTTTAG
TAAATCAGGTACATACCTGACATCTGAGACTGTCCTAAGCATCCTATCGTGCATCCTAATTTTAA
CAGTACCAAAACCGATTACCTTACTGAATGAACCGTTTCCCATGTACACAACTCCACCTTCAACC
GAACTGTATGTGAAGAACCATTCTCTGTTAGGACACATGTGAAAAGAACATCCCGAATCTAGGAT
CCACTCAGACATAAGCTCGAAGCTTTCACTCGTTGACACTAACAAGAAATAATCACCCCTTTCAT
CGACCAAATTAGCACTAGCTACAGCTTCTTTGTTACTCTCAACAATCATTTTATTTTGTAGTT
Found at i:39238631 original size:22 final size:22
Alignment explanation
Indices: 39238602--39238656 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
39238592 TTTTATATGG
39238602 AATT-TTGAATTGAAGAATTTT
1 AATTATTGAATTGAAGAATTTT
39238623 AATTATTGAATTGAAGAATTTT
1 AATTATTGAATTGAAGAATTTT
39238645 AATTATTGAATT
1 AATTATTGAATT
39238657 AAAAGTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (22 bp):
AATTATTGAATTGAAGAATTTT
Found at i:39239037 original size:6 final size:6
Alignment explanation
Indices: 39239017--39239092 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
39239007 TTAAATGGGT
* * * *
39239017 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTCACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
* *
39239065 TTTAAA TTT-AC TTTAAA TTTAAG TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
39239093 TCAAATTTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
5 12 0.22
6 38 0.70
8 4 0.07
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:39239037 original size:17 final size:17
Alignment explanation
Indices: 39239017--39239091 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
39239007 TTAAATGGGT
39239017 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
39239034 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
39239051 TTTAAATTCA-CTT--A
1 TTTAAATTTATTTTAAA
*
39239065 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
39239082 TTTAAGTTTA
1 TTTAAATTTA
39239092 ATCAAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 2 0.04
17 36 0.72
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:39241201 original size:30 final size:29
Alignment explanation
Indices: 39241167--39241616 Score: 155
Period size: 30 Copynumber: 15.3 Consensus size: 29
39241157 CAAAATTCTG
*
39241167 TTTTAACCCCGGTTTCATCAAAAATTACCA
1 TTTT-ACCCCGATTTCATCAAAAATTACCA
39241197 TTTTACCTCCGCACTTTC--C-AAAATT-CCA
1 TTTTACC-CCG-A-TTTCATCAAAAATTACCA
39241225 TTTTTAACCCCGATTTCATCAAAAATTACCA
1 -TTTT-ACCCCGATTTCATCAAAAATTACCA
*
39241256 TTTTACCCTCGAACTT--TCAAAAATT-CCA
1 TTTTACCC-CG-ATTTCATCAAAAATTACCA
* *
39241284 TTTTTAACCTCAATTTCA-CAAAAAATTACCA
1 -TTTT-ACCCCGATTTCATC-AAAAATTACCA
*
39241315 TTTTACCCCTAAACTTTC--C--AAATT-CCA
1 TTTTACCCC--GA-TTTCATCAAAAATTACCA
*
39241342 TTTTTAACCTCGATTTC-TCCAAAAATTACCA
1 -TTTT-ACCCCGATTTCAT-CAAAAATTACCA
39241373 TTTTACCCCCGAACTTTC--C-AAAATT-CCA
1 TTTTA-CCCCG-A-TTTCATCAAAAATTACCA
* * * *
39241401 TTTTTGACCTCAATTTCACCGAAAATTACCA
1 -TTTT-ACCCCGATTTCATCAAAAATTACCA
*
39241432 TTTTACCCCTAAACTTTC--C-AAAATT-CCA
1 TTTTACCCC--GA-TTTCATCAAAAATTACCA
* * *
39241460 TTTTTAAACCCGATTTCACCAAAAATTACCC
1 -TTTT-ACCCCGATTTCATCAAAAATTACCA
** * * *
39241491 TTTTACCCCCTGAACT-GTCCAAAATT-CTA
1 TTTTA-CCCC-GATTTCATCAAAAATTACCA
* * *
39241520 TTTTTGACCTCGATTTCA-CCAAAATTACTA
1 -TTTT-ACCCCGATTTCATCAAAAATTACCA
* *
39241550 TTTTACCCTTGAATTT--TCTAAAATT-CCA
1 TTTTACCC-CG-ATTTCATCAAAAATTACCA
* *
39241578 TTTTTAACCCTGATTTCATCGAAAATTACCA
1 -TTTT-ACCCCGATTTCATCAAAAATTACCA
39241609 TTTTACCC
1 TTTTACCC
39241617 TCGCGAGTCC
Statistics
Matches: 329, Mismatches: 32, Indels: 119
0.69 0.07 0.25
Matches are distributed among these distances:
26 4 0.01
27 16 0.05
28 37 0.11
29 109 0.33
30 117 0.36
31 30 0.09
32 16 0.05
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (29 bp):
TTTTACCCCGATTTCATCAAAAATTACCA
Found at i:39241230 original size:59 final size:58
Alignment explanation
Indices: 39241128--39241616 Score: 558
Period size: 59 Copynumber: 8.3 Consensus size: 58
39241118 GAACTGTCCG
* * *
39241128 AAAATTATCATTTTACCCCTAAAACTTTCCAAAATT-C-TGTTTTAACCCCGGTTTCATCA
1 AAAATTACCATTTTACCCC--GAACTTTCCAAAATTCCAT-TTTTAACCCCGATTTCATCA
*
39241187 AAAATTACCATTTTACCTCCGCACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACC-CCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
39241246 AAAATTACCATTTTACCCTCGAACTTTCAAAAATTCCATTTTTAACCTCAATTTCA-CAA
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC-A
* *
39241305 AAAATTACCATTTTACCCCTAAACTTTCC-AAATTCCATTTTTAACCTCGATTTC-TCCA
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT-CA
* * * * *
39241363 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACCG
1 AAAATTACCATTTTA-CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
39241422 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAAACCCGATTTCACCA
1 AAAATTACCATTTTACCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * * * *
39241481 AAAATTACCCTTTTACCCCCTGAACTGTCCAAAATTCTATTTTTGACCTCGATTTCA-CC
1 AAAATTACCATTTTA-CCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * * * *
39241540 AAAATTACTATTTTACCCTTGAATTTTCTAAAATTCCATTTTTAACCCTGATTTCATCG
1 AAAATTACCATTTTACCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
39241599 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
39241617 TCGCGAGTCC
Statistics
Matches: 373, Mismatches: 42, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
58 100 0.27
59 235 0.63
60 38 0.10
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:39241336 original size:118 final size:117
Alignment explanation
Indices: 39241128--39241619 Score: 616
Period size: 118 Copynumber: 4.2 Consensus size: 117
39241118 GAACTGTCCG
* ** * **
39241128 AAAATTATCATTTTACCCCTAAAACTTTCCAAAATT-C-TGTTTTAACCCCGGTTTCATCAAAAA
1 AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCAT-TTTTAACCTCAATTTCA-CAAAAA
**
39241191 TTACCATTTTACCTCC-GCACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
63 TTACCATTTTACC-CCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
*
39241246 AAAATTACCATTTTACCCTCGAACTTTCAAAAATTCCATTTTTAACCTCAATTTCACAAAAAATT
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCAC-AAAAATT
*
39241311 ACCATTTTACCCCTAAACTTTCC-AAATTCCATTTTTAACCTCGATTTC-TCCA
65 ACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT-CA
* * *
39241363 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCAATTTCACCGAAAATT
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCA-CAAAAATT
* *
39241428 ACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAAACCCGATTTCACCA
65 ACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * * * * *
39241481 AAAATTACCCTTTTACCCCCTGAACTGTCCAAAATTCTATTTTTGACCTCGATTTCACCAAAATT
1 AAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACAAAAATT
* * * * * * *
39241546 ACTATTTTACCCTTGAATTTTCTAAAATTCCATTTTTAACCCTGATTTCATCG
65 ACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
39241599 AAAATTACCATTTTACCCTCG
1 AAAATTACCATTTTACCCTCG
39241620 CGAGTCCAAA
Statistics
Matches: 332, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
116 1 0.00
117 129 0.39
118 168 0.51
119 34 0.10
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (117 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACAAAAATTA
CCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:39241572 original size:29 final size:29
Alignment explanation
Indices: 39241540--39241617 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
39241530 CGATTTCACC
* *
39241540 AAAATTACTATTTTACCCTTGAATTT-TCT
1 AAAATTACCATTTTACCCTTG-ATTTATCG
39241569 AAAATT-CCATTTTTAACCC-TGATTTCATCG
1 AAAATTACCA-TTTT-ACCCTTGATTT-ATCG
39241599 AAAATTACCATTTTACCCT
1 AAAATTACCATTTTACCCT
39241618 CGCGAGTCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
28 6 0.15
29 16 0.39
30 16 0.39
31 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTGATTTATCG
Found at i:39241749 original size:15 final size:16
Alignment explanation
Indices: 39241722--39241767 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
39241712 ATTTATTTGC
*
39241722 ATCTGCATTTTATATT
1 ATCTGCATATTATATT
*
39241738 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
39241752 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
39241768 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.57
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:39253914 original size:76 final size:76
Alignment explanation
Indices: 39253818--39254258 Score: 669
Period size: 76 Copynumber: 5.9 Consensus size: 76
39253808 AAGTCTTTAT
* * *
39253818 CTCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGAAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
39253883 CATTTCCTATC
66 CATTTCCTATC
* * *
39253894 CTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
*
39253959 TATTTCCTATC
66 CATTTCCTATC
* * *
39253970 CTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
39254035 CATTT-CTATC
66 CATTTCCTATC
* *
39254045 CTCTTGAAATTGAAGTAGAGTTGGATATCAAATATTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
39254110 CATTTCCTATC
66 CATTTCCTATC
* * *
39254121 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
39254186 CATTTCCTATC
66 CATTTCCTATC
* *
39254197 CTCGTGAAATT---G-A-AGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGCAAG
1 CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCTGAAATTGAAGTAAGAGCAAG
39254257 AT
64 AT
39254259 GAAGCCTCGA
Statistics
Matches: 338, Mismatches: 24, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
71 18 0.05
72 1 0.00
73 27 0.08
75 72 0.21
76 220 0.65
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (76 bp):
CTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATC
Found at i:39254104 original size:151 final size:152
Alignment explanation
Indices: 39253818--39254258 Score: 687
Period size: 151 Copynumber: 2.9 Consensus size: 152
39253808 AAGTCTTTAT
* * * * *
39253818 CTCTCGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGAAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
*
39253883 CATTTCCTATCCTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGT
66 CATTTCCTATCCTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
*
39253948 AAGAGCAAGATTATTTCCTATC
131 AAGAGCAAGATCATTTCCTATC
*
39253970 CTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
* * * *
39254035 CATTT-CTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAATATTTATCTCTGAAATTGAAGT
66 CATTTCCTATCCTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
39254099 AAGAGCAAGATCATTTCCTATC
131 AAGAGCAAGATCATTTCCTATC
*
39254121 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
* *
39254186 CATTTCCTATCCTCGTGAAATT---G-A-AGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAA
66 CATTTCCTATCCTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA--TCTCTGAAATTGAA
39254246 GTAAGAGCAAGAT
129 GTAAGAGCAAGAT
39254259 GAAGCCTCGA
Statistics
Matches: 268, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
147 17 0.06
148 1 0.00
149 28 0.10
151 143 0.53
152 79 0.29
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (152 bp):
CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATCCTCCTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
AAGAGCAAGATCATTTCCTATC
Found at i:39256803 original size:59 final size:59
Alignment explanation
Indices: 39256638--39257010 Score: 423
Period size: 59 Copynumber: 6.4 Consensus size: 59
39256628 GGACTGTCCG
* * * *
39256638 AAAATTACCATTTTACCCCTAGAACTTTCCAAAATTTC-GTTTTAACCTCGGTTTCATCA
1 AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
* * *
39256697 AAAATTACCATTTTTCCC-CGTACTTTTCAAAATTCCATTTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
* * ** *
39256755 AAAATTAGCATTTTACCCTTGAACTTTCCAAAATTTTATTTTTAACCTCGGTTTCATCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
* * *
39256814 AAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
* * ** * *
39256873 AAAGTTACTATTTTACCCTCGAACTTTCCAAAATTCCATTTTCGACTTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
* * * * * *
39256932 AAAATTACTATTTTACCCTCGAA-TTT-TAGAAATTCCATTTTTAACCCCAATTTCACCG
1 AAAATTACCATTTTACCCTCGAACTTTCCA-AAATTCCATTTTTAACCTCGATTTCATCA
* *
39256990 AAAATTACCGTTTTGCCCTCG
1 AAAATTACCATTTTACCCTCG
39257011 CGAGTCCAAA
Statistics
Matches: 270, Mismatches: 39, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
57 15 0.06
58 82 0.30
59 172 0.64
60 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.38
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCATCA
Found at i:39256894 original size:30 final size:29
Alignment explanation
Indices: 39256735--39256953 Score: 93
Period size: 30 Copynumber: 7.4 Consensus size: 29
39256725 AAAATTCCAT
* *
39256735 TTTTAACCTCGATTTCATCAAAAATTAGC-A
1 TTTTACCCTCGATTTCA-CCAAAATTA-CTA
* *
39256765 TTTTACCCTTGAACTTT--CCAAAATT-TTA
1 TTTTACCCTCG-A-TTTCACCAAAATTACTA
* * * *
39256793 TTTTTAACCTCGGTTTCATCAAAAATTACCA
1 -TTTTACCCTCGATTTCA-CCAAAATTACTA
** *
39256824 TTTTACCCCTAAACTTT--CCAAAATT-CCA
1 TTTTA-CCCTCGA-TTTCACCAAAATTACTA
39256852 TTTTTGA-CCTCGATTTCACCAAAAGTTACTA
1 -TTTT-ACCCTCGATTTCACCAAAA-TTACTA
*
39256883 TTTTACCCTCGAACTTT--CCAAAATT-CCA
1 TTTTACCCTCG-A-TTTCACCAAAATTACTA
*
39256911 TTTT-CGACTTCGATTTCACCAAAAATTACTA
1 TTTTAC--CCTCGATTTCACC-AAAATTACTA
39256942 TTTTACCCTCGA
1 TTTTACCCTCGA
39256954 ATTTTAGAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 52
0.66 0.10 0.24
Matches are distributed among these distances:
27 10 0.07
28 15 0.11
29 42 0.30
30 50 0.35
31 14 0.10
32 10 0.07
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTACCCTCGATTTCACCAAAATTACTA
Found at i:39260178 original size:52 final size:52
Alignment explanation
Indices: 39260095--39260281 Score: 261
Period size: 52 Copynumber: 3.6 Consensus size: 52
39260085 AAATGCAAAA
*
39260095 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
* *
39260147 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTA-TGTATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAG-ATTATG
* * * * *
39260199 AGTTCCGATGACTATGTGTCATCGTGAGCATATGGATCCTTTTACGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACAGATTATG
*
39260251 AGGTCCGATGACTTTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
39260282 TAAATGGGAA
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 111 0.93
53 7 0.06
54 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
Found at i:39261850 original size:30 final size:30
Alignment explanation
Indices: 39261804--39261900 Score: 128
Period size: 29 Copynumber: 3.3 Consensus size: 30
39261794 GGGTAAAGTG
*
39261804 GTAATTTTTG-GAAGTTTGAA-GGCAAAAAT
1 GTAATTTTTGAGAAGTTT-AAGGGAAAAAAT
*
39261833 GTAATTTTTGAGAAGTTTAAGGGTAAAAAT
1 GTAATTTTTGAGAAGTTTAAGGGAAAAAAT
*
39261863 GTAATTTTT-AAAAGTTTAAGGGAAAAAAT
1 GTAATTTTTGAGAAGTTTAAGGGAAAAAAT
*
39261892 ATAATTTTT
1 GTAATTTTT
39261901 AGATGTTCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
29 38 0.61
30 24 0.39
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (30 bp):
GTAATTTTTGAGAAGTTTAAGGGAAAAAAT
Found at i:39261901 original size:29 final size:28
Alignment explanation
Indices: 39261805--39261938 Score: 124
Period size: 29 Copynumber: 4.6 Consensus size: 28
39261795 GGTAAAGTGG
* * *
39261805 TAATTTTTGGAAGTTTGAAGGCAAAAATG
1 TAATTTTTAGAAGTTT-AAGGGAAAAATA
*
39261834 TAATTTTTGAGAAGTTTAAGGGTAAAAATG
1 TAATTTTT-AGAAGTTTAAGGG-AAAAATA
*
39261864 TAATTTTTAAAAGTTTAAGGGAAAAAATA
1 TAATTTTTAGAAGTTTAAGGG-AAAAATA
* ** *
39261893 TAATTTTTAGATGTTCGAGGGTAAAATA
1 TAATTTTTAGAAGTTTAAGGGAAAAATA
* *
39261921 TAGTTTTTGAAAAGTTTA
1 TAATTTTT-AGAAGTTTA
39261939 GGGGTTAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
28 13 0.15
29 52 0.60
30 22 0.25
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.38
Consensus pattern (28 bp):
TAATTTTTAGAAGTTTAAGGGAAAAATA
Found at i:39261934 original size:58 final size:59
Alignment explanation
Indices: 39261805--39261938 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
39261795 GGTAAAGTGG
** * * * *
39261805 TAATTTTTGGAAGTTTGAA-GGCAAAAATGTAATTTTTGAGAAGTTTAAGGGTAAAAATG
1 TAATTTTTAAAAGTTT-AAGGGAAAAAATATAATTTTTGAGAAGTTCAAGGGTAAAAATA
* *
39261864 TAATTTTTAAAAGTTTAAGGGAAAAAATATAATTTTT-AGATGTTCGAGGGT-AAAATA
1 TAATTTTTAAAAGTTTAAGGGAAAAAATATAATTTTTGAGAAGTTCAAGGGTAAAAATA
*
39261921 TAGTTTTTGAAAAGTTTA
1 TAATTTTT-AAAAGTTTA
39261939 GGGGTTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 12 0.19
58 22 0.34
59 30 0.47
ACGTcount: A:0.40, C:0.01, G:0.20, T:0.38
Consensus pattern (59 bp):
TAATTTTTAAAAGTTTAAGGGAAAAAATATAATTTTTGAGAAGTTCAAGGGTAAAAATA
Found at i:39261943 original size:29 final size:29
Alignment explanation
Indices: 39261828--39261971 Score: 96
Period size: 30 Copynumber: 4.9 Consensus size: 29
39261818 TTTGAAGGCA
* * *
39261828 AAAATGTAATTTTTGAGAAGTTTAAGGGT
1 AAAATATAATTTTTGAAAAGTTTAGGGGT
* **
39261857 AAAAATGTAATTTTT-AAAAGTTTAAGGGAA
1 -AAAATATAATTTTTGAAAAGTTT-AGGGGT
* * *
39261887 AAAATATAATTTTT-AGATG-TTCGAGGGT
1 AAAATATAATTTTTGAAAAGTTTAG-GGGT
*
39261915 AAAATATAGTTTTTGAAAAGTTTAGGGGTT
1 AAAATATAATTTTTGAAAAGTTTAGGGG-T
* ** * *
39261945 AAAACATGCTTTTTGGACAGTTTAGGG
1 AAAATATAATTTTTGAAAAGTTTAGGG
39261972 AACTTCTAGG
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
27 1 0.01
28 17 0.19
29 29 0.32
30 43 0.48
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAAGTTTAGGGGT
Found at i:39262271 original size:17 final size:17
Alignment explanation
Indices: 39262233--39262277 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39262223 AATTCATGGG
*
39262233 TAAATT-TAAAATTAAT
1 TAAATTGTAAAAATAAT
*
39262249 TAAAATTGTAAAAATGAT
1 T-AAATTGTAAAAATAAT
39262267 TAAATTGTAAA
1 TAAATTGTAAA
39262278 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.60
18 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
TAAATTGTAAAAATAAT
Found at i:39263690 original size:6 final size:6
Alignment explanation
Indices: 39263679--39263739 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
39263669 TAGATTTGAA
* *
39263679 TAAATT TAAATT TAAA-- TAATTT TAAATTT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
*
39263725 TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAA
39263740 CCTAAAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.07
5 8 0.18
6 27 0.61
7 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:39263745 original size:17 final size:17
Alignment explanation
Indices: 39263677--39263755 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
39263667 TTTAGATTTG
39263677 AATAAATTTAAATTT-A
1 AATAAATTTAAATTTAA
*
39263693 AATAATTTTAAATTTTAA
1 AATAAATTTAAA-TTTAA
39263711 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
**
39263728 AATAAATTTAAACCTAA
1 AATAAATTTAAATTTAA
*
39263745 AACAAATTTAA
1 AATAAATTTAA
39263756 GAAATGAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
16 11 0.20
17 33 0.59
18 12 0.21
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:39264302 original size:78 final size:78
Alignment explanation
Indices: 39264180--39264971 Score: 403
Period size: 78 Copynumber: 10.2 Consensus size: 78
39264170 CCCATGATCG
* ** * ** * * *
39264180 GGGTAAGAGATTGGCTGGCGACGATCTG-CCTTCGACTCGAGGTAAAAGATCGAATGGCTGTAAT
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCTAAG-CTCGGGGTAAGAGATCGAATGACTGTAAT
39264244 CTGCCCCAAGCTTA
65 CTGCCCCAAGCTTA
* * * * * * *
39264258 GGGTAAGAGATTTGTTGATAAGGATCTACCCTAGGCTCGGGGTAAGTGAT-TAGATGACTGTAAT
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGA-ATGACTGTAAT
* * *
39264322 TTACCCCAAG-TTC
65 CTGCCCCAAGCTTA
* ** * *
39264335 GCGGTAAGAGATTTACTGATGATGATC-GATCTCAAGCTCGGGGTAAGAGATCGGATAACTGTAA
1 G-GGTAAGAGATTTGCTGATGATGATCTGCCCT-AAGCTCGGGGTAAGAGATCGAATGACTGTAA
* * * * * *
39264399 TTTGCTCGAGGTTTG
64 TCTGCCCCAAGCTTA
* ** * * *
39264414 GGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTCACGGTAAGAGATCGGATGGCTGCAATC
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGACTGTAATC
*
39264479 TGCCCTAAG-TTA
66 TGCCCCAAGCTTA
* * * *
39264491 GGGGTAAGAGATTTGCTAATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCGAA-CAGCTGCAA
1 -GGGTAAGAGATTTGCTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGA-CTGTAA
* *
39264555 TTTGCCCCAGGCTT-
64 TCTGCCCCAAGCTTA
* * *
39264569 GAAGTAAGAGATTTGCTAATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCAAATGACTGTAAT
1 G-GGTAAGAGATTTGCTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGACTGTAAT
* * **
39264634 CTACCCCAGGCTCG
65 CTGCCCCAAGCTTA
* * * ** * ** * *
39264648 GGGTAAGAGA-TCGAATGGCT-ACAATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTG-GTGATG
1 GGGTAAGAGATTTG-CT-GATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGACTG-TA
* * *
39264710 ATCTGTCCCATG-TTCG
63 ATCTGCCCCAAGCTT-A
* * * * * * * * ** * * *
39264726 GGGTAAAAGA-TTGAACGGTTG-TAATCTACCCTAGGCTTGGGGTAAGAGATTGGCTGATTATGA
1 GGGTAAGAGATTTG--CTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGACTGTAA
* * *
39264789 TCTGCCTCATGCTCA
64 TCTGCCCCAAGCTTA
* * * * ** * * * *
39264804 GGGTAAGAGATTGGCTGGTGATGATTTG-CCTCATGCTCGGCATAAGAAATTGAATGGCTGCAAT
1 GGGTAAGAGATTTGCTGATGATGATCTGCCCT-AAGCTCGGGGTAAGAGATCGAATGACTGTAAT
**
39264868 CTGCCCCAAGCTCG
65 CTGCCCCAAGCTTA
* * * * * * *
39264882 GGGTAAGAGA-TTGACTGGTGATTAT-TAGCCCCATGCTCGGGGTAAGAGATCCAATGGCTGCAA
1 GGGTAAGAGATTTG-CTGATGATGATCT-GCCCTAAGCTCGGGGTAAGAGATCGAATGACTGTAA
* * *
39264945 TCTACCCCAGGC-TC
64 TCTGCCCCAAGCTTA
39264959 GAGGTAAGAGATT
1 G-GGTAAGAGATT
39264972 GGTTGGGGAT
Statistics
Matches: 553, Mismatches: 132, Indels: 57
0.75 0.18 0.08
Matches are distributed among these distances:
77 25 0.05
78 506 0.92
79 22 0.04
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (78 bp):
GGGTAAGAGATTTGCTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGACTGTAATC
TGCCCCAAGCTTA
Found at i:39264458 original size:39 final size:39
Alignment explanation
Indices: 39264242--39264931 Score: 139
Period size: 39 Copynumber: 17.7 Consensus size: 39
39264232 AATGGCTGTA
* * * *
39264242 ATCTGCCCCAAGCTTAGGGTAAGAGATTTGTTGATAAGG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
* * * * * * * *
39264281 ATCTACCCTAGGCTCGGGGTAAGTGATTAGATGACTG-TA
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGA-TGATG
* * * *
39264320 ATTTACCCCAAGTTC-GCGGTAAGAGATTTACTGATGATG
1 ATCTGCCCCAAGCTCAG-GGTAAGAGATTTGCTGATGATG
* * * ** * * *
39264359 ATC-GATCTCAAGCTCGGGGTAAGAGATCGGATAACTG-TA
1 ATCTG-CCCCAAGCTCAGGGTAAGAGATTTGCTGA-TGATG
* * * * * **
39264398 ATTTGCTCGAGGTTTGGGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
* * *
39264437 ATCTGCCCCAAGCTCACGGTAAGAGA--T-CGGATGGCTG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGAT-GATG
* * *
39264474 CAATCTGCCCTAAG-TTAGGGGTAAGAGATTTGCTAATGATG
1 --ATCTGCCCCAAGCTCA-GGGTAAGAGATTTGCTGATGATG
* * * *
39264515 ATCTGCCCCAAGCTCGGGGTAAGAGA-TCGAACAGCTGCA--
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTG--CTGATG-ATG
* * * * *
39264554 ATTTGCCCCAGGCT-TGAAGTAAGAGATTTGCTAATGATG
1 ATCTGCCCCAAGCTCAG-GGTAAGAGATTTGCTGATGATG
* * **** *
39264593 ATCTGCCCTAAGCTCGGGGTAAGAGATCAAATGACTG-TA
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGA-TGATG
* * * * * * **
39264632 ATCTACCCCAGGCTCGGGGTAAGAGA-TCGAATGGCT-ACA
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTG-CT-GATGATG
* * * * *
39264671 ATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTGGTGATG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
* * * * * * * *
39264710 ATCTGTCCCATGTTCGGGGTAAAAGA-TTGAACGGTTG-TA
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTG--CTGATGATG
* * * ** * *
39264749 ATCTACCCTAGGCTTGGGGTAAGAGATTGGCTGATTATG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
* * * *
39264788 ATCTGCCTCATGCTCAGGGTAAGAGATTGGCTGGTGATG
1 ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
* * * * * * *
39264827 ATTTGCCTCATGCTC-GGCATAAGA-AATTG--AATGGCTG
1 ATCTGCCCCAAGCTCAGG-GTAAGAGATTTGCTGAT-GATG
* * *
39264864 CAATCTGCCCCAAGCTCGGGGTAAGAGA-TTGACTGGTGATT
1 --ATCTGCCCCAAGCTCAGGGTAAGAGATTTG-CTGATGATG
* *
39264905 AT-TAGCCCCATGCTCGGGGTAAGAGAT
1 ATCT-GCCCCAAGCTCAGGGTAAGAGAT
39264932 CCAATGGCTG
Statistics
Matches: 458, Mismatches: 148, Indels: 89
0.66 0.21 0.13
Matches are distributed among these distances:
36 5 0.01
37 8 0.02
38 26 0.06
39 383 0.84
40 25 0.05
41 7 0.02
42 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCAGGGTAAGAGATTTGCTGATGATG
Found at i:39264635 original size:156 final size:156
Alignment explanation
Indices: 39264215--39264658 Score: 496
Period size: 156 Copynumber: 2.8 Consensus size: 156
39264205 CTGCCTTCGA
* * * * * * *
39264215 CTCGAGGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTT-AGGGTAAGAGATTTGTTGATAA
1 CTCGGGGTAAGAGATCGAATAGCTGTAATTTGCCCCAGGCTTGA-GGTAAGAGATTTGCTGATGA
* * * * * * *
39264279 GGATCTACCCTAGGCTCGGGGTAAGTGATTAGATGACTGTAATTTACCCCAAGTTCGCGGTAAGA
65 TGATCTGCCCTAAGCTCGGGGTAAGAGATCAGATGACTGTAATCTACCCCAAGTTCGGGGTAAGA
* * *
39264344 GATTTACTGATGATGATCGATCTCAAG
130 GATTTACTAATGATGATCGACCCCAAG
* * * * * *
39264371 CTCGGGGTAAGAGATCGGATAACTGTAATTTGCTCGAGGTTTGGGGTAAGAGATTTGCTGATGAT
1 CTCGGGGTAAGAGATCGAATAGCTGTAATTTGCCCCAGGCTTGAGGTAAGAGATTTGCTGATGAT
* ** * * * * * *
39264436 GATCTGCCCCAAGCTCACGGTAAGAGATCGGATGGCTGCAATCTGCCCTAAGTTAGGGGTAAGAG
66 GATCTGCCCTAAGCTCGGGGTAAGAGATCAGATGACTGTAATCTACCCCAAGTTCGGGGTAAGAG
*
39264501 ATTTGCTAATGATGATCTG-CCCCAAG
131 ATTTACTAATGATGATC-GACCCCAAG
* * * *
39264527 CTCGGGGTAAGAGATCGAACAGCTGCAATTTGCCCCAGGCTTGAAGTAAGAGATTTGCTAATGAT
1 CTCGGGGTAAGAGATCGAATAGCTGTAATTTGCCCCAGGCTTGAGGTAAGAGATTTGCTGATGAT
* * *
39264592 GATCTGCCCTAAGCTCGGGGTAAGAGATCAAATGACTGTAATCTACCCCAGGCTCGGGGTAAGAG
66 GATCTGCCCTAAGCTCGGGGTAAGAGATCAGATGACTGTAATCTACCCCAAGTTCGGGGTAAGAG
39264657 AT
131 AT
39264659 CGAATGGCTA
Statistics
Matches: 231, Mismatches: 55, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
156 230 1.00
157 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (156 bp):
CTCGGGGTAAGAGATCGAATAGCTGTAATTTGCCCCAGGCTTGAGGTAAGAGATTTGCTGATGAT
GATCTGCCCTAAGCTCGGGGTAAGAGATCAGATGACTGTAATCTACCCCAAGTTCGGGGTAAGAG
ATTTACTAATGATGATCGACCCCAAG
Found at i:39264678 original size:117 final size:116
Alignment explanation
Indices: 39264476--39264775 Score: 291
Period size: 117 Copynumber: 2.6 Consensus size: 116
39264466 GATGGCTGCA
* * * *
39264476 ATCTGCCCTAAGTTAGGGGTAAGAGATTTGCTAATGATG--ATCTGCCCCAAGCTCGGGGTAAGA
1 ATCTGCCCTAAGTTCGGGGTAAGAGA--T-CAAATGATGTAATCTACCCCAGGCTCGGGGTAAGA
* * * * *
39264539 GATCGAACAGCTGCAATTTGCCCCAGGCTTGAAGTAAGAGATTTGCTAATGATG
63 GATCGAACAGCTACAATCTGCCCCAAGCTCGAAGTAAGAGATTGGCTAATGATG
*
39264593 ATCTGCCCTAAGCTCGGGGTAAGAGATCAAATGACTGTAATCTACCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCTAAGTTCGGGGTAAGAGATCAAATGA-TGTAATCTACCCCAGGCTCGGGGTAAGAGA
** * ** * **
39264658 TCGAATGGCTACAATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTGGTGATG
65 TCGAACAGCTACAATCTGCCCCAAGCTCGAAGTAAGAGATTGGCTAATGATG
* * * ** * * *
39264710 ATCTGTCCC-ATGTTCGGGGTAAAAGATTGAACGGTTGTAATCTACCCTAGGCTTGGGGTAAGAG
1 ATCTG-CCCTAAGTTCGGGGTAAGAGA-TCAAATGATGTAATCTACCCCAGGCTCGGGGTAAGAG
39264774 AT
64 AT
39264776 TGGCTGATTA
Statistics
Matches: 151, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
114 6 0.04
115 3 0.02
117 135 0.89
118 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (116 bp):
ATCTGCCCTAAGTTCGGGGTAAGAGATCAAATGATGTAATCTACCCCAGGCTCGGGGTAAGAGAT
CGAACAGCTACAATCTGCCCCAAGCTCGAAGTAAGAGATTGGCTAATGATG
Found at i:39264792 original size:117 final size:117
Alignment explanation
Indices: 39264627--39264931 Score: 330
Period size: 117 Copynumber: 2.6 Consensus size: 117
39264617 GATCAAATGA
* * * * *
39264627 CTGTAATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCCTAAGCTCGGGGTA
1 CTGTAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGGTTATAATCTGCCCTATGCTCGGGGTA
* * **
39264692 AGAGATTGGTTGGTGATGATCTGTCC-CATGTTCGGGGTAA-AAGATTGAACGG
66 AGAGATTGGCTGGTGATGATCTG-CCTCATGCTCGGCATAAGAA-ATTGAACGG
* * * * * * *
39264744 TTGTAATCTACCCTAGGCTTGGGGTAAGAGATTGGCTGATTATGATCTG-CCTCATGCTCAGGGT
1 CTGTAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGGTTATAATCTGCCCT-ATGCTCGGGGT
* *
39264808 AAGAGATTGGCTGGTGATGATTTGCCTCATGCTCGGCATAAGAAATTGAATGG
65 AAGAGATTGGCTGGTGATGATCTGCCTCATGCTCGGCATAAGAAATTGAACGG
* * * * * *
39264861 CTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGGTGATTAT-TAGCCCCATGCTCGGGGT
1 CTGTAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGGTTATAATCT-GCCCTATGCTCGGGGT
39264925 AAGAGAT
65 AAGAGAT
39264932 CCAATGGCTG
Statistics
Matches: 153, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
116 6 0.04
117 143 0.93
118 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (117 bp):
CTGTAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGGTTATAATCTGCCCTATGCTCGGGGTA
AGAGATTGGCTGGTGATGATCTGCCTCATGCTCGGCATAAGAAATTGAACGG
Found at i:39264953 original size:39 final size:38
Alignment explanation
Indices: 39264437--39264972 Score: 253
Period size: 39 Copynumber: 13.8 Consensus size: 38
39264427 GCTGATGATG
* ** * *
39264437 ATCTGCCCCAAGCTCACGGTAAGAGATCGGATGGCTGCA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* * * * *
39264476 ATCTGCCCTAAGTTAGGGGTAAGAGATTTGCTAAT-GATG-
1 ATCTGCCCCATGCTCGGGGTAAGAGA-TTG--AATGGCTGA
* * **
39264515 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACAGCTGCA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* * * ** *
39264554 ATTTGCCCCAGGCTTGAAGTAAGAGATTTGCTAAT-GATG-
1 ATCTGCCCCATGCTCGGGGTAAGAGA-TTG--AATGGCTGA
* * ** *
39264593 ATCTGCCCTAAGCTCGGGGTAAGAGATCAAATGACTGTA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* * * *
39264632 ATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTACA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCT-GA
* * **
39264671 ATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTGG-TGA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTGA
* * * * *
39264708 TGATCTGTCCCATGTTCGGGGTAAAAGATTGAACGGTTGTA
1 --ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* * * * ** * *
39264749 ATCTACCCTAGGCTTGGGGTAAGAGATTGGCT-GATTA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTGA
* * **
39264786 TGATCTGCCTCATGCTCAGGGTAAGAGATTGGCTGG-TGA
1 --ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTGA
* * ** *
39264825 TGATTTGCCTCATGCTCGGCATAAGAAATTGAATGGCTGCA
1 --ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* *
39264866 ATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGG-TGA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTGA
**
39264903 TTAT-TAGCCCCATGCTCGGGGTAAGAGATCCAATGGCTGCA
1 --ATCT-GCCCCATGCTCGGGGTAAGAGATTGAATGGCTG-A
* * *
39264944 ATCTACCCCAGGCTCGAGGTAAGAGATTG
1 ATCTGCCCCATGCTCGGGGTAAGAGATTG
39264973 GTTGGGGATG
Statistics
Matches: 374, Mismatches: 95, Indels: 56
0.71 0.18 0.11
Matches are distributed among these distances:
36 5 0.01
37 8 0.02
38 9 0.02
39 327 0.87
40 12 0.03
41 9 0.02
42 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCATGCTCGGGGTAAGAGATTGAATGGCTGA
Found at i:39277009 original size:29 final size:28
Alignment explanation
Indices: 39276977--39277291 Score: 170
Period size: 29 Copynumber: 10.8 Consensus size: 28
39276967 GCTCGGGGGT
39276977 AAAATAGTAATTTTTGGAAGTTTAGAGGCA
1 AAAAT-GTAATTTTTGGAAGTTT-GAGGCA
** *
39277007 AAAATGTAATTTTTAATAAGTTTGAGGGTA
1 AAAATGTAATTTTT-GGAAGTTTGA-GGCA
* * *
39277037 AAATTGTGATTTTTGGAAGTTTGGGAGCA
1 AAAATGTAATTTTTGGAAGTTTGAG-GCA
* * **
39277066 AAAATGAAATTTTTGGATA-TTTGGGGGT
1 AAAATGTAATTTTTGGA-AGTTTGAGGCA
* * * * *
39277094 AAATTGGTAATTTTAGAAATTTTGAGGTTA
1 AAAAT-GTAATTTTTGGAAGTTTGAGG-CA
* *
39277124 AAAATGTAATTTTTGGATGTTCGAGG-A
1 AAAATGTAATTTTTGGAAGTTTGAGGCA
* * *
39277151 TAAATAGTAATTTTTGGATGTTTAGGGGCA
1 AAAAT-GTAATTTTTGGAAGTTT-GAGGCA
* *
39277181 AAAATGTAATTTTT-GAATATTTGGGGCA
1 AAAATGTAATTTTTGGAA-GTTTGAGGCA
* * * **
39277209 AAAATGT-ATTTTTAAGAAGTTCGGGGGTT
1 AAAATGTAATTTTT-GGAAGTT-TGAGGCA
* * **
39277238 AAAATGTAATTTTTAGAAATTTTGAGGGTT
1 AAAATGTAATTTTT-GGAAGTTTGA-GGCA
*
39277268 AAAATATAATTTTTGGAAAGTTTG
1 AAAATGTAATTTTTGG-AAGTTTG
39277292 GTGGTCAAAA
Statistics
Matches: 223, Mismatches: 45, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
27 11 0.05
28 40 0.18
29 102 0.46
30 70 0.31
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTGAGGCA
Found at i:39277016 original size:58 final size:58
Alignment explanation
Indices: 39276948--39277195 Score: 243
Period size: 58 Copynumber: 4.3 Consensus size: 58
39276938 AATTAAGGGT
* *
39276948 AAAATGGTAATTTTTGGATGCTCGGGGGTAAAATAGTAATTTTTGGAAGTTTAGAGGCA
1 AAAAT-GTAATTTTTGGATGTTCGAGGGTAAAATAGTAATTTTTGGAAGTTTAGAGGCA
* * * * *
39277007 AAAATGTAATTTTT-AATAAGTTTGAGGGTAAAATTGTGATTTTTGGAAGTTT-GGGAGCA
1 AAAATGTAATTTTTGGAT--GTTCGAGGGTAAAATAGTAATTTTTGGAAGTTTAGAG-GCA
* * * * * * * * * *
39277066 AAAATGAAATTTTTGGATATTTGGGGGTAAATTGGTAA-TTTTAGAAATTTTGAGGTTA
1 AAAATGTAATTTTTGGATGTTCGAGGGTAAAATAGTAATTTTTGGAAGTTTAGAGG-CA
* * *
39277124 AAAATGTAATTTTTGGATGTTCGAGGAT-AAATAGTAATTTTTGGATGTTTAGGGGCA
1 AAAATGTAATTTTTGGATGTTCGAGGGTAAAATAGTAATTTTTGGAAGTTTAGAGGCA
39277181 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
39277196 AATATTTGGG
Statistics
Matches: 151, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
57 36 0.24
58 64 0.42
59 49 0.32
60 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.39
Consensus pattern (58 bp):
AAAATGTAATTTTTGGATGTTCGAGGGTAAAATAGTAATTTTTGGAAGTTTAGAGGCA
Found at i:39277193 original size:28 final size:28
Alignment explanation
Indices: 39276948--39277221 Score: 187
Period size: 29 Copynumber: 9.5 Consensus size: 28
39276938 AATTAAGGGT
* * **
39276948 AAAATGGTAATTTTTGGATGCTCGGGGGT
1 AAAAT-GTAATTTTTGGATGTTTGGGGCA
* *
39276977 AAAATAGTAATTTTTGGAAGTTTAGAGGCA
1 AAAAT-GTAATTTTTGGATGTTT-GGGGCA
* *
39277007 AAAATGTAATTTTT-AATAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAT--GTTTG-GGGCA
* * *
39277037 AAATTGTGATTTTTGGAAGTTTGGGAGCA
1 AAAATGTAATTTTTGGATGTTTGGG-GCA
* * **
39277066 AAAATGAAATTTTTGGATATTTGGGGGT
1 AAAATGTAATTTTTGGATGTTTGGGGCA
* * * **
39277094 AAATTGGTAATTTTAGAAAT-TTTGAGGTTA
1 AAAAT-GTAATTTTTG-GATGTTTG-GGGCA
* *
39277124 AAAATGTAATTTTTGGATGTTCGAGG-A
1 AAAATGTAATTTTTGGATGTTTGGGGCA
*
39277151 TAAATAGTAATTTTTGGATGTTTAGGGGCA
1 AAAAT-GTAATTTTTGGATGTTT-GGGGCA
* *
39277181 AAAATGTAATTTTTGAATATTTGGGGCA
1 AAAATGTAATTTTTGGATGTTTGGGGCA
39277209 AAAATGT-ATTTTT
1 AAAATGTAATTTTT
39277222 AAGAAGTTCG
Statistics
Matches: 190, Mismatches: 42, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
27 11 0.06
28 40 0.21
29 98 0.52
30 40 0.21
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTGGATGTTTGGGGCA
Found at i:39277328 original size:30 final size:30
Alignment explanation
Indices: 39277244--39277332 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
39277234 GGTTAAAATG
* * *
39277244 TAATTTTTAGAAATTTTGAGGGTTAAAATA
1 TAATTTTTAGAAAGTTTGAGGGTCAAAACA
*
39277274 TAATTTTTGGAAAGTTTG-GTGGTCAAAACA
1 TAATTTTTAGAAAGTTTGAG-GGTCAAAACA
*
39277304 TAGTTTTTAGAAAGTTTGAGGGTCAAAAC
1 TAATTTTTAGAAAGTTTGAGGGTCAAAAC
39277333 GTGATTTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 1 0.02
30 49 0.96
31 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTGAGGGTCAAAACA
Found at i:39278447 original size:10 final size:10
Alignment explanation
Indices: 39278434--39278498 Score: 53
Period size: 12 Copynumber: 6.1 Consensus size: 10
39278424 TTTGCTTTCC
39278434 TTTTT-TTAT
1 TTTTTATTAT
39278443 TTTTTATTAT
1 TTTTTATTAT
39278453 TATTATTATTA-
1 T-TT-TTATTAT
*
39278464 TTATTATTAT
1 TTTTTATTAT
39278474 TGTTATTATTAT
1 T-TT-TTATTAT
39278486 TATTATTATTAT
1 T-TT-TTATTAT
39278498 T
1 T
39278499 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
9 11 0.23
10 7 0.15
11 4 0.09
12 25 0.53
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:39278452 original size:3 final size:3
Alignment explanation
Indices: 39278446--39278498 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
39278436 TTTTTATTTT
*
39278446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39278494 TTA TT
1 TTA TT
39278499 GTTGTTGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39279152 original size:16 final size:16
Alignment explanation
Indices: 39279128--39279227 Score: 71
Period size: 16 Copynumber: 6.3 Consensus size: 16
39279118 CATTATTTAT
* *
39279128 TTTAGATTTGAATAAA
1 TTTAAATTTAAATAAA
*
39279144 TTTAAATTTAAATAAT
1 TTTAAATTTAAATAAA
*
39279160 TTTAGATTT---TAAA
1 TTTAAATTTAAATAAA
* * * *
39279173 ATAAAATTAAAATTAA
1 TTTAAATTTAAATAAA
39279189 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
* *
39279206 TTTAAACTTAAAACAAA
1 TTTAAA-TTTAAATAAA
39279223 TTTAA
1 TTTAA
39279228 GAAATGAGTT
Statistics
Matches: 63, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
13 8 0.13
16 30 0.48
17 23 0.37
18 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:39279183 original size:28 final size:27
Alignment explanation
Indices: 39279146--39279216 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 27
39279136 TGAATAAATT
*
39279146 TAAATTTAAA-TAATTTTAGATTTTAAAA
1 TAAATTTAAATTAA-TTTA-AATTTAAAA
*
39279174 TAAAATTAAAATTAATTTAAATTTAAAA
1 T-AAATTTAAATTAATTTAAATTTAAAA
39279202 TAAATTTAAACTTAA
1 TAAATTTAAA-TTAA
39279217 AACAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.22
28 14 0.38
29 12 0.32
30 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTAATTTAAATTTAAAA
Found at i:39279183 original size:34 final size:32
Alignment explanation
Indices: 39279126--39279188 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
39279116 GACATTATTT
* * *
39279126 ATTTTAGATTTGAATAAATTTAAATTTAAATA
1 ATTTTAGATTTAAATAAAATTAAAATTAAATA
39279158 ATTTTAGATTTTAAAATAAAATTAAAATTAA
1 ATTTTAGA-TTT-AAATAAAATTAAAATTAA
39279189 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 8 0.31
33 3 0.12
34 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (32 bp):
ATTTTAGATTTAAATAAAATTAAAATTAAATA
Found at i:39279188 original size:17 final size:17
Alignment explanation
Indices: 39279174--39279227 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
39279164 GATTTTAAAA
*
39279174 TAAAATTAAAATTAATT
1 TAAAATTAAAATAAATT
*
39279191 TAAATTTAAAATAAATT
1 TAAAATTAAAATAAATT
* *
39279208 TAAACTTAAAACAAATT
1 TAAAATTAAAATAAATT
39279225 TAA
1 TAA
39279228 GAAATGAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATTAAAATAAATT
Found at i:39279223 original size:28 final size:28
Alignment explanation
Indices: 39279167--39279227 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
39279157 AATTTTAGAT
***
39279167 TTTAAAATAAAATTAAAATTAATTTAAA
1 TTTAAAATAAAATTAAAATTAAAACAAA
* *
39279195 TTTAAAATAAATTTAAACTTAAAACAAA
1 TTTAAAATAAAATTAAAATTAAAACAAA
39279223 TTTAA
1 TTTAA
39279228 GAAATGAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTAAAATAAAATTAAAATTAAAACAAA
Found at i:39279906 original size:21 final size:21
Alignment explanation
Indices: 39279858--39279908 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
39279848 GGAGTTTTTA
*
39279858 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
39279879 GTTTCGGTAGAAGTCA-CACTT
1 GTATCGGTAGAAG-CATCACAT
39279900 GTATCGGTA
1 GTATCGGTA
39279909 ATATTATCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:39281741 original size:24 final size:23
Alignment explanation
Indices: 39281700--39281760 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
39281690 TTTTAATTAG
* *
39281700 TTCTCCTATTTTTT--TTAAATT
1 TTCTCATATTTTTTAATTAAACT
*
39281721 TTCATTATATTTTTTAATTAAACT
1 TTC-TCATATTTTTTAATTAAACT
*
39281745 TTCTCAAATTTTTTAA
1 TTCTCATATTTTTTAA
39281761 AATTGTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 9 0.28
23 11 0.34
24 9 0.28
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (23 bp):
TTCTCATATTTTTTAATTAAACT
Found at i:39289172 original size:57 final size:57
Alignment explanation
Indices: 39289085--39289198 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
39289075 TACAAACTTA
39289085 ATATATATATATATATATTGCACTTTTAATTTGTGAAATTGTAGTATTAATGTTGTT
1 ATATATATATATATATATTGCACTTTTAATTTGTGAAATTGTAGTATTAATGTTGTT
39289142 ATATATATATATATATATTGCACTTTTAATTTGTGAAATTGTAGTATTAATGTTGTT
1 ATATATATATATATATATTGCACTTTTAATTTGTGAAATTGTAGTATTAATGTTGTT
39289199 GGTAATAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (57 bp):
ATATATATATATATATATTGCACTTTTAATTTGTGAAATTGTAGTATTAATGTTGTT
Found at i:39290422 original size:31 final size:30
Alignment explanation
Indices: 39290361--39290429 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
39290351 CATTTAACAT
39290361 AACAGTCACTCAACTTTGAAAATGTGACAA
1 AACAGTCACTCAACTTTGAAAATGTGACAA
39290391 AACAGTCACT-AACGTTATTGAAAA-GTGACAA
1 AACAGTCACTCAAC--T-TTGAAAATGTGACAA
39290422 AACAGTCA
1 AACAGTCA
39290430 TTGAAATCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.08
30 10 0.28
31 16 0.44
32 7 0.19
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (30 bp):
AACAGTCACTCAACTTTGAAAATGTGACAA
Found at i:39290800 original size:35 final size:35
Alignment explanation
Indices: 39290761--39290841 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
39290751 GATGTCAATA
* * *
39290761 TTGATTGTGATTTTTGATTTAGGGTTTATTTGATT
1 TTGATTGTGATTTTTGATTTAAGGTTAATTCGATT
* *
39290796 TTGATTTTTATTTTTGATTTAAGGTTAATTCGATT
1 TTGATTGTGATTTTTGATTTAAGGTTAATTCGATT
39290831 TTGATTG-GATT
1 TTGATTGTGATT
39290842 CTGATTACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 3 0.08
35 36 0.92
ACGTcount: A:0.20, C:0.01, G:0.20, T:0.59
Consensus pattern (35 bp):
TTGATTGTGATTTTTGATTTAAGGTTAATTCGATT
Found at i:39292076 original size:16 final size:16
Alignment explanation
Indices: 39292046--39292083 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39292036 ATTATAAAAG
*
39292046 AAAAAT-AATGGTATT
1 AAAAATAAATGATATT
*
39292061 AAGAATAAATGATATT
1 AAAAATAAATGATATT
39292077 AAAAATA
1 AAAAATA
39292084 TTCAATACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (16 bp):
AAAAATAAATGATATT
Found at i:39311783 original size:4 final size:4
Alignment explanation
Indices: 39311774--39311811 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
39311764 AGAGTAATGG
39311774 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
39311812 CGGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:39313215 original size:2 final size:2
Alignment explanation
Indices: 39313208--39313240 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39313198 AGTTTATTTA
39313208 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 A
39313241 CTTATGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39345571 original size:7 final size:7
Alignment explanation
Indices: 39345561--39345585 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39345551 TTAACACGAT
39345561 ACAACCA
1 ACAACCA
39345568 ACAACCA
1 ACAACCA
39345575 ACAACCA
1 ACAACCA
39345582 ACAA
1 ACAA
39345586 AAAGCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAACCA
Found at i:39345701 original size:60 final size:63
Alignment explanation
Indices: 39345565--39345688 Score: 185
Period size: 67 Copynumber: 1.9 Consensus size: 63
39345555 CACGATACAA
* *
39345565 CCAACAACCAACAACCAACAAAAAGCATAATTGAAAACATACATCAAATAAACATAACAGCCAAC
1 CCAACAACCAACAACCAACAAAAAACATAATTGAAAACATACATCAAACAAACATAACAG----C
39345630 AG
62 AG
*
39345632 CCAACAACCAACAACCAACAAAAAACATAATTGAACACATACATCAAACAAACATAA
1 CCAACAACCAACAACCAACAAAAAACATAATTGAAAACATACATCAAACAAACATAA
39345689 GAGGAACTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.58, C:0.27, G:0.04, T:0.10
Consensus pattern (63 bp):
CCAACAACCAACAACCAACAAAAAACATAATTGAAAACATACATCAAACAAACATAACAGCAG
Found at i:39346659 original size:35 final size:35
Alignment explanation
Indices: 39346613--39346684 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
39346603 ACATGTATTA
39346613 TTGCACACGAATAAAGTTAAATGATTTTGAGATTT
1 TTGCACACGAATAAAGTTAAATGATTTTGAGATTT
39346648 TTGCACACGAATAAAGTTAAATGATTTTGAGATTT
1 TTGCACACGAATAAAGTTAAATGATTTTGAGATTT
39346683 TT
1 TT
39346685 TTACTAGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (35 bp):
TTGCACACGAATAAAGTTAAATGATTTTGAGATTT
Found at i:39351240 original size:17 final size:17
Alignment explanation
Indices: 39351219--39351258 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
39351209 TTAAAAATGT
39351219 TAAAAAAT-ATAAAAAA
1 TAAAAAATCATAAAAAA
*
39351235 TAAAAAATCATTAAAAA
1 TAAAAAATCATAAAAAA
39351252 TAAAAAA
1 TAAAAAA
39351259 AGCACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAAATCATAAAAAA
Found at i:39352757 original size:23 final size:23
Alignment explanation
Indices: 39352731--39352782 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
39352721 TATATAAAGG
*
39352731 AATAAATATTATTTTAAGTTTTT
1 AATAAATATCATTTTAAGTTTTT
* *
39352754 AATAAA-CTCATTTTGAGTTTTT
1 AATAAATATCATTTTAAGTTTTT
39352776 AATAAAT
1 AATAAAT
39352783 CCACAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (23 bp):
AATAAATATCATTTTAAGTTTTT
Found at i:39359440 original size:33 final size:33
Alignment explanation
Indices: 39359403--39359467 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
39359393 TTATTGATAA
*
39359403 ATTTATAATAATATTTAAAATTAATAATAAAGG
1 ATTTACAATAATATTTAAAATTAATAATAAAGG
39359436 ATTTACAATAATATTTAAAATTAATAATAAAG
1 ATTTACAATAATATTTAAAATTAATAATAAAG
39359468 TATCACTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (33 bp):
ATTTACAATAATATTTAAAATTAATAATAAAGG
Found at i:39363205 original size:2 final size:2
Alignment explanation
Indices: 39363161--39363192 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39363151 GCACATCATA
39363161 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39363193 CGCGCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:39364933 original size:30 final size:32
Alignment explanation
Indices: 39364866--39364939 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
39364856 ATATTCAAAG
* **
39364866 TCATTAAATTATTTAAAAATTTTCATTTAAAT
1 TCATTAAATTATTCAAAAAAATTCATTTAAAT
39364898 T-ATTAAATTATTCAAAAAAATT-ATTT-AAT
1 TCATTAAATTATTCAAAAAAATTCATTTAAAT
*
39364927 TCATTAAACTATT
1 TCATTAAATTATT
39364940 AAATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 14 0.38
31 18 0.49
32 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (32 bp):
TCATTAAATTATTCAAAAAAATTCATTTAAAT
Found at i:39369397 original size:28 final size:28
Alignment explanation
Indices: 39369361--39369414 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
39369351 TAAAAAAAGT
* *
39369361 ACCTAAAGATATACATAAAATAATATTA
1 ACCTAAAGACATACATAAAAAAATATTA
* *
39369389 ACCTCAAGACATTCATAAAAAAATAT
1 ACCTAAAGACATACATAAAAAAATAT
39369415 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.26
Consensus pattern (28 bp):
ACCTAAAGACATACATAAAAAAATATTA
Found at i:39369694 original size:19 final size:19
Alignment explanation
Indices: 39369659--39369699 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39369649 TCGCAATTTC
*
39369659 AAAATTTTAAGAGTTAAAA
1 AAAATCTTAAGAGTTAAAA
39369678 AAAATCTT-AGAGATTAAAA
1 AAAATCTTAAGAG-TTAAAA
39369697 AAA
1 AAA
39369700 TGATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (19 bp):
AAAATCTTAAGAGTTAAAA
Found at i:39375158 original size:3 final size:3
Alignment explanation
Indices: 39375143--39375191 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
39375133 CAAATGTTAG
* *
39375143 TTA TTA TTG TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39375191 T
1 T
39375192 ATTCTATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39377562 original size:41 final size:40
Alignment explanation
Indices: 39377503--39377836 Score: 267
Period size: 41 Copynumber: 8.2 Consensus size: 40
39377493 AAATAAATTA
* * * *
39377503 GACCTTTAGCGGTGCTTTCACAGAAGCGTCGCTATTGCTCT
1 GACCTTTAGC-GCGCTTTCCCATAAGCGCCGCTATTGCTCT
* * *
39377544 GACCTTTAGCAGCACTTTCTCATAAGCGCCGCTATTGCTCA
1 GACCTTTAGC-GCGCTTTCCCATAAGCGCCGCTATTGCTCT
* ** * * * *
39377585 AATATTTAGCGTCGCTTGCCCATAAACCCCGCTATTGATCT
1 GACCTTTAGCG-CGCTTTCCCATAAGCGCCGCTATTGCTCT
* ** ** *
39377626 GACATTTAGCGATTCTTGACCATAAGCGCCGCTATTTCTCT
1 GACCTTTAGCG-CGCTTTCCCATAAGCGCCGCTATTGCTCT
* * * * * *
39377667 AACTTTTAGCGATGCTTTCCCATCAGTGCCGCTATTGTTCT
1 GACCTTTAGCG-CGCTTTCCCATAAGCGCCGCTATTGCTCT
* * *
39377708 GACCTTTAGAGGCGCTTGCCCATAAGCGCCGCTATTGATCT
1 GACCTTTAG-CGCGCTTTCCCATAAGCGCCGCTATTGCTCT
* *
39377749 GACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCT
1 GACCTTTAGC-GCGCTTTCCCATAAGCGCCGCTATTGCTCT
** *
39377790 GACCTTTAGCGACGCTTTTTCATAAGTC-CCGTTATTGCTCT
1 GACCTTTAGCG-CGCTTTCCCATAAG-CGCCGCTATTGCTCT
39377831 -ACCTTT
1 GACCTTT
39377837 TGCGGCGTTT
Statistics
Matches: 236, Mismatches: 52, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
40 8 0.03
41 226 0.96
42 2 0.01
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (40 bp):
GACCTTTAGCGCGCTTTCCCATAAGCGCCGCTATTGCTCT
Found at i:39377814 original size:82 final size:82
Alignment explanation
Indices: 39377504--39377843 Score: 308
Period size: 82 Copynumber: 4.2 Consensus size: 82
39377494 AATAAATTAG
* * * * * * * *
39377504 ACCTTTAGCGGTGCTTTCACAGAAGCGTCGCTATTGCTCTGACCTTTAGC-AGCACTTTCTCATA
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGA-CGCTTGCCCATA
*
39377568 AGCGCCGCTATTGCTCAA
65 AGCGCCGCTATTGCTCTA
** * * * * * ** *
39377586 ATATTTAGCGTCGCTTGCCCATAAACCCCGCTATTGATCTGACATTTAGCGATTCTTGACCATAA
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATAA
*
39377651 GCGCCGCTATTTCTCTA
66 GCGCCGCTATTGCTCTA
* ** * * * * * *
39377668 ACTTTTAGCGATGCTTTCCCATCAGTGCCGCTATTGTTCTGACCTTTAGAGGCGCTTGCCCATAA
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATAA
* *
39377733 GCGCCGCTATTGATCTG
66 GCGCCGCTATTGCTCTA
* ***
39377750 ACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTTTCATAA
1 ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATAA
*
39377815 GTC-CCGTTATTGCTCT-
66 G-CGCCGCTATTGCTCTA
*
39377831 ACCTTTTGCGGCG
1 ACCTTTAGCGGCG
39377844 TTTATGTAAA
Statistics
Matches: 202, Mismatches: 54, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
81 12 0.06
82 188 0.93
83 2 0.01
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (82 bp):
ACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATAA
GCGCCGCTATTGCTCTA
Found at i:39377826 original size:123 final size:122
Alignment explanation
Indices: 39377503--39377836 Score: 375
Period size: 123 Copynumber: 2.7 Consensus size: 122
39377493 AAATAAATTA
* * * *
39377503 GACCTTTAGCGGTGCTTTCACAGAAGCGTCGCTATTGCTCTGACCTTTAGC-AGCACTTTCTCAT
1 GACCTTTAGCGGTGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGA-CGCTTTCTCAT
* ** * *
39377567 AAG-CGCCGCTATTGCTCAAATATTTAGCGTCGCTTGCCCATAAACCCCGCTATTGATCT
65 AAGTC-CCGCTATTGCTC-TACCTTTAGAGGCGCTTGCCCATAAACCCCGCTATTGATCT
* * * * * * * * * * *
39377626 GACATTTAGCGATTCTTGACCATAAGCGCCGCTATTTCTCTAACTTTTAGCGATGCTTTCCCATC
1 GACCTTTAGCGGTGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTCTCATA
* * * *
39377691 AGTGCCGCTATTGTTCTGACCTTTAGAGGCGCTTGCCCATAAGCGCCGCTATTGATCT
66 AGTCCCGCTATTGCTCT-ACCTTTAGAGGCGCTTGCCCATAAACCCCGCTATTGATCT
* *
39377749 GACCTTTAGCGGCGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTTTCATA
1 GACCTTTAGCGGTGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTCTCATA
*
39377814 AGTCCCGTTATTGCTCTACCTTT
66 AGTCCCGCTATTGCTCTACCTTT
39377837 TGCGGCGTTT
Statistics
Matches: 168, Mismatches: 40, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
122 6 0.04
123 161 0.96
124 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (122 bp):
GACCTTTAGCGGTGCTTGCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTCTCATA
AGTCCCGCTATTGCTCTACCTTTAGAGGCGCTTGCCCATAAACCCCGCTATTGATCT
Found at i:39398812 original size:4 final size:4
Alignment explanation
Indices: 39398801--39398835 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
39398791 TATTTATATA
39398801 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
39398836 CTCAATATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:39399856 original size:29 final size:29
Alignment explanation
Indices: 39399824--39399915 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
39399814 ATCATATTTT
*
39399824 AAAATTATTTTTGACCCCCAAACTTTCCA
1 AAAATTATTTTTGACCCCCAAATTTTCCA
**
39399853 AAAATTATGTTTTGACCCTTAAATTTTCCA
1 AAAATTAT-TTTTGACCCCCAAATTTTCCA
** *
39399883 AAAATTTAAATTTGA-CCCCGAATTTTCCA
1 AAAA-TTATTTTTGACCCCCAAATTTTCCA
39399912 AAAA
1 AAAA
39399916 ATTCAAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.43
30 27 0.51
31 3 0.06
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTATTTTTGACCCCCAAATTTTCCA
Found at i:39399918 original size:60 final size:59
Alignment explanation
Indices: 39399833--39400027 Score: 186
Period size: 60 Copynumber: 3.3 Consensus size: 59
39399823 TAAAATTATT
* **
39399833 TTTGACCCCCAAACTTTCCAAAAATT-ATGTTTTGACCCTTAAATTTTCCAAAAATTTAAA
1 TTTGA-CCCCAAAATTTCCAAAAATTCA-AATTTGACCCTTAAATTTTCCAAAAATTTAAA
* * * * *
39399893 TTTGACCCCGAATTTTCCAAAAAATTCAAAATTGACCCCTAAACTCTTT--AAAAATTCT-AT
1 TTTGACCCCAAAATTTCC-AAAAATTCAAATTTGACCCTTAAA-T-TTTCCAAAAATT-TAAA
* * *
39399953 TTTAACCTCTAAAATTTCCAAAAATTCAAATTTAACCCTTAAATTTTCCAAAAATTTAAA
1 TTTGACC-CCAAAATTTCCAAAAATTCAAATTTGACCCTTAAATTTTCCAAAAATTTAAA
39400013 TTTGA-CCC-AAATTTC
1 TTTGACCCCAAAATTTC
39400028 ACTCGGATCA
Statistics
Matches: 109, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
57 7 0.06
58 4 0.04
59 14 0.13
60 70 0.64
61 11 0.10
62 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.36
Consensus pattern (59 bp):
TTTGACCCCAAAATTTCCAAAAATTCAAATTTGACCCTTAAATTTTCCAAAAATTTAAA
Found at i:39399976 original size:30 final size:30
Alignment explanation
Indices: 39399867--39400020 Score: 116
Period size: 30 Copynumber: 5.1 Consensus size: 30
39399857 TTATGTTTTG
* * *
39399867 ACCCTTAAATTTTCCAAAAATTTAAATTTG
1 ACCCTTAAAATTTCCAAAAATTCAAATTTA
** * * *
39399897 ACCC-CGAATTTTCCAAAAAATTCAAAATTG
1 ACCCTTAAAATTTCC-AAAAATTCAAATTTA
* * * * *
39399927 ACCCCTAAACTCTT-TAAAAATTCTATTTTA
1 ACCCTTAAAAT-TTCCAAAAATTCAAATTTA
39399957 A-CCTCTAAAATTTCCAAAAATTCAAATTTA
1 ACCCT-TAAAATTTCCAAAAATTCAAATTTA
* * *
39399987 ACCCTTAAATTTTCCAAAAATTTAAATTTG
1 ACCCTTAAAATTTCCAAAAATTCAAATTTA
39400017 ACCC
1 ACCC
39400021 AAATTTCACT
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
29 12 0.12
30 78 0.80
31 6 0.06
32 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (30 bp):
ACCCTTAAAATTTCCAAAAATTCAAATTTA
Found at i:39400877 original size:15 final size:15
Alignment explanation
Indices: 39400857--39400886 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39400847 TGATTTCAAC
39400857 TGGGTTCCGTTACTG
1 TGGGTTCCGTTACTG
*
39400872 TGGGTTCTGTTACTG
1 TGGGTTCCGTTACTG
39400887 GGATATGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.33, T:0.43
Consensus pattern (15 bp):
TGGGTTCCGTTACTG
Found at i:39401406 original size:105 final size:105
Alignment explanation
Indices: 39401224--39401436 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 105
39401214 AAGACTTTGA
*
39401224 GAAGAAAAGTTCCGAATTGGGGAAAAAGATAGAAGCATTAGAGGAGGAAAAGATGCAGTTGGGTT
1 GAAGAAAAGTTCCGAATTGGGGAAAAAGATAGAAGCATTAGAGGAGGAAAAGATACAGTTGGGTT
39401289 TGGATGTTGACGTCCAAAAGTTAGAAGCCGATAAGCTAAG
66 TGGATGTTGACGTCCAAAAGTTAGAAGCCGATAAGCTAAG
*
39401329 GAAGAAAAGTTTCGAATTGGGGAAAAAGATAGAAGCATTAGAGGAGGAAAAGATACAGTTGGGTT
1 GAAGAAAAGTTCCGAATTGGGGAAAAAGATAGAAGCATTAGAGGAGGAAAAGATACAGTTGGGTT
39401394 TGGATGTTGACGTCCAAAAGTTAGAAGCCGATAAGCTAAG
66 TGGATGTTGACGTCCAAAAGTTAGAAGCCGATAAGCTAAG
39401434 GAA
1 GAA
39401437 AGGGAAGAGA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.40, C:0.09, G:0.31, T:0.20
Consensus pattern (105 bp):
GAAGAAAAGTTCCGAATTGGGGAAAAAGATAGAAGCATTAGAGGAGGAAAAGATACAGTTGGGTT
TGGATGTTGACGTCCAAAAGTTAGAAGCCGATAAGCTAAG
Found at i:39410285 original size:50 final size:50
Alignment explanation
Indices: 39410145--39410288 Score: 207
Period size: 50 Copynumber: 2.9 Consensus size: 50
39410135 GGTAGAACGA
* * ** * **
39410145 CAAATCTTATACCCCTAAAGCTGTAGAGGAACGGATTGAAACCGTAATGG
1 CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAATGG
39410195 CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAATGG
1 CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAATGG
* *
39410245 CGAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGTCG
1 CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCG
39410289 CAAGAACAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (50 bp):
CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAATGG
Found at i:39410301 original size:50 final size:50
Alignment explanation
Indices: 39410143--39410306 Score: 186
Period size: 50 Copynumber: 3.3 Consensus size: 50
39410133 GCGGTAGAAC
* * ** * ** *
39410143 GACAAATCTTATACCCCTAAAGCTGTAGAGGAACGGATTGAAACCGTAAT
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAT
* *
39410193 GGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGTAAT
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAT
* * *
39410243 GGCGAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAA-
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAT
*
39410292 GAACAAATCTTATAC
1 G-ACAAATCTCATAC
39410307 TGAAATGAAG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 97 0.99
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (50 bp):
GACAAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGTCGCAAT
Found at i:39410415 original size:78 final size:79
Alignment explanation
Indices: 39410333--39410522 Score: 283
Period size: 79 Copynumber: 2.4 Consensus size: 79
39410323 TACAACTCCG
* * * **
39410333 AATCTTTTACCTTAACCAGAGGGTAGATTGAAGACCATCCAATCTCTTACCCTG-CCATGGGGTA
1 AATCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGACA
39410397 GATTAAAGCAATCC
66 GATTAAAGCAATCC
* *
39410411 AATCTTTTACCTTAACTAGAGGACAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGACA
1 AATCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGACA
*
39410476 GATTGAAGCAATCC
66 GATTAAAGCAATCC
* *
39410490 AATCTTTTACCCTAACTAAAGGGCAGATTGAAG
1 AATCTTTTACCTTAACTAGAGGGCAGATTGAAG
39410523 TTACAAAAGC
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 49 0.49
79 51 0.51
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
AATCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGACA
GATTAAAGCAATCC
Found at i:39410517 original size:39 final size:40
Alignment explanation
Indices: 39410324--39410522 Score: 154
Period size: 39 Copynumber: 5.0 Consensus size: 40
39410314 AAGTGAAGTT
* * *
39410324 ACAACTCCGAATCTTTTACCTTAACCAGAGGGTAGATTGAAG
1 ACAA-TCC-AATCTTTTACCCTAACCAAAGGGCAGATTGAAG
* * * ** * *
39410366 ACCATCCAATCTCTTACCCT-GCCATGGGGTAGATTAAAG
1 ACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG
* * * *
39410405 -CAATCCAATCTTTTACCTTAACTAGAGGACAGATTGAAG
1 ACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG
* * * ** *
39410444 ACCATCCGATCTCTTACCCCGACC-ATGGGACAGATTGAAG
1 ACAATCCAATCTTTTACCCTAACCAAAGGG-CAGATTGAAG
*
39410484 -CAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAG
1 ACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG
39410523 TTACAAAAGC
Statistics
Matches: 119, Mismatches: 34, Indels: 11
0.73 0.21 0.07
Matches are distributed among these distances:
38 16 0.13
39 56 0.47
40 41 0.34
41 3 0.03
42 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (40 bp):
ACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG
Found at i:39410947 original size:16 final size:17
Alignment explanation
Indices: 39410928--39410959 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39410918 TCCAATTTAA
39410928 TTTTTTATTT-ATTTTG
1 TTTTTTATTTCATTTTG
39410944 TTTTTTATTTCATTTT
1 TTTTTTATTTCATTTT
39410960 TATTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTTTATTTCATTTTG
Found at i:39411421 original size:13 final size:13
Alignment explanation
Indices: 39411382--39411423 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
39411372 TTAAGGTATA
39411382 TTATTT-TATATT
1 TTATTTATATATT
* *
39411394 CTATTTATCTATT
1 TTATTTATATATT
*
39411407 TTATTTATATTTT
1 TTATTTATATATT
39411420 TTAT
1 TTAT
39411424 CTTTCGAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATATATT
Found at i:39412204 original size:90 final size:89
Alignment explanation
Indices: 39412092--39412343 Score: 242
Period size: 90 Copynumber: 2.8 Consensus size: 89
39412082 TTTGACCTTA
* *
39412092 AACTTTTCAAAAATTATGTTTTGACCCCTAAATTTTTCAAAAATTTAAATTGGA-CCTTGAAA-T
1 AACTTTTCTAAAATTATATTTTGACCCCTAAATTTTTCAAAAATTTAAATTGGACCCTT-AAATT
*
39412155 TTCCAAAAAATTCAAAATTGACCCCTG
65 TTCCAAAAAATT-AAAATTGA-ACCTG
* * * * * *
39412182 AACTCTTCTAAAATTCTATTTTGATCCCTAAAATTTTCAAAAATTTGAATTTGACCCTTAAATTT
1 AACTTTTCTAAAATTATATTTTGACCCCTAAATTTTTCAAAAATTTAAATTGGACCCTTAAATTT
* *
39412247 TCCAAAAAATTTAAATTTAACCTG
66 TCCAAAAAATTAAAATTGAACCTG
* * * * ** * **
39412271 AA-TTTTTTGAAAATTTTGA-TTTGACCCCTAATTTTTTTAAAAATTTTGATTTGACCCTTGAGG
1 AACTTTTCT-AAAATTAT-ATTTTGACCCCTAAATTTTTCAAAAATTTAAATTGGACCCTT-AAA
39412334 TTTTCCAAAA
63 TTTTCCAAAA
39412344 TTCAAATTTG
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
88 4 0.03
89 47 0.35
90 67 0.50
91 17 0.13
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (89 bp):
AACTTTTCTAAAATTATATTTTGACCCCTAAATTTTTCAAAAATTTAAATTGGACCCTTAAATTT
TCCAAAAAATTAAAATTGAACCTG
Found at i:39412244 original size:29 final size:29
Alignment explanation
Indices: 39412082--39412329 Score: 123
Period size: 30 Copynumber: 8.3 Consensus size: 29
39412072 TTAAAATTGT
*
39412082 TTTGA-CCTTAAACTTTTCAAAAATTATG-T
1 TTTGACCCTTAAA-TTTTCAAAAATT-TGAA
* *
39412111 TTTGACCCCTAAATTTTTCAAAAATTTAAA
1 TTTGACCCTTAAA-TTTTCAAAAATTTGAA
* * **
39412141 TTGGA-CCTTGAAATTTCCAAAAAATTCAAA
1 TTTGACCCTT-AAATTTTC-AAAAATTTGAA
* * * * * *
39412171 ATTGACCCCTGAACTCTTCTAAAATTCT-AT
1 TTTGA-CCCTTAAATTTTCAAAAATT-TGAA
*
39412201 TTTGATCCCTAAAATTTTCAAAAATTTGAA
1 TTTGA-CCCTTAAATTTTCAAAAATTTGAA
*
39412231 TTTGACCCTTAAATTTTCCAAAAAATTTAAA
1 TTTGACCCTTAAATTTT-C-AAAAATTTGAA
* * * * *
39412262 TTT-AACCTGAATTTTTTGAAAATTTTG-A
1 TTTGACCCTTAA-ATTTTCAAAAATTTGAA
* * *
39412290 TTTGACCCCTAATTTTTTTAAAAATTTTG-A
1 TTTGACCCTTAA-ATTTTCAAAAA-TTTGAA
39412320 TTTGACCCTT
1 TTTGACCCTT
39412330 GAGGTTTTCC
Statistics
Matches: 168, Mismatches: 38, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
28 4 0.02
29 47 0.28
30 92 0.55
31 22 0.13
32 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (29 bp):
TTTGACCCTTAAATTTTCAAAAATTTGAA
Found at i:39412344 original size:30 final size:30
Alignment explanation
Indices: 39412280--39412345 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
39412270 GAATTTTTTG
** *
39412280 AAAATTTTGATTTGACCCCTAATTTTTTTA
1 AAAATTTTGATTTGACCCCTAAGGTTTTCA
* * *
39412310 AAAATTTTGATTTGACCCTTGAGGTTTTCC
1 AAAATTTTGATTTGACCCCTAAGGTTTTCA
39412340 AAAATT
1 AAAATT
39412346 CAAATTTGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (30 bp):
AAAATTTTGATTTGACCCCTAAGGTTTTCA
Found at i:39414156 original size:6 final size:6
Alignment explanation
Indices: 39414145--39414223 Score: 89
Period size: 6 Copynumber: 14.2 Consensus size: 6
39414135 TCATGATAAT
* * *
39414145 TAAGAA TAAGAA TAATAA TAAAAA TAAGAA TAAGAA T-A-AA -AATAA
1 TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA
39414190 TAAGAA TAAG-A -AA-AA TAAGAA TAAGAA TAAGAA T
1 TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA TAAGAA T
39414224 GATGATGATG
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 6 0.10
5 6 0.10
6 51 0.81
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (6 bp):
TAAGAA
Found at i:39414191 original size:15 final size:15
Alignment explanation
Indices: 39414140--39414219 Score: 83
Period size: 15 Copynumber: 5.3 Consensus size: 15
39414130 ACACATCATG
*
39414140 ATAATTAAGAATAAGA
1 ATAA-TAAGAATAAAA
*
39414156 ATAATAATAA-AAATA
1 ATAATAAGAATAAA-A
*
39414171 AGAATAAGAATAAAA
1 ATAATAAGAATAAAA
39414186 ATAATAAGAATAAGAA
1 ATAATAAGAATAA-AA
*
39414202 A-AATAAGAATAAGA
1 ATAATAAGAATAAAA
39414216 ATAA
1 ATAA
39414220 GAATGATGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
14 4 0.07
15 40 0.74
16 10 0.19
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
ATAATAAGAATAAAA
Found at i:39414191 original size:21 final size:22
Alignment explanation
Indices: 39414140--39414223 Score: 109
Period size: 21 Copynumber: 3.8 Consensus size: 22
39414130 ACACATCATG
39414140 ATAATTAAGAATAAGAATAATAATA
1 ATAA-TAAGAATAAGAAT-A-AATA
*
39414165 AAAATAAGAATAAGAATAAA-A
1 ATAATAAGAATAAGAATAAATA
39414186 ATAATAAGAATAAGAA-AAATA
1 ATAATAAGAATAAGAATAAATA
*
39414207 AGAATAAGAATAAGAAT
1 ATAATAAGAATAAGAAT
39414224 GATGATGATG
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
20 3 0.06
21 32 0.59
22 2 0.04
23 1 0.02
24 13 0.24
25 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
ATAATAAGAATAAGAATAAATA
Found at i:39414208 original size:9 final size:9
Alignment explanation
Indices: 39414149--39414210 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
39414139 GATAATTAAG
*
39414149 AATAAGAAT
1 AATAAGAAA
*
39414158 AATAATAAA
1 AATAAGAAA
*
39414167 AATAAGAAT
1 AATAAGAAA
* *
39414176 AAGAATAAA
1 AATAAGAAA
* *
39414185 AATAATAAG
1 AATAAGAAA
39414194 AATAAGAAA
1 AATAAGAAA
39414203 AATAAGAA
1 AATAAGAA
39414211 TAAGAATAAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.18
Consensus pattern (9 bp):
AATAAGAAA
Found at i:39414427 original size:124 final size:124
Alignment explanation
Indices: 39414231--39414482 Score: 488
Period size: 124 Copynumber: 2.0 Consensus size: 124
39414221 AATGATGATG
39414231 ATGATGATAAATCAGCTTCAACAAAGGTGAGCTCGGGGTTATTACCATGGGGTTCAACAATGGAT
1 ATGATGATAAATCAGCTTCAACAAAGGTGAGCTCGGGGTTATTACCATGGGGTTCAACAATGGAT
*
39414296 GATGATGGTCTTCAATCTTCCTGCTTTTTCACACTAGAATTCCTTATAAATAGGGTGTT
66 GATGATGGTCTTCAATCTTCCTGCTTTTTCACACTAGAATTCCTTATAAATACGGTGTT
39414355 ATGATGATAAATCAGCTTCAACAAAGGTGAGCTCGGGGTTATTACCATGGGGTTCAACAATGGAT
1 ATGATGATAAATCAGCTTCAACAAAGGTGAGCTCGGGGTTATTACCATGGGGTTCAACAATGGAT
39414420 GATGATGGTCTTCAATCTTCCTGCTTTTTCACACTAGAATTCCTTATAAATACGGTGTT
66 GATGATGGTCTTCAATCTTCCTGCTTTTTCACACTAGAATTCCTTATAAATACGGTGTT
39414479 -TGAT
1 ATGAT
39414483 CTGCAGATGC
Statistics
Matches: 127, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 4 0.03
124 123 0.97
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (124 bp):
ATGATGATAAATCAGCTTCAACAAAGGTGAGCTCGGGGTTATTACCATGGGGTTCAACAATGGAT
GATGATGGTCTTCAATCTTCCTGCTTTTTCACACTAGAATTCCTTATAAATACGGTGTT
Found at i:39416943 original size:22 final size:22
Alignment explanation
Indices: 39416900--39416960 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
39416890 AAAGTTTTAG
*
39416900 AAAAATAATAAACCTTAAAGAAATA
1 AAAAATAATAAA-ATT-AAGAAA-A
39416925 AAAAATAATAAAATT-AGAAAA
1 AAAAATAATAAAATTAAGAAAA
*
39416946 AAAAATTAATTAAAT
1 AAAAA-TAATAAAAT
39416961 GATAATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 6 0.18
22 13 0.39
24 2 0.06
25 12 0.36
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (22 bp):
AAAAATAATAAAATTAAGAAAA
Found at i:39424609 original size:14 final size:14
Alignment explanation
Indices: 39424590--39424618 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39424580 CATGCGAACC
39424590 ACAACATAAGAAGT
1 ACAACATAAGAAGT
39424604 ACAACATAAGAAGT
1 ACAACATAAGAAGT
39424618 A
1 A
39424619 TTTCACTCAC
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:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAACATAAGAAGT
Found at i:39434229 original size:3 final size:3
Alignment explanation
Indices: 39434193--39434261 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
39434183 ACAGGCAGAT
* * * * *
39434193 GAA GAA GAT GAA GAT GAA GAT GAA GAT GAT GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
39434241 GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA
39434262 AGACTCTGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:39434943 original size:60 final size:60
Alignment explanation
Indices: 39434820--39435005 Score: 180
Period size: 60 Copynumber: 3.1 Consensus size: 60
39434810 TTAATATAAC
* * * *
39434820 ATTTGATACTTGAATTTGACACTTTTTCCT-GATTTAGTACTTCAA-TTTATTTTTGATCCA
1 ATTTGATACTTGAACTTGACACTTTTTCCTAG-TTTGGTACTTAAACTTT-TTTTAGATCCA
* * *
39434880 ATTTGATATTTGAACTTGACGCTTTTTCCTAGTTTGGTATTTAAACTTTTTTTAGA-CCTA
1 ATTTGATACTTGAACTTGACACTTTTTCCTAGTTTGGTACTTAAACTTTTTTTAGATCC-A
* * * * * * * *
39434940 ATTTGGTACATGAACTTGACAATTTTTCCTAATTTGATACCTAAGCTTTTTTTAAGATTCA
1 ATTTGATACTTGAACTTGACACTTTTTCCTAGTTTGGTACTTAAACTTTTTTT-AGATCCA
39435001 ATTTG
1 ATTTG
39435006 GTACCTAAAT
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
59 2 0.02
60 87 0.84
61 13 0.13
62 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (60 bp):
ATTTGATACTTGAACTTGACACTTTTTCCTAGTTTGGTACTTAAACTTTTTTTAGATCCA
Found at i:39435284 original size:92 final size:91
Alignment explanation
Indices: 39435151--39435346 Score: 234
Period size: 92 Copynumber: 2.1 Consensus size: 91
39435141 TTAAAAAAGA
* * ***
39435151 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAAATTGGA-CCCCAAAAAGTTTAA
1 TTAGGTACCAAATTAGAAAAAAAAGTCAAGTTCAAGTACC-AAATTGGATCAAAAAAAAGTTTAA
*
39435215 GTATCAATTTTA-AAAAAAGTGTCAAGT
65 GTATCAA-ATTAGAAAAAAGTGTCAAGT
** *
39435242 TTAGGTACCAAATTAGAAAAAAAATGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAATTTTAA
1 TTAGGTACCAAATTAGAAAAAAAA-GTCAAGTTCAAGTACCAAATTGGATCAAAAAAAAGTTTAA
* *
39435307 GTATTAAATTAGGAAAAAGTGTCAAGT
65 GTATCAAATTAGAAAAAAGTGTCAAGT
* *
39435334 TCAAGTACCAAAT
1 TTAGGTACCAAAT
39435347 ATTATATTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
91 33 0.37
92 56 0.63
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (91 bp):
TTAGGTACCAAATTAGAAAAAAAAGTCAAGTTCAAGTACCAAATTGGATCAAAAAAAAGTTTAAG
TATCAAATTAGAAAAAAGTGTCAAGT
Found at i:39435297 original size:33 final size:33
Alignment explanation
Indices: 39435226--39435287 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
39435216 TATCAATTTT
39435226 AAAAAAAGTGTCAAGTTTAGGTACCAAATTAGA
1 AAAAAAAGTGTCAAGTTTAGGTACCAAATTAGA
39435259 AAAAAAA-TGTCAAGTTT-GAGTACCAAATT
1 AAAAAAAGTGTCAAGTTTAG-GTACCAAATT
39435288 GGATCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 1 0.04
32 20 0.71
33 7 0.25
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (33 bp):
AAAAAAAGTGTCAAGTTTAGGTACCAAATTAGA
Found at i:39435914 original size:19 final size:19
Alignment explanation
Indices: 39435880--39435926 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
39435870 CCAACAATAA
39435880 TTAAATAAATAATT-AAAATT
1 TTAAA-AAA-AATTAAAAATT
39435900 TATAAAAAAAATTAAAAATT
1 T-TAAAAAAAATTAAAAATT
39435920 TTAAAAA
1 TTAAAAA
39435927 TTTGTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.40
20 11 0.44
21 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAAAAAATTAAAAATT
Found at i:39441997 original size:71 final size:71
Alignment explanation
Indices: 39441906--39442051 Score: 177
Period size: 71 Copynumber: 2.1 Consensus size: 71
39441896 TACAAGTTTT
* * * * **
39441906 ATTCGATATTGCTCAATCAAGCTGTCTAGGATCCACAATATATGCTAGATCTCAGTCATCAATAA
1 ATTCGATATTGCTCAATCAAGCTGTCGAGAATCCACAACATATACTAGATCTCAACCATCAATAA
39441971 AGAATA
66 AGAATA
* * * * *
39441977 ATTCGATGTTGCT-AACTCAAGTTGTCGAGAATCCACAACATATATTAGATCTTAACCATCGATA
1 ATTCGATATTGCTCAA-TCAAGCTGTCGAGAATCCACAACATATACTAGATCTCAACCATCAATA
39442041 AAGAATA
65 AAGAATA
39442048 ATTC
1 ATTC
39442052 ATCTTCAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
70 2 0.03
71 61 0.97
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (71 bp):
ATTCGATATTGCTCAATCAAGCTGTCGAGAATCCACAACATATACTAGATCTCAACCATCAATAA
AGAATA
Found at i:39445132 original size:13 final size:13
Alignment explanation
Indices: 39445116--39445140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39445106 AATTCAAAAA
39445116 TAAAAATATTTTT
1 TAAAAATATTTTT
39445129 TAAAAATATTTT
1 TAAAAATATTTT
39445141 AAAAATAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAAATATTTTT
Found at i:39445622 original size:18 final size:18
Alignment explanation
Indices: 39445601--39445643 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39445591 TATTTTTGAA
*
39445601 TTTTAAAGAATTTTTATT
1 TTTTAAAGAATTGTTATT
** *
39445619 TTTTTCATAATTGTTATT
1 TTTTAAAGAATTGTTATT
39445637 TTTTAAA
1 TTTTAAA
39445644 AAAAGATATG
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTAAAGAATTGTTATT
Found at i:39446732 original size:15 final size:16
Alignment explanation
Indices: 39446709--39446743 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
39446699 GCTCCCTAAG
39446709 TTTAATTTTTT-TAAA
1 TTTAATTTTTTGTAAA
*
39446724 TTTAGTTTTTTGTAAA
1 TTTAATTTTTTGTAAA
39446740 TTTA
1 TTTA
39446744 TATTATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTAATTTTTTGTAAA
Found at i:39447764 original size:14 final size:13
Alignment explanation
Indices: 39447732--39447773 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
39447722 TATTTTGATA
*
39447732 TAATAAATTTTAT
1 TAATAAATTTTTT
39447745 T-ATAAATTTTTT
1 TAATAAATTTTTT
*
39447757 TAATTAAATTTGTT
1 TAA-TAAATTTTTT
39447771 TAA
1 TAA
39447774 ATTATTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TAATAAATTTTTT
Done.