Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 119 of 136
Found at i:40421931 original size:113 final size:114
Alignment explanation
Indices: 40421772--40422024 Score: 289
Period size: 113 Copynumber: 2.2 Consensus size: 114
40421762 ATAAATGAAG
* * * **
40421772 AATGAAATTGGACATCATAATTA-GCCTTCTAAAACAAAATGTAACATAAA-GAAAAATGAAACC
1 AATGAAATTGGACCTCAAAACTAGGCCTTCTAAAACAAAATACAACATAAATG-AAAATGAAACC
*
40421835 AAACCTCACAACCAAG-CTACTTAAATAGAATGCAACATAAATGAAAATGA
65 AAACCTCACAACCAAGCCT-CTAAAATAGAATGCAACATAAATGAAAATGA
* * ***
40421885 AATGAAATTGGACCTTAAAACTAGGCC-TCTAAAACAAAATACAACATAAATGGAAATGAAATTG
1 AATGAAATTGGACCTCAAAACTAGGCCTTCTAAAACAAAATACAACATAAATGAAAATGAAACCA
* * * * *
40421949 GACTTCATAACCAGGCCTCTAAAATAGGATGCAACATAAATGAAAATGA
66 AACCTCACAACCAAGCCTCTAAAATAGAATGCAACATAAATGAAAATGA
* * *
40421998 AATGAAACTAGACCTCACAACTAGGCC
1 AATGAAATTGGACCTCAAAACTAGGCC
40422025 CCTGGAAACA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
113 111 0.95
114 6 0.05
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (114 bp):
AATGAAATTGGACCTCAAAACTAGGCCTTCTAAAACAAAATACAACATAAATGAAAATGAAACCA
AACCTCACAACCAAGCCTCTAAAATAGAATGCAACATAAATGAAAATGA
Found at i:40429605 original size:27 final size:27
Alignment explanation
Indices: 40429545--40429605 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
40429535 ATCATCTCTT
*
40429545 GTTATTT-TATTATTATTTTATTCTAA
1 GTTATTTATATTATTATATTATTCTAA
* * *
40429571 ATTTTTTATAATTATTA-ATTATTTTAA
1 GTTATTTAT-ATTATTATATTATTCTAA
40429598 GTTATTTA
1 GTTATTTA
40429606 GGATTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 5 0.19
27 15 0.56
28 7 0.26
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (27 bp):
GTTATTTATATTATTATATTATTCTAA
Found at i:40431237 original size:13 final size:14
Alignment explanation
Indices: 40431216--40431252 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
40431206 TCCAAGTAAG
40431216 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
40431230 AT-AAATAACTAAA
1 ATAAAATAATTAAA
40431243 ATAAAATAAT
1 ATAAAATAAT
40431253 AAATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:40438314 original size:8 final size:9
Alignment explanation
Indices: 40438290--40438316 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40438280 GCAAAACAGT
40438290 TTATTTTTA
1 TTATTTTTA
40438299 TTATTTTTA
1 TTATTTTTA
40438308 TTATTTTTA
1 TTATTTTTA
40438317 ATTTTAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTA
Found at i:40443859 original size:24 final size:24
Alignment explanation
Indices: 40443764--40443859 Score: 102
Period size: 24 Copynumber: 3.9 Consensus size: 24
40443754 TAAATATTAA
* *
40443764 ATTATTTATATAGTTTTATTATAT
1 ATTATTTATATAATTTTATTGTAT
* * * *
40443788 ATTATATTTTTAAAATTTGTATTTTCT
1 A-T-TATTTATATAATTT-TATTGTAT
40443815 ATTATTTATATAATTTTATTGTAT
1 ATTATTTATATAATTTTATTGTAT
*
40443839 ATTATTTGTATAATTTTATTG
1 ATTATTTATATAATTTTATTG
40443860 CATTTTCCGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
24 27 0.46
25 13 0.22
26 12 0.20
27 7 0.12
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (24 bp):
ATTATTTATATAATTTTATTGTAT
Found at i:40446215 original size:11 final size:11
Alignment explanation
Indices: 40446199--40446224 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40446189 AAGTAAGAGC
40446199 TTCTTTTTTTT
1 TTCTTTTTTTT
40446210 TTCTTTTTTTT
1 TTCTTTTTTTT
40446221 TTCT
1 TTCT
40446225 GTAAACTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:40446331 original size:4 final size:4
Alignment explanation
Indices: 40446322--40446348 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40446312 GTAAGTTGAT
40446322 ATCC ATCC ATCC ATCC ATCC ATCC ATC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATC
40446349 AATACGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:40450235 original size:20 final size:20
Alignment explanation
Indices: 40450201--40450242 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40450191 AACTATTTAA
**
40450201 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAGTT
*
40450221 ATAATATTAAATGAATATTT
1 ATAATATTAAATGAATAGTT
40450241 AT
1 AT
40450243 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (20 bp):
ATAATATTAAATGAATAGTT
Found at i:40452142 original size:85 final size:86
Alignment explanation
Indices: 40452023--40452196 Score: 341
Period size: 85 Copynumber: 2.0 Consensus size: 86
40452013 TTTTTTCAAT
40452023 TTTGATTTTAATTCTAAAAAAATTTAAAGAAAAAACACAATTTTTCAATATTTTTAAAATGTTTT
1 TTTGATTTTAATTCTAAAAAAATTTAAAGAAAAAACACAATTTTTCAATATTTTTAAAATGTTTT
40452088 CAAAAAATATAAAATATATAA
66 CAAAAAATATAAAATATATAA
40452109 TTTGATTTTAATTC-AAAAAAATTTAAAGAAAAAACACAATTTTTCAATATTTTTAAAATGTTTT
1 TTTGATTTTAATTCTAAAAAAATTTAAAGAAAAAACACAATTTTTCAATATTTTTAAAATGTTTT
40452173 CAAAAAATATAAAATATATAA
66 CAAAAAATATAAAATATATAA
40452194 TTT
1 TTT
40452197 TCTTTAGATT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 74 0.84
86 14 0.16
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (86 bp):
TTTGATTTTAATTCTAAAAAAATTTAAAGAAAAAACACAATTTTTCAATATTTTTAAAATGTTTT
CAAAAAATATAAAATATATAA
Found at i:40457134 original size:132 final size:128
Alignment explanation
Indices: 40456839--40457196 Score: 562
Period size: 132 Copynumber: 2.8 Consensus size: 128
40456829 NNNNNNNNNA
40456839 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCAATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGC-ATCTT
40456904 CAATCTGCTCCACTACTGCTTAGGGAGAT-A-A--GATCTTCAATCTATTCCACTGTTGCCCAG
65 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCGATCTTCAATCTATTCCACTGTTGCCCAG
* *
40456964 GGAAGTAGAATTACTGGCTTTAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGTCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCG-CATCTT
* * *
40457029 CAATCTGCTCCACTACTGCTAAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCT
65 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATC-G--ATCTTCAATCTATTCCACTGTTGCCC
40457094 AG
127 AG
*
40457096 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCATAGGGAGGTAAAATCCGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCG-CATCTT
* *
40457161 CGATATGCTCCACTACTGCTTAGGGAGATAAGATCG
65 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCG
40457197 GTTTTAACCC
Statistics
Matches: 213, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
125 89 0.42
126 2 0.01
127 1 0.00
130 1 0.00
131 1 0.00
132 119 0.56
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (128 bp):
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCATCTTC
AATCTGCTCCACTACTGCTTAGGGAGATAAGATCGATCTTCAATCTATTCCACTGTTGCCCAG
Found at i:40457259 original size:44 final size:43
Alignment explanation
Indices: 40457182--40457533 Score: 228
Period size: 44 Copynumber: 8.3 Consensus size: 43
40457172 ACTACTGCTT
* * **
40457182 AGGGAGATAAGATCG--GTTTTAACCCACTCCACTGCAACTTC
1 AGGGAGATAAGATCGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
40457223 AGGGAGATAGGATCGTTGGCTTTAATCTACTCCACTGCAACTTC
1 AGGGAGATAAGATCG-TAGCTTTAATCTGCTCCACTGCAACTTC
* * * * *
40457267 AAGGAGATAAGA-C-TAGATGTGATCTGCT-CTCTGCAACTTC
1 AGGGAGATAAGATCGTAGCTTTAATCTGCTCCACTGCAACTTC
* * * ***
40457307 AGAGAGATAAGATTCGCCATCTTGGGTCTGC-CTCACTGCAACTTC
1 AGGGAGATAAGA-TCG-TAGCTTTAATCTGCTC-CACTGCAACTTC
* * * *
40457352 A-GGAGGATAAGACTTGTTTA-C-TTAGTTTGTTCCACTGCAACTTC
1 AGGGA-GATAAGA-TCG--TAGCTTTAATCTGCTCCACTGCAACTTC
* * * * *
40457396 AAGGAGATAAGA-C-TAGATGTGATCTGCT-CTCTGCAACTTC
1 AGGGAGATAAGATCGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
40457436 AGAGAGATAAGATCG--GCTTTAATCCGCTCCACTGTAACTTC
1 AGGGAGATAAGATCGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
40457477 AGGGAGATAGGATCGTTGGCTTTAATCTACTCCACTGCAACTTC
1 AGGGAGATAAGATCG-TAGCTTTAATCTGCTCCACTGCAACTTC
40457521 AGGGAGATAAGAT
1 AGGGAGATAAGAT
40457534 TTTCCATCTT
Statistics
Matches: 238, Mismatches: 52, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 51 0.21
41 53 0.22
42 1 0.00
43 1 0.00
44 103 0.43
45 26 0.11
46 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
AGGGAGATAAGATCGTAGCTTTAATCTGCTCCACTGCAACTTC
Found at i:40457314 original size:40 final size:42
Alignment explanation
Indices: 40457255--40457447 Score: 139
Period size: 40 Copynumber: 4.6 Consensus size: 42
40457245 TAATCTACTC
40457255 CACTGCAACTTCA-AGGAGATAAGACTAG-AT-GTGATCTGCT
1 CACTGCAACTTCAGA-GAGATAAGACTAGCATAGTGATCTGCT
* * * ** *
40457295 CTCTGCAACTTCAGAGAGATAAGATTCGCCATCTTGGGTCTGCCT
1 CACTGCAACTTCAGAGAGATAAGACTAG-CATAGT-GATCTG-CT
* ** * * * *
40457340 CACTGCAACTTCAG-GAGGATAAGACTTGTTTACTTAGTTTGTT
1 CACTGCAACTTCAGAGA-GATAAGACTAGCATAGTGA-TCTGCT
40457383 CCACTGCAACTTCA-AGGAGATAAGACTAG-AT-GTGATCTGCT
1 -CACTGCAACTTCAGA-GAGATAAGACTAGCATAGTGATCTGCT
*
40457424 CTCTGCAACTTCAGAGAGATAAGA
1 CACTGCAACTTCAGAGAGATAAGA
40457448 TCGGCTTTAA
Statistics
Matches: 118, Mismatches: 23, Indels: 24
0.72 0.14 0.15
Matches are distributed among these distances:
40 44 0.37
41 6 0.05
42 4 0.03
43 3 0.03
44 35 0.30
45 26 0.22
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (42 bp):
CACTGCAACTTCAGAGAGATAAGACTAGCATAGTGATCTGCT
Found at i:40457726 original size:50 final size:50
Alignment explanation
Indices: 40457573--40457747 Score: 154
Period size: 50 Copynumber: 3.5 Consensus size: 50
40457563 GTCGAGGATG
* * *
40457573 AGATTAGCCGTCGTAGCTTCAATCTGATCCACTGCACTGCCA-AGGAAATA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAGA-GAAATA
* ** * ** * * * * *
40457623 AGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTAGGGAAACA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAGAGAAATA
* *
40457673 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCTAGAGAAGTA
1 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAGAGAAATA
* * * *
40457723 AGATTCACTGTCGTGGTTTCAATCT
1 AGATTCGCCGTCGTAGCTTCAATCT
40457748 ACTTCACTGT
Statistics
Matches: 93, Mismatches: 31, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAGAGAAATA
Found at i:40465792 original size:18 final size:18
Alignment explanation
Indices: 40465771--40465814 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
40465761 ATATATATAT
40465771 GTAAGTATAA-TAATAATA
1 GTAAGTA-AATTAATAATA
40465789 GTAAGTAAATTAATAATA
1 GTAAGTAAATTAATAATA
*
40465807 ATAAGTAA
1 GTAAGTAA
40465815 CAGTAGCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
GTAAGTAAATTAATAATA
Found at i:40470147 original size:19 final size:21
Alignment explanation
Indices: 40470108--40470148 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40470098 CATTTGTATA
40470108 ATATAATTAAAATGCAAATATT
1 ATATAATTAAAAT-CAAATATT
40470130 ATAT-ATTAAAAT-AAATATT
1 ATATAATTAAAATCAAATATT
40470149 TTAGTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATAATTAAAATCAAATATT
Found at i:40475704 original size:21 final size:21
Alignment explanation
Indices: 40475680--40475723 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40475670 TAAGATAAAC
* *
40475680 AAATAAATACATAAATACATA
1 AAATAAAAACAAAAATACATA
40475701 AAATAAAAACAAAAATACATA
1 AAATAAAAACAAAAATACATA
40475722 AA
1 AA
40475724 TATCTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATAAAAACAAAAATACATA
Found at i:40478150 original size:22 final size:22
Alignment explanation
Indices: 40478124--40478177 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
40478114 ATATTCAAAC
**
40478124 AATAACAACAAAATAGTAGTAA
1 AATAACAACAAAATAGTAACAA
* * * *
40478146 TATAATAACGAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
40478168 AATAACAACA
1 AATAACAACA
40478178 TAACAACAAC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:40478177 original size:11 final size:11
Alignment explanation
Indices: 40478163--40478196 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40478153 ACGAAATGGT
*
40478163 AACAAAATAAC
1 AACAAAACAAC
*
40478174 AACATAACAAC
1 AACAAAACAAC
40478185 AACAAAACAAC
1 AACAAAACAAC
40478196 A
1 A
40478197 GGGGAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.24, G:0.00, T:0.06
Consensus pattern (11 bp):
AACAAAACAAC
Found at i:40479226 original size:43 final size:43
Alignment explanation
Indices: 40479179--40479290 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
40479169 GCCATGTTCA
*
40479179 TTAGCAACGCTTTTATAACAAACGCCGCCAAAGAACATGACTT
1 TTAGCAACGCTTTTATAACAAACGCCACCAAAGAACATGACTT
* * * * * *
40479222 TTAGCGATGCTTTTCTAACAATCGCCACTAAAGAACATGGCTT
1 TTAGCAACGCTTTTATAACAAACGCCACCAAAGAACATGACTT
* *
40479265 TTAACAACGCTTTTTATCACAAACGC
1 TTAGCAACGC-TTTTATAACAAACGC
40479291 TCTTTAGCGG
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
43 43 0.78
44 12 0.22
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (43 bp):
TTAGCAACGCTTTTATAACAAACGCCACCAAAGAACATGACTT
Found at i:40482870 original size:61 final size:62
Alignment explanation
Indices: 40482766--40482885 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 62
40482756 TTTCTGCTCT
40482766 TTTTGCCTCCATGGGGCCAGTTTTTTTTTCTTCATCTCTTCTTATATTGTTTATTTGAGTTG
1 TTTTGCCTCCATGGGGCCAGTTTTTTTTTCTTCATCTCTTCTTATATTGTTTATTTGAGTTG
*
40482828 TTTTGCCTCCATGGGGTCA-TTTTTTTTTCTTCATCTCTTCTTATATTGTTTATTTGAG
1 TTTTGCCTCCATGGGGCCAGTTTTTTTTTCTTCATCTCTTCTTATATTGTTTATTTGAG
40482886 CTGGATATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 39 0.68
62 18 0.32
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (62 bp):
TTTTGCCTCCATGGGGCCAGTTTTTTTTTCTTCATCTCTTCTTATATTGTTTATTTGAGTTG
Found at i:40483591 original size:60 final size:59
Alignment explanation
Indices: 40483496--40483687 Score: 266
Period size: 58 Copynumber: 3.3 Consensus size: 59
40483486 GTTGCGGTTG
*
40483496 CTTTTAGTGCCCAAACAAATTCAATCCTTGACATGCTGGTTATTGTGACTTGTGGTTTA
1 CTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTATTGTGACTTGTGGTTTA
* *
40483555 CTTTTAGTGCCAAAACAAAATTCAATCCTTGTCATGCTGGTTATTGTGA--AGTGGTTTA
1 CTTTTAGTGCCAAAAC-AAATTCAATCCTTGACATGCTGGTTATTGTGACTTGTGGTTTA
* * * * *
40483613 CTTTTAGTGCCAAAACAAATTTAATTCTTGACATGCTGG-TAGTTGTGGCTTGCGG-TTG
1 CTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTA-TTGTGACTTGTGGTTTA
40483671 CTTTTAGTGCCAAAACA
1 CTTTTAGTGCCAAAACA
40483688 TAGCAACTTT
Statistics
Matches: 119, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.02
57 25 0.21
58 43 0.36
59 18 0.15
60 31 0.26
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (59 bp):
CTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTATTGTGACTTGTGGTTTA
Found at i:40484873 original size:18 final size:17
Alignment explanation
Indices: 40484845--40484879 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40484835 ATTATTAAGA
*
40484845 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40484862 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40484880 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40485064 original size:16 final size:16
Alignment explanation
Indices: 40485043--40485095 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
40485033 CAAGAATACT
*
40485043 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTCC
*
40485059 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
40485075 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
40485091 ATTAC
1 ATTAC
40485096 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:40485711 original size:23 final size:24
Alignment explanation
Indices: 40485666--40485718 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
40485656 GTTCGTTTGA
*
40485666 AACATGTTCATGAATATTAAATT-
1 AACATGTTCATGAACATTAAATTG
40485689 AACATGTTCATGAACA-TATAATTG
1 AACATGTTCATGAACATTA-AATTG
40485713 AACATG
1 AACATG
40485719 CTCACAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 19 0.70
24 6 0.22
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (24 bp):
AACATGTTCATGAACATTAAATTG
Found at i:40488318 original size:6 final size:6
Alignment explanation
Indices: 40488285--40488329 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
40488275 ACACAACACC
* * *
40488285 TAACAG TAATCAG TAACGG TAGCAG TAACAG TAATAG TAACAG TA
1 TAACAG TAA-CAG TAACAG TAACAG TAACAG TAACAG TAACAG TA
40488330 TTCAACACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (6 bp):
TAACAG
Found at i:40488406 original size:45 final size:45
Alignment explanation
Indices: 40488309--40488413 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 45
40488299 AACGGTAGCA
*
40488309 GTAACAGTAATAGTAACAGTATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
*
40488354 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCT-AATC-
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGT-TGAATCT
*
40488398 GATGACAGTAACAGTA
1 G-TAACAGTAACAGTA
40488414 GTCGGCATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
Found at i:40488673 original size:40 final size:41
Alignment explanation
Indices: 40488613--40488720 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
40488603 AATTCATTAC
* ** *
40488613 TTCAGTAATTTCACTGTTCAATGT-AGTACAC-ATAACAATA
1 TTCAGTAACTTCACAATTCAAT-TCAGTACACAAAAACAATA
*
40488653 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATTCAGTACACAAAAACAATA
*
40488694 TTCAGT-A-TTCAATAATTCAATTCAGTA
1 TTCAGTAACTTC-ACAATTCAATTCAGTA
40488721 TCAGTCTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 4 0.07
40 41 0.69
41 14 0.24
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATTCAGTACACAAAAACAATA
Found at i:40488716 original size:20 final size:19
Alignment explanation
Indices: 40488652--40488721 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
40488642 ACATAACAAT
*
40488652 ATTCAGTAACTTCACAATTCA
1 ATTCAGT-A-TTCAAAATTCA
* *
40488673 ATTCAGTACTCAAAA-ACAA
1 ATTCAGTATTCAAAATTC-A
40488692 TATTCAGTATTCAATAATTCA
1 -ATTCAGTATTCAA-AATTCA
40488713 ATTCAGTAT
1 ATTCAGTAT
40488722 CAGTCTCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 22 0.55
21 10 0.25
22 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (19 bp):
ATTCAGTATTCAAAATTCA
Found at i:40490141 original size:101 final size:102
Alignment explanation
Indices: 40490026--40490210 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
40490016 AAAGTGATGG
* * *
40490026 TCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACC--AGAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGAT-GGTCACATGTGTAGT
*
40490089 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
40490127 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAATGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGATGGTCACATGTGTAGTA
40490192 CAATGTGCAGGCTACTATG
66 CAATGTGCAGGCTACTATG
40490211 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 37 0.48
102 33 0.43
103 7 0.09
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGATGGTCACATGTGTAGTA
CAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:40490147 original size:51 final size:50
Alignment explanation
Indices: 40490020--40490218 Score: 222
Period size: 51 Copynumber: 3.9 Consensus size: 50
40490010 AAAGTGAAAG
* * *
40490020 TGATGGTCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGA-A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * *
40490069 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * * * *
40490120 -GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAA
1 TG-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-A
* * *
40490172 TGATGGTCACATGTGTAGTACAATGTGCAGGCTACTATGTGAACCGG
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
40490219 TATCATTAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 4 0.03
50 39 0.32
51 76 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
Found at i:40490212 original size:26 final size:26
Alignment explanation
Indices: 40490132--40490212 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
40490122 TTCGATCACG
*
40490132 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACAATGTGCAGGCTACTA
* *
40490158 CGTGTA-T-CGAATAATG-ATGG-TCAC-A
1 TGTGTAGTAC-AAT-GTGCA-GGCT-ACTA
40490183 TGTGTAGTACAATGTGCAGGCTACTA
1 TGTGTAGTACAATGTGCAGGCTACTA
40490209 TGTG
1 TGTG
40490213 AACCGGTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 18
0.64 0.08 0.28
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACAATGTGCAGGCTACTA
Found at i:40490248 original size:101 final size:100
Alignment explanation
Indices: 40490028--40490218 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 100
40490018 AGTGATGGTC
* * * *
40490028 ACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACAAGAATGATAGGTCACATGTGTAGTACAA
* *
40490093 TGTGCAGGCTACTATGCGTACCGGATAGCTTCGATC
65 TGTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
*
40490129 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAATGAT-GGTCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTA-C-AAGAATGATAGGTCACATGTGTAGTAC
*
40490193 AATGTGCAGGCTACTATGTGAACCGG
63 AATGTGCAGGCTACTATGCGAACCGG
40490219 TATCATTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 34 0.42
102 40 0.49
103 7 0.09
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACGTGTACAAGAATGATAGGTCACATGTGTAGTACAAT
GTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
Found at i:40490286 original size:46 final size:43
Alignment explanation
Indices: 40490214--40490312 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
40490204 TACTATGTGA
*
40490214 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
40490257 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
40490303 ACCGTGTATC
1 ACCG-GTATC
40490313 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:40490456 original size:16 final size:16
Alignment explanation
Indices: 40490435--40490466 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40490425 TGATTGAAAG
*
40490435 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
40490451 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
40490467 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:40498361 original size:22 final size:22
Alignment explanation
Indices: 40498331--40498377 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40498321 GTCGAATTTA
*
40498331 TTTTATTAAAAAATTAAAATAT
1 TTTTATTAAAAAAATAAAATAT
* *
40498353 TTTTTTTAAAAAAATAAGATAT
1 TTTTATTAAAAAAATAAAATAT
40498375 TTT
1 TTT
40498378 CTTTCACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTATTAAAAAAATAAAATAT
Found at i:40498504 original size:13 final size:13
Alignment explanation
Indices: 40498473--40498497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40498463 TCAAACGAAC
40498473 ATAATTATATTTA
1 ATAATTATATTTA
40498486 ATAATTATATTT
1 ATAATTATATTT
40498498 GTTAATTTAC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTATATTTA
Found at i:40504883 original size:21 final size:21
Alignment explanation
Indices: 40504857--40504898 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40504847 TGACAAGTTC
* *
40504857 AAGTACCGAATCAGTAAAAAA
1 AAGTACCAAATCAGGAAAAAA
*
40504878 AAGTACCAAATTAGGAAAAAA
1 AAGTACCAAATCAGGAAAAAA
40504899 GAGTCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14
Consensus pattern (21 bp):
AAGTACCAAATCAGGAAAAAA
Found at i:40506604 original size:25 final size:25
Alignment explanation
Indices: 40506575--40506647 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 25
40506565 ATGCAAAAAC
*
40506575 AGTTTATAATAAATGATAAATAA-G-A
1 AGTTTA-AAAAAAT-ATAAATAAGGAA
40506600 AGTTTAAAACAAATA-ATAATGAAGGAA
1 AGTTTAAAA-AAATATA-AAT-AAGGAA
40506627 AGTTTAAAAAAATATAAATAA
1 AGTTTAAAAAAATATAAATAA
40506648 ATAAATAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 1 0.02
24 6 0.15
25 14 0.34
26 9 0.22
27 11 0.27
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.27
Consensus pattern (25 bp):
AGTTTAAAAAAATATAAATAAGGAA
Found at i:40508165 original size:40 final size:40
Alignment explanation
Indices: 40508118--40508232 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 40
40508108 TTCCTTCATT
40508118 TGCTCCACTACTGCTTAGGGAGATAAGACTGGATGC-GATC
1 TGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCTG-TC
* * * *
40508158 TGCTCCACTACTGCTTAGGGAGATAAGATATAGTTTCTTTTGTC
1 TGCTCCACTACTGCTTAGGGAGATAAGA-CTGGATGC---TGTC
40508202 TGCTCCACTACTGCTTAGGGAGATAAGACTG
1 TGCTCCACTACTGCTTAGGGAGATAAGACTG
40508233 CCGGCTTCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
40 28 0.44
41 4 0.06
43 1 0.02
44 30 0.47
45 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (40 bp):
TGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCTGTC
Found at i:40508300 original size:132 final size:129
Alignment explanation
Indices: 40508153--40508580 Score: 506
Period size: 132 Copynumber: 3.3 Consensus size: 129
40508143 AGACTGGATG
* * ** *
40508153 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATATAGTTTCTTTTGTCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTATCTTTAATCT-CTCCACTACTGCTA
*** *
40508218 AGGGAGATAAGACTGCCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATC
64 AGGGAGAT-AGACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
40508283 TT
128 TT
* * ** *
40508285 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGT-TTTAATC-CT--TTTAATTG-TA
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-ATCTTTAATCTCTCCACT-ACTGCTA
* * *
40508345 AGGTAGATAGGCTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGTCATCT
64 AGGGAGATAGACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCT
40508410 T
129 T
* * * * * * * **
40508411 CGATCTGCTCCACTACTGCTTACGGAGATAATATCGGGAATCTTCAATCTATTCCACTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGTATCTTTAATCT-CTCCACTACTGCTA
*
40508476 AGAGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
64 AGGGAGATAG-ACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
40508541 TT
128 TT
40508543 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
40508581 GGTTTTAATC
Statistics
Matches: 248, Mismatches: 38, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
126 85 0.34
127 16 0.06
128 3 0.01
129 3 0.01
130 2 0.01
131 17 0.07
132 122 0.49
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (129 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTTAATCTCTCCACTACTGCTAAG
GGAGATAGACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTT
Found at i:40508392 original size:126 final size:127
Alignment explanation
Indices: 40508235--40508603 Score: 523
Period size: 132 Copynumber: 2.9 Consensus size: 127
40508225 TAAGACTGCC
* *
40508235 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATCTTCAATCTGCTCCACTA
1 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
*
40508300 CTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCTTTTAATTGTAAG-GTAGATAG-GCTAAT
66 CTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCTTTTAATTGTAAGAG-AGATAGAACTAAT
*
40508361 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTA
1 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
* * * * * **
40508426 CTGCTTACGGAGATAATATC-G-GGAATCTTCAAT-CTATTCCACTGCTGCCCAGAGAGATAGAA
66 CTGCTTAGGGAGATAAGATCTGTGG--T-TTTAATCCT-TT-TAAT--TG-TAAGAGAGATAGAA
40508488 CTAAT
123 CTAAT
40508493 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
1 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
40508558 CTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCTTTTAATTGTAA
66 CTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCTTTTAATTGTAA
40508604 TGTCGGGGAA
Statistics
Matches: 211, Mismatches: 19, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
124 2 0.01
125 1 0.00
126 83 0.39
127 8 0.04
128 4 0.02
130 4 0.02
131 15 0.07
132 91 0.43
133 1 0.00
134 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (127 bp):
GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCTTTTAATTGTAAGAGAGATAGAACTAAT
Found at i:40508975 original size:87 final size:87
Alignment explanation
Indices: 40508844--40509236 Score: 671
Period size: 87 Copynumber: 4.5 Consensus size: 87
40508834 CACCAGTATG
* **
40508844 GGAAGACAAGATCTGC-ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
**
40508908 GATCTGCTTTGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
40508930 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTATTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
*
40508995 TATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
* * *
40509017 AGAAGGCAAGATCTGCTATATTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTT
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
40509082 GATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
40509104 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTT
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
40509169 GATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
40509191 GGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATG
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
40509237 AAGTAAAAAA
Statistics
Matches: 291, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
86 15 0.05
87 276 0.95
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
GATCTGCTCCGCTGTTAATGCA
Found at i:40515080 original size:26 final size:25
Alignment explanation
Indices: 40515038--40515120 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
40515028 ATTGGATCCA
* *
40515038 AAACTTTAAACCTTGAACCCTGGACCC
1 AAAC-TTAAACCATGAA-CCTGAACCC
40515065 AAACTTAAACCATGAACCTGAACCC
1 AAACTTAAACCATGAACCTGAACCC
* * * *
40515090 TAACTTCAAACCCTAAACATCGAACCC
1 AAACTT-AAACCATGAACCT-GAACCC
40515117 AAAC
1 AAAC
40515121 CACGAACCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 13 0.28
26 21 0.45
27 13 0.28
ACGTcount: A:0.41, C:0.34, G:0.07, T:0.18
Consensus pattern (25 bp):
AAACTTAAACCATGAACCTGAACCC
Found at i:40519941 original size:50 final size:50
Alignment explanation
Indices: 40519875--40520001 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 50
40519865 TCCTGTACTA
* * **
40519875 CCAATGCCATATCCCAGATATGGTCTTACATG-GGAGTTCTCATATCGGTG
1 CCAATGCCATATCCCAGACATGGTCTTAC-GGAGGACCTCTCATATCGGTG
* * * *
40519925 CCCATGCCATGTCCCAGACATGGTCGTACGGAGGACCTCTCATCTCGGTG
1 CCAATGCCATATCCCAGACATGGTCTTACGGAGGACCTCTCATATCGGTG
40519975 CCAATGCCATATCCCAGACATGGTCTT
1 CCAATGCCATATCCCAGACATGGTCTT
40520002 CTTACATGAG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 64 0.98
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAATGCCATATCCCAGACATGGTCTTACGGAGGACCTCTCATATCGGTG
Found at i:40522357 original size:85 final size:85
Alignment explanation
Indices: 40522262--40522787 Score: 1052
Period size: 85 Copynumber: 6.2 Consensus size: 85
40522252 AAAAATAATA
40522262 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522327 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522347 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522412 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522432 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522497 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522517 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522582 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522602 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522667 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522687 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
1 TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
40522752 CTATAAATAATATAATTTTT
66 CTATAAATAATATAATTTTT
40522772 TAAAATTTATAATATA
1 TAAAATTTATAATATA
40522788 AGAATTTTTT
Statistics
Matches: 441, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 441 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (85 bp):
TAAAATTTATAATATATAACCTTTATAAAAAAAAAGTTTTATATATTGTCCAAAACTTTTTATAA
CTATAAATAATATAATTTTT
Found at i:40525542 original size:113 final size:112
Alignment explanation
Indices: 40525398--40525989 Score: 497
Period size: 113 Copynumber: 5.3 Consensus size: 112
40525388 AAGAAAAAAA
* * *
40525398 ATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTACATTTTGG
1 ATTTT-GGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGG
* *
40525463 GCTATCATTGGCCAACACCAGTATACGAAAAAATTCAAAAAAATTTTAT
65 GCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTT-T
* * ****** *
40525512 ATTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATAT-ATAAAAAATTTTACATTTTGGG
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
** * *
40525576 CCCTCATTTGCCGGCACCAGTATACGAAAAAATTC-----AATTTTT
66 CTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
*
40525618 -TTTT-GTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTATATATTTTGGG
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
* * * *
40525681 TTGTCATTGGCTGGA-ACTAGTATACGAAAAAATT-----TAATTTTT
66 CTGTCATTGGC-CGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
* * * * ** * ***
40525723 TTTTTGCTGGTGGCCTAGCAATGGTCGATACCGCCTTTATGTAAAAAAGAGAAATTTTTTTTATA
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-----A-A-TTTTTTTTTTTATA
* * * *
40525788 TTTT-GGCTGTTATTGGTCGGCACCAGTATACGAAAAAATTCAAAACAAA-ATTT
59 TTTTGGGCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAA-AAATTTTT
** **
40525841 -TTTTGGTGGTGGCCTGGCAATGATCGGCACCATGTTTATGTAAACTTTTTTTATTTTATATTTT
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AA-TTTTTTT-TTTTATATTTT
* * **
40525905 GGGTTGTCATTGGCCGACACCAGTATACAAAAAAATT-AAAAAAA---AA
63 GGGCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
*
40525951 ATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTA
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTA
40525990 CGGGAAAAAA
Statistics
Matches: 382, Mismatches: 74, Indels: 47
0.76 0.15 0.09
Matches are distributed among these distances:
104 34 0.09
105 50 0.13
106 6 0.02
107 36 0.09
111 33 0.09
112 56 0.15
113 79 0.21
114 50 0.13
117 33 0.09
118 3 0.01
119 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (112 bp):
ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
CTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
Found at i:40525637 original size:104 final size:108
Alignment explanation
Indices: 40525398--40525655 Score: 299
Period size: 112 Copynumber: 2.4 Consensus size: 108
40525388 AAGAAAAAAA
* * * ******
40525398 ATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTACATTTTGG
1 ATTTT-GGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATAT-ATAAAAAATTTTACATTTTGG
*
40525463 GCTATCATTGGCCAACACCAGTATACGAAAAAATTCAAAAAAATTTTAT
64 GCCATCATTGGCCAACACCAGTATACGAAAAAATTC----AAATTTTAT
*
40525512 ATTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
* * **
40525577 CCTCATTTGCCGGCACCAGTATACGAAAAAATTC-AATTTT-T
66 CATCATTGGCCAACACCAGTATACGAAAAAATTCAAATTTTAT
40525618 -TTTT-GTGGTGGCCTGGCAATGGCCGGCACCACCTTTAT
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTAT
40525656 GTAATTTTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
104 33 0.26
105 4 0.03
106 1 0.01
107 6 0.05
112 46 0.36
113 33 0.26
114 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (108 bp):
ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
CATCATTGGCCAACACCAGTATACGAAAAAATTCAAATTTTAT
Found at i:40525955 original size:114 final size:109
Alignment explanation
Indices: 40525777--40525983 Score: 279
Period size: 114 Copynumber: 1.9 Consensus size: 109
40525767 AAAAGAGAAA
* * * * **
40525777 TTTTTTTTATATTTTGGCTGTTATTGGTCGGCACCAGTATACGAAAAAATTCAAAACAAAATTTT
1 TTTTTTTTATATTTTGGCTGTCATTGGCCGACACCAGTATACAAAAAAATT-AAAA-AAAA-AAT
* *
40525842 TTTGGTGGTGGCCTGGCAATGATCGGCACCATGTTTATGTAAACTTT
63 TTTGGTGGTGGCCTGCCAATGACCGGCACCATGTTTATGTAAACTTT
*
40525889 TTTTATTTTATATTTTGGGTTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATT
1 TTTT-TTTTATATTTT-GGCTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATT
*
40525954 TTGGTGGTGGCCTGCCAATGGCCGGCACCA
64 TTGGTGGTGGCCTGCCAATGACCGGCACCA
40525984 CCTTTACGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 29 0.35
112 8 0.10
113 15 0.18
114 31 0.37
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (109 bp):
TTTTTTTTATATTTTGGCTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATTTT
GGTGGTGGCCTGCCAATGACCGGCACCATGTTTATGTAAACTTT
Found at i:40526966 original size:22 final size:22
Alignment explanation
Indices: 40526948--40527012 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
40526938 AACAAATAAT
40526948 TATTTTAGATCCATTAAATTAA
1 TATTTTAGATCCATTAAATTAA
* *
40526970 TA-TTCA-A---A-CAAA-TAA
1 TATTTTAGATCCATTAAATTAA
40526985 TTATTTTAGATCCATTAAATTAA
1 T-ATTTTAGATCCATTAAATTAA
40527008 TATTT
1 TATTT
40527013 AAAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 16
0.61 0.08 0.31
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 4 0.13
18 1 0.03
20 1 0.03
21 4 0.13
22 9 0.29
23 4 0.13
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (22 bp):
TATTTTAGATCCATTAAATTAA
Found at i:40526977 original size:38 final size:38
Alignment explanation
Indices: 40526932--40527011 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
40526922 CGAATTCATG
40526932 TATTCAAACAAATAATTATTTTAGATCCATTAAATTAA
1 TATTCAAACAAATAATTATTTTAGATCCATTAAATTAA
40526970 TATTCAAACAAATAATTATTTTAGATCCATTAAATTAA
1 TATTCAAACAAATAATTATTTTAGATCCATTAAATTAA
40527008 TATT
1 TATT
40527012 TAAAAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (38 bp):
TATTCAAACAAATAATTATTTTAGATCCATTAAATTAA
Found at i:40527005 original size:19 final size:19
Alignment explanation
Indices: 40526945--40527006 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
40526935 TCAAACAAAT
40526945 AATTATTTTAGATCCATTA
1 AATTATTTTAGATCCATTA
* * * *
40526964 AATTAATATTCA-AACAAAT-
1 AATT-AT-TTTAGATCCATTA
40526983 AATTATTTTAGATCCATTA
1 AATTATTTTAGATCCATTA
40527002 AATTA
1 AATTA
40527007 ATATTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
19 13 0.42
20 6 0.19
21 3 0.10
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTATTTTAGATCCATTA
Found at i:40527098 original size:38 final size:38
Alignment explanation
Indices: 40527055--40527164 Score: 220
Period size: 38 Copynumber: 2.9 Consensus size: 38
40527045 ATTTACAGAA
40527055 TAATATTCAAACAAATAATTATTTTAGATCCATTAAAT
1 TAATATTCAAACAAATAATTATTTTAGATCCATTAAAT
40527093 TAATATTCAAACAAATAATTATTTTAGATCCATTAAAT
1 TAATATTCAAACAAATAATTATTTTAGATCCATTAAAT
40527131 TAATATTCAAACAAATAATTATTTTAGATCCATT
1 TAATATTCAAACAAATAATTATTTTAGATCCATT
40527165 GCTAGGCCAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (38 bp):
TAATATTCAAACAAATAATTATTTTAGATCCATTAAAT
Found at i:40527099 original size:22 final size:22
Alignment explanation
Indices: 40527074--40527137 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
40527064 AACAAATAAT
40527074 TATTTTAGATCCATTAAATTAA
1 TATTTTAGATCCATTAAATTAA
* *
40527096 TA-TTCA-A---A-CAAA-TAA
1 TATTTTAGATCCATTAAATTAA
40527111 TTATTTTAGATCCATTAAATTAA
1 T-ATTTTAGATCCATTAAATTAA
40527134 TATT
1 TATT
40527138 CAAACAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 16
0.60 0.08 0.32
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 4 0.13
18 1 0.03
20 1 0.03
21 4 0.13
22 8 0.27
23 4 0.13
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTAGATCCATTAAATTAA
Found at i:40527112 original size:19 final size:19
Alignment explanation
Indices: 40527055--40527151 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 19
40527045 ATTTACAGAA
40527055 TAATATTCAAACAAATAAT
1 TAATATTCAAACAAATAAT
* * * *
40527074 T-AT-TTTAGATCCATTAAAT
1 TAATATTCA-AACAAAT-AAT
40527093 TAATATTCAAACAAATAAT
1 TAATATTCAAACAAATAAT
* * * *
40527112 T-AT-TTTAGATCCATTAAAT
1 TAATATTCA-AACAAAT-AAT
40527131 TAATATTCAAACAAATAAT
1 TAATATTCAAACAAATAAT
40527150 TA
1 TA
40527152 TTTTAGATCC
Statistics
Matches: 54, Mismatches: 16, Indels: 16
0.63 0.19 0.19
Matches are distributed among these distances:
17 6 0.11
18 12 0.22
19 18 0.33
20 12 0.22
21 6 0.11
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATATTCAAACAAATAAT
Found at i:40527715 original size:109 final size:107
Alignment explanation
Indices: 40527160--40527957 Score: 825
Period size: 108 Copynumber: 7.3 Consensus size: 107
40527150 TATTTTAGAT
* * * *
40527160 CCATTGCTAGGCCACCACC-AAATTTTTTTTTTGAATTTTTTCGTATATTAGTGCCGACCAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* * *
40527224 CAGCTCAAAGTGTAAATTTTTTTTACATAAAGGTGGTGCCAG
66 CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
**** * * *
40527266 CCATTGCCAGGCCACCA-CAAAA-AAAATTTTTGAATTTTTTCGTACACTGGTGTCGGCTAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* *****
40527329 CAGCCAAAAATGTAAAAAAAAAATTTACATAAAGGTGGTGCCGG
66 CAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* *
40527373 CCATTGCCAGGCCAGCACCAAAA-TTTTTTTTTGAATTTTTTCGTATATTGGTGCCGGCCAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* *
40527437 TAGCCCAAAATGT-AATTTTTTTTACATAAAGGTGGTGCCAG
66 CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
* * * * * *
40527478 CCATTGCCATGCCACCACCAAAAAAATTTTTTTTTGAATTTTTTTGTATACTGATGTCGGCCAAG
1 CCATTGCCAGGCCACCACC--AAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAAT
* **** * *
40527543 GACAGCTCAAAATGTAAAAAAAAATTCTACATAAAGGTGGTGTCGG
64 GACAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* * * * *
40527589 CCATTGCCAAGCTACCACCAAAACTTTTTTTTTTTGAATTTTTTTCATATACTGGTGCTGGCAAA
1 CCATTGCCAGGCCACCACCAAAA--TTTTTTTTTTGAA-TTTTTTCGTATACTGGTGCCGGCCAA
*
40527654 TGACAACCCAAAATGT-AATTTTTTTTACATAAAGGTGGTGCCGG
63 TGACAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
* *
40527698 CAATTGCCAGGCCACCACCAAATTTTTTTTTCTTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
1 CCATTGCCAGGCCACCACCAAA--ATTTTTT-TTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
* * **** **
40527763 TGATAGCCCAAAATATATAAAAAAAAATTTTACATAAAATTGGTGCCGG
63 TGACAGCCC-AAA-ATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* *
40527812 CCATTGCCAGGCCACCACCAAAAAAATATTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCAAA
1 CCATTGCCAGGCCACCACC---AAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
*
40527877 TGACAGCCCAAAATGTAAAAATTTTTTTTACATAAAGGTGGTGTCGG
63 TGACAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* * * *
40527924 CTATTGACAGGTCAGCACCAAAATTTTTTTTTTG
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTG
40527958 TTCTTTCTTT
Statistics
Matches: 563, Mismatches: 105, Indels: 45
0.79 0.15 0.06
Matches are distributed among these distances:
105 81 0.14
106 19 0.03
107 43 0.08
108 96 0.17
109 95 0.17
110 10 0.02
111 53 0.09
112 75 0.13
113 3 0.01
114 80 0.14
115 5 0.01
117 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (107 bp):
CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
Found at i:40531103 original size:9 final size:9
Alignment explanation
Indices: 40531085--40531115 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40531075 TTTGGTTAAA
40531085 AATTAACCG
1 AATTAACCG
*
40531094 AATTACCCG
1 AATTAACCG
40531103 AATTAACCG
1 AATTAACCG
40531112 AATT
1 AATT
40531116 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40535566 original size:15 final size:15
Alignment explanation
Indices: 40535547--40535581 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40535537 TTTTTGGACT
*
40535547 TTTTTATTTTATTTTC
1 TTTTTATTCT-TTTTC
40535563 TTTTTATTCTTTTTC
1 TTTTTATTCTTTTTC
40535578 TTTT
1 TTTT
40535582 GGAGATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTCTTTTTC
Found at i:40563210 original size:4 final size:4
Alignment explanation
Indices: 40563203--40563228 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40563193 CACACTTTTT
40563203 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
40563229 ATGGTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:40571581 original size:14 final size:14
Alignment explanation
Indices: 40571553--40571585 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40571543 AAGGAATGTT
40571553 ATTAGTAGATTAAA
1 ATTAGTAGATTAAA
40571567 ATTAG-AGATTAAA
1 ATTAGTAGATTAAA
*
40571580 AATAGT
1 ATTAGT
40571586 TCTTCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTAGTAGATTAAA
Found at i:40574552 original size:39 final size:39
Alignment explanation
Indices: 40574498--40574577 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40574488 AGTTGTTTGT
40574498 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
1 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
40574537 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
1 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
40574576 AA
1 AA
40574578 CCTTCTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (39 bp):
AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
Found at i:40596190 original size:21 final size:23
Alignment explanation
Indices: 40596166--40596213 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
40596156 GCAGTGATTC
*
40596166 AGAACTTAAAAAG-ATAA-AAGA
1 AGAACTGAAAAAGAATAAGAAGA
*
40596187 AGAACTGAAGAAGAATAAGAAGA
1 AGAACTGAAAAAGAATAAGAAGA
40596210 AGAA
1 AGAA
40596214 GAAAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.65, C:0.04, G:0.21, T:0.10
Consensus pattern (23 bp):
AGAACTGAAAAAGAATAAGAAGA
Found at i:40598386 original size:11 final size:11
Alignment explanation
Indices: 40598370--40598411 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
40598360 TTAATAAATT
40598370 TAATTTTTTAA
1 TAATTTTTTAA
40598381 TAATTTTTT-A
1 TAATTTTTTAA
*
40598391 T-ATTGTTTAA
1 TAATTTTTTAA
*
40598401 TAATTATTTAA
1 TAATTTTTTAA
40598412 AAAACCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.22
10 4 0.15
11 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:40598706 original size:31 final size:30
Alignment explanation
Indices: 40598667--40598729 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
40598657 CAGGGGTTAA
*
40598667 AAAGACAAAATATAATCTAACTCCTAATAT
1 AAAGACAAAATACAATCTAACTCCTAATAT
*
40598697 AAAGAACAAAATACAATCTAACTCTTAATAT
1 AAAG-ACAAAATACAATCTAACTCCTAATAT
40598728 AA
1 AA
40598730 GGACGCATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAGACAAAATACAATCTAACTCCTAATAT
Found at i:40621792 original size:18 final size:19
Alignment explanation
Indices: 40621771--40621813 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
40621761 AAGGAAAAGC
*
40621771 ATTTTACCTTTTA-AATTT
1 ATTTTACCTTTTAGAATTA
**
40621789 ATTTTATTTTTTAGAATTA
1 ATTTTACCTTTTAGAATTA
40621808 ATTTTA
1 ATTTTA
40621814 ATTTTTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTACCTTTTAGAATTA
Found at i:40621811 original size:19 final size:19
Alignment explanation
Indices: 40621779--40621819 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40621769 GCATTTTACC
*
40621779 TTTTAAATTTATTTT-ATT
1 TTTTAAATTAATTTTAATT
40621797 TTTTAGAATTAATTTTAATT
1 TTTTA-AATTAATTTTAATT
40621817 TTT
1 TTT
40621820 CTATAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAAATTAATTTTAATT
Found at i:40625504 original size:23 final size:23
Alignment explanation
Indices: 40625476--40625527 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
40625466 TATGTACTAT
40625476 TGTATTAAAT-TATTTAAATATAA
1 TGTATTAAATATATTTAAA-ATAA
* **
40625499 TTTATTATTTATATTTAAAATAA
1 TGTATTAAATATATTTAAAATAA
40625522 TGTATT
1 TGTATT
40625528 TATCACTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TGTATTAAATATATTTAAAATAA
Found at i:40627384 original size:119 final size:122
Alignment explanation
Indices: 40627169--40627409 Score: 418
Period size: 119 Copynumber: 2.0 Consensus size: 122
40627159 GACTCGAGAG
40627169 AAAATTTCTGAGTTTTTTTTAGGGAAGAAAGAAAAATGAATTTAAAAAAAAAAATTGGTTTTATA
1 AAAATTTCTGAGTTTTTTTTAGGGAAGAAAGAAAAATGAATTT-AAAAAAAAAATTGGTTTTATA
40627234 AAGAGTTGAAACGGCGCCATTTTGGGGTTTAACCCCAGTAGCCAAAACGACGCCGTTA
65 AAGAGTTGAAACGGCGCCATTTTGGGGTTTAACCCCAGTAGCCAAAACGACGCCGTTA
40627292 AAAATTTCTGAG-TTTTTTTAGGGAAGAAA-AAAAATGAAATTT-AAAAAAAAA-TGGTTTTATA
1 AAAATTTCTGAGTTTTTTTTAGGGAAGAAAGAAAAATG-AATTTAAAAAAAAAATTGGTTTTATA
* *
40627353 AAGGGTTGAAACGGCGCCGTTTTGGGGTTTAACCCCAGTAGCCAAAACGACGCCGTT
65 AAGAGTTGAAACGGCGCCATTTTGGGGTTTAACCCCAGTAGCCAAAACGACGCCGTT
40627410 TTGGCCTTAG
Statistics
Matches: 115, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
119 65 0.57
120 9 0.08
121 7 0.06
122 22 0.19
123 12 0.10
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (122 bp):
AAAATTTCTGAGTTTTTTTTAGGGAAGAAAGAAAAATGAATTTAAAAAAAAAATTGGTTTTATAA
AGAGTTGAAACGGCGCCATTTTGGGGTTTAACCCCAGTAGCCAAAACGACGCCGTTA
Found at i:40627915 original size:25 final size:25
Alignment explanation
Indices: 40627882--40627974 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
40627872 TATATATATA
*
40627882 TATATGTTTACATACTCTTATATTT
1 TATAAGTTTACATACTCTTATATTT
* *
40627907 TATAAGTTTAAATAATTATCTTAGCT-TTAT
1 TATAAGTTTACAT-A--CTCTTA--TATT-T
40627937 ATATATATGTTTACATACTCTTATATTT
1 -TATA-A-GTTTACATACTCTTATATTT
40627965 TATAAGTTTA
1 TATAAGTTTA
40627975 AAGTATATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
25 16 0.30
26 2 0.04
27 4 0.08
28 7 0.13
29 4 0.08
30 7 0.13
31 4 0.08
32 2 0.04
33 7 0.13
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (25 bp):
TATAAGTTTACATACTCTTATATTT
Found at i:40630381 original size:9 final size:9
Alignment explanation
Indices: 40630349--40630380 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
40630339 TTTGGTTAAA
40630349 AATTAACCG
1 AATTAACCG
40630358 AATTAACCG
1 AATTAACCG
*
40630367 AATTACCCG
1 AATTAACCG
40630376 AATTA
1 AATTA
40630381 CGCGAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:40630418 original size:17 final size:17
Alignment explanation
Indices: 40630396--40630458 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
40630386 ATTGAATCAG
40630396 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
40630413 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
40630433 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
40630450 TACATAATT
1 TACATAATT
40630459 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:40630437 original size:37 final size:37
Alignment explanation
Indices: 40630387--40630461 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
40630377 ATTACGCGAA
* *
40630387 TTGAATCAGTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
40630424 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
40630461 T
1 T
40630462 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:40630671 original size:39 final size:39
Alignment explanation
Indices: 40630589--40630705 Score: 218
Period size: 39 Copynumber: 3.0 Consensus size: 39
40630579 ACTTAAGAGT
*
40630589 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40630627 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40630666 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40630705 T
1 T
40630706 TGGGTTGGAT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 27 0.35
39 50 0.65
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:40630704 original size:13 final size:13
Alignment explanation
Indices: 40630686--40630710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40630676 TTTTAGTTTT
40630686 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
40630699 ATTGGGTTGGGT
1 ATTGGGTTGGGT
40630711 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:40631142 original size:101 final size:99
Alignment explanation
Indices: 40630958--40631258 Score: 277
Period size: 101 Copynumber: 3.0 Consensus size: 99
40630948 AAAAATGAAT
* * * *
40630958 TGACAGATAAGACCATGGTTAGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGAC
1 TGAC-GATAAGACCATGGTTTGACCATGGC-AT-TATAAATGTAAGACCATAGTTGGGCTATGGC
* * * *
40631023 ATTTTAATGAAAATACCATAATTGAGG-TATGACAC-C
63 ATTCTGATGATAAGACCATAATTG-GGCTATGACACTC
* * *
40631059 TTGAACG-TAAGACCATGGTTTGATCATGACAGTATATATATGTAAGACCATAGTTGGGCTATGG
1 -TG-ACGATAAGACCATGGTTTGACCATGGCA-T-TATAAATGTAAGACCATAGTTGGGCTATGG
* * *
40631123 CATTCTGATGATAAGACCATAGTTGGGCTATGGCATTC
62 CATTCTGATGATAAGACCATAATTGGGCTATGACACTC
* * * * * * *
40631161 TGATGATAAGACCATAGTTGGGCTATGGCATTCT-GATGATAAGACCATAGTTGGGCTATGGCAT
1 TGACGATAAGACCATGGTTTGACCATGGCATTATAAATG-TAAGACCATAGTTGGGCTATGGCAT
* * *
40631225 TCTGATGATAAGACCATAACTGGGTTATGGCACT
65 TCTGATGATAAGACCATAATTGGGCTATGACACT
40631259 ACAAATGTAA
Statistics
Matches: 165, Mismatches: 28, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
98 3 0.02
99 57 0.35
100 6 0.04
101 93 0.56
102 4 0.02
103 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (99 bp):
TGACGATAAGACCATGGTTTGACCATGGCATTATAAATGTAAGACCATAGTTGGGCTATGGCATT
CTGATGATAAGACCATAATTGGGCTATGACACTC
Found at i:40631143 original size:33 final size:33
Alignment explanation
Indices: 40631101--40631256 Score: 285
Period size: 33 Copynumber: 4.7 Consensus size: 33
40631091 TATATATATG
40631101 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
40631134 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
40631167 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
40631200 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
** *
40631233 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAGTTGGGCTATGGCA
40631257 CTACAAATGT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 120 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCTATGGCATTCTGATGA
Found at i:40631270 original size:66 final size:66
Alignment explanation
Indices: 40631101--40631274 Score: 233
Period size: 66 Copynumber: 2.6 Consensus size: 66
40631091 TATATATATG
** * **
40631101 TAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGTTGGGCTATGGCATTCTGATG
1 TAAGACCATAACTGGGCTATGGCATACAAATGATAAGACCATAGTTGGGCTATGGCATTCTGATG
40631166 A
66 A
** * **
40631167 TAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGTTGGGCTATGGCATTCTGATG
1 TAAGACCATAACTGGGCTATGGCATACAAATGATAAGACCATAGTTGGGCTATGGCATTCTGATG
40631232 A
66 A
*
40631233 TAAGACCATAACTGGGTTATGGCACTACAAATG-TAAGACCAT
1 TAAGACCATAACTGGGCTATGGCA-TACAAATGATAAGACCAT
40631275 GGCAGGGCCA
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
66 96 0.95
67 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (66 bp):
TAAGACCATAACTGGGCTATGGCATACAAATGATAAGACCATAGTTGGGCTATGGCATTCTGATG
A
Found at i:40631272 original size:99 final size:99
Alignment explanation
Indices: 40631099--40631322 Score: 283
Period size: 99 Copynumber: 2.3 Consensus size: 99
40631089 AGTATATATA
** * **
40631099 TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGTTGGGCTATGGCATTCTGA
1 TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCATACAAA
** * *
40631164 TGATAAGACCATAGTTGGGCTATGGC-ATTC-TG
66 TGATAAGACCATAGCAGGGCCATGGCAATGCATG
*
40631196 ATGATAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTAC
1 -TG-TAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCA-TAC
*
40631261 AAATG-TAAGACCATGGCAGGGCCATGGCAATGCATG
63 AAATGATAAGACCATAGCAGGGCCATGGCAATGCATG
* *
40631297 TGTAAGACCTTAGTTGGACTATGGCA
1 TGTAAGACCATAGTTGGGCTATGGCA
40631323 CAAAAAGAAC
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
98 2 0.02
99 95 0.87
100 10 0.09
101 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (99 bp):
TGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCATACAAA
TGATAAGACCATAGCAGGGCCATGGCAATGCATG
Found at i:40632881 original size:5 final size:5
Alignment explanation
Indices: 40632869--40632932 Score: 121
Period size: 5 Copynumber: 13.0 Consensus size: 5
40632859 AAAAGTTAAG
40632869 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40632918 TATAT TATAT TATAT
1 TATAT TATAT TATAT
40632933 AATAAAAGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.07
5 55 0.93
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:40633726 original size:22 final size:22
Alignment explanation
Indices: 40633676--40633756 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
40633666 GAACTTTAGC
* *
40633676 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTG-TT--TAGCACTTTA
*
40633701 GTGCTATCTGTTTAGCACATTT-
1 GTGCTCTCTGTTTAGCAC-TTTA
*
40633723 GTGCTCTCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACTTTA
40633745 GTGCTCTCTGTT
1 GTGCTCTCTGTT
40633757 CATTAGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 3 0.06
22 33 0.69
23 1 0.02
24 2 0.04
25 9 0.19
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACTTTA
Found at i:40639279 original size:4 final size:4
Alignment explanation
Indices: 40639270--40639296 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40639260 TGGTTTGAGC
40639270 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
40639297 GAAGAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:40643563 original size:20 final size:20
Alignment explanation
Indices: 40643539--40643596 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
40643529 AATTCTATGA
40643539 AATTTTTATATATTCTTTAT
1 AATTTTTATATATTCTTTAT
* * *
40643559 CATTTTTAT-TTTTATTTTAT
1 AATTTTTATATATT-CTTTAT
40643579 AATTTTTA-A-ATTCTTTAT
1 AATTTTTATATATTCTTTAT
40643597 TCGCATGACA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 5 0.17
19 5 0.17
20 20 0.67
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTATATATTCTTTAT
Found at i:40644683 original size:21 final size:21
Alignment explanation
Indices: 40644658--40644699 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40644648 ATCTAGTAGA
40644658 GTCCCAGAATGAGTATAATTC
1 GTCCCAGAATGAGTATAATTC
40644679 GTCCCAGAATGAGTATAATTC
1 GTCCCAGAATGAGTATAATTC
40644700 TTCCATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
GTCCCAGAATGAGTATAATTC
Found at i:40662069 original size:2 final size:2
Alignment explanation
Indices: 40662062--40662087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40662052 NNNNNNNNNN
40662062 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40662088 ACTGTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40667139 original size:2 final size:2
Alignment explanation
Indices: 40667132--40667170 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40667122 CATTGCAAAG
40667132 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
40667171 GAGGGGAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40670633 original size:21 final size:22
Alignment explanation
Indices: 40670609--40670649 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40670599 AAATAGGAAG
*
40670609 AAAACAA-TAAAAAATAGCATT
1 AAAACAACAAAAAAATAGCATT
*
40670630 AAAATAACAAAAAAATAGCA
1 AAAACAACAAAAAAATAGCA
40670650 ATTTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (22 bp):
AAAACAACAAAAAAATAGCATT
Found at i:40673761 original size:15 final size:15
Alignment explanation
Indices: 40673728--40673776 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
40673718 TTTTTGAATA
40673728 TTGGGCTATAGGT--T
1 TTGGGCT-TAGGTGAT
40673742 TTGGGCTTAGGTGAT
1 TTGGGCTTAGGTGAT
*
40673757 TTGGGTTTAGGTGA-
1 TTGGGCTTAGGTGAT
40673771 TTGGGC
1 TTGGGC
40673777 ATTGTGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 12 0.39
15 14 0.45
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (15 bp):
TTGGGCTTAGGTGAT
Found at i:40674378 original size:50 final size:50
Alignment explanation
Indices: 40674232--40674565 Score: 147
Period size: 50 Copynumber: 6.7 Consensus size: 50
40674222 TTACCATCTC
* * * *
40674232 CAATCTGTTTAACTGCAATGTCA-GGAAATAAGATTTGTCGTCGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * ** * * * * *
40674281 CAATCTATTTCATTACACCGCCAGGGAAGTAAAATTCATTGTTGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * *
40674331 CAATCTATTTAACCACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * ** * ** * * * *
40674381 TAGTCTGTTCCACTGCACCACCT-A-GGAAGTAAGATTCGCCGTTGTGGCCT
1 CAATCTATTTAACT--ACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * * * * *
40674431 CAATCTTTTTAATTGCAATGTCGGGGAAAG-AAGATTCGCCTTTGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGG-AAGTAAGATTCGTCGTCGTAGCTT
** * ** * * * * * *
40674481 CAATCTATTCCACTGCACCGTC-TGGAAGTACGATTCGCCGTTGTGGCCT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * * *
40674530 CAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATT
40674566 TGCCGTTCTG
Statistics
Matches: 205, Mismatches: 72, Indels: 15
0.70 0.25 0.05
Matches are distributed among these distances:
48 6 0.03
49 50 0.24
50 141 0.69
51 4 0.02
52 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
Found at i:40674571 original size:50 final size:50
Alignment explanation
Indices: 40674405--40674785 Score: 286
Period size: 50 Copynumber: 7.6 Consensus size: 50
40674395 GCACCACCTA
*
40674405 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* * * * ** ** *
40674455 GGAAAG-AAGATTCGCCTTTGTAGCTTCAATCTATTCCACTGCACCGTC-T
1 GG-AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* *
40674504 GGAAGTACGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* * * * * * * * *
40674554 GGAAGCAAGATTTGCCGTTCTGACTTCAATCTGTTCAACTGCACTG-CATAG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTC--GG
* * *
40674605 GAAAGTAAGATTCGCCGTTGTGGCCTCAATC-TTTTAAATGCAATATCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
*** * * * * * ** ** *
40674654 GGAAACGAGATTCACCGTTATAGCTTCAATCTGTTCCACTGCACCGCCTGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTC-GG
* * * *
40674705 GAAAGTAAGATTCACCGTTGTGGCCTCAATC-TTTTAAATGCAATGTTGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
** * *
40674754 GGAAGCGAGATTCGCTGTTGTGGCTTCAATCT
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
40674786 GTTCCACTGT
Statistics
Matches: 241, Mismatches: 81, Indels: 18
0.71 0.24 0.05
Matches are distributed among these distances:
48 3 0.01
49 86 0.36
50 96 0.40
51 56 0.23
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
Found at i:40674589 original size:199 final size:200
Alignment explanation
Indices: 40674275--40674794 Score: 622
Period size: 199 Copynumber: 2.6 Consensus size: 200
40674265 TTTGTCGTCG
* * * * * ** * *
40674275 TAGCTTCAATCTATTTCATTACACCGCCAGGG-AAGTAAAATTCATTGTTGTAGCTTCAATCTAT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCT-T
*** * * *
40674339 TTAACCACAATGTCAGGGAAGCAAGATTCGCCG-TC-GTAGCTTTAGTCTGTTCCACTGCACCAC
65 TTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTG-A-CTTCAATCTGTTCCACTGCACCAC
* * *
40674402 CTAGG-AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGGGGAAA-GAAGA
128 ATAGGAAAGTAAGATTCGCCGTTGTGGCCTCAATC-TTTTAAATGCAATATCGGGGAAACG-AGA
* * *
40674465 TTCGCCTTTG
191 TTCACCGTTA
* * *
40674475 TAGCTTCAATCTATTCCACTGCACCGTCT-GG-AAGTACGATTCGCCGTTGTGGCCTCAATCTTT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATC-TT
* * * **
40674538 TTAATTGCAATGTCGGGGAAGCAAGATTTGCCGTTCTGACTTCAATCTGTTCAACTGCACTGCAT
65 TTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTGCACCACAT
40674603 AGGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCA
130 AGGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCA
40674668 CCGTTA
195 CCGTTA
*
40674674 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
* * * * *
40674739 TAAATGCAATGTTGGGGAAGCGAGATTCGCTGTTGTGGCTTCAATCTGTTCCACTG
66 TAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTG
40674795 TACTGCCTGA
Statistics
Matches: 273, Mismatches: 40, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
199 134 0.49
200 111 0.41
201 28 0.10
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (200 bp):
TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
TAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTGCACCACATA
GGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCAC
CGTTA
Found at i:40674803 original size:100 final size:100
Alignment explanation
Indices: 40674232--40674794 Score: 591
Period size: 100 Copynumber: 5.7 Consensus size: 100
40674222 TTACCATCTC
* * * ** * * * * * * *
40674232 CAATCTGTTTAACTGCAATGTC-AGGAAATAAGATTTGTCGTCGTAGCTTCAATCTATTTCATTA
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
* *** * *
40674296 CACCGCC-AGGGAAGTAAAATTCATTGTTGTAGCTT
66 CACCGCCTA-GGAAGTAAGATTCGCCGTTGTGGCCT
* *** * * * *
40674331 CAATCTATTTAACCACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAGTCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
*
40674396 CACCACCTAGGAAGTAAGATTCGCCGTTGTGGCCT
66 CACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
* * *
40674431 CAATCTTTTTAATTGCAATGTCGGGGAAAG-AAGATTCGCCTTTGTAGCTTCAATCTATTCCACT
1 CAATCTTTTTAAATGCAATGTCGGGG-AAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACT
* *
40674495 GCACCGTCT-GGAAGTACGATTCGCCGTTGTGGCCT
65 GCACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
* * * *
40674530 CAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTTGCCGTTCT-GACTTCAATCTGTTCAACT
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACT
* *
40674594 GCACTGCATAGGAAAGTAAGATTCGCCGTTGTGGCCT
65 GCACCGCCTAGG-AAGTAAGATTCGCCGTTGTGGCCT
* * * * *
40674631 CAATC-TTTTAAATGCAATATCGGGGAAACGAGATTCACCGTTATAGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
* *
40674695 CACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCT
66 CACCGCCTAGG-AAGTAAGATTCGCCGTTGTGGCCT
* * * *
40674731 CAATC-TTTTAAATGCAATGTTGGGGAAGCGAGATTCGCTGTTGTGGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
40674795 TACTGCCTGA
Statistics
Matches: 394, Mismatches: 62, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.01
99 103 0.26
100 254 0.64
101 33 0.08
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
CACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
Found at i:40675013 original size:88 final size:88
Alignment explanation
Indices: 40674890--40675572 Score: 1105
Period size: 88 Copynumber: 7.8 Consensus size: 88
40674880 ACTACCGCTT
*
40674890 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
40674955 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* *
40674978 AGGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCATGAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
40675043 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
** *
40675066 AAAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAAATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
40675131 TTTGACCTGCTCCACTACAACCA
66 TTTGACCTGCTCCACTACAACCG
* * *
40675154 AGGGAAGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGAATGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
40675219 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* *
40675242 AGGGAGGCAAGGCTTGTGTATTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
40675307 TTTGATCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* * *
40675330 AGGGAGGCAAAGCTTGTGTCTTCAATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
40675395 TTTGACCTACTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* ** * * * * *
40675418 AGGGAGGTAAGATTTGTGTTTTCGATCTGCTTCGCTGTCAATACAAGAAGGCAAAATCTACTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
40675483 TTTGACCTGCTCCACTACAACTG
66 TTTGACCTGCTCCACTACAACCG
* * *
40675506 AGGGAGGTAAGGCTTGTGTCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCGATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
40675571 TT
66 TT
40675573 CATTGATCTG
Statistics
Matches: 546, Mismatches: 49, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 546 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (88 bp):
AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
TTTGACCTGCTCCACTACAACCG
Found at i:40676241 original size:327 final size:327
Alignment explanation
Indices: 40675648--40676627 Score: 1800
Period size: 327 Copynumber: 3.0 Consensus size: 327
40675638 GGAATGATCA
* * *
40675648 AAATGAATCAAATACTCCTAAATAGACATGTGTGAATAGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
*
40675713 TTTCCGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGG-TTTGTGACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
40675777 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
40675842 TGAACCTCAAAGTTTAATCCATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
* * *
40675907 GAGTAGAAATATGTAGCCTTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTATGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
40675972 CT
326 CT
40675974 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
*
40676039 TTTCTGAGAATGATCCCACTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
* *
40676104 GCTACGACGCCTTCTTGCTTGACTGGTTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCTCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
40676169 TGAACCTCAAAGTTTAATCTATTAGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
40676234 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
40676299 CT
326 CT
*
40676301 AAATGAATCAAATGCTCCTAAATAGACATTTGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
* *
40676366 TTTCTGAGAATGATCCCGCTTAGGTTGCCATTACTCGAAGTTTATTAAGGCTTTGTAACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
*
40676431 GCTACGATGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
40676496 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTATCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
40676561 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
40676626 CT
326 CT
40676628 TTATGCCATT
Statistics
Matches: 632, Mismatches: 21, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
326 110 0.17
327 522 0.83
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (327 bp):
AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
CT
Found at i:40677467 original size:7 final size:7
Alignment explanation
Indices: 40677454--40677487 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40677444 TTATCCTCTC
40677454 CATTTTT
1 CATTTTT
*
40677461 TATTTTT
1 CATTTTT
40677468 CATTTTT
1 CATTTTT
40677475 CA-TTTT
1 CATTTTT
40677481 CATTTTT
1 CATTTTT
40677488 TTGACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
CATTTTT
Found at i:40677480 original size:13 final size:14
Alignment explanation
Indices: 40677454--40677487 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
40677444 TTATCCTCTC
*
40677454 CATTTTTTATTTTT
1 CATTTTTCATTTTT
40677468 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
40677481 CATTTTT
1 CATTTTT
40677488 TTGACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:40690209 original size:25 final size:24
Alignment explanation
Indices: 40690181--40690228 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40690171 ATCCAGGCAA
40690181 TATAACGGAAAGCTCACAAAGAGCT
1 TATAACGGAAAGCTC-CAAAGAGCT
* **
40690206 TATAATGGGTAGCTCCAAAGAGC
1 TATAACGGAAAGCTCCAAAGAGC
40690229 AATTAATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (24 bp):
TATAACGGAAAGCTCCAAAGAGCT
Found at i:40690235 original size:24 final size:24
Alignment explanation
Indices: 40690191--40690258 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
40690181 TATAACGGAA
*
40690191 AGCTCACAAAGAGC-TTATAATGGGT
1 AGCTC-CAAAGAGCAAT-TAATGGGT
40690216 AGCTCCAAAGAGCAATTAATGGGT
1 AGCTCCAAAGAGCAATTAATGGGT
* *
40690240 AGCTCCGAAGAGTAATTAA
1 AGCTCCAAAGAGCAATTAA
40690259 CAAGAAGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 33 0.85
25 6 0.15
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAATGGGT
Found at i:40690843 original size:21 final size:21
Alignment explanation
Indices: 40690817--40690856 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40690807 TATACGAGTA
40690817 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
40690838 AATTTACATTCAATTTAAT
1 AATTTACATTCAATTTAAT
40690857 CCAAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:40690867 original size:21 final size:21
Alignment explanation
Indices: 40690826--40690867 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40690816 AAATTTAACA
* *
40690826 TCAATTTAATACAATTTACAT
1 TCAATTTAATACAAGTCACAT
*
40690847 TCAATTTAATCCAAGTCACAT
1 TCAATTTAATACAAGTCACAT
40690868 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
TCAATTTAATACAAGTCACAT
Found at i:40693302 original size:20 final size:22
Alignment explanation
Indices: 40693268--40693315 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
40693258 TGCTGCACCC
*
40693268 TTTTAAAAAATTA-TTAT-TAT
1 TTTTTAAAAATTATTTATGTAT
40693288 ATTTTTAAAAA-TATTTATGTAT
1 -TTTTTAAAAATTATTTATGTAT
40693310 TTTTTA
1 TTTTTA
40693316 TTTTTTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTTAAAAATTATTTATGTAT
Found at i:40693550 original size:31 final size:32
Alignment explanation
Indices: 40693457--40693550 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 32
40693447 CAATTAACAG
* * * *
40693457 AAATGGAAAAAAGAATCGATTAGTTGGGTGATC
1 AAATGAAAAAAAAAATCCA-TAGTTGGGTGACC
* * *
40693490 AAATTAAAAAAAAAATTCATAATTGGGTGACC
1 AAATGAAAAAAAAAATCCATAGTTGGGTGACC
* *
40693522 AAA-GAAGAAACAAATCCATAGTTGGGTGA
1 AAATGAAAAAAAAAATCCATAGTTGGGTGA
40693551 TCAATTTTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 21 0.43
32 14 0.29
33 14 0.29
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (32 bp):
AAATGAAAAAAAAAATCCATAGTTGGGTGACC
Found at i:40702238 original size:17 final size:16
Alignment explanation
Indices: 40702202--40702250 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
40702192 TGATAAATAC
40702202 AAATTTAAAAATAAAA
1 AAATTTAAAAATAAAA
* *
40702218 AAATCTTAAAAATATAT
1 AAAT-TTAAAAATAAAA
40702235 AAA-TTAATAAATAAAA
1 AAATTTAA-AAATAAAA
40702251 GTATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTTAAAAATAAAA
Found at i:40710012 original size:84 final size:80
Alignment explanation
Indices: 40709835--40710073 Score: 217
Period size: 80 Copynumber: 3.0 Consensus size: 80
40709825 AACCAAAGTC
* * * * *
40709835 TTTACAA-AAAATATTATTATGTGGACTATC--T-ATC-TAAAATCTAAAATAATG-CAATGTCT
1 TTTACAATAAAATA-AATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCAAGGTCT
*
40709894 TTTATTTAATTA-ATT
65 TTTATTTAATTATTTT
* * * *
40709909 TTTACAATAAAATATATTATGTGAAATATCTATCTTTCAACGTGCAATATAAAATAATGCCATAG
1 TTTACAATAAAATAAATTATGTG---GA-CTATCTTTCAACATACAATATAAAATAATGCCA-AG
*
40709974 GTCTTTTATTTATTTATTTAT
61 GTCTTTTATTTAATTATTT-T
* * *
40709995 TTTACAA-AAAA-AAATTATGTGGACTATCTTTCAACATACAATCTACAATAATGCCACAGGTAT
1 TTTACAATAAAATAAATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCA-AGGTCT
40710058 TTTATTTAATTATTTT
65 TTTATTTAATTATTTT
40710074 GATTTGATTT
Statistics
Matches: 135, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
74 16 0.12
75 6 0.04
77 1 0.01
78 5 0.04
79 1 0.01
80 49 0.36
81 3 0.02
82 14 0.10
83 2 0.01
84 25 0.19
85 5 0.04
86 8 0.06
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (80 bp):
TTTACAATAAAATAAATTATGTGGACTATCTTTCAACATACAATATAAAATAATGCCAAGGTCTT
TTATTTAATTATTTT
Found at i:40710770 original size:25 final size:23
Alignment explanation
Indices: 40710742--40710787 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
40710732 ACTTTATATT
*
40710742 TTTATTTTTATTTTTAAGAATTTAA
1 TTTATTTAT-TTTTTAA-AATTTAA
40710767 TTTATTTATTTTTTAAAATTT
1 TTTATTTATTTTTTAAAATTT
40710788 TTAAATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTATTTTTTAAAATTTAA
Found at i:40715520 original size:19 final size:19
Alignment explanation
Indices: 40715496--40715534 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
40715486 TGACAGGCGC
40715496 AAATTATT-TTTTTATATTA
1 AAATTATTATTTTTAT-TTA
40715515 AAATTATTATTTTTATTTA
1 AAATTATTATTTTTATTTA
40715534 A
1 A
40715535 TAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATTATTATTTTTATTTA
Found at i:40715526 original size:22 final size:21
Alignment explanation
Indices: 40715498--40715546 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
40715488 ACAGGCGCAA
*
40715498 ATTATTTTT-TTATATTAAAATT
1 ATTATTTTTATT-TAATAAAA-T
40715520 ATTATTTTTATTTAATAAAAT
1 ATTATTTTTATTTAATAAAAT
40715541 ATTATT
1 ATTATT
40715547 AATCTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTTTTATTTAATAAAAT
Found at i:40715634 original size:27 final size:27
Alignment explanation
Indices: 40715604--40715728 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 27
40715594 CAGGTTGCGG
* * *
40715604 CTATTTGATAGGCGCGACTAGTTAAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
40715631 CTATCTCAGAGGCGCGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
40715658 TTATCTGACAGGCGTGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
40715685 CTATCTGACAGGAGCGACTAGTTGTGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* * *
40715712 CTAACTCAGAGGCGCGA
1 CTATCTGACAGGCGCGA
40715729 ATGGTGGGGC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (27 bp):
CTATCTGACAGGCGCGACTAGTTGAGC
Found at i:40720238 original size:60 final size:60
Alignment explanation
Indices: 40720145--40720277 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 60
40720135 ATACTAAATT
* * * *
40720145 AAACACAACAATTTATAACTTAACCCTAAATTACTAATAAATAAATTTTAAAATAATTAC
1 AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
* * *
40720205 AAACACAAAAAATTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAT
1 AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
*
40720265 AAAAAGCAAAAAA
1 AAACA-CAAAAAA
40720278 AAAATACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 57 0.89
61 7 0.11
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.29
Consensus pattern (60 bp):
AAACACAAAAAATTATAACATAACCCTAAATTACTAACAAATAAATTTTAAAATAATTAC
Found at i:40720382 original size:16 final size:16
Alignment explanation
Indices: 40720357--40720394 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40720347 TGATACATTA
*
40720357 CTCTTTTTTTTCTTTCT
1 CTCTTCTTTTT-TTTCT
40720374 -TCTTCTTTTTTTTCT
1 CTCTTCTTTTTTTTCT
40720389 CTCTTC
1 CTCTTC
40720395 CGAATGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
CTCTTCTTTTTTTTCT
Found at i:40720382 original size:19 final size:19
Alignment explanation
Indices: 40720358--40720394 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40720348 GATACATTAC
*
40720358 TCTTTTTTTTCTTTCTTCT
1 TCTTTTTTTTCTCTCTTCT
40720377 TCTTTTTTTTCTCTCTTC
1 TCTTTTTTTTCTCTCTTC
40720395 CGAATGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTTTTCTCTCTTCT
Found at i:40720566 original size:27 final size:27
Alignment explanation
Indices: 40720536--40720592 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
40720526 GCCTACCTAT
*
40720536 CAGGCTCGATTAGTCGCGCCTATTTGA
1 CAGGCTCGATTAGTCGCGCCCATTTGA
*
40720563 CAGGCTCGATTAGTCGTGCCCATTTGA
1 CAGGCTCGATTAGTCGCGCCCATTTGA
40720590 CAG
1 CAG
40720593 ACGCGACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (27 bp):
CAGGCTCGATTAGTCGCGCCCATTTGA
Found at i:40720808 original size:19 final size:17
Alignment explanation
Indices: 40720766--40720799 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40720756 ATAGACGCGA
40720766 TTAAAAAATATATCATT
1 TTAAAAAATATATCATT
40720783 TTAAAAAATATAT-ATT
1 TTAAAAAATATATCATT
40720799 T
1 T
40720800 AAGTAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAAATATATCATT
Found at i:40727328 original size:24 final size:24
Alignment explanation
Indices: 40727283--40727330 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
40727273 AATCATTTTA
40727283 ATAAAAAAGAAAACATTTTCTTTAGT
1 ATAAAAAAGAAAACA--TTCTTTAGT
40727309 ATAAAAAAGAAAGACA-TCTTTA
1 ATAAAAAAGAAA-ACATTCTTTA
40727331 AATGTCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
26 12 0.57
27 3 0.14
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAAAAAAGAAAACATTCTTTAGT
Found at i:40733295 original size:20 final size:21
Alignment explanation
Indices: 40733241--40733298 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
40733231 TTAATATTTT
* *
40733241 TAAATCTTTATATAT-TTAGA
1 TAAATCTTTAAAAATATTAGA
40733261 TAAAGTC-TT-AAAATATT-GA
1 TAAA-TCTTTAAAAATATTAGA
40733280 TAAATCTTTAAAAATATTA
1 TAAATCTTTAAAAATATTA
40733299 TTAAATTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TAAATCTTTAAAAATATTAGA
Found at i:40737285 original size:22 final size:22
Alignment explanation
Indices: 40737259--40737314 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
40737249 AAATTAAATC
40737259 TCTAAGATTGCAGATCATATCT
1 TCTAAGATTGCAGATCATATCT
40737281 TCTAAGATTGCAGATCATATCT
1 TCTAAGATTGCAGATCATATCT
40737303 TCTAAGATTGCA
1 TCTAAGATTGCA
40737315 TATCTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
TCTAAGATTGCAGATCATATCT
Found at i:40745335 original size:3 final size:3
Alignment explanation
Indices: 40745327--40745363 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
40745317 ATTTTCCCCA
*
40745327 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40745364 TCATGTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40746385 original size:31 final size:31
Alignment explanation
Indices: 40746350--40746447 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
40746340 GATTCGTCTA
40746350 TGTATGCTTGAAAAATATGAAGTTGGTGGTC
1 TGTATGCTTGAAAAATATGAAGTTGGTGGTC
* *
40746381 TGTA----T-AAAATATATGCAG-TGAGATTCGTC
1 TGTATGCTTGAAAA-ATATGAAGTTG-G--TGGTC
40746410 TATGTATGCTTGAAAAATATGAAGTTGGTGGTC
1 --TGTATGCTTGAAAAATATGAAGTTGGTGGTC
40746443 TGTAT
1 TGTAT
40746448 AAAATTCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
26 6 0.12
27 9 0.18
29 4 0.08
31 13 0.25
33 4 0.08
35 9 0.18
36 6 0.12
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.37
Consensus pattern (31 bp):
TGTATGCTTGAAAAATATGAAGTTGGTGGTC
Found at i:40746413 original size:62 final size:62
Alignment explanation
Indices: 40746327--40746452 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
40746317 TCTGATCAAG
40746327 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
1 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
40746389 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
1 ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
40746451 AT
1 AT
40746453 TCAGATTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.36
Consensus pattern (62 bp):
ATATATGCAGTGAGATTCGTCTATGTATGCTTGAAAAATATGAAGTTGGTGGTCTGTATAAA
Found at i:40757132 original size:20 final size:19
Alignment explanation
Indices: 40757087--40757156 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
40757077 GAAGAAAAAA
40757087 AAAAAAGAAAATGGGAAAG
1 AAAAAAGAAAATGGGAAAG
40757106 AATAAAAGAAAA-GGGAAA-
1 AA-AAAAGAAAATGGGAAAG
**
40757124 AGGAAA-AAAATGGGAAAG
1 AAAAAAGAAAATGGGAAAG
* *
40757142 TGAAATAGAAAATGG
1 -AAAAAAGAAAATGG
40757157 ACTATGATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.10
17 9 0.22
18 1 0.03
19 10 0.25
20 16 0.40
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (19 bp):
AAAAAAGAAAATGGGAAAG
Found at i:40758100 original size:52 final size:51
Alignment explanation
Indices: 40758022--40758123 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 51
40758012 CTTGTAGTTC
* * *
40758022 ATAAAAGAAAAAATAGTTTGTGGGTCA-GCAGATGCACTAAAGAGTTATAT
1 ATAAAAAAAAAAATAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATAT
* *
40758072 ATAAAAAAAAAAATGTAGTTAGTGGGTCAGGGAAATGCACTCAAGAGTTATA
1 ATAAAAAAAAAAA--TAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATA
40758124 AAATCTGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
50 12 0.27
52 13 0.30
53 19 0.43
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (51 bp):
ATAAAAAAAAAAATAGTTAGTGGGTCAGGCAAATGCACTAAAGAGTTATAT
Found at i:40758557 original size:20 final size:22
Alignment explanation
Indices: 40758534--40758584 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
40758524 TTTTTTTGTA
40758534 TTTTATATTATA-TTTT-TAAT
1 TTTTATATTATATTTTTATAAT
*
40758554 TTTT-TA-AATATTTTTATAAT
1 TTTTATATTATATTTTTATAAT
*
40758574 TTTTAAATTAT
1 TTTTATATTAT
40758585 TTGTTGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.12
19 6 0.25
20 12 0.50
21 1 0.04
22 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATATTATATTTTTATAAT
Done.