Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 24 of 147
Found at i:5150757 original size:21 final size:21
Alignment explanation
Indices: 5150709--5150767 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
5150699 ATTTATTGAT
5150709 TTATTTTTATATTATATAAATAA
1 TTATTTTTA-ATTATA-AAATAA
5150732 --A--TTTAATTATAAAATAA
1 TTATTTTTAATTATAAAATAA
*
5150749 TTATTTTTACTTGATAAAA
1 TTATTTTTAATT-ATAAAA
5150768 ATTTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
17 6 0.20
18 6 0.20
19 5 0.17
21 7 0.23
22 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTTTTAATTATAAAATAA
Found at i:5151193 original size:14 final size:14
Alignment explanation
Indices: 5151174--5151221 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
5151164 AATAAAAGTT
5151174 AATTAATTACAAAA
1 AATTAATTACAAAA
5151188 AATTAATTATCAAATAAA
1 AATTAATTA-C--A-AAA
*
5151206 AATAAATTACAAAA
1 AATTAATTACAAAA
5151220 AA
1 AA
5151222 GAAATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 14 0.48
15 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
AATTAATTACAAAA
Found at i:5151206 original size:18 final size:18
Alignment explanation
Indices: 5151185--5151236 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
5151175 ATTAATTACA
*
5151185 AAAAATTAATTATCAAAT
1 AAAAATAAATTATCAAAT
*
5151203 AAAAATAAATTA-CAAAA
1 AAAAATAAATTATCAAAT
5151220 AAGAAATAAATT-TCAAA
1 AA-AAATAAATTATCAAA
5151237 AGGGTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATAAATTATCAAAT
Found at i:5152029 original size:370 final size:370
Alignment explanation
Indices: 5151339--5152337 Score: 1293
Period size: 370 Copynumber: 2.7 Consensus size: 370
5151329 CAGGGTCCTG
* * * * ** * * *
5151339 TGTCACGGGTCGAGACTTAATCTTCTAACCCGCGCGGCTTCAAGACCCGGGCATTCACCCTTCCG
1 TGTCACGGGTCGAGACTTAAGCTCCGAACTCGCGTAGCTCCGAGACCCGGGCATTCACCCTTTCG
* * * *
5151404 GCGTCTCGAATCAACCTGACCTTCACGGTTCACACCCTTGTAAAGTATTGTTCGCTCTGGCCCCC
66 GCGTCCCGAATCAACCTGACCTTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCCCC
* *
5151469 TTAGCCTCACGGTTTTGTCCTACAAAAAATGCCTCACAAGGCAGAGGTGGTGTGAACCATTTTAT
131 -TGGCCTCACGGTTTTGTCCTACAAAAAATGCCTCACAAGGCAGAGGTGGTGTGAACCCTTTTAT
* *
5151534 ACTCCAGTGACCCTCCTATTATGTTTGATGTGGGATTCAGGACTCTTCCTTAAGTCCGTGACATT
195 ACCCCAGTGACCCTCCTATTATGTTTGATGTGGGATTCAGGACTCTTTCTTAAGTCCGTGACATT
* * * *
5151599 CTCCCGCATCCAACCTCGTGACGCCCTCGTCACGGAGGCTGACCACCCTGCCTGCCTCCCT-TGA
260 CTCCCCCACCCAACCTCATGACGCCCTCGTCACGGAGGCTGACCACCCTGCCTACCTCCCTCT-A
** * * * * *
5151663 GGTGCTTGGCATGGATCGAACGGTTTAGGACTGACTCTGATATCACT
324 GACGCTCGACATGAATCGAACGATTTAGGACTGACTCTGATACCACT
* *
5151710 TTTCACGGGTCGAGACTTAAGCTCCGAA-TCGACGTAGCTCCGAGACCCGGGCATTCACCTTTTC
1 TGTCACGGGTCGAGACTTAAGCTCCGAACTCG-CGTAGCTCCGAGACCCGGGCATTCACCCTTTC
* *
5151774 GGCGTCCCGAATCAGCCT-TCCTTCCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCC
65 GGCGTCCCGAATCAACCTGACCTT-CACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCC
* * ** * * * *
5151838 CCTGGCCTCATGGTTTTATCCTACAAAAGGTGCCTCACAAGACGGAGATGGTGTGAACCCTTATA
129 CCTGGCCTCACGGTTTTGTCCTACAAAAAATGCCTCACAAGGCAGAGGTGGTGTGAACCCTTTTA
* * * *
5151903 TACCCCAGTGACCTTCATATTATGTTCGATGTGGGATTCAGGACTCTTTCTTAGGTCCGTGACAT
194 TACCCCAGTGACCCTCCTATTATGTTTGATGTGGGATTCAGGACTCTTTCTTAAGTCCGTGACAT
* * *
5151968 TCTCCCCCACCCAACCTCATGACGCCCTCGTCACGGAGGCTGGCCATCCTGCTTACCTCCCTCTA
259 TCTCCCCCACCCAACCTCATGACGCCCTCGTCACGGAGGCTGACCACCCTGCCTACCTCCCTCTA
* *
5152033 GACGCTCGACGTGAATCGAACGATTTAGGGCTGACTCTGATACCACT
324 GACGCTCGACATGAATCGAACGATTTAGGACTGACTCTGATACCACT
* * * * * *
5152080 TGTCACGGGTCGAGACTTAATCTCCTAACTCGCGTGGCTTCGGGACCCGGGCATTCACCCTTTCA
1 TGTCACGGGTCGAGACTTAAGCTCCGAACTCGCGTAGCTCCGAGACCCGGGCATTCACCCTTTCG
* * * * *
5152145 ACGTCCCGAATCAACCTGACCGTCACAGTTCACATCTTTGTGAGGTATTGTCCGCTCTGGCCCCT
66 GCGTCCCGAATCAACCTGACCTTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCCC-
* * * *
5152210 TTGGCCTCACGATTTTGTCTTACAAAAAATACCTCACAAGGCAGAGGTGGTGTGAACCCTTTTAT
130 CTGGCCTCACGGTTTTGTCCTACAAAAAATGCCTCACAAGGCAGAGGTGGTGTGAACCCTTTTAT
** * ** * *
5152275 ACCTTAGTGACCCTCCTATTATATTTGATGTAAGATTCAGGACTCTTTCTTAATTCTGTGACA
195 ACCCCAGTGACCCTCCTATTATGTTTGATGTGGGATTCAGGACTCTTTCTTAAGTCCGTGACA
5152338 CTTGCACTTC
Statistics
Matches: 535, Mismatches: 87, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
370 318 0.59
371 217 0.41
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.28
Consensus pattern (370 bp):
TGTCACGGGTCGAGACTTAAGCTCCGAACTCGCGTAGCTCCGAGACCCGGGCATTCACCCTTTCG
GCGTCCCGAATCAACCTGACCTTCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCCCC
TGGCCTCACGGTTTTGTCCTACAAAAAATGCCTCACAAGGCAGAGGTGGTGTGAACCCTTTTATA
CCCCAGTGACCCTCCTATTATGTTTGATGTGGGATTCAGGACTCTTTCTTAAGTCCGTGACATTC
TCCCCCACCCAACCTCATGACGCCCTCGTCACGGAGGCTGACCACCCTGCCTACCTCCCTCTAGA
CGCTCGACATGAATCGAACGATTTAGGACTGACTCTGATACCACT
Found at i:5154783 original size:18 final size:18
Alignment explanation
Indices: 5154740--5154787 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5154730 ATTATATTTT
**
5154740 TAATAAATTTTGATTAATT
1 TAATAAATTTT-ATTAAAA
*
5154759 TTA-AAATTTTATTAAAA
1 TAATAAATTTTATTAAAA
5154776 TAATAAATTTTA
1 TAATAAATTTTA
5154788 ATGAATCATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 15 0.62
19 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATAAATTTTATTAAAA
Found at i:5155287 original size:29 final size:29
Alignment explanation
Indices: 5155255--5155314 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
5155245 AATCAATTGA
5155255 ATTAAATTAA-TTTGATTAATTAATTTATT
1 ATTAAATTAATTTTGATTAATT-ATTTATT
*
5155284 ATTAAATTAATTTTGATTGATTATTTATT
1 ATTAAATTAATTTTGATTAATTATTTATT
5155313 AT
1 AT
5155315 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTAAATTAATTTTGATTAATTATTTATT
Found at i:5155558 original size:19 final size:18
Alignment explanation
Indices: 5155531--5155569 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5155521 AATTAGTAAA
5155531 AAATTAATTAAATCAATT
1 AAATTAATTAAATCAATT
**
5155549 AAATTAAATTTGATCAATT
1 AAATT-AATTAAATCAATT
5155568 AA
1 AA
5155570 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTAATTAAATCAATT
Found at i:5155792 original size:42 final size:42
Alignment explanation
Indices: 5155745--5155869 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
5155735 ATTCCATTTG
* *
5155745 TGTTGATTCTAAGATATAATGATTAAGTTCACCATCATAGGC
1 TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGGC
5155787 TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGGC
1 TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGGC
5155829 TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGG
1 TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGG
5155870 ATGCACCCAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (42 bp):
TGTTGATTCTAACATATAATGATTAAGTTCGCCATCATAGGC
Found at i:5156197 original size:23 final size:22
Alignment explanation
Indices: 5156155--5156206 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
5156145 AATTATATAT
* *
5156155 TATAAATTTTAAAATTATTAAA
1 TATAATTTTTAAAATAATTAAA
*
5156177 TATAATTTTTAAAAATAATTACA
1 TATAATTTTT-AAAATAATTAAA
*
5156200 TAAAATT
1 TATAATT
5156207 ATTTCAGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAATTTTTAAAATAATTAAA
Found at i:5160094 original size:68 final size:65
Alignment explanation
Indices: 5159938--5160103 Score: 149
Period size: 69 Copynumber: 2.5 Consensus size: 65
5159928 TTAATTAAAA
* * * *
5159938 TGGATTATTGAAGATCTTTTTTGTCAAAAAAGCTTTTAATAATCCCTTCAAAGTCTAATTTTTTT
1 TGGATTATTGAAGGTTTTTTTTGTCAAAAAAGCTTTCAATAATCCCTTCAAAGTCAAATTTTTTT
* * * *
5160003 TAGGAGATTATTAAATGTATTTTTTTGTCAAAAATA-CTTTCATTAATCCCGTT-AAATTTCAAA
1 T--G-GATTATTGAAGGT-TTTTTTTGTCAAAAA-AGCTTTCAATAATCCC-TTCAAA-GTCAAA
5160066 TTTTTTAT
59 TTTTTT-T
* *
5160074 TGGATTATTGAAGGTGTTTTTGGT-AAAAAA
1 TGGATTATTGAAGGTTTTTTTTGTCAAAAAA
5160104 TGTCTTCACT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
65 2 0.02
66 5 0.06
67 8 0.10
68 21 0.26
69 30 0.37
70 13 0.16
71 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (65 bp):
TGGATTATTGAAGGTTTTTTTTGTCAAAAAAGCTTTCAATAATCCCTTCAAAGTCAAATTTTTTT
Found at i:5160176 original size:24 final size:24
Alignment explanation
Indices: 5160144--5160189 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5160134 GAGGATTATT
5160144 GAAGGCGTTTTAAAGTTTTTTACC
1 GAAGGCGTTTTAAAGTTTTTTACC
5160168 GAAGGCGTTTTAAAGTTTTTTA
1 GAAGGCGTTTTAAAGTTTTTTA
5160190 TCAAAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (24 bp):
GAAGGCGTTTTAAAGTTTTTTACC
Found at i:5160204 original size:25 final size:24
Alignment explanation
Indices: 5160149--5160205 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5160139 TTATTGAAGG
* **
5160149 CGTTTTAAAGTTTTTTACCGAAGG
1 CGTTTTAAAGTTTTTTACCAAAAA
*
5160173 CGTTTTAAAGTTTTTTATCAAAAA
1 CGTTTTAAAGTTTTTTACCAAAAA
5160197 CGTCTTTAA
1 CGT-TTTAA
5160206 TAATCCTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (24 bp):
CGTTTTAAAGTTTTTTACCAAAAA
Found at i:5161363 original size:139 final size:138
Alignment explanation
Indices: 5161086--5161366 Score: 472
Period size: 139 Copynumber: 2.0 Consensus size: 138
5161076 ATAAGGTTAA
* * *
5161086 CAATATGAGCAATGCATCTCAAATGAAGATATTTGCCTCTTACAATACTAGTTTCTGTATTGTTA
1 CAATATGAGCAATGCATATCAAATGAAGATATTTGCCTCTTACAATACTAGTTCCTGCATTGTTA
*
5161151 AGTTTTTTTCTCAAGTATGCGACTGCAACATCATTATAACTAACATTATCAATTGTAATAGCAAA
66 AGTTTTTTTCTCAAGTATGAGACTGCAACATCATTATAACTAACATTATCAATTGTAATAGCAAA
*
5161216 AACTTTAT
131 AACCTTAT
* *
5161224 CAATATGAGCAATGCGTATCAAATGAAGATATTTGCTTCTTACAATACTAGTTCCTGCATTGTTA
1 CAATATGAGCAATGCATATCAAATGAAGATATTTGCCTCTTACAATACTAGTTCCTGCATTGTTA
* *
5161289 AGTTTTTTTTCTCAAGTATGAGATTGCAACATCATTATAACTAGCATTATCAATTGTAATAGCAA
66 AG-TTTTTTTCTCAAGTATGAGACTGCAACATCATTATAACTAACATTATCAATTGTAATAGCAA
5161354 AAACCTTAT
130 AAACCTTAT
5161363 CAAT
1 CAAT
5161367 CATTCAATCA
Statistics
Matches: 133, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
138 62 0.47
139 71 0.53
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (138 bp):
CAATATGAGCAATGCATATCAAATGAAGATATTTGCCTCTTACAATACTAGTTCCTGCATTGTTA
AGTTTTTTTCTCAAGTATGAGACTGCAACATCATTATAACTAACATTATCAATTGTAATAGCAAA
AACCTTAT
Found at i:5162298 original size:21 final size:22
Alignment explanation
Indices: 5162274--5162314 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5162264 ACCCAGATCC
*
5162274 AAAAGTTATGA-AAAAGAAAAA
1 AAAAGTGATGACAAAAGAAAAA
*
5162295 AAAAGTGATTACAAAAGAAA
1 AAAAGTGATGACAAAAGAAA
5162315 GAAAGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (22 bp):
AAAAGTGATGACAAAAGAAAAA
Found at i:5164023 original size:13 final size:13
Alignment explanation
Indices: 5164013--5164037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5164003 TTAAAATATG
5164013 ATATAAAAATAAA
1 ATATAAAAATAAA
5164026 ATATAAAAATAA
1 ATATAAAAATAA
5164038 TACGATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATATAAAAATAAA
Found at i:5164158 original size:32 final size:32
Alignment explanation
Indices: 5164122--5164196 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
5164112 TTTAATACAT
5164122 AATTTTCATATAAAATACGATATAAATATATA
1 AATTTTCATATAAAATACGATATAAATATATA
* *** * *
5164154 AATTTTAATATTTTATACTATATAAATATATG
1 AATTTTCATATAAAATACGATATAAATATATA
*
5164186 AATTATCATAT
1 AATTTTCATAT
5164197 TTAATTATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (32 bp):
AATTTTCATATAAAATACGATATAAATATATA
Found at i:5164197 original size:32 final size:32
Alignment explanation
Indices: 5164136--5164198 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5164126 TTCATATAAA
*
5164136 ATACGATATAAATATATAAATTTTAATATTTT
1 ATACGATATAAATATATAAATTATAATATTTT
* * *
5164168 ATACTATATAAATATATGAATTATCATATTT
1 ATACGATATAAATATATAAATTATAATATTT
5164199 AATTATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (32 bp):
ATACGATATAAATATATAAATTATAATATTTT
Found at i:5169954 original size:24 final size:24
Alignment explanation
Indices: 5169927--5169972 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5169917 ATTTATTAAG
5169927 TTTAATAAATAATTATAAATAATA
1 TTTAATAAATAATTATAAATAATA
* * *
5169951 TTTAATAATTTATTTTAAATAA
1 TTTAATAAATAATTATAAATAA
5169973 ATAAATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAATAAATAATTATAAATAATA
Found at i:5170267 original size:29 final size:28
Alignment explanation
Indices: 5170235--5170292 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
5170225 ATATAAAAAT
5170235 AATATAATT-TAAAATCTTAAAAAATTATA
1 AATATAATTATAAAA--TTAAAAAATTATA
5170264 AATATAATTAATAAAATTAAAAAATTATA
1 AATATAATT-ATAAAATTAAAAAATTATA
5170293 TTTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 22 0.81
31 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATAATTATAAAATTAAAAAATTATA
Found at i:5173900 original size:32 final size:31
Alignment explanation
Indices: 5173843--5173907 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
5173833 AATATGATAT
*
5173843 GAAAATAATATAAAAAATACAAAAATAATAC
1 GAAAATAATATAAAAAAAACAAAAATAATAC
* *
5173874 GAAAATGATA-AAAAAAAACATGAAAATTATAC
1 GAAAATAATATAAAAAAAACA--AAAATAATAC
5173906 GA
1 GA
5173908 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.31
31 9 0.31
32 11 0.38
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (31 bp):
GAAAATAATATAAAAAAAACAAAAATAATAC
Found at i:5177549 original size:19 final size:18
Alignment explanation
Indices: 5177525--5177571 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
5177515 GTAAAATATG
5177525 TTTTTTAATTTTTAACTTA
1 TTTTTTAATTTTTAAC-TA
*
5177544 TTTTTT-GTTATTTAACTA
1 TTTTTTAATT-TTTAACTA
5177562 -TTTTTAATTT
1 TTTTTTAATTT
5177572 AATACAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 12 0.50
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTTAATTTTTAACTA
Found at i:5179221 original size:22 final size:22
Alignment explanation
Indices: 5179191--5179234 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5179181 TTTCATAGAA
*
5179191 AATTGATTGGTCAACGAAAAAT
1 AATTGATTGATCAACGAAAAAT
* *
5179213 AATTTATTGATCAATGAAAAAT
1 AATTGATTGATCAACGAAAAAT
5179235 GAAACTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (22 bp):
AATTGATTGATCAACGAAAAAT
Found at i:5179358 original size:18 final size:18
Alignment explanation
Indices: 5179281--5179480 Score: 106
Period size: 18 Copynumber: 11.3 Consensus size: 18
5179271 AAAAGACTAT
5179281 TAATATATATATTAATAAA
1 TAATAT-TATATTAATAAA
5179300 TAATATTATA--AAT--A
1 TAATATTATATTAATAAA
5179314 -AATA-T-TA-TAAT-AA
1 TAATATTATATTAATAAA
*
5179327 T-TTATTAATATTAATAAA
1 TAATATT-ATATTAATAAA
*
5179345 TAATATTGTATTAATAAA
1 TAATATTATATTAATAAA
*
5179363 TACATA--ATATTATATTAA
1 TA-ATATTATATTA-ATAAA
* *
5179381 TAAATAGTATATTAATATA
1 T-AATATTATATTAATAAA
* *
5179400 TAATATTATAATATATTAA
1 TAATATTATATTA-ATAAA
* *
5179419 TAGATGATT-TATT-GTTAA
1 TA-AT-ATTATATTAATAAA
*
5179437 T-ATAGTATATTAATAAA
1 TAATATTATATTAATAAA
5179454 TAATATTGTTATATTAATAAA
1 TAATA---TTATATTAATAAA
5179475 TAATAT
1 TAATAT
5179481 AATACTAAAT
Statistics
Matches: 141, Mismatches: 17, Indels: 47
0.69 0.08 0.23
Matches are distributed among these distances:
11 2 0.01
12 4 0.03
13 7 0.05
14 2 0.01
15 2 0.01
16 11 0.08
17 13 0.09
18 46 0.33
19 23 0.16
20 11 0.08
21 20 0.14
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (18 bp):
TAATATTATATTAATAAA
Found at i:5179369 original size:22 final size:21
Alignment explanation
Indices: 5179294--5179386 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 21
5179284 TATATATATT
*
5179294 AATAAATAATA-TTATAAATA
1 AATAAATAATATTTATTAATA
*
5179314 AATATTATAATAATTTATTAATA
1 AATA-AATAAT-ATTTATTAATA
5179337 TTAATAAATAATATTGTATTAATA
1 --AATAAATAATATT-TATTAATA
*
5179361 AATACATAATATTATATTAATA
1 AATAAATAATATT-TATTAATA
5179383 AATA
1 AATA
5179387 GTATATTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.06
21 5 0.08
22 25 0.40
23 11 0.18
24 13 0.21
25 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
AATAAATAATATTTATTAATA
Found at i:5179457 original size:87 final size:85
Alignment explanation
Indices: 5179281--5179543 Score: 229
Period size: 87 Copynumber: 3.0 Consensus size: 85
5179271 AAAAGACTAT
* *
5179281 TAATATATATATTAATAAATAATATT-ATAAATAAATATTATAATAATTTATTAATATTAATAAA
1 TAATAT-TATATTAATAAATAATATTAATATAT-AATATTATAATAATTTAATAATATTAATAAA
* *
5179345 TAATATTGTATTAATAAATACA
64 TAATATAGTATTAATAAATAAA
*
5179367 TAATATTATATTAATAAATAGTATATTAATATATAATATTATAAT-ATATTAATAGATGATTTAT
1 TAATATTATATTAATAAATA--ATATTAATATATAATATTATAATAAT-TTAATA-AT-ATTAAT
***
5179431 TGTTAATATAGTATATTAATAAAT-AA
61 AAATAATATAG--TATTAATAAATAAA
* * * *
5179457 TATTGTTATATTAATAAATAATA-TAATACTA-AATATTAT--TAATTTAATTACTA-AAATATA
1 TAATATTATATTAATAAATAATATTAATA-TATAATATTATAATAATTTAA-TAATATTAATA-A
5179517 ATAATAATA-TATTAATAAATAATA
63 ATAAT-ATAGTATTAATAAATAA-A
5179541 TAA
1 TAA
5179544 AAAATAATAA
Statistics
Matches: 145, Mismatches: 17, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
82 11 0.08
83 3 0.02
84 8 0.06
85 23 0.16
86 12 0.08
87 34 0.23
88 12 0.08
89 12 0.08
90 19 0.13
91 11 0.08
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (85 bp):
TAATATTATATTAATAAATAATATTAATATATAATATTATAATAATTTAATAATATTAATAAATA
ATATAGTATTAATAAATAAA
Found at i:5179468 original size:21 final size:20
Alignment explanation
Indices: 5179281--5179481 Score: 81
Period size: 21 Copynumber: 10.3 Consensus size: 20
5179271 AAAAGACTAT
5179281 TAATATA-TATATTAATAAA
1 TAATATAGTATATTAATAAA
* *
5179300 TAATATTA-TAAATAAATATTATAA
1 TAATA-TAGT--AT-ATTAATA-AA
* *
5179324 TAATTTATTAATATTAATAAA
1 TAATATAGT-ATATTAATAAA
*
5179345 TAATAT--TGTATTAATAAA
1 TAATATAGTATATTAATAAA
* *
5179363 T-ACATA--ATATTATATTAA
1 TAATATAGTATATTA-ATAAA
*
5179381 TAA-ATAGTATATTAATATA
1 TAATATAGTATATTAATAAA
*
5179400 T-A-ATA-T-TA-TAATATA
1 TAATATAGTATATTAATAAA
* * ***
5179415 TTA-ATAG-ATGATTTATTGT
1 TAATATAGTAT-ATTAATAAA
5179434 TAATATAGTATATTAATAAA
1 TAATATAGTATATTAATAAA
*
5179454 TAATATTGTTATATTAATAAA
1 TAATATAG-TATATTAATAAA
5179475 TAATATA
1 TAATATA
5179482 ATACTAAATA
Statistics
Matches: 140, Mismatches: 23, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
15 8 0.06
16 6 0.04
17 10 0.07
18 24 0.17
19 16 0.11
20 25 0.18
21 27 0.19
22 7 0.05
23 10 0.07
24 7 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAATATAGTATATTAATAAA
Found at i:5179496 original size:28 final size:26
Alignment explanation
Indices: 5179282--5179552 Score: 78
Period size: 24 Copynumber: 10.7 Consensus size: 26
5179272 AAAGACTATT
*
5179282 AATATATATATTAATAAATAATATT-ATA
1 AATA-ATATAATAAT-AAT-ATATTAATA
* *
5179310 AATAAATATTATAATAATTTATTAAT-
1 AAT-AATATAATAATAATATATTAATA
* * *
5179336 ATTAATA-AATAATATTGTATTAATA
1 AATAATATAATAATAATATATTAATA
*
5179361 AAT-ACATAAT-AT--TATATTAATA
1 AATAATATAATAATAATATATTAATA
* *
5179383 AATAGTATATTAATATATAATATT-AT-
1 AATAATATAATAATA-AT-ATATTAATA
* * **
5179409 AAT-ATATTAATAGATGATTTATTGTTA
1 AATAATA-TAATA-ATAATATATTAATA
* * *
5179436 ATATAGTATATTAATAAATAATATT-GT-
1 A-ATAATATAATAAT-AAT-ATATTAATA
* * *
5179463 TAT-AT-TAATAAATAATATAATACTA
1 AATAATATAAT-AATAATATATTAATA
* * *
5179488 AAT-AT-TATTAAT-TTA-ATTACT-
1 AATAATATAATAATAATATATTAATA
5179509 AA-AATATAATAATAATATATTAATA
1 AATAATATAATAATAATATATTAATA
*
5179534 AATAATATAAAAAATAATA
1 AATAATAT-AATAATAATA
5179553 AATAGTTTTA
Statistics
Matches: 179, Mismatches: 36, Indels: 57
0.66 0.13 0.21
Matches are distributed among these distances:
21 4 0.02
22 23 0.13
23 12 0.07
24 35 0.20
25 28 0.16
26 23 0.13
27 22 0.12
28 25 0.14
29 7 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (26 bp):
AATAATATAATAATAATATATTAATA
Found at i:5179539 original size:15 final size:15
Alignment explanation
Indices: 5179282--5179542 Score: 104
Period size: 15 Copynumber: 16.6 Consensus size: 15
5179272 AAAGACTATT
5179282 AATATATATATTAATA
1 AATA-ATATATTAATA
*
5179298 AATAATATTATAAATA
1 AATAATA-TATTAATA
* * *
5179314 AATATTATAATAATT
1 AATAATATATTAATA
* *
5179329 TATTA-ATATTAATA
1 AATAATATATTAATA
5179343 AATAATATTGTATTAATA
1 AATAATA---TATTAATA
*
5179361 AATACATAATATTATATT
1 AATA-AT-ATATTA-ATA
*
5179379 AATAA-ATAGT-AT-
1 AATAATATATTAATA
*
5179391 ATTAATATA-TAATA
1 AATAATATATTAATA
*
5179405 TTATAATATATTAATA
1 -AATAATATATTAATA
* * * **
5179421 GATGATTTATTGTTA
1 AATAATATATTAATA
*
5179436 ATATAGTATATTAATA
1 A-ATAATATATTAATA
5179452 AATAATATTGTTATATTAATA
1 AAT-A-A----TATATTAATA
* *
5179473 AATAATATAATACTA
1 AATAATATATTAATA
* *
5179488 AATATTATTAATTTAATT
1 AATAATA-T-A-TTAATA
* *
5179506 ACTAAAATA-TAAT-
1 AATAATATATTAATA
5179519 AATAATATATTAATA
1 AATAATATATTAATA
5179534 AATAATATA
1 AATAATATA
5179543 AAAAATAATA
Statistics
Matches: 180, Mismatches: 40, Indels: 51
0.66 0.15 0.19
Matches are distributed among these distances:
12 5 0.03
13 14 0.08
14 18 0.10
15 57 0.32
16 35 0.19
17 8 0.04
18 25 0.14
19 3 0.02
20 2 0.01
21 13 0.07
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:5179548 original size:35 final size:35
Alignment explanation
Indices: 5179470--5179549 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
5179460 TGTTATATTA
* * * *
5179470 ATAAATAATATAATACTAAATATTATTAATTTAAT
1 ATAAAAAATATAATAATAAATATTAATAATATAAT
*
5179505 -TACTAAAATATAATAATAATATATTAATAA-ATAAT
1 ATA-AAAAATATAATAATAA-ATATTAATAATATAAT
5179540 ATAAAAAATA
1 ATAAAAAATA
5179550 ATAAATAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
34 2 0.06
35 23 0.64
36 11 0.31
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
ATAAAAAATATAATAATAAATATTAATAATATAAT
Found at i:5179600 original size:19 final size:18
Alignment explanation
Indices: 5179573--5179660 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 18
5179563 TTTTAAGTAT
*
5179573 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
5179592 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
5179610 TTATTAA-A--AAATAATTA
1 TT-TTAATATTAAATAA-TA
5179627 TTTTTTAATATT-AAT-A-A
1 --TTTTAATATTAAATAATA
*
5179644 TTTTAATAATAAATAAT
1 TTTTAATATTAAATAAT
5179661 TTCAATATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
15 9 0.16
16 8 0.15
17 4 0.07
18 12 0.22
19 19 0.35
20 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:5179642 original size:20 final size:19
Alignment explanation
Indices: 5179570--5179645 Score: 52
Period size: 18 Copynumber: 4.1 Consensus size: 19
5179560 TTATTTTAAG
*
5179570 TATTTTTT-ATATTAACAT
1 TATTTTTTAATATTAAAAT
* *
5179588 AATATTTTAATATTAAATAT
1 TATTTTTTAATATTAAA-AT
* *
5179608 TA-TTATTAA-A-AAATAAT
1 TATTTTTTAATATTAA-AAT
5179625 TATTTTTTAATATTAATAAT
1 TATTTTTTAATATTAA-AAT
5179645 T
1 T
5179646 TTAATAATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 13 0.30
20 10 0.23
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTTTAATATTAAAAT
Found at i:5179649 original size:15 final size:15
Alignment explanation
Indices: 5179629--5179669 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
5179619 AATAATTATT
*
5179629 TTTTAATATTAATAA
1 TTTTAATATAAATAA
5179644 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
5179660 TTTCAATATA
1 TTTTAATATA
5179670 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:5179658 original size:16 final size:16
Alignment explanation
Indices: 5179629--5179694 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
5179619 AATAATTATT
*
5179629 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
5179644 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
*
5179660 -TTT--CAAT--AT-A
1 TTTTAATAATAAATAA
5179670 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
5179686 TTTTTAATA
1 -TTTTAATA
5179695 TTTTGATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 5 0.12
13 6 0.15
15 12 0.30
16 8 0.20
17 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:5179672 original size:26 final size:25
Alignment explanation
Indices: 5179639--5179688 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
5179629 TTTTAATATT
5179639 AATAATTTTAATAATAAATAATTTC
1 AATAATTTTAATAATAAATAATTTC
5179664 AATATATTTTAATAATAAATAATTT
1 AATA-ATTTTAATAATAAATAATTT
5179689 TTAATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAATTTTAATAATAAATAATTTC
Found at i:5181628 original size:2 final size:2
Alignment explanation
Indices: 5181621--5181658 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5181611 ATTGACAGTT
* *
5181621 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5181659 GCCCTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5182194 original size:13 final size:12
Alignment explanation
Indices: 5182169--5182210 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 12
5182159 TTTCATCTGC
5182169 ATATTAT-TTTT
1 ATATTATATTTT
5182180 ATATTATATTATT
1 ATATTATATT-TT
5182193 ATATTATATTTT
1 ATATTATATTTT
*
5182205 AAATTA
1 ATATTA
5182211 CCGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 7 0.25
12 9 0.32
13 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:5185239 original size:23 final size:23
Alignment explanation
Indices: 5185204--5185250 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5185194 AAACATAAAA
** * *
5185204 TATATATTTTTATTTTTTAAATT
1 TATATATAATTATTGTTAAAATT
5185227 TATATATAATTATTGTTAAAATT
1 TATATATAATTATTGTTAAAATT
5185250 T
1 T
5185251 TAAAACGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TATATATAATTATTGTTAAAATT
Found at i:5187584 original size:20 final size:21
Alignment explanation
Indices: 5187534--5187585 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5187524 TGATTAAATT
*
5187534 TATT-ATTTTTTTAAATTAAA
1 TATTAATTTATTTAAATTAAA
* *
5187554 TATTAAATTATTTAAATTCAA
1 TATTAATTTATTTAAATTAAA
5187575 T-TTAATTTATT
1 TATTAATTTATT
5187586 ATTTAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTAATTTATTTAAATTAAA
Found at i:5188096 original size:16 final size:16
Alignment explanation
Indices: 5188075--5188105 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5188065 TTTTATATAT
5188075 TTTTTTAGTAAATAAA
1 TTTTTTAGTAAATAAA
*
5188091 TTTTTTATTAAATAA
1 TTTTTTAGTAAATAA
5188106 TATAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTTAGTAAATAAA
Found at i:5188181 original size:27 final size:26
Alignment explanation
Indices: 5188135--5188196 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
5188125 TAAGTAAAAC
* ** *
5188135 TAATATATTTTTATTTAAAATATATAT
1 TAATATATATTTATAAAAAAT-TACAT
5188162 TAATATATATTTATAAAAAATTACAT
1 TAATATATATTTATAAAAAATTACAT
*
5188188 AAATATATA
1 TAATATATA
5188197 AGATAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATATATATTTATAAAAAATTACAT
Found at i:5189365 original size:32 final size:33
Alignment explanation
Indices: 5189329--5189390 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
5189319 ATTTCATATT
* *
5189329 TATCATTAC-TTTTTTTTAATATAATTTTATGG
1 TATCACTACATTTTTTTTAATACAATTTTATGG
*
5189361 TATCACTACATTTTTTTTAATGCAATTTTA
1 TATCACTACATTTTTTTTAATACAATTTTA
5189391 GTCAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (33 bp):
TATCACTACATTTTTTTTAATACAATTTTATGG
Found at i:5191803 original size:18 final size:19
Alignment explanation
Indices: 5191780--5191821 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
5191770 CCAAATCAAA
5191780 TTATATATTTATT-AATTT
1 TTATATATTTATTAAATTT
*
5191798 TTATATATTTTTTAAATTT
1 TTATATATTTATTAAATTT
5191817 TTATA
1 TTATA
5191822 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATTTATTAAATTT
Found at i:5191877 original size:12 final size:12
Alignment explanation
Indices: 5191860--5191898 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5191850 TCTATTTAAA
5191860 TATATTAAAAAT
1 TATATTAAAAAT
*
5191872 TATATTAAAATAA
1 TATATTAAAA-AT
*
5191885 TATATAAAAAAT
1 TATATTAAAAAT
5191897 TA
1 TA
5191899 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:5193978 original size:23 final size:22
Alignment explanation
Indices: 5193932--5193990 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
5193922 ATCATATAAA
*
5193932 ATAT-TAATAATTTAT-ATATT
1 ATATATAATAATTTATAAAATT
5193952 -TATATAATAATTTATAAAAATT
1 ATATATAATAATTTAT-AAAATT
*
5193974 ATATATCATAATTTATA
1 ATATATAATAATTTATA
5193991 TGAATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 11 0.33
22 5 0.15
23 14 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATAATAATTTATAAAATT
Found at i:5194055 original size:16 final size:16
Alignment explanation
Indices: 5194026--5194063 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
5194016 TTTTTTTATG
*
5194026 ATTTTTGCTAAAATTGT
1 ATTTTTGATAAAATT-T
5194043 ATTTTTGAT-AAATTT
1 ATTTTTGATAAAATTT
5194058 ATTTTT
1 ATTTTT
5194064 TATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTTTTGATAAAATTT
Found at i:5195552 original size:154 final size:154
Alignment explanation
Indices: 5195268--5195571 Score: 500
Period size: 154 Copynumber: 2.0 Consensus size: 154
5195258 CTGAACAGGT
* * * * *
5195268 TAAAAGTACTAGTAGCTACAGCAGGCATCTACCAAAGAAAGGATCTATTGGAGTAACAATACTTG
1 TAAAAGTACTACTAGCTACAGCAGGCATCTACCAAAGAAAGGATCTATTAGAATAACAATACGTC
* * *
5195333 ACCAAACATATATGATGGATTAGATGGACCCAACTTGATAAGATTGGGGAGAGAGAGTGGCTGTG
66 ACCAAACATAAATGATGGATTAGAAGGACCCAACTTGATAAGATTGGGGAGAGAGAGTGGATGTG
5195398 GTGAAGTGACACCAATCCACAAAC
131 GTGAAGTGACACCAATCCACAAAC
* *
5195422 TAAAAGTACTACTAGCTAGAGCAGGCATCTACTAAAGAAAGGATCTATTAGAATAACAATACGTC
1 TAAAAGTACTACTAGCTACAGCAGGCATCTACCAAAGAAAGGATCTATTAGAATAACAATACGTC
*
5195487 ACCAAACATAAATGATGGCTTAGAAGGACCCAACTTGATAAGATTGGGGAGAGAGAGTGGATGTG
66 ACCAAACATAAATGATGGATTAGAAGGACCCAACTTGATAAGATTGGGGAGAGAGAGTGGATGTG
*
5195552 GTGAAGTGATACCAATCCAC
131 GTGAAGTGACACCAATCCAC
5195572 TTCTAAGTGA
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
154 138 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (154 bp):
TAAAAGTACTACTAGCTACAGCAGGCATCTACCAAAGAAAGGATCTATTAGAATAACAATACGTC
ACCAAACATAAATGATGGATTAGAAGGACCCAACTTGATAAGATTGGGGAGAGAGAGTGGATGTG
GTGAAGTGACACCAATCCACAAAC
Found at i:5197079 original size:17 final size:17
Alignment explanation
Indices: 5197059--5197092 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5197049 TGTTTCTATT
5197059 ACATAG-TTGTTCAAGAA
1 ACATAGATT-TTCAAGAA
5197076 ACATAGATTTTCAAGAA
1 ACATAGATTTTCAAGAA
5197093 TAGCCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (17 bp):
ACATAGATTTTCAAGAA
Found at i:5200969 original size:23 final size:24
Alignment explanation
Indices: 5200943--5200990 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
5200933 TGTTTAAAAA
*
5200943 TAAATACATAAAATAAT-AAATAT
1 TAAAAACATAAAATAATAAAATAT
*
5200966 TAAAAATATAAAATAATAAAATAT
1 TAAAAACATAAAATAATAAAATAT
5200990 T
1 T
5200991 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAAACATAAAATAATAAAATAT
Found at i:5201012 original size:17 final size:18
Alignment explanation
Indices: 5200981--5201021 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5200971 ATATAAAATA
5200981 ATAAAATATTTTTTTATT
1 ATAAAATATTTTTTTATT
5200999 ATAAAATA-TTTTTTATT
1 ATAAAATATTTTTTTATT
*
5201016 ACAAAA
1 ATAAAA
5201022 GCACCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAAATATTTTTTTATT
Found at i:5201381 original size:12 final size:12
Alignment explanation
Indices: 5201364--5201397 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5201354 ATTATAAATT
*
5201364 TTTAAATTTTAC
1 TTTAAATTTTAA
*
5201376 TTTAAATTTAAA
1 TTTAAATTTTAA
5201388 TTTAAATTTT
1 TTTAAATTTT
5201398 TATACGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:5205996 original size:12 final size:12
Alignment explanation
Indices: 5205979--5206005 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5205969 TAAAATATAT
5205979 TAATGTTTTCTC
1 TAATGTTTTCTC
5205991 TAATGTTTTCTC
1 TAATGTTTTCTC
5206003 TAA
1 TAA
5206006 AATGAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (12 bp):
TAATGTTTTCTC
Found at i:5206338 original size:16 final size:17
Alignment explanation
Indices: 5206311--5206359 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5206301 AAAGAATAGT
*
5206311 AGTGTTGATCCATGAAA
1 AGTGTTGTTCCATGAAA
5206328 A-TGTTGTTCCAT-AAA
1 AGTGTTGTTCCATGAAA
*
5206343 AGGTGTTATTCCATGAA
1 A-GTGTTGTTCCATGAA
5206360 GTTGCTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 11 0.41
18 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (17 bp):
AGTGTTGTTCCATGAAA
Found at i:5208130 original size:2 final size:2
Alignment explanation
Indices: 5208123--5208149 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5208113 AGAGATAACT
5208123 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5208150 TTGTATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5209514 original size:25 final size:25
Alignment explanation
Indices: 5209479--5209540 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 25
5209469 TTTTTTTATG
5209479 AAATTATATTATAAGCACTAAATTTT
1 AAATT-TATTATAAGCACTAAATTTT
*
5209505 AAATTTATTATAAGCACTCAATTTT
1 AAATTTATTATAAGCACTAAATTTT
*
5209530 AAATTTTTTAT
1 AAATTTATTAT
5209541 GAATATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 29 0.85
26 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (25 bp):
AAATTTATTATAAGCACTAAATTTT
Found at i:5209951 original size:21 final size:21
Alignment explanation
Indices: 5209925--5209972 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5209915 AATGCAATGC
5209925 AAGGATGGGCATCATCTAGCT
1 AAGGATGGGCATCATCTAGCT
5209946 AAGGATGGGCATCATCTAGCT
1 AAGGATGGGCATCATCTAGCT
5209967 AAGGAT
1 AAGGAT
5209973 TTGTCATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (21 bp):
AAGGATGGGCATCATCTAGCT
Found at i:5215191 original size:2 final size:2
Alignment explanation
Indices: 5215186--5215224 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5215176 AAAAGTTTAC
* *
5215186 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5215225 CCGTCTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5215842 original size:28 final size:30
Alignment explanation
Indices: 5215782--5215842 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
5215772 TTTTAGTTTA
5215782 TTAAATTAATATATAATTTTTATTAAAATT
1 TTAAATTAATATATAATTTTTATTAAAATT
*
5215812 TTAAATT-ATA-AT-ATTTTATATTAAATTT
1 TTAAATTAATATATAATTTT-TATTAAAATT
5215840 TTA
1 TTA
5215843 TTTTATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 14 0.48
29 3 0.10
30 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTAAATTAATATATAATTTTTATTAAAATT
Found at i:5220031 original size:23 final size:23
Alignment explanation
Indices: 5219987--5220031 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5219977 ATTTATATAT
* **
5219987 ATTCGTTTAATATTCACTAATGA
1 ATTCATTTAATATTCAAGAATGA
*
5220010 ATTCATTTAATATTTAAGAATG
1 ATTCATTTAATATTCAAGAATG
5220032 TGTTTATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (23 bp):
ATTCATTTAATATTCAAGAATGA
Found at i:5223149 original size:29 final size:29
Alignment explanation
Indices: 5223084--5223150 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
5223074 TTATTTTTTA
* * *
5223084 AAATAAAAATATTATTTTATATATATAAAT
1 AAAT-AAAATATCATTATATAAATATAAAT
** *
5223114 ATTTAAAATATCATTATATAAATATATAT
1 AAATAAAATATCATTATATAAATATAAAT
5223143 AAATAAAA
1 AAATAAAA
5223151 AATTAAATAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATAAAATATCATTATATAAATATAAAT
Found at i:5225233 original size:17 final size:16
Alignment explanation
Indices: 5225209--5225244 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5225199 AATATTTATA
*
5225209 TTTTTGACTTCTGATT
1 TTTTTGACTTATGATT
5225225 TTTTATGACTTATGATT
1 TTTT-TGACTTATGATT
5225242 TTT
1 TTT
5225245 CATCTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (16 bp):
TTTTTGACTTATGATT
Found at i:5227170 original size:21 final size:22
Alignment explanation
Indices: 5227128--5227170 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5227118 ACATATTTTT
5227128 AATTTTATTATATTTCAATTAA
1 AATTTTATTATATTTCAATTAA
5227150 AATTTTGATTA-ATTT-AATTAA
1 AATTTT-ATTATATTTCAATTAA
5227171 TTCCATTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTTATTATATTTCAATTAA
Found at i:5228525 original size:22 final size:22
Alignment explanation
Indices: 5228484--5228525 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5228474 GTTCATTTCT
*
5228484 CAACTTTATTTTCTCTTCTACC
1 CAACTTTATTTTCTCGTCTACC
5228506 CAACTTTATTTTAC-CGTCTA
1 CAACTTTATTTT-CTCGTCTA
5228526 TTATCACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (22 bp):
CAACTTTATTTTCTCGTCTACC
Found at i:5229126 original size:28 final size:28
Alignment explanation
Indices: 5229071--5229126 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
5229061 CAAAAATCAA
* * *
5229071 ATTAATTGAATTATATTATATTATTTTT
1 ATTAATTGAATCAAATTATATTAATTTT
* *
5229099 ATTAATTGAATCAAATTTTTTTAATTTT
1 ATTAATTGAATCAAATTATATTAATTTT
5229127 GAAAACTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (28 bp):
ATTAATTGAATCAAATTATATTAATTTT
Found at i:5230245 original size:114 final size:117
Alignment explanation
Indices: 5230106--5230345 Score: 389
Period size: 114 Copynumber: 2.1 Consensus size: 117
5230096 TTGAATCAAC
*
5230106 AATTTATAAAATAGTTAAATGTTATTTTATAAAAAATTAC-AAAATAAATCAATTTTGATGAAAA
1 AATTTATAAAATAGTTAAAAGTTATTTTATAAAAAATTACTAAAA-AAATCAATTTTGATGAAAA
*
5230170 TAATTTCTAAAAAAATTATTAAATAAATTCA-T-TTTT-TTCTAATCAATATA
65 TAAATTCTAAAAAAATTATTAAATAAATTCATTATTTTCTTCTAATCAATATA
*
5230220 AATTTATAAAATAGTTAAAAGTTATTTTATAAAGAATTACTAAAAAAATCAATTTTGATGAAAAT
1 AATTTATAAAATAGTTAAAAGTTATTTTATAAAAAATTACTAAAAAAATCAATTTTGATGAAAAT
* * *
5230285 AAATTCTAAATAAATTATTAAATGAATTCATTATTTTCTTCTAATTAATATA
66 AAATTCTAAAAAAATTATTAAATAAATTCATTATTTTCTTCTAATCAATATA
5230337 AATTTATAA
1 AATTTATAA
5230346 CATAAAACCG
Statistics
Matches: 116, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
114 85 0.73
115 5 0.04
116 4 0.03
117 22 0.19
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (117 bp):
AATTTATAAAATAGTTAAAAGTTATTTTATAAAAAATTACTAAAAAAATCAATTTTGATGAAAAT
AAATTCTAAAAAAATTATTAAATAAATTCATTATTTTCTTCTAATCAATATA
Found at i:5232409 original size:17 final size:17
Alignment explanation
Indices: 5232387--5232440 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
5232377 TAAAACATCT
*
5232387 TAAATAATTCTATTATA
1 TAAATAATTCTATTAAA
*
5232404 TAAATAATT-GATTAAA
1 TAAATAATTCTATTAAA
*
5232420 TTAAATAATCCTATTAAA
1 -TAAATAATTCTATTAAA
5232438 TAA
1 TAA
5232441 TTGATGCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.16
17 20 0.65
18 6 0.19
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATAATTCTATTAAA
Found at i:5235843 original size:38 final size:39
Alignment explanation
Indices: 5235771--5235844 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
5235761 AAGATGAGCA
*
5235771 TTTTATAAAAAAGTTATTGAGCATTTGTTAAGAGAAATC
1 TTTTATAAAAAAGTTATTGAGCATCTGTTAAGAGAAATC
*
5235810 TTTTAT-AAAAAGTTATTGAGTC-TCTGTTGAGAGAA
1 TTTTATAAAAAAGTTATTGAG-CATCTGTTAAGAGAA
5235845 GCTTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (39 bp):
TTTTATAAAAAAGTTATTGAGCATCTGTTAAGAGAAATC
Found at i:5237313 original size:3 final size:3
Alignment explanation
Indices: 5237305--5237350 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5237295 GGATTTGTTC
5237305 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5237351 CATATAGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5242241 original size:18 final size:18
Alignment explanation
Indices: 5242218--5242253 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5242208 TAAAAATGTC
5242218 AAATATCCCAACTAAGAT
1 AAATATCCCAACTAAGAT
5242236 AAATATCCCAACTAAGAT
1 AAATATCCCAACTAAGAT
5242254 CGTAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
AAATATCCCAACTAAGAT
Found at i:5243250 original size:24 final size:24
Alignment explanation
Indices: 5243222--5243272 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5243212 ACATTAATTT
*
5243222 AATAAAAATAATAAATATAACACA
1 AATAAAAATAATAAACATAACACA
* *
5243246 AATAAAAGTAATAAACATAATACA
1 AATAAAAATAATAAACATAACACA
5243270 AAT
1 AAT
5243273 GATAACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.22
Consensus pattern (24 bp):
AATAAAAATAATAAACATAACACA
Found at i:5245652 original size:28 final size:27
Alignment explanation
Indices: 5245614--5245669 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
5245604 TTAAAATTAA
* *
5245614 ATTAATTGAATT-ATATTATATTATTTTT
1 ATTAATAGAATTGA-ATT-TATTAATTTT
5245642 ATTAATAGAATTGAATTTATTAATTTT
1 ATTAATAGAATTGAATTTATTAATTTT
5245669 A
1 A
5245670 AAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.40
28 14 0.56
29 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (27 bp):
ATTAATAGAATTGAATTTATTAATTTT
Found at i:5245763 original size:7 final size:7
Alignment explanation
Indices: 5245751--5245786 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
5245741 TTAAATTAAA
5245751 TTAAATT
1 TTAAATT
5245758 TTAAATT
1 TTAAATT
5245765 TTAAATTTT
1 TTAAA--TT
5245774 TTAAATT
1 TTAAATT
5245781 TTAAAT
1 TTAAAT
5245787 AAATTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 20 0.74
9 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTAAATT
Found at i:5245775 original size:16 final size:16
Alignment explanation
Indices: 5245756--5245786 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5245746 TTAAATTAAA
5245756 TTTTAAATTTTAAATT
1 TTTTAAATTTTAAATT
5245772 TTTTAAATTTTAAAT
1 TTTTAAATTTTAAAT
5245787 AAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATTTTAAATT
Found at i:5245822 original size:13 final size:14
Alignment explanation
Indices: 5245790--5245822 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5245780 TTTAAATAAA
5245790 TTAAATAAAATTAT
1 TTAAATAAAATTAT
5245804 TT-AATAAAA-TAT
1 TTAAATAAAATTAT
5245816 TTAAATA
1 TTAAATA
5245823 CTAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 11 0.61
14 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAATAAAATTAT
Found at i:5246565 original size:18 final size:19
Alignment explanation
Indices: 5246494--5246567 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 19
5246484 ATTATTAATT
* *
5246494 TATTAATTAAAATAATTTT
1 TATTAATTAATATAATTTA
*
5246513 TATT-ATTAATATAATTAA
1 TATTAATTAATATAATTTA
*
5246531 TATTACA--CA-ATAATTTA
1 TATTA-ATTAATATAATTTA
5246548 TATTAATTAATA-AATTTA
1 TATTAATTAATATAATTTA
5246566 TA
1 TA
5246568 ATTTATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.02
17 12 0.27
18 25 0.57
19 5 0.11
20 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAATTAATATAATTTA
Found at i:5246977 original size:20 final size:20
Alignment explanation
Indices: 5246932--5246969 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5246922 TTCAATCATC
*
5246932 TAAATAATAAAATAAAAAAT
1 TAAAAAATAAAATAAAAAAT
*
5246952 TAAAAAATAAATTAAAAA
1 TAAAAAATAAAATAAAAA
5246970 CTTCAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAAATAAAATAAAAAAT
Found at i:5247351 original size:16 final size:16
Alignment explanation
Indices: 5247330--5247362 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5247320 TTTATTAAAA
5247330 TTTTAAATTTTATTAT
1 TTTTAAATTTTATTAT
5247346 TTTTAAATTTTATTAT
1 TTTTAAATTTTATTAT
5247362 T
1 T
5247363 GTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAAATTTTATTAT
Found at i:5251382 original size:15 final size:15
Alignment explanation
Indices: 5251364--5251409 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5251354 ATTCTATGTT
5251364 TTTCTCTTTTTTTCC
1 TTTCTCTTTTTTTCC
5251379 TTTCT-TTTTTTTCTC
1 TTTCTCTTTTTTTC-C
* *
5251394 TTTTTC-TCTTTTCC
1 TTTCTCTTTTTTTCC
5251408 TT
1 TT
5251410 CCCAGTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTCTTTTTTTCC
Found at i:5251389 original size:24 final size:26
Alignment explanation
Indices: 5251344--5251398 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 26
5251334 CGAGAGTTAT
5251344 TTTTTTTCCTATTCTATGTTTTTCTC
1 TTTTTTTCCTATTCTATGTTTTTCTC
*
5251370 TTTTTTTCCT-TTCT-TTTTTTTCTC
1 TTTTTTTCCTATTCTATGTTTTTCTC
5251394 TTTTT
1 TTTTT
5251399 CTCTTTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 14 0.50
25 4 0.14
26 10 0.36
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTTTTCCTATTCTATGTTTTTCTC
Found at i:5251507 original size:16 final size:17
Alignment explanation
Indices: 5251476--5251509 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5251466 CTTTTTTCTC
*
5251476 TTCTCTTTCTTTCTTTT
1 TTCTATTTCTTTCTTTT
5251493 TTCTATTTC-TTCTTTT
1 TTCTATTTCTTTCTTTT
5251509 T
1 T
5251510 CTTCTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTATTTCTTTCTTTT
Found at i:5251510 original size:22 final size:22
Alignment explanation
Indices: 5251458--5251517 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
5251448 ACTTTTCTTA
*
5251458 TTTCTTATCTTTTTTCTCTTCTC
1 TTTCTT-TCTTTTTTCTATTCTC
5251481 TTTCTTTCTTTTTTCTATT-TC
1 TTTCTTTCTTTTTTCTATTCTC
*
5251502 TTCTTTTTCTTCTTTT
1 TT-TCTTTCTT-TTTT
5251518 ATGGTTGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.12
22 19 0.58
23 10 0.30
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCTTTCTTTTTTCTATTCTC
Found at i:5252749 original size:13 final size:13
Alignment explanation
Indices: 5252731--5252760 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5252721 GGTACTACTT
5252731 TATTTTATTAAAA
1 TATTTTATTAAAA
5252744 TATTTTATTAAAA
1 TATTTTATTAAAA
5252757 -ATTT
1 TATTT
5252761 GAATTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTATTAAAA
Found at i:5252885 original size:167 final size:167
Alignment explanation
Indices: 5252669--5252977 Score: 415
Period size: 167 Copynumber: 1.9 Consensus size: 167
5252659 TAAAGCTTTC
* * * * *
5252669 CAATATATTGGTAAAGCCTTGTTTTGAAATTAAAATTACCTTTCAATATGTTGGT-ACTACTTTA
1 CAATATATTGGTAAAACCTTATTTTAAAATTAAAATTACCTTTCAATATGTTGATAACGA-TTTA
* * * * * * *
5252733 TTTTATTAAAATATTTTATTAAAAATTTGAATTTTTCAATATGTTGGTAAGAGTCAGTTTTTATG
65 TTTAATTAAAATAATTTATTAAAAATTTAAATATTCCAATATGTTGGTAAGAGTAAGCTTTTATG
5252798 TAAAAATTTATATTTTTTAAAAACTTGAACCCATTCTA
130 TAAAAATTTATATTTTTTAAAAACTTGAACCCATTCTA
* * ** *
5252836 CAATATGTTGGTAAAATCTTATTTTAAAATTAAAATT-TTTTTCCAATATGTTGATAAGGATTTA
1 CAATATATTGGTAAAACCTTATTTTAAAATTAAAATTACCTTT-CAATATGTTGATAACGATTTA
* *
5252900 TTTAATTAAAATAATTTATTAAAATTTTAAATATTCCAATATGTTGGTAAGAGTAAGCTTTTATT
65 TTTAATTAAAATAATTTATTAAAAATTTAAATATTCCAATATGTTGGTAAGAGTAAGCTTTTATG
5252965 TAAAAATTTATAT
130 TAAAAATTTATAT
5252978 ATATATTTTT
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
166 3 0.02
167 116 0.96
168 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (167 bp):
CAATATATTGGTAAAACCTTATTTTAAAATTAAAATTACCTTTCAATATGTTGATAACGATTTAT
TTAATTAAAATAATTTATTAAAAATTTAAATATTCCAATATGTTGGTAAGAGTAAGCTTTTATGT
AAAAATTTATATTTTTTAAAAACTTGAACCCATTCTA
Found at i:5253667 original size:19 final size:18
Alignment explanation
Indices: 5253643--5253686 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
5253633 AATGTTTGTC
5253643 AAAAATTAAAAAATTCCAA
1 AAAAATTAAAAAATT-CAA
**
5253662 AAAAATCCAAAAATTCAA
1 AAAAATTAAAAAATTCAA
5253680 AAAAATT
1 AAAAATT
5253687 TGCAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATTAAAAAATTCAA
Found at i:5254281 original size:14 final size:14
Alignment explanation
Indices: 5254262--5254291 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5254252 ATAAATGCAC
*
5254262 TAAAAATAAAACAA
1 TAAAAATAAAAAAA
5254276 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
5254290 TA
1 TA
5254292 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:5254530 original size:17 final size:18
Alignment explanation
Indices: 5254503--5254540 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5254493 TTTCTTTTGT
5254503 TTTTGTTTTTT-TATTTTA
1 TTTTGTTTTTTGT-TTTTA
5254521 TTTT-TTTTTTGTTTTTA
1 TTTTGTTTTTTGTTTTTA
5254538 TTT
1 TTT
5254541 ATGACAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.87
Consensus pattern (18 bp):
TTTTGTTTTTTGTTTTTA
Found at i:5254602 original size:40 final size:41
Alignment explanation
Indices: 5254556--5254662 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 41
5254546 AAGCTCCTAA
* * *
5254556 AAAATAGAGGCACATAACTTTAAAAAATAAAAGCTCTTTAT
1 AAAATAGAGGCACACAACTTTAAAAAATAAAAGCTCATCAT
* *
5254597 -TAATAGAGGCACACAAC-TT-AAAAATAAAGGCTCATCAT
1 AAAATAGAGGCACACAACTTTAAAAAATAAAAGCTCATCAT
*
5254635 AAATATAGAGGCACACAACTTGAAAAAA
1 AAA-ATAGAGGCACACAACTTTAAAAAA
5254663 AAATAAAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
38 16 0.29
39 3 0.05
40 30 0.55
41 1 0.02
42 5 0.09
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.21
Consensus pattern (41 bp):
AAAATAGAGGCACACAACTTTAAAAAATAAAAGCTCATCAT
Found at i:5256010 original size:74 final size:74
Alignment explanation
Indices: 5255842--5256016 Score: 199
Period size: 74 Copynumber: 2.4 Consensus size: 74
5255832 AAAAAATATT
* ** * **
5255842 GATCCCCTCTTAAAAGGGATCGATCGGTTGCTTTGATAGAATATTCCTCAAGTTTGAAAACCCAA
1 GATCCCTTCTTAAAAGGGATCGATCGGTTGCTCAGACAGAATATTCCTCAAGTTCAAAAACCCAA
*
5255907 AAAATGGAC
66 AAAAGGGAC
* * *** *
5255916 GATCCCTTCTTAAAAAGGATCGATCGGTTGCTCAGACAGAATGTTCCTCAAGTTCAAAAATTTAG
1 GATCCCTTCTTAAAAGGGATCGATCGGTTGCTCAGACAGAATATTCCTCAAGTTCAAAAACCCAA
5255981 AAAAGGGATC
66 AAAAGGGA-C
* *
5255991 GATCTCTT-TTTAAAGGGATCGATCGG
1 GATCCCTTCTTAAAAGGGATCGATCGG
5256017 GTAAGGCATT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 76 0.90
75 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (74 bp):
GATCCCTTCTTAAAAGGGATCGATCGGTTGCTCAGACAGAATATTCCTCAAGTTCAAAAACCCAA
AAAAGGGAC
Found at i:5263134 original size:75 final size:75
Alignment explanation
Indices: 5263004--5263181 Score: 223
Period size: 75 Copynumber: 2.4 Consensus size: 75
5262994 TAAGAAAAAT
* * *
5263004 GATCGATCTCCTCTTAAAAGGGATCGATCAGTTGCTCAAACAAAATGTTCCTCAAGTTTGAAAAC
1 GATCGATCTCCTCTTAAAAGGGATCGATCAGTTGCTCAAACAAAATGGTCATCAAGTTCGAAAAC
*
5263069 CCAGAAAAGG
66 CCAAAAAAGG
* * ** * * *
5263079 GATCGATTTCCTCTTAAAAGGGATTGATTGGTTGCTTAGACAGAATGGTCATCAAGTTCGAAAAC
1 GATCGATCTCCTCTTAAAAGGGATCGATCAGTTGCTCAAACAAAATGGTCATCAAGTTCGAAAAC
*
5263144 CTAAAAAAGG
66 CCAAAAAAGG
* *
5263154 GATTGATCCCCTCTT-AAAGGGATCGATC
1 GATCGATCTCCTCTTAAAAGGGATCGATC
5263182 GGGTAAGGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
74 11 0.13
75 75 0.87
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (75 bp):
GATCGATCTCCTCTTAAAAGGGATCGATCAGTTGCTCAAACAAAATGGTCATCAAGTTCGAAAAC
CCAAAAAAGG
Found at i:5270799 original size:59 final size:58
Alignment explanation
Indices: 5270695--5271031 Score: 480
Period size: 59 Copynumber: 5.7 Consensus size: 58
5270685 TTGCGTAGGA
* *
5270695 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
5270753 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCT-TTTTTTGAAAATTTATTTTTAAGG
* * ** * *
5270812 AAAATTGATACTTTCAACTTTT-TTCTAAAAAT-ATTTTTCAAAAATTTTGACTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATCTTTTTTTGAAAA-TTT-ATTTTTAAGG
5270871 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC--TTTTTTTGAAAATTTATTTTTAAGG
* *
5270931 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTATTTTTATGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTTGAAAATTTATTTTTAAGG
* *
5270990 AAAATTGATACTTTCAACTTTTTCTTAAAAATCATTTTTTTG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC-TTTTTTTG
5271032 CTTTTTATTT
Statistics
Matches: 251, Mismatches: 18, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
57 9 0.04
58 38 0.15
59 149 0.59
60 42 0.17
61 4 0.02
62 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGG
Found at i:5270945 original size:119 final size:116
Alignment explanation
Indices: 5270695--5271031 Score: 478
Period size: 119 Copynumber: 2.9 Consensus size: 116
5270685 TTGCGTAGGA
* *
5270695 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTTCCTAAAAATA-TTTTTTGAAAATTTATTTTTAAGGAAAATTG
*
5270760 ATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGG
* ** * *
5270812 AAAATTGATACTTTCAACTTTTTTCTAAAAATATTTTTCAAAAATTTTGACTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTGAAAA-TTT-ATTTTTAAGGAAAATT
5270877 GATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG
64 GATACTTTCAACTTTTCCTCAAAAATC-TTTTTTTTGAAAATTTATTTTTAAGG
* * *
5270931 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATCCTTTTTTTGAAAATTTATTTTTATGAAAAAT
1 AAAATTGATACTTTCAACTTTTTCCT-AAAAAT--ATTTTTTGAAAATTTATTTTTAAGGAAAAT
* * *
5270995 TGATACTTTCAACTTTTTCTTAAAAATCATTTTTTTG
63 TGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTG
5271032 CTTTTTATTT
Statistics
Matches: 195, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
116 9 0.05
117 33 0.17
118 55 0.28
119 86 0.44
120 3 0.02
121 9 0.05
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGG
Found at i:5270996 original size:178 final size:177
Alignment explanation
Indices: 5270695--5271028 Score: 575
Period size: 178 Copynumber: 1.9 Consensus size: 177
5270685 TTGCGTAGGA
5270695 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTG
*
5270760 ATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATTTATTTTTAAGGAAAATTGATACTT
66 ATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTT
5270825 TCAACTTTTT-TCTAAAAAT-ATTTTTCAAAAATTTTGACTTTCAAGG
131 TCAACTTTTTCT-TAAAAATCATTTTTCAAAAATTTTGACTTTCAAGG
* *
5270871 AAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTTGAAAATTTATTTTTAAGGAAAAT
*
5270936 TGATACTTTCAACTTTTCCTCAAAAATC-CTTTTTTTGAAAATTTATTTTTATGAAAAATTGATA
64 TGATACTTTCAACTTTTCCTCAAAAATCTC-TTTTTTGAAAATTTATTTTTAAGAAAAATTGATA
5271000 CTTTCAACTTTTTCTTAAAAATCATTTTT
128 CTTTCAACTTTTTCTTAAAAATCATTTTT
5271029 TTGCTTTTTA
Statistics
Matches: 149, Mismatches: 4, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
176 30 0.20
177 1 0.01
178 111 0.74
179 7 0.05
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (177 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAATTG
ATACTTTCAACTTTTCCTCAAAAATCTCTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTT
TCAACTTTTTCTTAAAAATCATTTTTCAAAAATTTTGACTTTCAAGG
Found at i:5271061 original size:5 final size:5
Alignment explanation
Indices: 5271046--5271125 Score: 51
Period size: 5 Copynumber: 15.6 Consensus size: 5
5271036 TTATTTAAAG
*
5271046 AAAAT AGAAT AAAAT AAAAGT GAAAAT -AAAT AAAGAT -AAA- AAAAT
1 AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAA-AT AAAAT AAAAT
* *
5271091 AAAA- AAAAGT AAAACA AAAAT AAAAAT AAGAT AAA
1 AAAAT AAAA-T AAAA-T AAAAT -AAAAT AAAAT AAA
5271126 GGTAAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
4 12 0.20
5 26 0.44
6 17 0.29
7 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:5271061 original size:10 final size:9
Alignment explanation
Indices: 5271041--5271206 Score: 71
Period size: 9 Copynumber: 18.1 Consensus size: 9
5271031 GCTTTTTATT
*
5271041 TAAAGAAAA
1 TAAATAAAA
5271050 TAGAATAAAA
1 TA-AATAAAA
5271060 TAAAAGTGAAAA
1 T-AAA-T-AAAA
5271072 TAAATAAAGA
1 TAAATAAA-A
5271082 TAAA-AAAA
1 TAAATAAAA
*
5271090 TAAAAAAAA
1 TAAATAAAA
*
5271099 GTAAA-ACAA
1 -TAAATAAAA
5271108 -AAATAAAAA
1 TAAAT-AAAA
*
5271117 TAAGATAAAGG
1 TAA-ATAAA-A
*
5271128 TAAA-AATAT
1 TAAATAA-AA
**
5271137 TAAATGAATC
1 TAAAT-AAAA
*
5271147 TAACCT--AA
1 TAA-ATAAAA
5271155 TAAATAAAA
1 TAAATAAAA
5271164 TAAAT-AAA
1 TAAATAAAA
5271172 TAAAT-AAA
1 TAAATAAAA
5271180 TAAATAAAA
1 TAAATAAAA
*
5271189 CAAAT-AAA
1 TAAATAAAA
*
5271197 TAAAAAAAA
1 TAAATAAAA
5271206 T
1 T
5271207 TTTGAAAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
7 4 0.03
8 30 0.24
9 42 0.34
10 29 0.24
11 13 0.11
12 5 0.04
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (9 bp):
TAAATAAAA
Found at i:5271070 original size:22 final size:22
Alignment explanation
Indices: 5271045--5271086 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5271035 TTTATTTAAA
5271045 GAAAATAGAATAAA-ATAAAAGT
1 GAAAATA-AATAAAGATAAAAGT
5271067 GAAAATAAATAAAGATAAAA
1 GAAAATAAATAAAGATAAAA
5271087 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (22 bp):
GAAAATAAATAAAGATAAAAGT
Found at i:5271080 original size:35 final size:35
Alignment explanation
Indices: 5271053--5271119 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
5271043 AAGAAAATAG
* *
5271053 AATAAAATAAAAGTGAAA-ATAAATAAAGATAAAAA
1 AATAAAA-AAAAGTAAAACAAAAATAAAGATAAAAA
*
5271088 AATAAAAAAAAGTAAAACAAAAATAAAAATAA
1 AATAAAAAAAAGTAAAACAAAAATAAAGATAA
5271120 GATAAAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (35 bp):
AATAAAAAAAAGTAAAACAAAAATAAAGATAAAAA
Found at i:5271111 original size:21 final size:22
Alignment explanation
Indices: 5271085--5271125 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5271075 ATAAAGATAA
5271085 AAAAATAAAAAAAAG-TAAAAC
1 AAAAATAAAAAAAAGATAAAAC
*
5271106 AAAAATAAAAATAAGATAAA
1 AAAAATAAAAAAAAGATAAA
5271126 GGTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAAAAGATAAAAC
Found at i:5271162 original size:4 final size:4
Alignment explanation
Indices: 5271153--5271200 Score: 69
Period size: 4 Copynumber: 11.5 Consensus size: 4
5271143 AATCTAACCT
*
5271153 AATA AATAA AATA AATA AATA AATA AATA AATAA AACA AATA AATA AA
1 AATA AAT-A AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AA
5271201 AAAAATTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 33 0.82
5 7 0.17
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:5271171 original size:13 final size:13
Alignment explanation
Indices: 5271153--5271206 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
5271143 AATCTAACCT
5271153 AATAAATAAAATA
1 AATAAATAAAATA
5271166 AATAAAT-AAATA
1 AATAAATAAAATA
*
5271178 AATAAATAAAACA
1 AATAAATAAAATA
*
5271191 AATAAATAAAAAA
1 AATAAATAAAATA
5271204 AAT
1 AAT
5271207 TTTGAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 12 0.32
13 26 0.68
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:5271175 original size:17 final size:17
Alignment explanation
Indices: 5271153--5271206 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
5271143 AATCTAACCT
5271153 AATAAATAAAATAAAT-A
1 AATAAAT-AAATAAATAA
5271170 AATAAATAAATAAATAA
1 AATAAATAAATAAATAA
* *
5271187 AACAAATAAATAAAAAA
1 AATAAATAAATAAATAA
5271204 AAT
1 AAT
5271207 TTTGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 8 0.24
17 25 0.76
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAATAAATAAATAA
Found at i:5271181 original size:25 final size:25
Alignment explanation
Indices: 5271153--5271200 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5271143 AATCTAACCT
*
5271153 AATAAATAAAATAAATAAATAAATA
1 AATAAATAAAACAAATAAATAAATA
5271178 AATAAATAAAACAAATAAATAAA
1 AATAAATAAAACAAATAAATAAA
5271201 AAAAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (25 bp):
AATAAATAAAACAAATAAATAAATA
Found at i:5272142 original size:35 final size:33
Alignment explanation
Indices: 5272069--5272182 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 33
5272059 TAAAAATCAA
* **
5272069 ATAAATATAAAAAAAAAAATAGATA-ATTAGAACAG
1 ATAAATA-AAAAAAAAAAAAAGATATA-TA-ATTAG
*
5272104 ATAAATCAAAAAAGAAAAAAAAGATATATTA-TAGG
1 ATAAAT-AAAAAA-AAAAAAAAGATATATAATTA-G
* *
5272139 ATAAATAAAAAAAAATAACAGATATATAATTAG
1 ATAAATAAAAAAAAAAAAAAGATATATAATTAG
5272172 ATAAATAAAAA
1 ATAAATAAAAA
5272183 TATAAAAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
33 26 0.38
34 9 0.13
35 19 0.28
36 13 0.19
37 1 0.01
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (33 bp):
ATAAATAAAAAAAAAAAAAAGATATATAATTAG
Found at i:5272195 original size:4 final size:4
Alignment explanation
Indices: 5272172--5272350 Score: 69
Period size: 4 Copynumber: 45.2 Consensus size: 4
5272162 ATATAATTAG
*
5272172 ATAA AT-A A-AA ATATA A-AA ATAA ATAA A-AT ATAA A-ATA AT-A AT-A
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA
* * *
5272215 AT-A AT-A ATAA ATAA ATTATA ATATA ATAT ATAA CTAT ATAA ATAAA
1 ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA ATAA ATAA AT-AA
* * * *
5272261 ATACA TATAA AT-A TTAA CAGAA A-AA ATAA ATAA ATAA ATAA ATAA AGAT
1 ATA-A -ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
5272310 ATAC ATAT ATTA ATAA ATAGTA AT-A ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA ATAA A
5272351 ATACATAAAA
Statistics
Matches: 136, Mismatches: 19, Indels: 40
0.70 0.10 0.21
Matches are distributed among these distances:
3 32 0.24
4 77 0.57
5 19 0.14
6 8 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:5272220 original size:19 final size:19
Alignment explanation
Indices: 5272175--5272263 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 19
5272165 TAATTAGATA
*
5272175 AATAAAAATAT-AAA-AAT
1 AATAATAATATAAAATAAT
5272192 AAATAA-AATATAAAATAAT
1 -AATAATAATATAAAATAAT
5272211 AATAATAATA-ATAAAT-A-
1 AATAATAATATA-AAATAAT
* *
5272228 AATTATAATATAATAT-AT
1 AATAATAATATAAAATAAT
5272246 AACTATATAA-ATAAAATA
1 AA-TA-ATAATATAAAATA
5272264 CATATAAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
17 18 0.31
18 18 0.31
19 18 0.31
20 4 0.07
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATAATATAAAATAAT
Found at i:5272227 original size:31 final size:30
Alignment explanation
Indices: 5272174--5272263 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 30
5272164 ATAATTAGAT
* *
5272174 AAATAAAAATATAAAAATAAATAAAATATA
1 AAATAATAATATAATAATAAATAAAATATA
*
5272204 AAATAATAATAATAATAATAAATAAATTATA
1 AAATAATAAT-ATAATAATAAATAAAATATA
*
5272235 ATATAAT-ATATAACTATATAAATAAAATA
1 AAATAATAATATAA-TA-ATAAATAAAATA
5272264 CATATAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.08
30 13 0.25
31 35 0.67
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (30 bp):
AAATAATAATATAATAATAAATAAAATATA
Found at i:5272238 original size:36 final size:33
Alignment explanation
Indices: 5272175--5272240 Score: 87
Period size: 36 Copynumber: 1.9 Consensus size: 33
5272165 TAATTAGATA
5272175 AATAAAAATATAAAAATAAATAAAATATAAAAT
1 AATAAAAATATAAAAATAAATAAAATATAAAAT
* *
5272208 AATAATAATAATAATAAATAAATTATAATATAA
1 AATAAAAAT-ATAA-AAATAAA-TAAAATATAA
5272241 TATATAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.29
34 4 0.14
35 7 0.25
36 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (33 bp):
AATAAAAATATAAAAATAAATAAAATATAAAAT
Found at i:5272274 original size:31 final size:29
Alignment explanation
Indices: 5272190--5272278 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 29
5272180 AAATATAAAA
* *
5272190 ATAAATAAAATATAAAATAATAATAA-TAAT
1 ATAAAT-AAATATAATATAATATTAACT-AT
5272220 AATAAATAAATTATAATATAATATATAACTAT
1 -ATAAATAAA-TATAATATAATAT-TAACTAT
5272252 ATAAATAAA-ATACATATAAATATTAAC
1 ATAAATAAATATA-ATAT-AATATTAAC
5272279 AGAAAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
29 3 0.06
30 11 0.22
31 31 0.61
32 5 0.10
33 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
ATAAATAAATATAATATAATATTAACTAT
Found at i:5272758 original size:41 final size:41
Alignment explanation
Indices: 5272614--5273004 Score: 463
Period size: 41 Copynumber: 9.4 Consensus size: 41
5272604 GACTTAAAAA
* * * * *
5272614 AAAAATAAATGGCTCCTCTAATCAGAGGCTCAACGACTTTGG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-G
*
5272656 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-G
*
5272698 AAAAGTAAATTGCTTCTCTAAACAGAGGCACCACGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* *
5272739 AAAAATAAATTGCTCCTCTAAACAGATGCACCACGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* * *
5272780 AAAAATAAAATGCTCCTCTAATCAGAGGCA--ACGAAACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG--ACTTTG
* *
5272821 GAAAGTAAAATGCTCCTCTAATA-AGAGGCA--ACGGAACTTTG
1 AAAAGTAAATTGCTCCTCTAA-ACAGAGGCACCAC-G-ACTTTG
* *
5272862 GAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTG
*
5272904 AGAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGG
1 A-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-G
*
5272947 GAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAAACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG--ACTTTG
5272988 AAAAGTAAATTGCTCCT
1 AAAAGTAAATTGCTCCT
5273005 TGACAATCAT
Statistics
Matches: 315, Mismatches: 22, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
39 3 0.01
40 4 0.01
41 153 0.49
42 118 0.37
43 37 0.12
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
Found at i:5278276 original size:60 final size:59
Alignment explanation
Indices: 5278098--5278375 Score: 438
Period size: 59 Copynumber: 4.7 Consensus size: 59
5278088 TCTTGCGTAG
* * *
5278098 GGAAAACTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
*
5278156 GG-AAATTGATACTTTCAAACTTTTTCCTC-AAAATCTCTTTTTT-AAAATTTATTTTTAA
1 GGAAAATTGATACTTTC-AAC-TTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
5278214 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATC-TTTTTTTTGAAAATTTATTTTTAA
*
5278274 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
* *
5278333 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATCCTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTT
5278376 ACTTTTTATT
Statistics
Matches: 205, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
57 21 0.10
58 36 0.18
59 98 0.48
60 50 0.24
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.47
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
Found at i:5278339 original size:119 final size:118
Alignment explanation
Indices: 5278098--5278375 Score: 438
Period size: 119 Copynumber: 2.4 Consensus size: 118
5278088 TCTTGCGTAG
* * *
5278098 GGAAAACTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTTGAAAATTTATTTTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGGAAA
5278161 TTGATACTTTCAAACTTTTTCCTCAAAATCTCTTTTTTAAAATTTATTTTTAA
66 TTGATACTTTCAAACTTTTTCCTCAAAATCTCTTTTTTAAAATTTATTTTTAA
5278214 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGG-AA
* *
5278279 ATTGATACTTTC-AAC-TTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTTTAT
65 ATTGATACTTTCAAACTTTTTCCTC-AAAATCTCTTTTTT-AAAATTTATTTTTAA
* *
5278333 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATCCTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTT
5278376 ACTTTTTATT
Statistics
Matches: 150, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
116 31 0.21
117 8 0.05
118 42 0.28
119 69 0.46
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.47
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTGAAAATTTATTTTTAAGGAAA
TTGATACTTTCAAACTTTTTCCTCAAAATCTCTTTTTTAAAATTTATTTTTAA
Found at i:5278406 original size:10 final size:9
Alignment explanation
Indices: 5278386--5278553 Score: 64
Period size: 9 Copynumber: 18.0 Consensus size: 9
5278376 ACTTTTTATT
*
5278386 TAAAGAAAA
1 TAAATAAAA
5278395 TAGAATAAAA
1 TA-AATAAAA
5278405 TAAAAGTGAAAA
1 T-AAA-T-AAAA
5278417 TAAATAAAGA
1 TAAATAAA-A
5278427 TAAA-AAAA
1 TAAATAAAA
*
5278435 TAAAGAAAA
1 TAAATAAAA
*
5278444 GTAAA-ACAA
1 -TAAATAAAA
5278453 -AAATAAAAA
1 TAAAT-AAAA
*
5278462 TAAGATAAAGG
1 TAA-ATAAA-A
*
5278473 TAAA-AATAT
1 TAAATAA-AA
**
5278482 TAAATGAATC
1 TAAAT-AAAA
*
5278492 TAACCT--AA
1 TAA-ATAAAA
5278500 TAAATAAAA
1 TAAATAAAA
5278509 TAAAT-AAA
1 TAAATAAAA
5278517 TAAAT-AAA
1 TAAATAAAA
*
5278525 TAAAACAAAA
1 T-AAATAAAA
5278535 TAAATAAAA
1 TAAATAAAA
*
5278544 AAAATTAAAA
1 TAAA-TAAAA
5278554 AAAAAAACCT
Statistics
Matches: 124, Mismatches: 14, Indels: 41
0.69 0.08 0.23
Matches are distributed among these distances:
7 4 0.03
8 20 0.16
9 44 0.35
10 38 0.31
11 13 0.10
12 5 0.04
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (9 bp):
TAAATAAAA
Found at i:5278415 original size:22 final size:22
Alignment explanation
Indices: 5278390--5278431 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5278380 TTTATTTAAA
5278390 GAAAATAGAATAAA-ATAAAAGT
1 GAAAATA-AATAAAGATAAAAGT
5278412 GAAAATAAATAAAGATAAAA
1 GAAAATAAATAAAGATAAAA
5278432 AAATAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (22 bp):
GAAAATAAATAAAGATAAAAGT
Found at i:5278437 original size:14 final size:15
Alignment explanation
Indices: 5278413--5278477 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
5278403 AATAAAAGTG
5278413 AAAATAAATAAAGAT
1 AAAATAAATAAAGAT
5278428 AAAA-AAATAAAGA-
1 AAAATAAATAAAGAT
* * *
5278441 AAAGTAAAACAAAAAT
1 AAAAT-AAATAAAGAT
*
5278457 AAAAATAAGATAAAGGT
1 -AAAATAA-ATAAAGAT
5278474 AAAA
1 AAAA
5278478 ATATTAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
13 3 0.08
14 9 0.24
15 11 0.29
16 6 0.16
17 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAATAAATAAAGAT
Found at i:5278507 original size:4 final size:4
Alignment explanation
Indices: 5278498--5278542 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
5278488 AATCTAACCT
*
5278498 AATA AATAA AATA AATA AATA AATA AATA AA-A CA-A AATA AATA AA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
5278543 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 4 0.11
4 29 0.78
5 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:5278556 original size:22 final size:21
Alignment explanation
Indices: 5278504--5278556 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
5278494 ACCTAATAAA
*
5278504 TAAAATAAATAAATAAATAAAT
1 TAAAA-AAATAAATAAAAAAAT
*
5278526 AAAACAAAATAAATAAAAAAAAT
1 TAAA-AAAATAAAT-AAAAAAAT
5278549 TAAAAAAA
1 TAAAAAAA
5278557 AAAACCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAAAAAATAAATAAAAAAAT
Found at i:5279400 original size:28 final size:27
Alignment explanation
Indices: 5279357--5279424 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
5279347 TCAAATAAAT
*
5279357 ATAAA-AAAAAATAGAT-AATTAGAACAG
1 ATAAATAAAAAAAAGATAAATTA-AA-AG
* *
5279384 ATAAATAAAAAAAAGATAAATTATAGG
1 ATAAATAAAAAAAAGATAAATTAAAAG
5279411 ATAAATAAAAAAAA
1 ATAAATAAAAAAAA
5279425 CAACAGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 20 0.56
28 11 0.31
29 5 0.14
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.19
Consensus pattern (27 bp):
ATAAATAAAAAAAAGATAAATTAAAAG
Found at i:5279466 original size:4 final size:4
Alignment explanation
Indices: 5279443--5279630 Score: 78
Period size: 4 Copynumber: 47.2 Consensus size: 4
5279433 ATATAATTAG
*
5279443 ATAA AT-A A-AA ATATA A-AA ATAA ATAA A-AT ATAA A-ATA AT-A AT-A
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA
* * * *
5279486 AT-A AT-A ATAA ATTATA ATATA AT-A ATGA ATAT ATAA CTAT ATAA ATAAA
1 ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA ATAA ATAA ATAA ATAA AT-AA
*
5279535 ATACA TATAA ATATTA ACAA A-AA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATA-A -ATAA ATA--A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * *
5279582 ATAA AGAT ATAC ATAT ATTA ATAA ATAGTA AT-A ATAA ATAA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA ATAA
5279630 A
1 A
5279631 ATACATAAAA
Statistics
Matches: 145, Mismatches: 18, Indels: 42
0.71 0.09 0.20
Matches are distributed among these distances:
3 33 0.23
4 85 0.59
5 16 0.11
6 11 0.08
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:5279542 original size:23 final size:22
Alignment explanation
Indices: 5279452--5279639 Score: 95
Period size: 20 Copynumber: 8.7 Consensus size: 22
5279442 GATAAATAAA
5279452 AATATAAA-A-ATAAATAAAAT
1 AATATAAATATATAAATAAAAT
5279472 -ATA-AAATA-AT-AAT--AAT
1 AATATAAATATATAAATAAAAT
5279488 AATAATAAAT-TATAATATAATAAT
1 AAT-ATAAATATATAA-ATAA-AAT
5279512 GAATATATAACTATATAAATAAAAT
1 -AATATA-AA-TATATAAATAAAAT
*
5279537 ACATATAAATAT-TAACAAAAAAT
1 A-ATATAAATATATAA-ATAAAAT
*
5279560 AA-ATAAATAAATAAAT-AAAT
1 AATATAAATATATAAATAAAAT
* *
5279580 AA-ATAAAGATATACATATATTAAT
1 AATATAAATATATA-A-ATA-AAAT
5279604 AA-ATAGTAATA-ATAAAT-AAAT
1 AATATA--AATATATAAATAAAAT
*
5279625 AATA-AAATACATAAA
1 AATATAAATATATAAA
5279640 ATACAAAAGA
Statistics
Matches: 135, Mismatches: 8, Indels: 50
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.02
17 2 0.01
18 7 0.05
19 16 0.12
20 21 0.16
21 17 0.13
22 10 0.07
23 12 0.09
24 18 0.13
25 16 0.12
26 8 0.06
27 5 0.04
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (22 bp):
AATATAAATATATAAATAAAAT
Found at i:5287074 original size:11 final size:11
Alignment explanation
Indices: 5287058--5287083 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5287048 TAAAAATCAA
5287058 TTAATATTCTT
1 TTAATATTCTT
5287069 TTAATATTCTT
1 TTAATATTCTT
5287080 TTAA
1 TTAA
5287084 CGATAAGAAA
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:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAATATTCTT
Found at i:5289727 original size:27 final size:27
Alignment explanation
Indices: 5289697--5289752 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5289687 AAATGATAAT
5289697 TTTTTATTAAAATTTT-AAATTATATTA
1 TTTTTA-TAAAATTTTCAAATTATATTA
** *
5289724 TTTTTATATTATTTTCATATTATATTA
1 TTTTTATAAAATTTTCAAATTATATTA
5289751 TT
1 TT
5289753 ATATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTATAAAATTTTCAAATTATATTA
Found at i:5289730 original size:11 final size:11
Alignment explanation
Indices: 5289716--5289771 Score: 69
Period size: 11 Copynumber: 4.9 Consensus size: 11
5289706 AAATTTTAAA
5289716 TTATATTATTT
1 TTATATTATTT
5289727 TTATATTATTT
1 TTATATTATTT
*
5289738 TCATATTATATT
1 TTATATTAT-TT
5289750 ATTATATTATATT
1 -TTATATTAT-TT
5289763 TTA-ATTATT
1 TTATATTATT
5289772 AAATGTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
10 1 0.02
11 24 0.59
12 5 0.12
13 11 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTATTT
Done.