Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 12 of 173
Found at i:3280503 original size:73 final size:73
Alignment explanation
Indices: 3280285--3280603 Score: 469
Period size: 73 Copynumber: 4.4 Consensus size: 73
3280275 AAAATAATCA
* ** ***
3280285 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACATCGTTTCCCGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
* *
3280349 TCGGGGAA
66 TCAGGGAT
* * * *
3280357 TTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACCATAAGCCCAACGACGCCATTTTGTGAGCT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTGTGAGCT
*
3280422 TTCGGGGAT
65 TTCAGGGAT
*
3280431 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
*
3280496 TTAGGGAT
66 TCAGGGAT
* *
3280504 TTAGCGGCGTTTTTAAGGAAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
3280569 TCAGGGAT
66 TCAGGGAT
3280577 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
3280604 TAATGCTTTG
Statistics
Matches: 224, Mismatches: 21, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
72 25 0.11
73 136 0.61
74 63 0.28
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (73 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
TCAGGGAT
Found at i:3280702 original size:113 final size:113
Alignment explanation
Indices: 3280498--3280805 Score: 422
Period size: 113 Copynumber: 2.7 Consensus size: 113
3280488 GTGAGCTTTT
* * * *
3280498 AGGGATTTAGCGGCGTTTTTAAGG-AAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTG
1 AGGGCTTTAGCGGCGTTTTT-GGGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTC
* * *
3280562 TGAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTT-
64 TGAGCTTTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATG-TTC
* **
3280612 TGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCTATTTTCTG
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
*
3280677 AGCTTTCGGGGATTTAACGATGTTTTTAAGAAAGCGCCGCTAATGTTC
66 AGCTTTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTC
* * *** *
3280725 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCTGCAAAAATTATAAGCCCAACGACGCCGTTTTTTG
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
3280790 AGCTTTCGGGGATTTA
66 AGCTTTCGGGGATTTA
3280806 GCGGCCAAAA
Statistics
Matches: 172, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
112 2 0.01
113 143 0.83
114 27 0.16
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (113 bp):
AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
AGCTTTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTC
Found at i:3281146 original size:14 final size:14
Alignment explanation
Indices: 3281127--3281158 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3281117 AAGTATGGGT
3281127 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3281141 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3281155 TTAG
1 TTAG
3281159 AGGTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:3281186 original size:7 final size:7
Alignment explanation
Indices: 3281176--3281224 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3281166 GATTTAAGGT
3281176 TTAGGGG
1 TTAGGGG
3281183 TTAGAGGG
1 TTAG-GGG
3281191 TTAGGGG
1 TTAGGGG
3281198 TTTAGGGG
1 -TTAGGGG
*
3281206 TTAGACGTG
1 TTAG--GGG
3281215 TTAGGGG
1 TTAGGGG
3281222 TTA
1 TTA
3281225 AAAGTTAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 16 0.44
8 14 0.39
9 6 0.17
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:3281196 original size:15 final size:15
Alignment explanation
Indices: 3281176--3281224 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
3281166 GATTTAAGGT
3281176 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
3281191 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
3281206 TTAGACGTGTTAGGGG
1 TTAGGGGT-TTAGGGG
3281222 TTA
1 TTA
3281225 AAAGTTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:3281200 original size:23 final size:24
Alignment explanation
Indices: 3281173--3281223 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
3281163 TGGGATTTAA
3281173 GGTTTAGGGGTTAGA-GGGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
*
3281196 GGTTTAGGGGTTAGACGTGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
3281220 GGTT
1 GGTT
3281224 AAAAGTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.16, C:0.02, G:0.49, T:0.33
Consensus pattern (24 bp):
GGTTTAGGGGTTAGACGGGTTAGG
Found at i:3281633 original size:303 final size:299
Alignment explanation
Indices: 3281005--3281636 Score: 959
Period size: 303 Copynumber: 2.1 Consensus size: 299
3280995 ATTATTTAAA
* *
3281005 ATAATTGTAAAAGAGATAATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTA
1 ATAATTGTAAAAGAG---ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAA
* *
3281070 TTTAAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGGTTTAGGGAT
63 TTTAAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAAT
*
3281135 TATGGATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTT
128 TATGAATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTT
* * * *
3281200 TAGGGGTTAGACGTGTTAGGGGTTAAAAGTTAAGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTT
193 TAGGGGTTAGACGAGTTAGGGATTAAAAGTTAAGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTT
3281265 AGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
258 AGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
3281307 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
*
3281372 AAGATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGG-AGTATGGATTTAGGAATTAT
66 AAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTAT
* * *
3281436 GAATTAGGGATTATGGTTTA-AGGGTTGGGATTTAATGTTTAGGGGTTAGTA-GTTTATGGGTTA
131 GAATTAGGGATTATGGATTAGA-GGTTGGGATTTAAGGTTTAGGGGTTAG-AGGGTTA-GGG---
* * *
3281499 GATGTTAGGGGTTA-A-GAGTTAGGGATTTAAGGTTTAGGGATTCAGGGGTCGAGTTAAGGTTTT
190 G-T-TTAGGGGTTAGACGAGTTAGGGATTAAAAG-TTAAGGATTCAGGGGTCGAGTTAAGGTTTT
3281562 GAGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
252 GAGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
* *
3281610 ATAATTGTAAAATAGGTAATAATAAAT
1 ATAATTGTAAAAGAGATAATAATAAAT
3281637 CAAATATATT
Statistics
Matches: 303, Mismatches: 18, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
297 1 0.00
298 66 0.22
299 95 0.31
302 29 0.10
303 102 0.34
304 10 0.03
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.41
Consensus pattern (299 bp):
ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTT
AAGATTTAAGGCCGATTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTAT
GAATTAGGGATTATGGATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAG
GGGTTAGACGAGTTAGGGATTAAAAGTTAAGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGA
TTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
Found at i:3281840 original size:107 final size:106
Alignment explanation
Indices: 3281649--3281847 Score: 335
Period size: 106 Copynumber: 1.9 Consensus size: 106
3281639 AATATATTGA
* *
3281649 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCATA
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
* *
3281714 GCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGCGTT
66 GCAAAACAGCGTCATTTTGTTCAAAATTAAATAGCGGCGTT
* *
3281755 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAATTGAAAAAATTTTAGCAG
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAAT-AAAAAATTTTAGCAG
3281820 AGCAAAACAGCGTCATTTTGTTCAAAAT
65 AGCAAAACAGCGTCATTTTGTTCAAAAT
3281848 GAAAAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
106 46 0.53
107 40 0.47
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (106 bp):
TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
GCAAAACAGCGTCATTTTGTTCAAAATTAAATAGCGGCGTT
Found at i:3282106 original size:104 final size:107
Alignment explanation
Indices: 3281900--3282109 Score: 354
Period size: 104 Copynumber: 2.0 Consensus size: 107
3281890 GTAAGCAATA
*
3281900 GCGGCGTTTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAAA
1 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTAT-AAACAAATAAAATAAAAAAA
* * *
3281965 TTTTAGCATAACAAAACGGCGTCATTTTGTTGAAAATGAAATT
65 TTTTAGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAATT
3282008 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTAT-AA-AAA-AAAATAAAAAAAT
1 GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAACAAATAAAATAAAAAAAT
3282070 TTTAGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAA
66 TTTAGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAA
3282110 AAATTTTTGC
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
104 50 0.51
105 3 0.03
106 2 0.02
108 43 0.44
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (107 bp):
GCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAACAAATAAAATAAAAAAAT
TTTAGCAGAACAAAACGACGTCATTTTGTTCAAAATGAAATT
Found at i:3282225 original size:243 final size:248
Alignment explanation
Indices: 3281649--3282302 Score: 925
Period size: 243 Copynumber: 2.6 Consensus size: 248
3281639 AATATATTGA
* *
3281649 TTTAT-AAAAAACGCCACAAAAAATTAATCAATTTATAAAA-AAATAAAATAAAAAATTTTAGCA
1 TTTATAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAATTTTAGCA
*
3281712 TAGCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGCG-TTTTTATAAAAAACGCCGCAAAA
66 TAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTAT-AAAAACGCCGCAAAA
* *
3281776 AATAAATCAATTTATAAAAAAATAAATTGAAAAAATTTTAGCAGAGCAAAACAGCGTCATTTTGT
130 AATAAATCAATTTAT-AAAAAA-AAATTAAAAAAATTTTAGCAGAACAAAACAGCGTCATTTTGT
3281841 TCAAAATGAAAAAAAAATTACGGCGTTTTTCATAAAAACGCCGCTAAAGGTAAGCAATAGCGGCG
193 TCAAAATGAAAAAAAAATTACGGCGTTTTT-AT---AA-----CT--AGGTAAGCAATAGCGGCG
3281906 TT
247 TT
* *
3281908 TTT-TATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAAATTTTAGC
1 TTTATAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAT-AAAAAATTTTAGC
* *
3281972 ATAACAAAACGGCGTCATTTTGTTGAAAATGAAATTGCGGCGTTTTTTATAAAAACGCCGCAAAA
65 ATAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAA
3282037 AATAAATCAATTTATAAAAAAAAA-TAAAAAAATTTTAGCAGAACAAAAC-GACGTCATTTTGTT
130 AATAAATCAATTTATAAAAAAAAATTAAAAAAATTTTAGCAGAACAAAACAG-CGTCATTTTGTT
*** *
3282100 CAAAATGAAAAAATTTTTGCGGCG-TTTT-T-A-T-GGTAAGCAATAGCGGCGTT
194 CAAAATGAAAAAAAAATTACGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
*
3282150 TTTATAAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAATTTTTAGC
1 TTTATAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAA-TTTTAGC
* *
3282215 ATAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGAGGCGTTTTTATAAAAAAACGCCGCAAA
65 ATAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTT-TATAAAAACGCCGCAAA
3282280 AAATAAATCAATTTATAAAAAAA
129 AAATAAATCAATTTATAAAAAAA
3282303 TAAAATATAA
Statistics
Matches: 367, Mismatches: 20, Indels: 31
0.88 0.05 0.07
Matches are distributed among these distances:
242 28 0.08
243 95 0.26
244 39 0.11
245 1 0.00
251 1 0.00
255 1 0.00
257 5 0.01
258 56 0.15
259 37 0.10
260 15 0.04
261 82 0.22
262 7 0.02
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (248 bp):
TTTATAAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAATTTTAGCA
TAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAA
ATAAATCAATTTATAAAAAAAAATTAAAAAAATTTTAGCAGAACAAAACAGCGTCATTTTGTTCA
AAATGAAAAAAAAATTACGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
Found at i:3283544 original size:30 final size:31
Alignment explanation
Indices: 3283483--3283547 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
3283473 ATCTCCAAAC
* *
3283483 TATATATGAACTTTGATTTTATGTATAATTT
1 TATATAGGAACTTTGATTTTATGAATAATTT
*
3283514 TATATAGGAAC-TTGATTTTGTGCAAT-ATTT
1 TATATAGGAACTTTGATTTTATG-AATAATTT
3283544 TATA
1 TATA
3283548 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATAGGAACTTTGATTTTATGAATAATTT
Found at i:3302419 original size:20 final size:21
Alignment explanation
Indices: 3302396--3302439 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3302386 AAAAATTACA
3302396 AAAAAATT-AAAATAATTTTC
1 AAAAAATTCAAAATAATTTTC
*
3302416 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTC
3302436 AAAA
1 AAAA
3302440 TTGAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTC
Found at i:3302421 original size:19 final size:19
Alignment explanation
Indices: 3302397--3302467 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
3302387 AAAATTACAA
3302397 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
3302415 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
3302435 TAAAATTGAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
3302454 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
3302468 TAAAGAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 25 0.56
20 16 0.36
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:3302530 original size:9 final size:9
Alignment explanation
Indices: 3302518--3302547 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3302508 TTTTTTGAAT
3302518 TTAAATAAG
1 TTAAATAAG
3302527 TT-AATAAG
1 TTAAATAAG
3302535 TTAAATAAG
1 TTAAATAAG
3302544 TTAA
1 TTAA
3302548 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (9 bp):
TTAAATAAG
Found at i:3305987 original size:20 final size:19
Alignment explanation
Indices: 3305964--3306031 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
3305954 TTACAAATAG
3305964 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTT-AAA
* *
3305984 AATTCAAAATAATTTTTAA
1 AATTTAAAATAATTTTAAA
*
3306003 AATTGAAAAT-ATTTGTAAA
1 AATTTAAAATAATTT-TAAA
3306022 AATTCTAAAA
1 AATT-TAAAA
3306032 ATTCTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTAAAATAATTTTAAA
Found at i:3306023 original size:19 final size:19
Alignment explanation
Indices: 3305964--3306041 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
3305954 TTACAAATAG
*
3305964 AATTTAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
3305984 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
*
3306003 AATTGAAAAT-ATTTGTAAA
1 AATTCAAAATAATTT-TAAA
* *
3306022 AATTCTAAA-AATTCTAAA
1 AATTCAAAATAATTTTAAA
3306040 AA
1 AA
3306042 AAAGGGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 10 0.20
19 24 0.49
20 15 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:3309508 original size:40 final size:40
Alignment explanation
Indices: 3309457--3309537 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3309447 AATTAGTAAA
3309457 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3309497 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3309537 T
1 T
3309538 AGAGAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
Found at i:3309548 original size:40 final size:40
Alignment explanation
Indices: 3309454--3309548 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
3309444 TTAAATTAGT
*
3309454 AAATT-GAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTAGAATAAAATATTAATTTAGATCAAGATTGGGTGG
* *
3309493 AAATTTGAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTAGAATAAAATATTAATTTAGATCAAGATTGGGTGG
3309533 AAATTAGAGA-AAAATA
1 AAATTAGA-ATAAAATA
3309549 GAAATTTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 5 0.10
40 46 0.88
41 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (40 bp):
AAATTAGAATAAAATATTAATTTAGATCAAGATTGGGTGG
Found at i:3323184 original size:6 final size:6
Alignment explanation
Indices: 3323173--3323277 Score: 131
Period size: 6 Copynumber: 17.0 Consensus size: 6
3323163 ATAATTACAC
* *
3323173 ATTTTA ATTTTA ATTTTT A-TTTA TTTTTA ATTTTA ATTTTTA TATATTCTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A-TTTTA -AT-TT-TA
* *
3323224 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTT ATTTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
3323272 ATTTTA
1 ATTTTA
3323278 CATGTAGACA
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
5 3 0.03
6 70 0.80
7 8 0.09
8 5 0.06
9 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:3332676 original size:47 final size:47
Alignment explanation
Indices: 3332617--3332970 Score: 568
Period size: 47 Copynumber: 7.6 Consensus size: 47
3332607 ATTCATGACT
* ** **
3332617 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3332664 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
3332711 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* *
3332758 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3332804 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3332851 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* * *
3332897 TTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3332944 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
3332971 TTCAACTCAT
Statistics
Matches: 288, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 88 0.31
47 200 0.69
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
Found at i:3332819 original size:93 final size:94
Alignment explanation
Indices: 3332617--3332970 Score: 586
Period size: 93 Copynumber: 3.8 Consensus size: 94
3332607 ATTCATGACT
* ** **
3332617 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3332682 ACAAATTGGGCAGCATTTAGGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
3332711 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3332775 ACAAATTGGGCAGCTTTTATGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
*
3332804 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
3332868 ACAAATTGGGCAGCATTTATGCATCAAAA
66 ACAAATTGGGCAGCATTTATGCATCAAAA
* * *
3332897 TTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
3332962 ATAAATTGG
66 ACAAATTGG
3332971 TTCAACTCAT
Statistics
Matches: 247, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
93 180 0.73
94 67 0.27
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (94 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
ACAAATTGGGCAGCATTTATGCATCAAAA
Found at i:3332914 original size:140 final size:140
Alignment explanation
Indices: 3332640--3332970 Score: 583
Period size: 140 Copynumber: 2.4 Consensus size: 140
3332630 ATAAAACAGT
* * *
3332640 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
*
3332705 TCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATT
66 TCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATA
3332770 ATGTAACAAA
131 ATGTAACAAA
*
3332780 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
*
3332845 TCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATA
66 TCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-
*
3332909 AATGTAATAAA
130 AATGTAACAAA
3332920 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGG
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGG
3332971 TTCAACTCAT
Statistics
Matches: 182, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
139 45 0.25
140 137 0.75
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (140 bp):
TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATA
ATGTAACAAA
Found at i:3333881 original size:43 final size:42
Alignment explanation
Indices: 3333815--3333929 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 42
3333805 AACTCGTACA
* *
3333815 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
*
3333858 ATGCCACTGTCCCAGACAG-GGTCTTAGACGTAAACACAAGTCG
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
* *
3333901 ATGCCAACGTTCCAAACGTGGTCTTACAC
1 ATGCC-ACGTCCCAGACGTGGTCTTACAC
3333930 AATGATTAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 4 0.07
43 54 0.89
44 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:3334191 original size:15 final size:16
Alignment explanation
Indices: 3334159--3334191 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3334149 AGTGGGAGAA
3334159 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
3334176 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
3334191 T
1 T
3334192 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:3337769 original size:18 final size:17
Alignment explanation
Indices: 3337746--3337788 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3337736 AAAATTCCTA
3337746 TTATTTTTTTTT-ACTATT
1 TTATTTTTTTTTCA-T-TT
*
3337764 TTATTTTATTTTCATTT
1 TTATTTTTTTTTCATTT
3337781 TTATTTTT
1 TTATTTTT
3337789 GCAGGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTTTTTCATTT
Found at i:3338993 original size:15 final size:16
Alignment explanation
Indices: 3338961--3338993 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3338951 AGTGGGAGAA
3338961 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
3338978 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
3338993 T
1 T
3338994 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:3342676 original size:16 final size:16
Alignment explanation
Indices: 3342655--3342756 Score: 177
Period size: 16 Copynumber: 6.2 Consensus size: 16
3342645 TTTGGTTCGC
3342655 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
3342671 TGTATTGGATTATAGG
1 TGTATTGGATTAGAGG
3342687 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
3342704 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3342720 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
3342737 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3342753 TGTA
1 TGTA
3342757 ATAGCTAATC
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
16 51 0.62
17 31 0.38
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3342701 original size:33 final size:33
Alignment explanation
Indices: 3342655--3342756 Score: 188
Period size: 33 Copynumber: 3.1 Consensus size: 33
3342645 TTTGGTTCGC
*
3342655 TGTATT-GGATTAGAGGTGTATTGGATTATAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
3342687 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
3342720 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
3342753 TGTA
1 TGTA
3342757 ATAGCTAATC
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 6 0.09
33 62 0.91
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (33 bp):
TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
Found at i:3342727 original size:49 final size:49
Alignment explanation
Indices: 3342655--3342756 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 49
3342645 TTTGGTTCGC
*
3342655 TGTATTGGATTAGAGGTGTATT-GGATTATAGGTGTATTGGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGGATTAGAGGTGTATT-GGATTAGAGG
3342704 TGTATTGGATTAGAGGTGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGGATTAGAGGTGTATTGGATTAGAGG
3342753 TGTA
1 TGTA
3342757 ATAGCTAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 36 0.71
50 15 0.29
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (49 bp):
TGTATTGGATTAGAGGTGTATTGGGATTAGAGGTGTATTGGATTAGAGG
Found at i:3342821 original size:44 final size:45
Alignment explanation
Indices: 3342737--3342827 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3342727 GGATTAGAGG
* * *
3342737 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
3342782 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
3342826 TG
1 TG
3342828 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:3343001 original size:15 final size:15
Alignment explanation
Indices: 3342981--3343022 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3342971 TTTAAACATA
3342981 ATTATAATTAAATAT
1 ATTATAATTAAATAT
3342996 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3343010 A-TATAATTTAATA
1 ATTATAATTAAATA
3343023 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3343009 original size:16 final size:16
Alignment explanation
Indices: 3342972--3343013 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
3342962 TTAATCATAT
3342972 TTAAACATA-ATTATAA
1 TTAAA-ATATATTATAA
3342988 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3343003 TTAAAATATAT
1 TTAAAATATAT
3343014 AATTTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3343021 original size:18 final size:18
Alignment explanation
Indices: 3342978--3343026 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
3342968 ATATTTAAAC
3342978 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
*
3342996 AT--TATAATTAAAATAT
1 ATAATTTAATTAAAATAT
3343012 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
3343027 TCTTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 6 0.23
18 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:3343257 original size:14 final size:15
Alignment explanation
Indices: 3343208--3343259 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3343198 ATAAAATATA
3343208 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3343223 TATTAAATATATTAT
1 AATTAAATATATTAT
3343238 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3343251 AATTTAATA
1 AATTAAATA
3343260 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3343368 original size:16 final size:17
Alignment explanation
Indices: 3343343--3343383 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
3343333 AAATAATTAA
3343343 AATT-AAATATAT-TTT
1 AATTAAAATATATATTT
3343358 AATTAAAATATATGATTT
1 AATTAAAATATAT-ATTT
3343376 AA-TAAAAT
1 AATTAAAAT
3343384 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 6 0.26
18 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAAAATATATATTT
Found at i:3343395 original size:120 final size:120
Alignment explanation
Indices: 3342975--3343384 Score: 711
Period size: 120 Copynumber: 3.4 Consensus size: 120
3342965 ATCATATTTA
3342975 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
3343040 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
3343095 AACATAA-T-T-ATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
3343157 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
3343212 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* * *
3343277 TATTCTTATATGAATTTACTCAAATCATAATATATTATACTATAAAAGATAATTTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA-ATT
* * *
3343333 AA-ATAATTAAAATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
3343385 TAAAATAATT
Statistics
Matches: 278, Mismatches: 8, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
117 115 0.41
118 2 0.01
119 2 0.01
120 155 0.56
121 4 0.01
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:3345573 original size:21 final size:21
Alignment explanation
Indices: 3345547--3345589 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3345537 GGTTCGTTGT
*
3345547 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
3345568 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
3345589 A
1 A
3345590 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:3345589 original size:16 final size:16
Alignment explanation
Indices: 3345570--3345602 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3345560 TGTATTGGAT
*
3345570 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
3345586 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
3345602 T
1 T
3345603 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:3345647 original size:45 final size:44
Alignment explanation
Indices: 3345581--3345675 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
3345571 GGATTAGAGG
* *
3345581 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
3345626 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
3345670 TGTAAT
1 TGTAAT
3345676 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:3345858 original size:18 final size:17
Alignment explanation
Indices: 3345837--3345871 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3345827 TTATTATTTA
*
3345837 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3345855 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3345872 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3345865 original size:28 final size:27
Alignment explanation
Indices: 3345795--3345867 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3345785 TTTATTATCA
*
3345795 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
3345823 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
3345850 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
3345868 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:3345984 original size:144 final size:147
Alignment explanation
Indices: 3345756--3346027 Score: 469
Period size: 144 Copynumber: 1.9 Consensus size: 147
3345746 ATGATTATTG
3345756 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
3345821 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
3345886 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
3345905 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
3345967 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
3346028 ATATTCTTAT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
144 90 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:3346002 original size:18 final size:17
Alignment explanation
Indices: 3345981--3346015 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3345971 TTATTATTAA
*
3345981 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3345999 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3346016 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3349733 original size:17 final size:17
Alignment explanation
Indices: 3349707--3349740 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3349697 ACTCGTTATC
3349707 TAATACATAGATAGGAT
1 TAATACATAGATAGGAT
*
3349724 TAATATATAGATAGGAT
1 TAATACATAGATAGGAT
3349741 CCTAAATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (17 bp):
TAATACATAGATAGGAT
Found at i:3358909 original size:13 final size:13
Alignment explanation
Indices: 3358874--3358919 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3358864 TTAAATAAAA
3358874 ATTTT-AAAATA-
1 ATTTTAAAAATAT
*
3358885 ATTTTATTAAATAT
1 ATTTTA-AAAATAT
3358899 ATTTTAAAAATAT
1 ATTTTAAAAATAT
*
3358912 ACTTTAAA
1 ATTTTAAA
3358920 CTTTTACATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.17
13 18 0.62
14 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:3365912 original size:17 final size:19
Alignment explanation
Indices: 3365892--3365947 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 19
3365882 ATATGGGACA
3365892 ATTTTTTAAAAAA-A-AAT
1 ATTTTTTAAAAAATATAAT
3365909 A--TTTTAAAAAATATAAT
1 ATTTTTTAAAAAATATAAT
*
3365926 A-TTTTT-ACAAATAT-AT
1 ATTTTTTAAAAAATATAAT
3365942 ATTTTT
1 ATTTTT
3365948 ACAAAGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 10 0.29
16 4 0.12
17 16 0.47
18 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTTTAAAAAATATAAT
Found at i:3365949 original size:16 final size:17
Alignment explanation
Indices: 3365906--3365958 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
3365896 TTTAAAAAAA
* *
3365906 AATATTTTAAAAAATAT
1 AATATTTTTACAAATAT
3365923 AATATTTTTACAAATAT
1 AATATTTTTACAAATAT
*
3365940 -ATATTTTTACAAAGAT
1 AATATTTTTACAAATAT
3365956 AAT
1 AAT
3365959 GAATTTTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTTTTACAAATAT
Found at i:3368535 original size:18 final size:17
Alignment explanation
Indices: 3368509--3368546 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3368499 CACTCTAGAC
*
3368509 ATATTTTTTAATATTTTT
1 ATATATTTTAA-ATTTTT
3368527 ATATATTTTAAATTTTT
1 ATATATTTTAAATTTTT
3368544 ATA
1 ATA
3368547 ACATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATATTTTAAATTTTT
Found at i:3368811 original size:9 final size:9
Alignment explanation
Indices: 3368799--3368836 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3368789 GTGTTATACG
3368799 TTTTATATA
1 TTTTATATA
*
3368808 TTTT-TAGA
1 TTTTATATA
*
3368816 TTTTATTTA
1 TTTTATATA
3368825 TTTTATATA
1 TTTTATATA
3368834 TTT
1 TTT
3368837 GGACAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTATATA
Found at i:3371167 original size:30 final size:32
Alignment explanation
Indices: 3371126--3371213 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
3371116 TAGAAACAGT
3371126 ACATA-AA-TCTTAAAAGTTAACAATGAC-A-
1 ACATAGAAGTCTTAAAAGTTAACAATGACAAC
**
3371154 ACATAGAAGTCTTAAAAGTTTAA-AAAAACAAC
1 ACATAGAAGTCTTAAAAG-TTAACAATGACAAC
* *
3371186 ACAAAGTAAGTCTTGAAAGTTAACAATG
1 ACATAG-AAGTCTTAAAAGTTAACAATG
3371214 GTAGAACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 13 0.28
31 5 0.11
32 9 0.19
33 13 0.28
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (32 bp):
ACATAGAAGTCTTAAAAGTTAACAATGACAAC
Found at i:3372442 original size:23 final size:22
Alignment explanation
Indices: 3372414--3372477 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3372404 AACATGAAAT
* *
3372414 TTTGTGAAACCTTTGTGGCGTAA
1 TTTGTGAAGCCTTTGTGGCAT-A
* *
3372437 TTTGTGACGCCTTTGTAGCATA
1 TTTGTGAAGCCTTTGTGGCATA
3372459 TTCTGTGAAGCCTTTGTGG
1 TT-TGTGAAGCCTTTGTGG
3372478 TCTGGTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (22 bp):
TTTGTGAAGCCTTTGTGGCATA
Found at i:3375045 original size:89 final size:89
Alignment explanation
Indices: 3374894--3375071 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
3374884 CTCCAACATG
3374894 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3374959 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3374983 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3375048 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3375072 CTATCATAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (89 bp):
AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
CATTTAACAACCTAACCATTCCAA
Found at i:3380697 original size:74 final size:74
Alignment explanation
Indices: 3380570--3380707 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 74
3380560 ACCAATTTTA
* * *
3380570 TTTTACTTTAATATTTTGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAAGTCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATG-AAGGCTTCTT
3380635 CCATCGTGTT
65 CCATCGTGTT
** *
3380645 TTTTA-TTTAATAATTCGACCGAAAGGT-ATCTATTAGGGGTAAAAGTGGAAATGAAGGCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGA-AGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTT
3380708 ATAGATGACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
73 10 0.18
74 41 0.73
75 5 0.09
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTTC
CATCGTGTT
Found at i:3380839 original size:7 final size:7
Alignment explanation
Indices: 3380823--3380869 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
3380813 AATATGTTCG
3380823 TAAA-TT
1 TAAATTT
3380829 TAAATTT
1 TAAATTT
3380836 TAAATTTT
1 TAAA-TTT
3380844 TAAATTTTT
1 TAAA--TTT
3380853 TAAATTT
1 TAAATTT
*
3380860 TAAAATT
1 TAAATTT
3380867 TAA
1 TAA
3380870 GTTTAATTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
6 4 0.11
7 18 0.49
8 7 0.19
9 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TAAATTT
Found at i:3380846 original size:8 final size:8
Alignment explanation
Indices: 3380827--3380867 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
3380817 TGTTCGTAAA
3380827 TTTAAA-T
1 TTTAAATT
3380834 TTTAAATT
1 TTTAAATT
3380842 TTTAAATTT
1 TTTAAA-TT
3380851 TTTAAATT
1 TTTAAATT
*
3380859 TTAAAATT
1 TTTAAATT
3380867 T
1 T
3380868 AAGTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
7 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTAAATT
Found at i:3380855 original size:17 final size:17
Alignment explanation
Indices: 3380833--3380867 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3380823 TAAATTTAAA
*
3380833 TTTTAAATTTTTAAATT
1 TTTTAAATTTTAAAATT
3380850 TTTTAAATTTTAAAATT
1 TTTTAAATTTTAAAATT
3380867 T
1 T
3380868 AAGTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTTAAAATT
Found at i:3383535 original size:62 final size:63
Alignment explanation
Indices: 3383406--3383571 Score: 183
Period size: 62 Copynumber: 2.6 Consensus size: 63
3383396 CATGGTTAAA
* * * * * *
3383406 GTTCGAATGTATGATACAAGTTTATTGAGCTGAACTTAATATTATGAATTTCATATATATATGTG
1 GTTCGAATATAT-ATTCAAG-TTCTTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
* *
3383471 GTTCGAATATATATTCAAGTTCTTGAGCTGAATTTAAT-GTATGAATTTTATATACATATATG
1 GTTCGAATATATATTCAAGTTCTTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
* *
3383533 GTTCGAATAT-TAGTTACAAATTCCTTGAGCTGAAGTTAA
1 GTTCGAATATATA-TT-CAAGTT-CTTGAGCTGAACTTAA
3383572 AGTTGTGAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
61 2 0.02
62 32 0.36
63 22 0.25
64 21 0.24
65 11 0.12
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (63 bp):
GTTCGAATATATATTCAAGTTCTTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
Found at i:3383776 original size:41 final size:40
Alignment explanation
Indices: 3383719--3383832 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
3383709 TGAGATTTTT
3383719 AGACTTTACGTCTAGCATGCTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTGAAATATTTC
3383760 AGACTTTACGTCTAGCAGACTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAG-CTTAATGCCGGTGAAATATTTC
* *
3383801 AGACCTTACGTCTAGCAGGTTTAATGCCGGTG
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTG
3383833 TATTGAATCA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
40 1 0.01
41 67 0.97
42 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (40 bp):
AGACTTTACGTCTAGCAGCTTAATGCCGGTGAAATATTTC
Found at i:3389176 original size:41 final size:41
Alignment explanation
Indices: 3389142--3389299 Score: 253
Period size: 41 Copynumber: 3.9 Consensus size: 41
3389132 ACTGGCACTT
* * * * *
3389142 AGCCTGCTAGACATAAAGTTTGAAATATTTCACTGGCGTCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCA
3389183 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCA
*
3389224 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCA
*
3389265 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCG
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCG
3389300 ACAATAAACC
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCA
Found at i:3389331 original size:82 final size:82
Alignment explanation
Indices: 3389164--3389315 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
3389154 ATAAAGTTTG
* * * *
3389164 AAATATTTCACTGGCGTCAAGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGGCATCAAGCCT
1 AAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGACATCAAACCT
* *
3389229 GCTAGACTTAAAGTCTA
66 GATAGACTTAAAGCCTA
* *
3389246 AAATGTTTCACCGGCATCAAGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCGACAAT-AAACC
1 AAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGAC-ATCAAACC
3389310 TGATAG
65 TGATAG
3389316 GCATTGAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 60 0.97
83 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (82 bp):
AAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATGTTTCACCGACATCAAACCT
GATAGACTTAAAGCCTA
Found at i:3390891 original size:19 final size:20
Alignment explanation
Indices: 3390854--3390897 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3390844 CTTTTGTTTT
3390854 ATTTAGTTATCATTATACTA
1 ATTTAGTTATCATTATACTA
* *
3390874 ATTTA-TTATTATTTTACTA
1 ATTTAGTTATCATTATACTA
3390893 ATTTA
1 ATTTA
3390898 ACCTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTAGTTATCATTATACTA
Found at i:3391142 original size:14 final size:15
Alignment explanation
Indices: 3391123--3391151 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3391113 TCACAAAACT
3391123 TTCACACAT-ATAAA
1 TTCACACATAATAAA
3391137 TTCACACATAATAAA
1 TTCACACATAATAAA
3391152 CATAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:3393301 original size:2 final size:2
Alignment explanation
Indices: 3393294--3393327 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3393284 CAAACAAGGG
3393294 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3393328 ATTCCATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3400867 original size:13 final size:13
Alignment explanation
Indices: 3400845--3400877 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3400835 CCCCATATAC
*
3400845 AGATAAATATAAT
1 AGATACATATAAT
3400858 AGATACATATAAT
1 AGATACATATAAT
3400871 AGATACA
1 AGATACA
3400878 AATATACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (13 bp):
AGATACATATAAT
Found at i:3408355 original size:27 final size:26
Alignment explanation
Indices: 3408325--3408381 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
3408315 AATTTCGAGG
*
3408325 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
*
3408351 ATTTACATTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
3408378 TTTA
1 TTTA
3408382 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:3408537 original size:22 final size:23
Alignment explanation
Indices: 3408498--3408540 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3408488 TTTAAAAAAT
*
3408498 AAAACATAATATAATATTTATCA
1 AAAAAATAATATAATATTTATCA
*
3408521 AAAAAATAA-ATATTATTTAT
1 AAAAAATAATATAATATTTAT
3408541 TTGATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATAATATAATATTTATCA
Found at i:3408648 original size:43 final size:43
Alignment explanation
Indices: 3408599--3408800 Score: 244
Period size: 43 Copynumber: 4.7 Consensus size: 43
3408589 CGAGAAGCAT
* * * *
3408599 CGCTAAAGGT-TTGTTCTATAGCGGCGTTTGTGATAAAAAGCGC
1 CGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTG-GAAAAAGCGC
* * *
3408642 CGCTAAAGATCATGGTCTTTAGCGGCATTTGTGGTAAAAGCGC
1 CGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
* ** * **
3408685 CACTAAAGAACATGGTCTTTAGCGGCGTTTGTGGGAAAAGTTC
1 CGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
* *
3408728 CGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGC
1 CGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
*
3408771 CACTAAAGGTCATGGTCTTTAGCGGCGTTT
1 CGCTAAAGGTCATGGTCTTTAGCGGCGTTT
3408801 ATTTCCAAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
43 116 0.87
44 18 0.13
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
CGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGC
Found at i:3409119 original size:18 final size:20
Alignment explanation
Indices: 3409091--3409128 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3409081 TTAATTAAGA
3409091 AATTAAATAAAT-ATATTTT
1 AATTAAATAAATAATATTTT
3409110 AATT-AATAAATAATATTTT
1 AATTAAATAAATAATATTTT
3409129 TTTAGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAAATAAATAATATTTT
Found at i:3415518 original size:26 final size:26
Alignment explanation
Indices: 3415482--3415536 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
3415472 TCTTCAATGA
3415482 TTAATTTCTAACCGGTTTTTTGGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
*
3415508 TTAATTTCTAACCGGTTTTTTTGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
3415534 TTA
1 TTA
3415537 TTAGTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (26 bp):
TTAATTTCTAACCGGTTTTTTGGTGG
Found at i:3419345 original size:54 final size:54
Alignment explanation
Indices: 3419281--3419387 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
3419271 TTTGAACAGT
* *
3419281 AGTCTCCCCCT-AAGCAGTAGCTT-CCCTTCGAACAATGGTGTTTTCTGGAATAAC
1 AGTCTCCCCCTGAA-CAATAACTTCCCCTT-GAACAATGGTGTTTTCTGGAATAAC
*
3419335 AGTCTTCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
1 AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
3419388 AGTTTTCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
54 41 0.85
55 7 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (54 bp):
AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAAC
Found at i:3439677 original size:10 final size:10
Alignment explanation
Indices: 3439624--3439689 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
3439614 ACGTTATTTT
3439624 TATTTTTAAA
1 TATTTTTAAA
*
3439634 AATTTTTAAA
1 TATTTTTAAA
* *
3439644 GAGTTTT-AA
1 TATTTTTAAA
*
3439653 T-TTTTCACAA
1 TATTTTTA-AA
3439663 T-TTTTTAAA
1 TATTTTTAAA
3439672 TATTTTCT-AA
1 TATTTT-TAAA
3439682 TATTTTTA
1 TATTTTTA
3439690 TTGAAAATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
8 3 0.07
9 6 0.14
10 34 0.77
11 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:3439677 original size:27 final size:26
Alignment explanation
Indices: 3439618--3439677 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
3439608 TAAATAACGT
*
3439618 TATTTTTATTTTTAAAAATTTTTAAA
1 TATTTTAATTTTTAAAAATTTTTAAA
* * *
3439644 GAGTTTTAATTTTTCACAATTTTTTAAA
1 TA-TTTTAATTTTT-AAAAATTTTTAAA
3439672 TATTTT
1 TATTTT
3439678 CTAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.04
27 14 0.52
28 12 0.44
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TATTTTAATTTTTAAAAATTTTTAAA
Found at i:3446811 original size:23 final size:23
Alignment explanation
Indices: 3446797--3446842 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3446787 GTTTGCGAAT
* *
3446797 GTTAAATGAACATGTTCGTAAAC
1 GTTAAATGAAAATGTTCGCAAAC
*
3446820 GTTAAATGAAAATGTTCACAAAC
1 GTTAAATGAAAATGTTCGCAAAC
3446843 AATAAACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (23 bp):
GTTAAATGAAAATGTTCGCAAAC
Found at i:3446848 original size:23 final size:23
Alignment explanation
Indices: 3446799--3446848 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
3446789 TTGCGAATGT
* ** **
3446799 TAAATGAACATGTTCGTAAACGT
1 TAAATGAAAATGTTCACAAACAA
3446822 TAAATGAAAATGTTCACAAACAA
1 TAAATGAAAATGTTCACAAACAA
3446845 TAAA
1 TAAA
3446849 CCAACCAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (23 bp):
TAAATGAAAATGTTCACAAACAA
Found at i:3453376 original size:16 final size:18
Alignment explanation
Indices: 3453353--3453392 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
3453343 TTTTTATTTT
3453353 TATTTTGATAATT-TAAA
1 TATTTTGATAATTGTAAA
*
3453370 T-TTTTGATGATTGTAAA
1 TATTTTGATAATTGTAAA
3453387 TATTTT
1 TATTTT
3453393 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 10 0.50
17 6 0.30
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TATTTTGATAATTGTAAA
Found at i:3454593 original size:69 final size:68
Alignment explanation
Indices: 3454508--3454635 Score: 175
Period size: 69 Copynumber: 1.9 Consensus size: 68
3454498 AGCATTTTCC
* * *
3454508 ATTGATTTAGTATATTTTACACAATCAAATACAAAAAAAATGAAAAAAATATTTTCCGTAAAATT
1 ATTGATCTAGTATATTTTACACAATCAAACAC-AAAAAAATGAAAAAAATAATTTCCGTAAAATT
3454573 TTAA
65 TTAA
* * ** *
3454577 ATTGATCTATTATATTTTACACAATTAAACACCGAAAAATGAGAAAAATAATTTCCGTA
1 ATTGATCTAGTATATTTTACACAATCAAACACAAAAAAATGAAAAAAATAATTTCCGTA
3454636 CAGAAACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
68 23 0.45
69 28 0.55
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (68 bp):
ATTGATCTAGTATATTTTACACAATCAAACACAAAAAAATGAAAAAAATAATTTCCGTAAAATTT
TAA
Found at i:3459914 original size:2 final size:2
Alignment explanation
Indices: 3459907--3459935 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3459897 AATCTAAAAC
3459907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3459936 GAAAAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3466436 original size:45 final size:45
Alignment explanation
Indices: 3466386--3466487 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 45
3466376 AACGGTAGCA
* * ** *
3466386 GTAACAATAGCAGTGACAGTATTC-AGCACACAAAGTGTTGAATCT
1 GTAACAATAACAGTAACAGTATTCGA-CACACAAAGTGCCGAATCG
* **
3466431 GTAACAGTAATGGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAATAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
3466476 GTAACAGTAACA
1 GTAACAATAACA
3466488 ATAGTTCGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.22
Consensus pattern (45 bp):
GTAACAATAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
Found at i:3467998 original size:25 final size:23
Alignment explanation
Indices: 3467954--3468014 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
3467944 ATTTTAATTC
*
3467954 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
3467978 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
3468002 ATATAAATTATAT
1 AT-TTAATTATAT
3468015 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:3468003 original size:35 final size:33
Alignment explanation
Indices: 3467962--3468045 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 33
3467952 TCATTTAATA
* *
3467962 ATATAATATCATTATAATTTAATTATCATAAATT
1 ATATAATATAATTAT-ATTTAAATATCATAAATT
*
3467996 CATATAATATAAATTATATTTAAATATCATTAATT
1 -ATATAATAT-AATTATATTTAAATATCATAAATT
3468031 ATATATATATAATTA
1 ATATA-ATATAATTA
3468046 AACAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
34 10 0.23
35 29 0.66
36 5 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAATTATATTTAAATATCATAAATT
Found at i:3472353 original size:43 final size:43
Alignment explanation
Indices: 3472268--3472353 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
3472258 AATCATGACA
* * * *
3472268 ACTTTACGTAAAAGTATTTATGATAAAATATATTTAATTTTTT
1 ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
3472311 ACTTTATCATAAAAGTATCTATAAGAAAATATATTTAATTTTT
1 ACTTTA-CATAAAAGTATCTATAAGAAAATATATTTAATTTTT
3472354 CTACATTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (43 bp):
ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
Found at i:3476940 original size:19 final size:20
Alignment explanation
Indices: 3476916--3476961 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
3476906 ACATATTGCC
3476916 TTAGATTATGTCAAAGGCA-
1 TTAGATTATGTCAAAGGCAT
3476935 TTAGATTATGTCAAAGGCAT
1 TTAGATTATGTCAAAGGCAT
3476955 TTAGATT
1 TTAGATT
3476962 GAGTTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (20 bp):
TTAGATTATGTCAAAGGCAT
Found at i:3477778 original size:28 final size:29
Alignment explanation
Indices: 3477720--3477778 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
3477710 AAATGTATAT
* *
3477720 AAAAAAGTATGTAACAATTTTTTTTCCTGA
1 AAAAAAGTATGTAACAATATTTTAT-CTGA
3477750 AAAAAATGTATGTAACAA-ATTTTAT-TGA
1 AAAAAA-GTATGTAACAATATTTTATCTGA
3477778 A
1 A
3477779 TTAAATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
30 11 0.42
31 11 0.42
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAAAAGTATGTAACAATATTTTATCTGA
Found at i:3479504 original size:17 final size:17
Alignment explanation
Indices: 3479484--3479538 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
3479474 AAATTGTGAT
*
3479484 AAAATTAAAATTTATTA
1 AAAATTAAAATATATTA
3479501 AAAATTACAAA-ATACTTAA
1 AAAATTA-AAATATA-TT-A
*
3479520 AAAATAAAAATATATTA
1 AAAATTAAAATATATTA
3479537 AA
1 AA
3479539 GTTATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 12 0.38
18 10 0.31
19 10 0.31
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTAAAATATATTA
Found at i:3479537 original size:18 final size:18
Alignment explanation
Indices: 3479484--3479538 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
3479474 AAATTGTGAT
* *
3479484 AAAATTAAAATTTATTAA
1 AAAATAAAAATATATTAA
* *
3479502 AAATTACAAAATA-CTTAA
1 AAAATA-AAAATATATTAA
3479520 AAAATAAAAATATATTAA
1 AAAATAAAAATATATTAA
3479538 A
1 A
3479539 GTTATTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAAAAATATATTAA
Found at i:3480048 original size:24 final size:24
Alignment explanation
Indices: 3480020--3480068 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3480010 ATATGAGTAC
3480020 AATATATTA--TAT-AAATTATATA
1 AATATATTATTTATGAAATT-TATA
3480042 AATATATTATTTATGAAATTTATA
1 AATATATTATTTATGAAATTTATA
3480066 AAT
1 AAT
3480069 GATCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATATTATTTATGAAATTTATA
Found at i:3481863 original size:23 final size:23
Alignment explanation
Indices: 3481837--3481883 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3481827 ATGTTATAAC
3481837 TTTTTTTTATTTACCAAAATATA
1 TTTTTTTTATTTACCAAAATATA
3481860 TTTTTTTTATTTACCAAAATATA
1 TTTTTTTTATTTACCAAAATATA
3481883 T
1 T
3481884 CAAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTTTATTTACCAAAATATA
Found at i:3482046 original size:19 final size:19
Alignment explanation
Indices: 3482024--3482101 Score: 104
Period size: 19 Copynumber: 4.2 Consensus size: 19
3482014 TATTCTCCTT
* *
3482024 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
3482043 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
* * *
3482062 TAA-ACTATTCTCATTTAA
1 TAACTCTATTTTAATTTAA
3482080 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
3482099 TAA
1 TAA
3482102 ACTATTAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
18 15 0.30
19 35 0.70
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:3482081 original size:37 final size:37
Alignment explanation
Indices: 3482037--3482107 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
3482027 CTCTTTTTTT
3482037 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
3482074 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
3482108 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:3482362 original size:18 final size:18
Alignment explanation
Indices: 3482325--3482393 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
3482315 TCAACTCAAT
* *
3482325 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
3482344 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
* *
3482362 TTCTCATTTAATAAATCTA
1 TTTTAATTTAATAAA-CTA
3482381 TTTTAATTTAATA
1 TTTTAATTTAATA
3482394 TAATATTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.37
19 27 0.63
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:3482711 original size:37 final size:37
Alignment explanation
Indices: 3482664--3482734 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
3482654 AGTATTACTT
*
3482664 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
3482701 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
3482735 AAAAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (37 bp):
AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:3482739 original size:19 final size:19
Alignment explanation
Indices: 3482670--3482738 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3482660 ACTTAATAGT
3482670 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
3482689 TTATTAAATGAGAATAG-C
1 TTATTAAATTAAAATAGAG
3482707 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
3482726 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
3482739 AAAAGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:3482745 original size:20 final size:19
Alignment explanation
Indices: 3482670--3482747 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
3482660 ACTTAATAGT
* *
3482670 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
* * * *
3482689 TTATTAAATGAGAATAG-C
1 TTATTAAATAAAAAAAGAG
* *
3482707 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
3482726 TTATTAAATAAAAAAAAGAG
1 TTATTAAAT-AAAAAAAGAG
3482746 TT
1 TT
3482748 GAAGGGGAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
18 15 0.31
19 24 0.49
20 10 0.20
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.35
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:3482861 original size:27 final size:28
Alignment explanation
Indices: 3482812--3482882 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
3482802 ACTTTTTTTC
*
3482812 CTTTGGCACCA-TGGTGCCGCCAA-TGA
1 CTTTGGCACCATTGGTGCCACCAATTGA
*
3482838 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCACCAATTGA
*
3482866 -TTTGGCACCTTTGGTGC
1 CTTTGGCACCATTGGTGC
3482883 TGCCAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.28
27 27 0.68
28 2 0.05
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (28 bp):
CTTTGGCACCATTGGTGCCACCAATTGA
Found at i:3482888 original size:27 final size:26
Alignment explanation
Indices: 3482813--3482898 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
3482803 CTTTTTTTCC
* *
3482813 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
3482838 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
*
3482866 TTTGGCACCTTTGGTGCTGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
3482893 ATTGGC
1 TTTGGC
3482899 CTGATCAGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.78
28 2 0.04
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:3482969 original size:24 final size:24
Alignment explanation
Indices: 3482936--3482983 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3482926 TTTGTTTTTT
3482936 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
*
3482960 TATATTTTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
3482984 AGTTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAAAA
Found at i:3488230 original size:16 final size:17
Alignment explanation
Indices: 3488191--3488230 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
3488181 TTTTATAACA
3488191 TAAT-AAATTATTATTT
1 TAATAAAATTATTATTT
3488207 TAATAAAATT-TTATTT
1 TAATAAAATTATTATTT
3488223 TAATAAAA
1 TAATAAAA
3488231 AAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAAAATTATTATTT
Found at i:3488456 original size:16 final size:18
Alignment explanation
Indices: 3488433--3488473 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3488423 ATTATGTCTA
3488433 TATAAAATA-T-AATTAT
1 TATAAAATATTAAATTAT
*
3488449 TTTAAAATATTAAATTAT
1 TATAAAATATTAAATTAT
3488467 TATAAAA
1 TATAAAA
3488474 AATACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATATTAAATTAT
Found at i:3488466 original size:18 final size:16
Alignment explanation
Indices: 3488433--3488486 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 16
3488423 ATTATGTCTA
3488433 TATAAAATATAATTAT
1 TATAAAATATAATTAT
*
3488449 TTTAAAATATTAAATTAT
1 TATAAAATA-T-AATTAT
* *
3488467 TATAAAAAATACTT-T
1 TATAAAATATAATTAT
3488482 TATAA
1 TATAA
3488487 TATTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 2 0.06
18 13 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAAAATATAATTAT
Found at i:3489037 original size:2 final size:2
Alignment explanation
Indices: 3489032--3489058 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3489022 GTAAGCCCCC
3489032 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3489059 ACATCACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3493956 original size:20 final size:21
Alignment explanation
Indices: 3493919--3493957 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3493909 ACATAAAATC
*
3493919 GTTAAATGGTATCTATACTAG
1 GTTAAATGGTATCGATACTAG
3493940 GTTAAAT-GTATCGATACT
1 GTTAAATGGTATCGATACT
3493958 TTAAGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (21 bp):
GTTAAATGGTATCGATACTAG
Found at i:3500112 original size:72 final size:70
Alignment explanation
Indices: 3499994--3500137 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 70
3499984 TAGAAAAGAA
* *
3499994 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGGGAAAGAAAAAGAGAAAGAAAAAAAGAGA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAG--AGAAAAAAAGAGA
*
3500059 GAAGCTT
64 AAAGCTT
*
3500066 AGAAACATATGAAACGGAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
*
3500131 AGGTT
66 AGCTT
3500136 AG
1 AG
3500138 GGTTTTAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
70 20 0.30
72 47 0.70
ACGTcount: A:0.61, C:0.06, G:0.28, T:0.06
Consensus pattern (70 bp):
AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
AGCTT
Found at i:3507260 original size:19 final size:19
Alignment explanation
Indices: 3507225--3507262 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3507215 CCTAAATGAT
*
3507225 TTTAAATTGTTTTTAAAAC
1 TTTAAATTGTTTCTAAAAC
3507244 TTTAAATAT-TTTCTAAAAC
1 TTTAAAT-TGTTTCTAAAAC
3507263 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAATTGTTTCTAAAAC
Found at i:3509343 original size:19 final size:20
Alignment explanation
Indices: 3509321--3509362 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3509311 TTATTTAGGA
3509321 ATTTATATT-ATTATAT-CAT
1 ATTTA-ATTAATTATATACAT
*
3509340 ATTTAATTAATTTTATACAT
1 ATTTAATTAATTATATACAT
3509360 ATT
1 ATT
3509363 AAAGCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATTAATTATATACAT
Found at i:3511708 original size:30 final size:30
Alignment explanation
Indices: 3511630--3511716 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
3511620 TATTTATTTT
*
3511630 TATTTTTT-AAA-TTTTAAAATACTTTTAAAA
1 TATTTTTTAAAATTTTTTAAA-A-TTTTAAAA
*
3511660 TACTTTTTTTAAATTTTTT-AAATTTTAAAA
1 TA-TTTTTTAAAATTTTTTAAAATTTTAAAA
3511690 T-TTTTTTAAAATACTTTTTAAAATTTT
1 TATTTTTTAAAAT--TTTTTAAAATTTT
3511717 TTTAATTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
28 10 0.20
30 16 0.33
31 14 0.29
32 5 0.10
33 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTTTTTAAAATTTTTTAAAATTTTAAAA
Found at i:3511708 original size:40 final size:40
Alignment explanation
Indices: 3511631--3511757 Score: 200
Period size: 40 Copynumber: 3.1 Consensus size: 40
3511621 ATTTATTTTT
* *
3511631 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTAAA
*
3511672 ATTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
* *
3511712 ATTTTTTTAATTTTAAAATATTTTTAAAATGCTTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
3511752 ATTTTT
1 ATTTTT
3511758 ATTTTAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 50 0.62
41 30 0.38
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (40 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTAAA
Found at i:3511726 original size:29 final size:29
Alignment explanation
Indices: 3511693--3511750 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3511683 TTTAAAATTT
*
3511693 TTTTAAAATACTTTTTAAAAT-TTTTTTAA
1 TTTTAAAATA-TTTTTAAAATGCTTTTTAA
3511722 TTTTAAAATATTTTTAAAATGCTTTTTAA
1 TTTTAAAATATTTTTAAAATGCTTTTTAA
3511751 AATTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTAAAATATTTTTAAAATGCTTTTTAA
Found at i:3511749 original size:12 final size:11
Alignment explanation
Indices: 3511641--3511757 Score: 76
Period size: 11 Copynumber: 11.3 Consensus size: 11
3511631 ATTTTTTAAA
*
3511641 TTTTAAAATAC
1 TTTTAAAATAT
3511652 TTTTAAAATACTT
1 TTTTAAAATA--T
*
3511665 TTTTTAAAT-T
1 TTTTAAAATAT
3511675 TTTT--AA-A-
1 TTTTAAAATAT
*
3511682 TTTTAAAATTT
1 TTTTAAAATAT
3511693 TTTTAAAATACT
1 TTTTAAAATA-T
3511705 TTTTAAAAT-T
1 TTTTAAAATAT
*
3511715 TTTT----TAA
1 TTTTAAAATAT
3511722 TTTTAAAATAT
1 TTTTAAAATAT
*
3511733 TTTTAAAATGCT
1 TTTTAAAAT-AT
3511745 TTTTAAAAT-T
1 TTTTAAAATAT
3511755 TTT
1 TTT
3511758 ATTTTAATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 29
0.70 0.06 0.24
Matches are distributed among these distances:
6 1 0.01
7 8 0.09
8 2 0.02
9 2 0.02
10 14 0.16
11 30 0.35
12 20 0.24
13 8 0.09
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3513454 original size:152 final size:152
Alignment explanation
Indices: 3513197--3513787 Score: 1069
Period size: 152 Copynumber: 3.9 Consensus size: 152
3513187 TGTCATGGAT
* * *
3513197 GGTATTTTAAATGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTCTGAAGCTGAG-
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTG-GT
* * *
3513261 CACAATGT-AAAGTTCGGATATCTTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTG
65 GACAATGTGAAA-TTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTG
3513325 ATCTATTTCTTTGCTGTCATGTTC
129 ATCTATTTCTTTGCTGTCATGTTC
*
3513349 AGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
3513414 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
3513479 CTATTTCTTTGCTGTCATGTTC
131 CTATTTCTTTGCTGTCATGTTC
3513501 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
3513566 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
3513631 CTATTTCTTTGCTGTCATGTTC
131 CTATTTCTTTGCTGTCATGTTC
3513653 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
1 GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
* *
3513718 ACAATGTGAAATTCGGATTTCCTTTGGCCTTTACCACCTCCATGCTTTCGTGGAATGTGATTGAT
66 ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
3513783 CTATT
131 CTATT
3513788 GCTAAAAAAT
Statistics
Matches: 427, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
151 1 0.00
152 423 0.99
153 3 0.01
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (152 bp):
GGTATCTTAAGTGTGAAATATGGAGATGAGGGTTGATTTGGTTGGAGGATACTATGAAGCTGGTG
ACAATGTGAAATTCGGATTTCCTTTGGCCTTCACCACCTCCATGCTTTCGTGGAGTGTGATTGAT
CTATTTCTTTGCTGTCATGTTC
Found at i:3518594 original size:14 final size:15
Alignment explanation
Indices: 3518572--3518648 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3518562 CAATCAAACA
3518572 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
3518586 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
3518601 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
3518621 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
3518635 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
3518649 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:3518613 original size:20 final size:20
Alignment explanation
Indices: 3518588--3518627 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3518578 AATATTTTCC
*
3518588 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3518608 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3518628 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3518633 original size:34 final size:35
Alignment explanation
Indices: 3518576--3518642 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3518566 CAAACACCAG
*
3518576 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3518611 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3518643 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3520557 original size:138 final size:138
Alignment explanation
Indices: 3520309--3520581 Score: 485
Period size: 138 Copynumber: 2.0 Consensus size: 138
3520299 GAGATGCGTT
* *
3520309 TTGCAGTTATGTCTTTTAAGTAGTTTCCTATAGAGTATTAATGGAGATGATTGGCATTTCTTAAT
1 TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
3520374 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTT-CTC
66 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCT-
3520438 AAGAAACTA
130 AAGAAACTA
* *
3520447 TTGCAGTTATGTCTTTTAGGTAGTTCCCTGTAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
1 TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
*
3520512 TCCATTGAGTGCAATTCGAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
66 TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
3520577 AGAAA
131 AGAAA
3520582 TTGTAAAAGA
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
138 127 0.98
139 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (138 bp):
TTGCAGTTATGTCTTTTAAGTAGTTCCCTATAGAGTATTAATGGAGATGATTGCCATTTCTTAAT
TCCATTGAGTGCAATTCAAGTGAATTCAATATTTTCTAGCTTGTACCAATGTGTCAAATTTCCTA
AGAAACTA
Found at i:3520895 original size:30 final size:28
Alignment explanation
Indices: 3520841--3520935 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
3520831 AAATTATTAA
3520841 AATATTAATATAAA-ATAT-TATAATTTTT
1 AATATT-AT-TAAACATATATATAATTTTT
3520869 AATATTATTAAACATACATATATAATTATTT
1 AATATTATTAAACAT--ATATATAATT-TTT
*
3520900 -ATA-T-TTAATCATATA-ATAATTTATT
1 AATATTATTAAACATATATATAATTT-TT
*
3520925 AATATAATTAA
1 AATATTATTAA
3520936 TATAATTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
24 1 0.02
25 8 0.14
26 10 0.18
27 4 0.07
28 17 0.30
29 3 0.05
30 10 0.18
31 3 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATTATTAAACATATATATAATTTTT
Found at i:3520938 original size:25 final size:25
Alignment explanation
Indices: 3520910--3520967 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
3520900 ATATTTAATC
3520910 ATATAATAATT-TATTAATATAATTA
1 ATATAATAATTATATTAATA-AATTA
* *
3520935 ATATAATTTATTATTTTAATAAATTA
1 ATATAA-TAATTATATTAATAAATTA
3520961 AT-TAATA
1 ATATAATA
3520968 TTTCAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 1 0.04
25 9 0.32
26 11 0.39
27 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATATAATAATTATATTAATAAATTA
Found at i:3520954 original size:22 final size:22
Alignment explanation
Indices: 3520888--3520963 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
3520878 AAACATACAT
*
3520888 ATATAA-TTATTTATATTTAATCAT
1 ATATAATTTA-TTAT-TTTAAT-AA
* * *
3520912 ATAATAATTTATTAATATAATTA
1 AT-ATAATTTATTATTTTAATAA
3520935 ATATAATTTATTATTTTAATAA
1 ATATAATTTATTATTTTAATAA
3520957 AT-TAATT
1 ATATAATT
3520964 AATATTTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.12
22 19 0.44
23 2 0.05
24 7 0.16
25 7 0.16
26 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAATTTATTATTTTAATAA
Found at i:3524304 original size:14 final size:15
Alignment explanation
Indices: 3524285--3524313 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3524275 TTCTTTTGAT
3524285 AAATAAAAA-ATAAA
1 AAATAAAAACATAAA
3524299 AAATAAAAACATAAA
1 AAATAAAAACATAAA
3524314 TTTTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAATAAAAACATAAA
Found at i:3526555 original size:19 final size:19
Alignment explanation
Indices: 3526524--3526572 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3526514 AAAAATATAA
*
3526524 ATTTTGAAATTTTTATAAAT
1 ATTTTG-AATTTTTAAAAAT
3526544 ATTTTGAA-TTTTAAAAAT
1 ATTTTGAATTTTTAAAAAT
3526562 -TATTTGAATTT
1 AT-TTTGAATTT
3526573 ATTTTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 15 0.58
19 4 0.15
20 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAAAT
Found at i:3536354 original size:21 final size:22
Alignment explanation
Indices: 3536306--3536358 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
3536296 GCAATATAAT
3536306 AACAAAATAGCAACAAAACAAC
1 AACAAAATAGCAACAAAACAAC
* *
3536328 ATCAAAAT-GCCAAC-AAACGAC
1 AACAAAATAG-CAACAAAACAAC
3536349 AACAAAATAG
1 AACAAAATAG
3536359 TAGTAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (22 bp):
AACAAAATAGCAACAAAACAAC
Found at i:3545832 original size:3 final size:3
Alignment explanation
Indices: 3545824--3545855 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3545814 GTTTGCTCGT
3545824 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3545856 TGAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Done.