Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 14 of 106
Found at i:2210081 original size:41 final size:40
Alignment explanation
Indices: 2209990--2210123 Score: 234
Period size: 40 Copynumber: 3.4 Consensus size: 40
2209980 GGGCCACCTT
*
2209990 GTGATGTAGATGCAACTAAGGCAAACATCTTTTTTTTTT-
1 GTGATGCAGATGCAACTAAGGCAAACATCTTTTTTTTTTA
*
2210029 GTGATGTAGATGCAACTAAGGCAAACATCTTTTTTTTTTTA
1 GTGATGCAGATGCAACTAAGGCAAACATC-TTTTTTTTTTA
2210070 GTGATGCAGATGCAACTAAGGCAAACATCTTTTTTTTTTA
1 GTGATGCAGATGCAACTAAGGCAAACATCTTTTTTTTTTA
2210110 GTGATGCAGATGCA
1 GTGATGCAGATGCA
2210124 CTGGGCTTAA
Statistics
Matches: 92, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
39 29 0.32
40 35 0.38
41 28 0.30
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (40 bp):
GTGATGCAGATGCAACTAAGGCAAACATCTTTTTTTTTTA
Found at i:2210199 original size:34 final size:34
Alignment explanation
Indices: 2210161--2210265 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 34
2210151 AACTAATTTA
2210161 GGCTTAAATATTTCTTTGAAAGCTAGCTAAACTG
1 GGCTTAAATATTTCTTTGAAAGCTAGCTAAACTG
* * * * * *
2210195 GGCTT--ATATTT-ATTGGAGGTTAGCTAATCTA
1 GGCTTAAATATTTCTTTGAAAGCTAGCTAAACTG
* *
2210226 GGCTTAAATTTTTCTTTGAAAGCTAGCTAAATTG
1 GGCTTAAATATTTCTTTGAAAGCTAGCTAAACTG
2210260 GGCTTA
1 GGCTTA
2210266 TTATTTCATT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
31 19 0.35
32 6 0.11
33 5 0.09
34 24 0.44
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (34 bp):
GGCTTAAATATTTCTTTGAAAGCTAGCTAAACTG
Found at i:2210230 original size:65 final size:67
Alignment explanation
Indices: 2210123--2210291 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 67
2210113 ATGCAGATGC
* * * * *
2210123 ACTGGGCTTAATATTTCATTGAAGGGCCAACTAATTTAGGCTTAAATATTTCTTTGAAAGCTAGC
1 ACTGGGCTTATTATTTCATT-AGGGGCTAGCTAATCTAGGCTTAAATATTTCTTTGAAAGCTAGC
2210188 TAA
65 TAA
* *
2210191 ACTGGGCTTA-TATTT-ATT-GGAGGTTAGCTAATCTAGGCTTAAATTTTTCTTTGAAAGCTAGC
1 ACTGGGCTTATTATTTCATTAGG-GGCTAGCTAATCTAGGCTTAAATATTTCTTTGAAAGCTAGC
2210253 TAA
65 TAA
*
2210256 ATTGGGCTTATTATTTCATTAGGGGCTAGCTAATCT
1 ACTGGGCTTATTATTTCATTAGGGGCTAGCTAATCT
2210292 GGGTCTAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
64 1 0.01
65 48 0.54
66 8 0.09
67 20 0.22
68 12 0.13
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (67 bp):
ACTGGGCTTATTATTTCATTAGGGGCTAGCTAATCTAGGCTTAAATATTTCTTTGAAAGCTAGCT
AA
Found at i:2210350 original size:63 final size:64
Alignment explanation
Indices: 2210270--2210394 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 64
2210260 GGCTTATTAT
*
2210270 TTCATTAGGGGCTAGCTAATCTGGG-TCTAAAATTTCATT-AGAGGCCAACTAA-CTAGGCTTAC
1 TTCATTAGGGGCCAGCTAATCTGGGCT-TAAAATTTCATTAAG-GGCCAACTAATCTAGGCTTAC
2210332 A
64 A
* *
2210333 TTCATT-GGAGGCCAGCTAATTTGGGCTTAATATTTCATTAAGGGCCAACTAATCTAGGCTTA
1 TTCATTAGG-GGCCAGCTAATCTGGGCTTAAAATTTCATTAAGGGCCAACTAATCTAGGCTTA
2210395 ATATTTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
62 2 0.04
63 41 0.75
64 12 0.22
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (64 bp):
TTCATTAGGGGCCAGCTAATCTGGGCTTAAAATTTCATTAAGGGCCAACTAATCTAGGCTTACA
Found at i:2210379 original size:33 final size:33
Alignment explanation
Indices: 2210124--2210400 Score: 146
Period size: 33 Copynumber: 8.5 Consensus size: 33
2210114 TGCAGATGCA
*
2210124 CTGGGCTTAATATTTCATTGAAGGGCCAACTAAT
1 CTGGGCTTAATATTTCATT-AAGGGCCAGCTAAT
* * * * * *
2210158 TTAGGCTTAAATATTTCTTTGAA-AGCTAGCTAAA
1 CTGGGCTT-AATATTTCATT-AAGGGCCAGCTAAT
* **
2210192 CTGGGCTT-ATATTT-ATT-GGAGGTTAGCTAAT
1 CTGGGCTTAATATTTCATTAAG-GGCCAGCTAAT
* * * * *
2210223 CTAGGCTTAAATTTTTCTTTGAA-AGCTAGCTAAAT
1 CTGGGCTT-AATATTTCATT-AAGGGCCAGCT-AAT
* * *
2210258 -TGGGCTTATTATTTCATTAGGGGCTAGCTAAT
1 CTGGGCTTAATATTTCATTAAGGGCCAGCTAAT
* *
2210290 CTGGG-TCTAAAATTTCATT-AGAGGCCAACTAA-
1 CTGGGCT-TAATATTTCATTAAG-GGCCAGCTAAT
* * *
2210322 CTAGGCTT-ACA-TTCATT-GGAGGCCAGCTAAT
1 CTGGGCTTAATATTTCATTAAG-GGCCAGCTAAT
* *
2210353 TTGGGCTTAATATTTCATTAAGGGCCAACTAAT
1 CTGGGCTTAATATTTCATTAAGGGCCAGCTAAT
*
2210386 CTAGGCTTAATATTT
1 CTGGGCTTAATATTT
2210401 TTTTTCAAGG
Statistics
Matches: 183, Mismatches: 42, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
30 17 0.09
31 25 0.14
32 19 0.10
33 72 0.39
34 34 0.19
35 16 0.09
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
CTGGGCTTAATATTTCATTAAGGGCCAGCTAAT
Found at i:2211302 original size:12 final size:11
Alignment explanation
Indices: 2211263--2211345 Score: 53
Period size: 12 Copynumber: 7.4 Consensus size: 11
2211253 CACCCACTCA
2211263 TTTTTTTCTTT
1 TTTTTTTCTTT
*
2211274 CTTTTATTCTTT
1 -TTTTTTTCTTT
**
2211286 ATTTTTTT-TCA
1 -TTTTTTTCTTT
*
2211297 TTTTTTCCTTT
1 TTTTTTTCTTT
**
2211308 CCTTTTTCTTT
1 TTTTTTTCTTT
*
2211319 TTTGCTTTACTTT
1 TTT--TTTTCTTT
2211332 TTTTTTT-TTT
1 TTTTTTTCTTT
2211342 TTTT
1 TTTT
2211346 GCATTTGAAT
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
10 13 0.25
11 14 0.26
12 16 0.30
13 10 0.19
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2211340 original size:19 final size:19
Alignment explanation
Indices: 2211290--2211339 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2211280 TTCTTTATTT
*
2211290 TTTTTCATTTTTTCCTTTCC
1 TTTTTC-TTTTTTCCTTTAC
*
2211310 TTTTTCTTTTTTGCTTTAC
1 TTTTTCTTTTTTCCTTTAC
2211329 TTTTT-TTTTTT
1 TTTTTCTTTTTT
2211340 TTTTTTGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTTTCCTTTAC
Found at i:2212314 original size:146 final size:146
Alignment explanation
Indices: 2212074--2212379 Score: 373
Period size: 146 Copynumber: 2.1 Consensus size: 146
2212064 GGTAAGGAAT
* *
2212074 TGAAAGGTTGGTAAGTTTCGTAATCAACATAACCCTGACAACATATAGGTCTGGCCAACTTTTTG
1 TGAAAGATTGGTAAGTTTCGCAATCAACATAACCCTGACAACATATAGGTCTGGCCAACTTTTTG
* ** * * ** *
2212139 GGTAAAGGGGCTGAAAGGTTGGTAAATATAAGCAATATGTCTTGAAAACACATAAGCTAGGCAAA
66 GGTAAAAGGGCTGAAAAATTGGTAAATATAAGCAACATGCCACGAAAACACATAAGCCAGGCAAA
2212204 AGTTTT-GGTAAAAGAC
131 A-TTTTGGGTAAAAGAC
* * * * * ** *
2212220 TGAAAGTTTGGTAAGTTTTGCGATCAACATGACCTTGATGACATATGGGT-TAGGCCAACTTTTT
1 TGAAAGATTGGTAAGTTTCGCAATCAACATAACCCTGACAACATATAGGTCT-GGCCAACTTTTT
* * *
2212284 GGGTAAAAGGGTTGAAAAATTGGTAAATATAAGCAACATGCCACGGAAACACATGAGCCAGGCAA
65 GGGTAAAAGGGCTGAAAAATTGGTAAATATAAGCAACATGCCACGAAAACACATAAGCCAGGCAA
* *
2212349 AATTTTGGGTAACAGAT
130 AATTTTGGGTAAAAGAC
2212366 TGAAAGATTGGTAA
1 TGAAAGATTGGTAA
2212380 ATCTGTGGTC
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
145 5 0.04
146 130 0.96
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (146 bp):
TGAAAGATTGGTAAGTTTCGCAATCAACATAACCCTGACAACATATAGGTCTGGCCAACTTTTTG
GGTAAAAGGGCTGAAAAATTGGTAAATATAAGCAACATGCCACGAAAACACATAAGCCAGGCAAA
ATTTTGGGTAAAAGAC
Found at i:2214952 original size:17 final size:18
Alignment explanation
Indices: 2214932--2214972 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2214922 TTAATTAGTG
2214932 ATAAA-TAATTTTTAAAA
1 ATAAATTAATTTTTAAAA
*
2214949 ATAAATTTAATTTTTAAAT
1 ATAAA-TTAATTTTTAAAA
2214968 ATAAA
1 ATAAA
2214973 ATTATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
19 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATTAATTTTTAAAA
Found at i:2216476 original size:21 final size:20
Alignment explanation
Indices: 2216417--2216476 Score: 50
Period size: 23 Copynumber: 2.8 Consensus size: 20
2216407 TTTATTAATT
*
2216417 TAATTTTTATTATATAAAATA
1 TAATTTTTATTTTA-AAAATA
*
2216438 -AATTTTAAATTTAATAAAATATA
1 TAATTTT-TATTT--TAAAA-ATA
2216461 TAATTTTTATTTTAAA
1 TAATTTTTATTTTAAA
2216477 TTTTTATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 3 0.10
23 9 0.29
24 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTTTATTTTAAAAATA
Found at i:2218148 original size:4 final size:4
Alignment explanation
Indices: 2218139--2218164 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2218129 TATTATTATT
2218139 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
2218165 ATTAAAAAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2219148 original size:13 final size:12
Alignment explanation
Indices: 2219132--2219184 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
2219122 TTTTTTTTCA
2219132 TTTTATATTTATT
1 TTTTATATTT-TT
* *
2219145 TTTTAAATTTTA
1 TTTTATATTTTT
2219157 TTTTAT-TTTTT
1 TTTTATATTTTT
2219168 TGTTTAATATTTTT
1 T-TTT-ATATTTTT
2219182 TTT
1 TTT
2219185 ACAATTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 5 0.15
12 9 0.27
13 13 0.39
14 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTATATTTTT
Found at i:2219148 original size:20 final size:19
Alignment explanation
Indices: 2219118--2219168 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2219108 TATGTAAGTT
* *
2219118 TTTTTTTTTTTTCATTTTA
1 TTTTATTTTTTTAATTTTA
*
2219137 TATTTATTTTTTAAATTTTA
1 T-TTTATTTTTTTAATTTTA
2219157 TTTTATTTTTTT
1 TTTTATTTTTTT
2219169 GTTTAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTTTAATTTTA
Found at i:2219159 original size:25 final size:25
Alignment explanation
Indices: 2219126--2219185 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
2219116 TTTTTTTTTT
2219126 TTTTCATTTTATATTTATTT-TTTAA-A
1 TTTT-ATTTTAT-TTT-TTTGTTTAATA
2219152 TTTTATTTTATTTTTTTGTTTAATA
1 TTTTATTTTATTTTTTTGTTTAATA
2219177 TTTT-TTTTA
1 TTTTATTTTA
2219186 CAATTTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.09
24 13 0.41
25 12 0.38
26 4 0.12
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTATTTTATTTTTTTGTTTAATA
Found at i:2219808 original size:19 final size:19
Alignment explanation
Indices: 2219769--2219832 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
2219759 TTATTCATTC
2219769 AAATAAT-A-AAAAAGATAA
1 AAATAATCACAAAAA-ATAA
*
2219787 AAATAATCACAAAAAATTA
1 AAATAATCACAAAAAATAA
2219806 AAATAATCACAATAAAA-AA
1 AAATAATCACAA-AAAATAA
2219825 TAAATAAT
1 -AAATAAT
2219833 TAATTAAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.17
19 17 0.43
20 16 0.40
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAATCACAAAAAATAA
Found at i:2219829 original size:20 final size:19
Alignment explanation
Indices: 2219769--2219832 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
2219759 TTATTCATTC
*
2219769 AAATAAT-A-AAAAAGATAA
1 AAATAATCACAAAAAAAT-A
*
2219787 AAATAATCACAAAAAATTA
1 AAATAATCACAAAAAAATA
2219806 AAATAATCACAATAAAAA-A
1 AAATAATCACAA-AAAAATA
2219825 TAAATAAT
1 -AAATAAT
2219833 TAATTAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.18
19 15 0.38
20 17 0.44
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAATCACAAAAAAATA
Found at i:2244163 original size:20 final size:20
Alignment explanation
Indices: 2244138--2244233 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
2244128 CATGCTAGTA
* *
2244138 AATCATGCAAATATATTAAT
1 AATCATGCAATTATATTTAT
* *
2244158 AATCATACAAATATATTTAT
1 AATCATGCAATTATATTTAT
2244178 AATCATGCAATTATATTTAT
1 AATCATGCAATTATATTTAT
*
2244198 AATCGTGCAATTATATTTAT
1 AATCATGCAATTATATTTAT
2244218 AATCATGCAATTATAT
1 AATCATGCAATTATAT
2244234 AATATATTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
AATCATGCAATTATATTTAT
Found at i:2244421 original size:24 final size:23
Alignment explanation
Indices: 2244384--2244430 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2244374 ATCACATAAT
*
2244384 TAAAATAAAAAATAATAAAAAATA
1 TAAAATAAAAAAT-AGAAAAAATA
**
2244408 TAAAATAATGAATAGAAAAAATA
1 TAAAATAAAAAATAGAAAAAATA
2244431 AAACAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAATAAAAAATAGAAAAAATA
Found at i:2244426 original size:21 final size:19
Alignment explanation
Indices: 2244385--2244433 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
2244375 TCACATAATT
2244385 AAAATAAAAAATAATAAAA
1 AAAATAAAAAATAATAAAA
* *
2244404 AATATAAAATAATGAATAGAA
1 AAAATAAAA-AAT-AATAAAA
2244425 AAAATAAAA
1 AAAATAAAA
2244434 CAAAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 3 0.12
21 14 0.56
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAATAAAAAATAATAAAA
Found at i:2244483 original size:55 final size:53
Alignment explanation
Indices: 2244385--2244497 Score: 131
Period size: 55 Copynumber: 2.1 Consensus size: 53
2244375 TCACATAATT
* ** *
2244385 AAAATAAAAAATAATAAAAAATATAAAATAATGAATAGAAAAAATAAAACAAAGA
1 AAAACAAAAAATAATAAAAAATATAAAATAAAAAAAAGAAAAAA-AAAA-AAAGA
*
2244440 AAAACAAAAAATAA-AATCAAAAT-TAAAATAAAAAAAAGGAAAAAAAAAAAAGA
1 AAAACAAAAAATAATAA--AAAATATAAAATAAAAAAAAGAAAAAAAAAAAAAGA
2244493 AAAAC
1 AAAAC
2244498 CTGCGATTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 10 0.20
54 6 0.12
55 30 0.59
56 5 0.10
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (53 bp):
AAAACAAAAAATAATAAAAAATATAAAATAAAAAAAAGAAAAAAAAAAAAAGA
Found at i:2245444 original size:6 final size:6
Alignment explanation
Indices: 2245430--2245559 Score: 109
Period size: 6 Copynumber: 21.8 Consensus size: 6
2245420 ACTAAAACAA
* **
2245430 AAAAT- AAAATC AAAATC AAAATC AAAATT GGAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* ** * * * ** *
2245477 AAAATT GGAATC AAAGTC AAAATT AAAATT AAAATC AACGTC AAAATT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * * *
2245525 AAAATC AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
2245560 TTTTTTGCTT
Statistics
Matches: 101, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
5 5 0.05
6 96 0.95
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (6 bp):
AAAATC
Found at i:2245560 original size:6 final size:6
Alignment explanation
Indices: 2245410--2245560 Score: 95
Period size: 6 Copynumber: 25.2 Consensus size: 6
2245400 TGACTTTGAC
* * * * * * * *
2245410 TAAACT TAAAAC TAAAAC AAAAAA TAAAAT CAAAAT CAAAAT CAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
** * * * ** * * *
2245458 TGGAAT CAAAAT CAAAAT CAAAAT TGGAAT CAAAGT CAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* ** * *
2245506 TAAAAT CAACGT CAAAAT TAAAAT CAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
2245554 TAAAAT T
1 TAAAAT T
2245561 TTTTTGCTTT
Statistics
Matches: 115, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 115 1.00
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.24
Consensus pattern (6 bp):
TAAAAT
Found at i:2245560 original size:24 final size:24
Alignment explanation
Indices: 2245429--2245559 Score: 145
Period size: 24 Copynumber: 5.5 Consensus size: 24
2245419 AACTAAAACA
* *
2245429 AAAAATAAAATCAAAATCAAAATC
1 AAAATTAAAATCAAAATCAAAATT
** *
2245453 AAAATTGGAATCAAAATCAAAATC
1 AAAATTAAAATCAAAATCAAAATT
** *
2245477 AAAATTGGAATCAAAGTCAAAATT
1 AAAATTAAAATCAAAATCAAAATT
**
2245501 AAAATTAAAATCAACGTCAAAATT
1 AAAATTAAAATCAAAATCAAAATT
* * *
2245525 AAAATCAAAATTAAAATTAAAATT
1 AAAATTAAAATCAAAATCAAAATT
2245549 AAAATTAAAAT
1 AAAATTAAAAT
2245560 TTTTTTGCTT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.24
Consensus pattern (24 bp):
AAAATTAAAATCAAAATCAAAATT
Found at i:2245857 original size:41 final size:42
Alignment explanation
Indices: 2245811--2246034 Score: 197
Period size: 41 Copynumber: 5.3 Consensus size: 42
2245801 AACTTTGAGT
**
2245811 AAAT-AAATGCTCTTCCCACTAGAGGCTTTGAAACTTTTGAA
1 AAATAAAATGCTCCCCCCACTAGAGGCTTTGAAACTTTTGAA
* ** *
2245852 AAAT-AAATGCTCCCCCCATTTTAGGCTTTAAAACTTTTGAGA
1 AAATAAAATGCTCCCCCCACTAGAGGCTTTGAAACTTTTGA-A
** * * * *
2245894 AAATAAAACACTCACCCCACCAAAGGCTTTGAAGC-TTTGAA
1 AAATAAAATGCTCCCCCCACTAGAGGCTTTGAAACTTTTGAA
* * *
2245935 AAAT-AAATGCTCCCCCCAC-CGAAAGTTTTGAAACTTTTGAAA
1 AAATAAAATGCTCCCCCCACTAG-AGGCTTTGAAACTTTTG-AA
* * * *
2245977 AAATAAAATGCTCCCCCTAATTGGAGGCTTTGAAACTTTCGAGA
1 AAATAAAATGCTCCCCC-CACTAGAGGCTTTGAAACTTTTGA-A
2246021 AAATAAAATGCTCC
1 AAATAAAATGCTCC
2246035 TTAGGATTTT
Statistics
Matches: 145, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
40 21 0.14
41 43 0.30
42 16 0.11
43 34 0.23
44 30 0.21
45 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (42 bp):
AAATAAAATGCTCCCCCCACTAGAGGCTTTGAAACTTTTGAA
Found at i:2245898 original size:83 final size:83
Alignment explanation
Indices: 2245799--2246034 Score: 235
Period size: 83 Copynumber: 2.8 Consensus size: 83
2245789 TAGAAGCCTC
* *
2245799 AAAAC-TTTGAGTAAAT-AAATGCTCTTCCCACTAGAGGCTTTGAAACTTTTGAAAAATAAATGC
1 AAAACTTTTGAGAAAATAAAATGCTC-CCCCACTAGAGGCTTTGAAACTTTTGAAAAATAAATGC
**** *
2245862 TCCCCCCATTTTAGGCTTT
65 TCCCCCCACCGAAAGCTTT
** * * *
2245881 AAAACTTTTGAGAAAATAAAACACTCACCCCACCAAAGGCTTTGAAGC-TTTGAAAAATAAATGC
1 AAAACTTTTGAGAAAATAAAATGCTC-CCCCACTAGAGGCTTTGAAACTTTTGAAAAATAAATGC
*
2245945 TCCCCCCACCGAAAGTTTT
65 TCCCCCCACCGAAAGCTTT
* * * * *
2245964 GAAACTTTTGAAAAAATAAAATGCTCCCCCTAATTGGAGGCTTTGAAACTTTCGAGAAAATAAAA
1 AAAACTTTTGAGAAAATAAAATGCTCCCCC--ACTAGAGGCTTTGAAACTTTTGA-AAAAT-AAA
2246029 TGCTCC
62 TGCTCC
2246035 TTAGGATTTT
Statistics
Matches: 123, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
82 9 0.07
83 61 0.50
84 35 0.28
85 4 0.03
86 5 0.04
87 9 0.07
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
AAAACTTTTGAGAAAATAAAATGCTCCCCCACTAGAGGCTTTGAAACTTTTGAAAAATAAATGCT
CCCCCCACCGAAAGCTTT
Found at i:2256659 original size:10 final size:10
Alignment explanation
Indices: 2256644--2256678 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2256634 AATATATATA
2256644 TTTTATTTTT
1 TTTTATTTTT
2256654 TTTTA-TTTT
1 TTTTATTTTT
2256663 TTTTATTTTT
1 TTTTATTTTT
*
2256673 GTTTAT
1 TTTTAT
2256679 CTAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:2256662 original size:9 final size:9
Alignment explanation
Indices: 2256644--2256678 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
2256634 AATATATATA
2256644 TTTTATTTTT
1 TTTTA-TTTT
2256654 TTTTATTTT
1 TTTTATTTT
2256663 TTTTATTTT
1 TTTTATTTT
2256672 TGTTTAT
1 T-TTTAT
2256679 CTAATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.58
10 10 0.42
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTATTTT
Found at i:2256760 original size:3 final size:3
Alignment explanation
Indices: 2256746--2256779 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
2256736 ATCTTTTCTA
2256746 ATT ATCT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
2256780 TTTTATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2258593 original size:59 final size:59
Alignment explanation
Indices: 2258498--2258672 Score: 239
Period size: 60 Copynumber: 2.9 Consensus size: 59
2258488 TTTTGCAAAA
*
2258498 AAAT-AAAATTTCAAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-G
1 AAATCAAAATTTCAAAAAAAA-TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGG
**
2258557 AGAATCAAAATTTC-CGAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 A-AATCAAAATTTCAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTGG
**
2258617 AAATCAACGTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAATCAAAATTTCAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
2258673 CTACGCAAGA
Statistics
Matches: 103, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
59 45 0.44
60 50 0.49
61 8 0.08
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (59 bp):
AAATCAAAATTTCAAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGG
Found at i:2258666 original size:60 final size:60
Alignment explanation
Indices: 2258502--2258672 Score: 247
Period size: 59 Copynumber: 2.9 Consensus size: 60
2258492 GCAAAAAAAT
* *
2258502 AAAATTTCAAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAATC
1 AAAATTTCAAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAATC
** *
2258563 AAAATTTC-CGAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG-GAAATC
1 AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAG-AATC
**
2258622 AACGTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
2258673 CTACGCAAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.01
59 45 0.46
60 44 0.45
61 8 0.08
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (60 bp):
AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAATC
Found at i:2263173 original size:42 final size:42
Alignment explanation
Indices: 2263127--2263542 Score: 668
Period size: 42 Copynumber: 10.0 Consensus size: 42
2263117 GTCTAGGAGT
*
2263127 ATTTACTTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
2263169 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAAAGGAACA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263210 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263252 ATTTA-TTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263292 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263334 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263376 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
2263417 ATTTACCTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAAGAGCA
1 ATTTA-CTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263459 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
2263501 ATTTA-TGTTTCTCAAAGTCATTGAGCCTCTGTTTAGAGGAGC
1 ATTTACT-TTTC-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
2263543 TTTGGTAAAA
Statistics
Matches: 353, Mismatches: 10, Indels: 21
0.92 0.03 0.05
Matches are distributed among these distances:
40 38 0.11
41 86 0.24
42 199 0.56
43 30 0.08
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:2263229 original size:83 final size:83
Alignment explanation
Indices: 2263127--2263542 Score: 685
Period size: 83 Copynumber: 5.0 Consensus size: 83
2263117 GTCTAGGAGT
*
2263127 ATTTACTTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
* *
2263192 CCTCTGTTTAAAGGAACA
66 CCTCTGTTTAGAGGAGCA
2263210 ATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAGTCGTGGT
1 ATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGT
2263273 GCCTCTGTTTAGAGGAGCA
65 GCCTCTGTTTAGAGGAGCA
*
2263292 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGT
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTGGT
2263357 GCCTCTGTTTAGAGGAGCA
65 GCCTCTGTTTAGAGGAGCA
2263376 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACCTTTTCAAAGTCGTGGT
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGT
*
2263440 GCCTCTGTTTAGAAGAGCA
65 GCCTCTGTTTAGAGGAGCA
* * *
2263459 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATGTTTCTCAAAGTCATTG
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTT-TCAAAGTCGTGG
*
2263524 AGCCTCTGTTTAGAGGAGC
64 TGCCTCTGTTTAGAGGAGC
2263543 TTTGGTAAAA
Statistics
Matches: 314, Mismatches: 12, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
82 79 0.25
83 124 0.39
84 84 0.27
85 27 0.09
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (83 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
CCTCTGTTTAGAGGAGCA
Found at i:2263449 original size:125 final size:124
Alignment explanation
Indices: 2263127--2263542 Score: 692
Period size: 125 Copynumber: 3.3 Consensus size: 124
2263117 GTCTAGGAGT
*
2263127 ATTTACTTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
* *
2263192 CCTCTGTTTAAAGGAACAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263252 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTG
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTG
2263316 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2263376 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACCTTTTCAAAGTCGTGGTG
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGTG
*
2263441 CCTCTGTTTAGAAGAGCAATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * * *
2263501 ATTTATGTTTCTCAAAGTCATTGAGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
2263543 TTTGGTAAAA
Statistics
Matches: 277, Mismatches: 8, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
123 40 0.14
124 80 0.29
125 116 0.42
126 13 0.05
127 28 0.10
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (124 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGC
CTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:2263555 original size:1 final size:1
Alignment explanation
Indices: 2263549--2263629 Score: 72
Period size: 1 Copynumber: 81.0 Consensus size: 1
2263539 GAGCTTTGGT
* * * * * * * *
2263549 AAAAAAAAAAAACAAAAAAACAAAAAAAAATAAAAACAAAACAAAACAAAACAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2263614 ACAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAA
2263630 TGACAATGTT
Statistics
Matches: 60, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:2263573 original size:15 final size:15
Alignment explanation
Indices: 2263549--2263621 Score: 96
Period size: 15 Copynumber: 4.9 Consensus size: 15
2263539 GAGCTTTGGT
2263549 AAAAAA-AAAAAACA
1 AAAAAACAAAAAACA
*
2263563 AAAAAACAAAAAAAA
1 AAAAAACAAAAAACA
2263578 ATAAAAACAAAACAA-A
1 A-AAAAACAAAA-AACA
*
2263594 ACAAAACAAAAAACA
1 AAAAAACAAAAAACA
2263609 AAAAAACAAAAAA
1 AAAAAACAAAAAA
2263622 ATAAAAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.15
15 30 0.58
16 12 0.23
17 2 0.04
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (15 bp):
AAAAAACAAAAAACA
Found at i:2263937 original size:45 final size:45
Alignment explanation
Indices: 2263840--2263937 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
2263830 TATGTATTTA
* **
2263840 TTATTTATTTATTATTACTAATATATATATTTTTTATTTTTTATT
1 TTATTTATTTATTATTACTAATATATATATCTGATATTTTTTATT
* *
2263885 TTTTTTATTT-TTGTTTATCTAAT-TATATATCTGATATTATTTT-TT
1 TTATTTATTTATT-ATTA-CTAATATATATATCTGATATT-TTTTATT
2263930 TTATTTAT
1 TTATTTAT
2263938 CCTATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
44 2 0.05
45 33 0.75
46 9 0.20
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (45 bp):
TTATTTATTTATTATTACTAATATATATATCTGATATTTTTTATT
Found at i:2266458 original size:59 final size:57
Alignment explanation
Indices: 2266381--2266537 Score: 203
Period size: 59 Copynumber: 2.7 Consensus size: 57
2266371 AATTTCAAAA
*
2266381 AAAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAG-AATCAAAATTTCC
1 AAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAAT--AAATTTCC
* *
2266439 GAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT-CTTTAGAAATAAATTTTC
1 -AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAATAAATTTCC
*
2266496 AAAAATGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAT--ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
2266538 CTACGCAAGA
Statistics
Matches: 89, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
56 6 0.07
57 7 0.08
58 36 0.40
59 39 0.44
60 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (57 bp):
AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAATAAATTTCC
Found at i:2266529 original size:58 final size:59
Alignment explanation
Indices: 2266366--2266537 Score: 217
Period size: 58 Copynumber: 2.9 Consensus size: 59
2266356 TTTGCAAAAA
** * *
2266366 AATAAAATTTCAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAG
1 AATAAAATTTC-CGAAAAATGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAG
* *
2266426 AATCAAAATTTCCGAAAAAT-ATTTTTAGGGAAAAGTTGAAAGTATCAATTTT-CTTTAG
1 AAT-AAAATTTCCGAAAAATGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAG
*
2266484 AA-ATAAATTTTC-AAAAATGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
1 AATA-AAATTTCCGAAAAAT-GATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
2266538 CTACGCAAGA
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
56 7 0.07
57 7 0.07
58 38 0.38
59 31 0.31
60 8 0.08
61 8 0.08
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (59 bp):
AATAAAATTTCCGAAAAATGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAG
Found at i:2268973 original size:22 final size:22
Alignment explanation
Indices: 2268889--2268975 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
2268879 CAGTTAAAAA
*
2268889 TTAGTAGTAAATCAATT-CTAAT
1 TTAGTAGTAAATC-ATTGATAAT
* *
2268911 TTAATAGTAAATCATTAATAAT
1 TTAGTAGTAAATCATTGATAAT
* * *
2268933 TTTGTAGCATATCATTGATAAT
1 TTAGTAGTAAATCATTGATAAT
2268955 TTAGTAGTAAATCGA-TGATAA
1 TTAGTAGTAAATC-ATTGATAA
2268976 CATAATAATG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 3 0.06
22 49 0.92
23 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (22 bp):
TTAGTAGTAAATCATTGATAAT
Found at i:2271557 original size:160 final size:159
Alignment explanation
Indices: 2270971--2271544 Score: 511
Period size: 160 Copynumber: 3.6 Consensus size: 159
2270961 CATTTGGGCC
* * *
2270971 TTTCACACATATCAA-TCATGAAAACCAAGTTCAATCATTGA-AAAAAGTTTAATATCATGTATT
1 TTTCACACATATCAACT-GTGAAAACCAAGTTCAATCATTCAGACAAA-TTTAATATCATGTATT
** * * ** * * * * * * ** *
2271034 AAAGCCATCCAAACTATTAAAATAGATTAATCTTAGCAAATTTGTATTTTTGCTTTTTAGTGGCA
64 GGAGCTATCCAAACTGTTAAAATAGAACAAT-ATATCAAATTTGCA-GTTTGCCTCTTAACGACA
* * * * *
2271099 -AAAATAGTTCTAAATAGATGTAAATGATAACTT
127 TAAAA-AATCCTAAACAAACGTAAATGATAACTT
* * * *
2271132 TTTCAAACATATCAACTGT-AGAAATCAAGTTCAATCATTCAGATAAGTTTAATATCATGTATTG
1 TTTCACACATATCAACTGTGA-AAACCAAGTTCAATCATTCAGACAAATTTAATATCATGTATTG
* * * * *
2271196 AAGCTATCTAAACTGTTAAAATAG-ACAATAATATTAAATTTGTAGTTTGCCTTTTAACGACATA
65 GAGCTATCCAAACTGTTAAAATAGAACAAT-ATATCAAATTTGCAGTTTGCCTCTTAACGACATA
** * * * *
2271260 AAATGTCCTAAACAAGCGTAAA-CATTAGTT
129 AAAAATCCTAAACAAACGTAAATGATAACTT
* * *
2271290 TTTCCACACATATGAACTATGAAAACCAAGTTCAATTATTCTAG-CAAATTTAATATCATGTATT
1 TTT-CACACATATCAACTGTGAAAACCAAGTTCAATCATTC-AGACAAATTTAATATCATGTATT
* * * * *
2271354 -GAGGCTATGCAAATTGTTAAAATAGAATAATAACAACAAATTTGCA-TATTGCCTCTTAAC-AG
64 GGA-GCTATCCAAACTGTTAAAATAGAACAAT-ATATCAAATTTGCAGT-TTGCCTCTTAACGA-
*
2271416 CATAAAAAATCTTAAACAAACGTAAATGATAACTT
125 CATAAAAAATCCTAAACAAACGTAAATGATAACTT
* * *
2271451 TTTCACACATATCAATTGTGAAAACCAATTTTAATCATTCAGACAAATTTAATATCATGTATTGG
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAGACAAATTTAATATCATGTATTGG
2271516 AGCTATCCAAACTGTTAAAATAGAACAAT
66 AGCTATCCAAACTGTTAAAATAGAACAAT
2271545 TTGTCCAAAT
Statistics
Matches: 336, Mismatches: 63, Indels: 29
0.79 0.15 0.07
Matches are distributed among these distances:
158 9 0.03
159 97 0.29
160 146 0.43
161 80 0.24
162 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (159 bp):
TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAGACAAATTTAATATCATGTATTGG
AGCTATCCAAACTGTTAAAATAGAACAATATATCAAATTTGCAGTTTGCCTCTTAACGACATAAA
AAATCCTAAACAAACGTAAATGATAACTT
Found at i:2271665 original size:319 final size:319
Alignment explanation
Indices: 2271118--2271727 Score: 689
Period size: 319 Copynumber: 1.9 Consensus size: 319
2271108 CTAAATAGAT
* * *
2271118 GTAAATGATAACTTTTTCAAACATATCAACTGTAGAAATCAAGTTCAATCATTCAGATAAGTTTA
1 GTAAATGATAACTTTTTCAAACATATCAACTGTAGAAACCAAGTTCAATCATTCAGACAAATTTA
* * *
2271183 ATATCATGTATTGAAGCTATCTAAACTGTTAAAATAGACAATAATATTAAATTTGTAGTTTGCCT
66 ATATCATGTATTGAAGCTATCCAAACTGTTAAAATAGACAATAATATCAAATTTGTAGTTTGACT
* * * * * * *
2271248 TTTAACGACATAAAATGTCCTAAACAAGCGTAAACATTAGTTTTTCCACACATATGAACTATGAA
131 TATAACGACA-AAAATGTACTAAACAAGCATAAACATAACTTTTTCCACACATATCAACCATGAA
* ** ** * *
2271313 AACCAAGTTCAATTATTCTAGCAAATTTAATATCATGTATTGAGGCTATGC-AAATTGTTAAAAT
195 AACCAAGTTCAATAATTCTAGCAAACCTAATATCATGTATTGAAACTAT-CAAAACTATTAAAAT
*
2271377 AGAATAATAACAACAAATTTGCA-TATTGCCTCTTAACAGCATAAAAAATCTTAAACAAAC
259 AGAACAATAACAACAAATTTGCATTATTGCCTCTTAACAGCATAAAAAATCTTAAACAAAC
* * * *
2271437 GTAAATGATAACTTTTTCACACATATCAATTGT-GAAAACCAATTTTAATCATTCAGACAAATTT
1 GTAAATGATAACTTTTTCAAACATATCAACTGTAG-AAACCAAGTTCAATCATTCAGACAAATTT
* * * * *
2271501 AATATCATGTATTGGAGCTATCCAAACTGTTAAAATAGAACAAT-TTGTCCAAATTTGTATTTTT
65 AATATCATGTATTGAAGCTATCCAAACTGTTAAAATAG-ACAATAATAT-CAAATTTGTAGTTTG
* * * * *
2271565 ACTTAATAATGAC-ACAATGTACTAAATAGGCATAAACAATAACTTTTT-CATACATATCAACCA
128 ACTT-ATAACGACAAAAATGTACTAAACAAGCATAAAC-ATAACTTTTTCCACACATATCAACCA
* * *
2271628 T-AGAAACTAAGTTTAATAATT-T-GGATCAACCTAATATCATGTATTGAAACTATCAAAACTAT
191 TGA-AAACCAAGTTCAATAATTCTAGCA--AACCTAATATCATGTATTGAAACTATCAAAACTAT
** * *
2271690 TACTATAGAACAATAACTATAAATTTGCATTATTGCCT
253 TAAAATAGAACAATAACAACAAATTTGCATTATTGCCT
2271728 TGTAATGGCA
Statistics
Matches: 239, Mismatches: 42, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
317 2 0.01
318 4 0.02
319 191 0.80
320 36 0.15
321 6 0.03
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (319 bp):
GTAAATGATAACTTTTTCAAACATATCAACTGTAGAAACCAAGTTCAATCATTCAGACAAATTTA
ATATCATGTATTGAAGCTATCCAAACTGTTAAAATAGACAATAATATCAAATTTGTAGTTTGACT
TATAACGACAAAAATGTACTAAACAAGCATAAACATAACTTTTTCCACACATATCAACCATGAAA
ACCAAGTTCAATAATTCTAGCAAACCTAATATCATGTATTGAAACTATCAAAACTATTAAAATAG
AACAATAACAACAAATTTGCATTATTGCCTCTTAACAGCATAAAAAATCTTAAACAAAC
Found at i:2272926 original size:13 final size:13
Alignment explanation
Indices: 2272891--2272927 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2272881 ATAAAAGCGA
*
2272891 ATATATAAAAAAC
1 ATATATAAAGAAC
*
2272904 ATATGTAAAGAAC
1 ATATATAAAGAAC
2272917 ATATATAAAGA
1 ATATATAAAGA
2272928 CATTGAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:2275188 original size:21 final size:21
Alignment explanation
Indices: 2275164--2275206 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2275154 CACTTTGAAC
*
2275164 ATCAAAATCACCACCTTGAGT
1 ATCAAAATCACCAACTTGAGT
** *
2275185 ATCATTATCATCAACTTGAGT
1 ATCAAAATCACCAACTTGAGT
2275206 A
1 A
2275207 ATAGAAAGCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.30
Consensus pattern (21 bp):
ATCAAAATCACCAACTTGAGT
Found at i:2278163 original size:65 final size:63
Alignment explanation
Indices: 2277749--2278194 Score: 274
Period size: 62 Copynumber: 7.1 Consensus size: 63
2277739 GCAAAAAACA
* * * ***
2277749 CCTTCAATAATCCCCTT-AAATTTTGATGAAGAGATTATTGAAGGTATTTTTCACT-AAAAATG
1 CCTTCAATAATCCCTTTCAAATTTTTATCAAGAGATTATTGAAGGT-TTTTTTTGTAAAAAATG
* * * *
2277811 CCTTTAATAATCTCTTCCAAATTTTTATC-AGAGGATTATTGAAGG-TTTTTTTGCAAAAAATG
1 CCTTCAATAATCCCTTTCAAATTTTTATCAAGA-GATTATTGAAGGTTTTTTTTGTAAAAAATG
* * * * * *
2277873 CCTTCAATAAT-CCTCTGAAATTTGTTAT-AAAAAATTATT-AAGGGTGTATTTTG-AAGAAAAT
1 CCTTCAATAATCCCTTTCAAATTT-TTATCAAGAGATTATTGAA-GGTTTTTTTTGTAA-AAAAT
2277934 G
63 G
* * * * * * * ** **
2277935 CCTTCAATAA-CCCTCTT--AATTTTTTTTAAAAAATTATTCAAGGTGTTTTTTGCATGAAACA
1 CCTTCAATAATCCCT-TTCAAATTTTTATCAAGAGATTATTGAAGGTTTTTTTTGTAAAAAATG
* * * * *
2277996 CCTTTAATAATCCCTTTCAAA-TTTTATTAGGGGATTATCGAAGGTGTTTTTTTTAGTAAAAAAT
1 CCTTCAATAATCCCTTTCAAATTTTTATCAAGAGATTATTGAA-G-GTTTTTTTT-GTAAAAAAT
2278060 G
63 G
* * ** * * * *
2278061 CCTTCAATAATCTCATAAAAAATTTTA-AAAGAAATTATTGAAGGCATTTTTTTTGTAAAAAATA
1 CCTTCAATAATCCCTTTCAAATTTTTATCAAGAGATTATTGAAGG--TTTTTTTTGTAAAAAATG
* * *
2278125 CCTTCAATAATCCCTTTCAATTTTTTATCAAGGGATTATTGAAGACCTTTTTTTTGGT--AAAAT
1 CCTTCAATAATCCCTTTCAAATTTTTATCAAGAGATTATTGAAG--GTTTTTTTT-GTAAAAAAT
2278188 G
63 G
2278189 CCTTCA
1 CCTTCA
2278195 CTGATCATTT
Statistics
Matches: 296, Mismatches: 62, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
60 5 0.02
61 63 0.21
62 85 0.29
63 26 0.09
64 50 0.17
65 60 0.20
66 7 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (63 bp):
CCTTCAATAATCCCTTTCAAATTTTTATCAAGAGATTATTGAAGGTTTTTTTTGTAAAAAATG
Found at i:2281907 original size:35 final size:35
Alignment explanation
Indices: 2281850--2281916 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
2281840 ATATATAAAC
* *
2281850 TAAATATTTTTTGAGCATAAACCTACAATTGAATT
1 TAAATATTTTATGAGCACAAACCTACAATTGAATT
* *
2281885 TAAATGTTTTATGGGCACAAACCTACAATTGA
1 TAAATATTTTATGAGCACAAACCTACAATTGA
2281917 CTTCACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (35 bp):
TAAATATTTTATGAGCACAAACCTACAATTGAATT
Found at i:2282168 original size:64 final size:62
Alignment explanation
Indices: 2282040--2282188 Score: 171
Period size: 64 Copynumber: 2.4 Consensus size: 62
2282030 ATTTCTGGTT
* *
2282040 AAAAACGCCTTT-AATAATCCACTCTAAAAGATTTTGTAGGGATTGTTGAAGACGTTTTTGACC
1 AAAAACG-CTTTCAATAATCC-CTCTAAAAGATTTTGTAGGGATTATTGAAGACGTTTTCGACC
2282103 AAAAACGCTTTCAATAATCCCTCATAAAA-ATTTAT-TGAGTGGATTATTGAAAGA-GTTTTCGA
1 AAAAACGCTTTCAATAATCCCTC-TAAAAGATTT-TGT-AG-GGATTATTG-AAGACGTTTTCGA
2282165 CC
61 CC
* *
2282167 AAAAATGCCTTCAATAATCCCT
1 AAAAACGCTTTCAATAATCCCT
2282189 TCCAAATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
62 12 0.16
63 23 0.30
64 37 0.49
65 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (62 bp):
AAAAACGCTTTCAATAATCCCTCTAAAAGATTTTGTAGGGATTATTGAAGACGTTTTCGACC
Found at i:2282284 original size:64 final size:65
Alignment explanation
Indices: 2282093--2282312 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 65
2282083 TGTTGAAGAC
* * * * * *
2282093 GTTTTT-GACCAAAAACGCTTTCAATAATCCCTCATAAAAATTTATTGAGTGGATTATTGAAAGA
1 GTTTTTCGACCAAAAATGCCTTCAATAATCCCTCACAAAAATTTTTTGAATGGATTATTGAAAGT
*
2282157 G-TTTTCGACCAAAAATGCCTTCAATAATCCCTTC-C--AAATTTTTCT--ATGGATTATTGAAG
1 GTTTTTCGACCAAAAATGCCTTCAATAATCCC-TCACAAAAATTTTT-TGAATGGATTATTGAAA
2282216 GT
64 GT
* *** * *
2282218 GTTTTTTG-TTGAAAATGCCTTCAATATTCTCTCACAAAAATTTTTTGAATGGATTATTGAAAGT
1 GTTTTTCGACCAAAAATGCCTTCAATAATCCCTCACAAAAATTTTTTGAATGGATTATTGAAAGT
* * *
2282282 GTTTTT-AACTAGAAAATGCCTTGAATAATCC
1 GTTTTTCGACCA-AAAATGCCTTCAATAATCC
2282313 TTTACAAATA
Statistics
Matches: 125, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
60 2 0.02
61 33 0.26
62 13 0.10
63 13 0.10
64 46 0.37
65 18 0.14
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (65 bp):
GTTTTTCGACCAAAAATGCCTTCAATAATCCCTCACAAAAATTTTTTGAATGGATTATTGAAAGT
Found at i:2282634 original size:63 final size:61
Alignment explanation
Indices: 2282567--2282712 Score: 141
Period size: 62 Copynumber: 2.3 Consensus size: 61
2282557 AGACACCTTT
* *
2282567 AATAATCGCCTTCATTTTTTTATGAGGGGATTATTCAAAGTGTTGTCTGCTAAAAACGCATTC
1 AATAATC-CCTTCATTTTTTTATGA-GGGATTATTCAAAGTGTTGTCTGCCAAAAACACATTC
* * * * * * * *
2282630 AATAATCTCTT-ATCCATTTTAATGAGTGATTATTCAAGGTGTTTTCTGCCAAAAATACCTTC
1 AATAATCCCTTCAT--TTTTTTATGAGGGATTATTCAAAGTGTTGTCTGCCAAAAACACATTC
*
2282692 AATAATCACTTTCATTTTTTT
1 AATAATC-CCTTCATTTTTTT
2282713 GAAAAGATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
61 2 0.03
62 44 0.68
63 17 0.26
64 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (61 bp):
AATAATCCCTTCATTTTTTTATGAGGGATTATTCAAAGTGTTGTCTGCCAAAAACACATTC
Found at i:2283062 original size:9 final size:10
Alignment explanation
Indices: 2283037--2283160 Score: 73
Period size: 11 Copynumber: 12.3 Consensus size: 10
2283027 CATCAAGAGG
*
2283037 TTATTAAAATT
1 TTATCAAAA-T
2283048 TTATCAAAA-
1 TTATCAAAAT
2283057 TTATCAAAAT
1 TTATCAAAAT
2283067 TATATCATAAA-
1 T-TATCA-AAAT
2283078 TTA-CTAAAAT
1 TTATC-AAAAT
*
2283088 TGTATCAAAAG
1 T-TATCAAAAT
*
2283099 TTACCAAAATT
1 TTATCAAAA-T
**
2283110 TTATCAAAGG
1 TTATCAAAAT
2283120 TTATC-AAA-
1 TTATCAAAAT
2283128 --ATCAAAAT
1 TTATCAAAAT
*
2283136 TATATAAAAAT
1 T-TATCAAAAT
2283147 ATTATCAAAAT
1 -TTATCAAAAT
2283158 TTA
1 TTA
2283161 CTTAAATTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 29
0.70 0.08 0.23
Matches are distributed among these distances:
6 3 0.03
7 3 0.03
9 15 0.17
10 20 0.22
11 43 0.48
12 5 0.06
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (10 bp):
TTATCAAAAT
Found at i:2283068 original size:42 final size:42
Alignment explanation
Indices: 2283005--2283129 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 42
2282995 TATCATAAGT
* * * *
2283005 TATCAACAGATTACAAAAATTACATCAAGAGGTTATTAAAATTT
1 TATCAAAAG-TTACCAAAATTATATCAA-AGGTTATTAAAATTG
* * *
2283049 TATCAAAA-TTATCAAAATTATATCATAA-ATTACTAAAATTG
1 TATCAAAAGTTACCAAAATTATATCA-AAGGTTATTAAAATTG
* *
2283090 TATCAAAAGTTACCAAAATTTTATCAAAGGTTATCAAAAT
1 TATCAAAAGTTACCAAAATTATATCAAAGGTTATTAAAAT
2283130 CAAAATTATA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
41 20 0.30
42 38 0.58
43 1 0.02
44 7 0.11
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (42 bp):
TATCAAAAGTTACCAAAATTATATCAAAGGTTATTAAAATTG
Found at i:2283080 original size:21 final size:20
Alignment explanation
Indices: 2283037--2283129 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
2283027 CATCAAGAGG
*
2283037 TTATTAAAATTTTATCAAAA
1 TTATCAAAATTTTATCAAAA
*
2283057 TTATCAAAATTATATCATAAA
1 TTATCAAAATTTTATCA-AAA
*
2283078 TTA-CTAAAATTGTATCAAAA
1 TTATC-AAAATTTTATCAAAA
* *
2283098 GTTACCAAAATTTTATCAAAGG
1 -TTATCAAAATTTTATCAAA-A
2283120 TTATCAAAAT
1 TTATCAAAAT
2283130 CAAAATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 19 0.31
21 42 0.68
22 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (20 bp):
TTATCAAAATTTTATCAAAA
Found at i:2285581 original size:16 final size:16
Alignment explanation
Indices: 2285544--2285588 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2285534 AAAATAATAG
*
2285544 TTTATATATAAATTTA
1 TTTATATTTAAATTTA
**
2285560 CATATATTTAAATTTA
1 TTTATATTTAAATTTA
2285576 TTTATACTTTAAA
1 TTTATA-TTTAAA
2285589 AAAATGTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATATTTAAATTTA
Found at i:2296131 original size:6 final size:5
Alignment explanation
Indices: 2296112--2296171 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
2296102 CAAATGGAAT
* *
2296112 TTTTA TTTTA TTTTA CTTT- TTTAA TTTTA -TTTA TTTTA TTATT- TTTT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA
*
2296159 TCTTA TTTTA TTT
1 TTTTA TTTTA TTT
2296172 CTTCTTGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 11 0.24
5 32 0.71
6 2 0.04
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:2296132 original size:18 final size:16
Alignment explanation
Indices: 2296111--2296171 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
2296101 CCAAATGGAA
2296111 TTTTTATTTTATTTTACT
1 TTTTTATTTTA-TTTA-T
2296129 TTTTTAATTTTATTTAT
1 TTTTT-ATTTTATTTAT
*
2296146 TTTATTATTTT-TTTCT
1 TTT-TTATTTTATTTAT
2296162 TATTTTATTT
1 T-TTTTATTT
2296172 CTTCTTGTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 11 0.28
17 11 0.28
18 11 0.28
19 6 0.15
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTATTTAT
Found at i:2296156 original size:23 final size:24
Alignment explanation
Indices: 2296112--2296171 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
2296102 CAAATGGAAT
2296112 TTTTATTTTATTTTACTTTTTTAA
1 TTTTATTTTATTTTACTTTTTTAA
*
2296136 TTTTA-TTTATTTTA-TTATTTT-T
1 TTTTATTTTATTTTACTT-TTTTAA
2296158 TTCTTATTTTATTT
1 TT-TTATTTTATTT
2296172 CTTCTTGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.12
23 16 0.50
24 12 0.38
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTATTTTATTTTACTTTTTTAA
Found at i:2296159 original size:28 final size:28
Alignment explanation
Indices: 2296113--2296171 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2296103 AAATGGAATT
2296113 TTTATTTTATTTTACTTTT-TTAATTTTA
1 TTTATTTTATTTTACTTTTCTT-ATTTTA
*
2296141 TTTATTTTATTATT-TTTTTCTTATTTTA
1 TTTATTTTATT-TTACTTTTCTTATTTTA
2296169 TTT
1 TTT
2296172 CTTCTTGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTATTTTATTTTACTTTTCTTATTTTA
Found at i:2297836 original size:28 final size:29
Alignment explanation
Indices: 2297788--2297842 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2297778 ATAGAATAAT
* *
2297788 AAAAAATAATAATAATGAAAATCAACACA
1 AAAAAATAATAATAATAAAAACCAACACA
2297817 AAAAAATAA-AATTAA-AAAAACCAACA
1 AAAAAATAATAA-TAATAAAAACCAACA
2297843 TTACAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.15
Consensus pattern (29 bp):
AAAAAATAATAATAATAAAAACCAACACA
Found at i:2299416 original size:359 final size:360
Alignment explanation
Indices: 2298738--2299463 Score: 1402
Period size: 359 Copynumber: 2.0 Consensus size: 360
2298728 ACATGCATAA
2298738 ATAAAAAATCATGTATTAAAAAAAAAAGAAAAATCTCACAAAAGAACTTTTTTTTCTAATCTCGA
1 ATAAAAAATCATGTATTAAAAAAAAAAGAAAAATCTCACAAAAGAACTTTTTTTTCTAATCTCGA
2298803 ACCACATTTTTACGCTAACTTAATCTTGTTTTCCTATTTTTTTCTTCTTCTTTTTCCTTTTGCAT
66 ACCACATTTTTACGCTAACTTAATCTTGTTTTCCTA-TTTTTTCTTCTTCTTTTTCCTTTTGCAT
*
2298868 AAATCACATTATATAGTCCCACATTGAGATATTTATTCTAAAACTTTTTTTTCCAAGAAATTCTT
130 AAATCACATTATATAATCCCACATTGAGATATTTATTCTAAAACTTTTTTTTCCAAGAAATTCTT
2298933 TCATAGATCCCATAAAACTATAGATTTACTCATCTTCTATGAACATCCCATGTGACTTATATAAT
195 TCATAGATCCCATAAAACTATAGATTTACTCATCTTCTATGAACATCCCATGTGACTTATATAAT
2298998 GAGATACTTATTTGGTCAAAAGAAGCCCAACAAAAGAATGGAGATTTTTTGCCTATCGGTTATGT
260 GAGATACTTATTTGGTCAAAAGAAGCCCAACAAAAGAATGGAGATTTTTTGCCTATCGGTTATGT
2299063 GTCTGGGTTGCCCAAAAATGTGCATTTGGATCTTAC
325 GTCTGGGTTGCCCAAAAATGTGCATTTGGATCTTAC
2299099 ATAAAAAATCATGTATTAAAAAAAAAAAGAAAAATCTCACAAAAGAACTTTTTTTTCTAATCTCG
1 ATAAAAAATCATGTATT-AAAAAAAAAAGAAAAATCTCACAAAAGAACTTTTTTTTCTAATCTCG
2299164 AACCACATTTTTACGCTAACTTAATCTTGTTTTCCTA-TTTTT-TTCTTCTTTTTCCTTTTGCAT
65 AACCACATTTTTACGCTAACTTAATCTTGTTTTCCTATTTTTTCTTCTTCTTTTTCCTTTTGCAT
2299227 AAATCACATTATATAATCCCACATTGAGATATTTATTCTAAAACTTTTTTTTCCAAGAAATTCTT
130 AAATCACATTATATAATCCCACATTGAGATATTTATTCTAAAACTTTTTTTTCCAAGAAATTCTT
2299292 TCATAGATCCCATAAAACTATAGATTTACTCATCTTCTATGAACATCCCATGTGACTTATATAAT
195 TCATAGATCCCATAAAACTATAGATTTACTCATCTTCTATGAACATCCCATGTGACTTATATAAT
*
2299357 GAGATACTTATTTGGTCAAAAGAAGCCTAACAAAAGAATGGAGATTTTTTGCCTATCGGTTATGT
260 GAGATACTTATTTGGTCAAAAGAAGCCCAACAAAAGAATGGAGATTTTTTGCCTATCGGTTATGT
2299422 GTCTGGGTTGCCCAAAAATGTGCATTTGGATCTTAC
325 GTCTGGGTTGCCCAAAAATGTGCATTTGGATCTTAC
2299458 ATAAAA
1 ATAAAA
2299464 TAATTTAAAA
Statistics
Matches: 362, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
359 256 0.71
360 5 0.01
361 17 0.05
362 84 0.23
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (360 bp):
ATAAAAAATCATGTATTAAAAAAAAAAGAAAAATCTCACAAAAGAACTTTTTTTTCTAATCTCGA
ACCACATTTTTACGCTAACTTAATCTTGTTTTCCTATTTTTTCTTCTTCTTTTTCCTTTTGCATA
AATCACATTATATAATCCCACATTGAGATATTTATTCTAAAACTTTTTTTTCCAAGAAATTCTTT
CATAGATCCCATAAAACTATAGATTTACTCATCTTCTATGAACATCCCATGTGACTTATATAATG
AGATACTTATTTGGTCAAAAGAAGCCCAACAAAAGAATGGAGATTTTTTGCCTATCGGTTATGTG
TCTGGGTTGCCCAAAAATGTGCATTTGGATCTTAC
Found at i:2306973 original size:15 final size:15
Alignment explanation
Indices: 2306955--2306984 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2306945 ATACATTATG
2306955 TGTATACTTACAAAT
1 TGTATACTTACAAAT
2306970 TGTATACTTACAAAT
1 TGTATACTTACAAAT
2306985 CACCAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TGTATACTTACAAAT
Found at i:2308825 original size:19 final size:19
Alignment explanation
Indices: 2308801--2308840 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2308791 AAAGTTAATA
2308801 AGATAATGTGAACTATGAG
1 AGATAATGTGAACTATGAG
*
2308820 AGATAATGTGAATTATGAG
1 AGATAATGTGAACTATGAG
2308839 AG
1 AG
2308841 GGAGGGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.28
Consensus pattern (19 bp):
AGATAATGTGAACTATGAG
Found at i:2312297 original size:48 final size:50
Alignment explanation
Indices: 2312180--2312322 Score: 164
Period size: 48 Copynumber: 2.8 Consensus size: 50
2312170 AAATATATCT
* *
2312180 AATTATTTCACCATTTGGGTCAAATTAGAAATATTTTCTTATTTTGAATTTCAA
1 AATT-TTTCACCATTTGGGTCTATTTAGAAAT-TTTT-TTATTTT-AATTTCAA
* * * *
2312234 AATTCTCCACCATTTGGGCCTATTTAGAAATTTTTTT-TTTT-ATTTCTA
1 AATTTTTCACCATTTGGGTCTATTTAGAAATTTTTTTATTTTAATTTCAA
* *
2312282 AATTTTTCACCATTTGGGTCTATTTATAAATTCTTTTATTT
1 AATTTTTCACCATTTGGGTCTATTTAGAAATTTTTTTATTT
2312323 CTTCTTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
48 38 0.49
49 3 0.04
50 4 0.05
51 2 0.03
52 4 0.05
53 22 0.29
54 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.51
Consensus pattern (50 bp):
AATTTTTCACCATTTGGGTCTATTTAGAAATTTTTTTATTTTAATTTCAA
Found at i:2312907 original size:196 final size:196
Alignment explanation
Indices: 2312533--2312900 Score: 433
Period size: 196 Copynumber: 1.9 Consensus size: 196
2312523 AAAAAAATAC
* *
2312533 AATTACTTTTATTGAAATTTCATCCAAATTATTCCATAATTTGGGACAAATTTAGATAAAATTTC
1 AATTACTTTTATTGAAATTTCATCCAAATTATTCCACAATTTGGGACAAATTTAGACAAAATTTC
* * * * *
2312598 TTACCTAGAGATTTCTTAGGAATTTTCCATTTGAAATTTTTAAGAATCTCATCATTGGATAATTT
66 TCACCTAGAGATTTCTTAGAAATTTACCATTTGAAATTTTTAAGAATCTCATCATTAGATAATTA
* * *
2312663 GTATTTAATTTCAAATTTTTTAATTTTTTTTTATTTTTGTTATTTTTTGGTTTGAAAATAGACAT
131 ATATTTAATTTAAAATATTTTAATTTTTTTTTATTTTTGTTATTTTTTGGTTTGAAAATAGACAT
2312728 T
196 T
* * * * *
2312729 AATTA-TTGTTATTGAAACTTT-ATCTAAATTATTCTACCATTTGGGACGAATTTAGCCAAAATT
1 AATTACTT-TTATTGAAA-TTTCATCCAAATTATTCCACAATTTGGGACAAATTTAGACAAAATT
* *
2312792 TCTCACCTAG-GAATTT-TATAGAAATTTACCATTTGAAATTTCTATA-AAT-TCCATTATTAGA
64 TCTCACCTAGAG-ATTTCT-TAGAAATTTACCATTTGAAATTTTTA-AGAATCT-CATCATTAGA
* *
2312853 TAATTAATATTTATTCTTAAACATATTTTATTTTTTATTTTTATTTTT
125 TAATTAATATTTAAT-TTAAA-ATATTTTA-ATTTT-TTTTTATTTTT
2312901 TTTTTTGAAT
Statistics
Matches: 143, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
195 5 0.03
196 108 0.76
197 8 0.06
198 7 0.05
199 4 0.03
200 11 0.08
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (196 bp):
AATTACTTTTATTGAAATTTCATCCAAATTATTCCACAATTTGGGACAAATTTAGACAAAATTTC
TCACCTAGAGATTTCTTAGAAATTTACCATTTGAAATTTTTAAGAATCTCATCATTAGATAATTA
ATATTTAATTTAAAATATTTTAATTTTTTTTTATTTTTGTTATTTTTTGGTTTGAAAATAGACAT
T
Found at i:2313828 original size:9 final size:9
Alignment explanation
Indices: 2313814--2313838 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2313804 ACACACCCTT
2313814 TTTTTTTAA
1 TTTTTTTAA
2313823 TTTTTTTAA
1 TTTTTTTAA
2313832 TTTTTTT
1 TTTTTTT
2313839 GAAAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:2313913 original size:41 final size:41
Alignment explanation
Indices: 2313854--2314067 Score: 243
Period size: 41 Copynumber: 5.2 Consensus size: 41
2313844 AGTAAACAAA
* * * * * **
2313854 GCTCATCTAAATAGAGGCACCATAACATTGAAAAAGAAACG
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
* * *
2313895 GCTCCTCTAAACAAAGGCACGACAA-TTGTGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTT-TGAAAAATAAATT
* *
2313936 GCTCCTCTAAAAAGAGGGC-CCATAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGA-GGCACCACAACTTTGAAAAATAAATT
*
2313977 GCTCCTATAAACAGAGGCACCACAACTTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAATT
**
2314019 ATTCCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
1 GCT-CCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
2314061 GCTCCTC
1 GCTCCTC
2314068 GACAATCATG
Statistics
Matches: 145, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.03
41 82 0.57
42 37 0.26
43 22 0.15
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
Found at i:2326099 original size:17 final size:16
Alignment explanation
Indices: 2326073--2326104 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2326063 ATTTAATTCC
2326073 ATTTTTTTATTTTTGT
1 ATTTTTTTATTTTTGT
2326089 ATTTTTATTATTTTTG
1 ATTTTT-TTATTTTTG
2326105 GTTTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
ATTTTTTTATTTTTGT
Found at i:2326230 original size:26 final size:25
Alignment explanation
Indices: 2326196--2326250 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2326186 CTCACCTATG
2326196 AATTTTATAAAAATT-TATCATTTGA-
1 AATTTTAT--AAATTCTATCATTTGAT
2326221 AATTTCTATAAATTCTATCATTTGAT
1 AATTT-TATAAATTCTATCATTTGAT
2326247 AATT
1 AATT
2326251 AATATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (25 bp):
AATTTTATAAATTCTATCATTTGAT
Found at i:2326339 original size:15 final size:14
Alignment explanation
Indices: 2326306--2326344 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2326296 TTCAATCATG
2326306 TAAAAATAAACACA
1 TAAAAATAAACACA
* *
2326320 TAAAAATAAATAGA
1 TAAAAATAAACACA
2326334 TAAAAAATAAA
1 T-AAAAATAAA
2326345 AAATACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAAAATAAACACA
Found at i:2335383 original size:22 final size:21
Alignment explanation
Indices: 2335342--2335383 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2335332 TAGAATCTAA
*
2335342 ATCGATGATTATCATCTAACC
1 ATCGATGATTATCATATAACC
*
2335363 ATCGATGATGTCTCATATAAC
1 ATCGATGAT-TATCATATAAC
2335384 AGAACTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
ATCGATGATTATCATATAACC
Found at i:2340691 original size:8 final size:8
Alignment explanation
Indices: 2340678--2340707 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2340668 TAAATTACAT
2340678 AAAATAAA
1 AAAATAAA
2340686 AAAATAAA
1 AAAATAAA
2340694 AAAGATAAA
1 AAA-ATAAA
2340703 AAAAT
1 AAAAT
2340708 GTGAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:2341132 original size:15 final size:16
Alignment explanation
Indices: 2341106--2341137 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2341096 TGTAGCAACG
2341106 AAAATTTATGTCACTA
1 AAAATTTATGTCACTA
2341122 AAAATTT-TGTCACTA
1 AAAATTTATGTCACTA
2341137 A
1 A
2341138 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAATTTATGTCACTA
Found at i:2342727 original size:8 final size:8
Alignment explanation
Indices: 2342714--2342739 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2342704 ATCAATATTA
2342714 AAAATTTT
1 AAAATTTT
2342722 AAAATTTT
1 AAAATTTT
2342730 AAAATTTT
1 AAAATTTT
2342738 AA
1 AA
2342740 TATAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAAATTTT
Found at i:2344056 original size:64 final size:64
Alignment explanation
Indices: 2343878--2344056 Score: 147
Period size: 61 Copynumber: 2.8 Consensus size: 64
2343868 TGCCTTTAAT
* * * * *
2343878 AATATATTCAATAATCTTCTCATAAATTTTTATGATGTGATTACTC-AAGACATTTTTCATCAAA
1 AATATTTTCAATAATCCTCTCATATATTTTTATGATGTGATTACTCAAAG-CATTTCTCATAAAA
** * * * * * *
2343942 AATGCTTTGAATAAT-CTCACA-AT-TTTTTTTAAT-TGGATTA-TTAATGGCATTTCT-AGTAA
1 AATATTTTCAATAATCCTCTCATATATTTTTATGATGT-GATTACTCAA-AGCATTTCTCA-TAA
2344001 AA
63 AA
*
2344003 AATATTTTCAATAATCCTCTTATATATTTTTATGATGTGATTACTCAAAGCATT
1 AATATTTTCAATAATCCTCTCATATATTTTTATGATGTGATTACTCAAAGCATT
2344057 GTTTTGCCAA
Statistics
Matches: 84, Mismatches: 22, Indels: 18
0.68 0.18 0.15
Matches are distributed among these distances:
60 3 0.04
61 36 0.43
62 6 0.07
63 6 0.07
64 29 0.35
65 4 0.05
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (64 bp):
AATATTTTCAATAATCCTCTCATATATTTTTATGATGTGATTACTCAAAGCATTTCTCATAAAA
Found at i:2344131 original size:126 final size:125
Alignment explanation
Indices: 2343878--2344154 Score: 292
Period size: 126 Copynumber: 2.2 Consensus size: 125
2343868 TGCCTTTAAT
* * * *
2343878 AATATATTCAATAATCTTCTCATAAATTTTTATGATGTGATTACTCAAGACATTTTTCATCAAAA
1 AATATTTTCAATAATCATCTTATAAATTTTTATGATGTGATTACTCAAGACATTTTTCACCAAAA
* * *** * *
2343943 ATGCTTTGAATAATCTCACAATTTTTTTTAATTGGATTATTAATGGCATTTCTAGTAAAA
66 ATACATTGAATAATCTCACAAAAATTTTTAATCGGATTATTAAAGGCATTTCTAGTAAAA
* * **
2344003 AATATTTTCAATAATCCTCTTATATATTTTTATGATGTGATTACTCAA-AGCATTGTTTTGCCAA
1 AATATTTTCAATAATCATCTTATAAATTTTTATGATGTGATTACTCAAGA-CATT-TTTCACCAA
* * * * **
2344067 AAATACATTGAATAATCTTGA-AAAAATTTTTAATACGG-TTATTAAAGGTATTTTTGGTCTAA
64 AAATACATTGAATAATC-TCACAAAAATTTTTAAT-CGGATTATTAAAGGCATTTCTAGTAAAA
2344129 AATATCTTT-AATAATCATCTTATAAA
1 AATAT-TTTCAATAATCATCTTATAAA
2344155 AATAAAAGAT
Statistics
Matches: 125, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
124 1 0.01
125 48 0.38
126 69 0.55
127 7 0.06
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (125 bp):
AATATTTTCAATAATCATCTTATAAATTTTTATGATGTGATTACTCAAGACATTTTTCACCAAAA
ATACATTGAATAATCTCACAAAAATTTTTAATCGGATTATTAAAGGCATTTCTAGTAAAA
Found at i:2344253 original size:16 final size:16
Alignment explanation
Indices: 2344232--2344272 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2344222 TCCTTCAGCC
2344232 AAATGAATAAATC-TAA
1 AAATGAA-AAATCTTAA
*
2344248 AAATGAAATATCTTAA
1 AAATGAAAAATCTTAA
2344264 AAAT-AAAAA
1 AAATGAAAAA
2344273 CAACTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATGAAAAATCTTAA
Found at i:2352786 original size:22 final size:22
Alignment explanation
Indices: 2352758--2352801 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2352748 CTAAATCTTC
*
2352758 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
2352780 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
2352802 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:2356474 original size:25 final size:25
Alignment explanation
Indices: 2356434--2356482 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2356424 TTTCTTTGAA
2356434 AGGATTCGACAATGAAGGCCTAAAC
1 AGGATTCGACAATGAAGGCCTAAAC
* *
2356459 AGGATTCGGCAGTGAAGGCCTAAA
1 AGGATTCGACAATGAAGGCCTAAA
2356483 AAAGTCAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (25 bp):
AGGATTCGACAATGAAGGCCTAAAC
Found at i:2356528 original size:22 final size:23
Alignment explanation
Indices: 2356443--2356521 Score: 104
Period size: 23 Copynumber: 3.3 Consensus size: 23
2356433 AAGGATTCGA
* * *
2356443 CAATGAAGGCCTAAACAGGATTCGG
1 CAATGAAGGCCTAAA-A-AAGTCAG
*
2356468 CAGTGAAGGCCTAAAAAAGTCAG
1 CAATGAAGGCCTAAAAAAGTCAG
2356491 CAATGAAGGCCTAAAAAAGTCAG
1 CAATGAAGGCCTAAAAAAGTCAG
2356514 CAATGAAG
1 CAATGAAG
2356522 CTGAAAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
23 34 0.69
24 1 0.02
25 14 0.29
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (23 bp):
CAATGAAGGCCTAAAAAAGTCAG
Found at i:2356724 original size:22 final size:22
Alignment explanation
Indices: 2356696--2356739 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2356686 CTAAATCTTC
*
2356696 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
*
2356718 CTTAATTCTAGAGATATAAATA
1 CTTAATTCTAGAGATACAAATA
2356740 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:2356762 original size:8 final size:8
Alignment explanation
Indices: 2356749--2356773 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2356739 ATAAATATAC
2356749 AGATTACA
1 AGATTACA
2356757 AGATTACA
1 AGATTACA
2356765 AGATTACA
1 AGATTACA
2356773 A
1 A
2356774 CCTGCTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
AGATTACA
Found at i:2358859 original size:65 final size:65
Alignment explanation
Indices: 2358751--2358879 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 65
2358741 GACCGTGTTG
* * *
2358751 GTAAAAATGACTCTCATAATGATTAAATTTGGAATCTCTTGGGATCTTTAATATGATTTAGGCCA
1 GTAAAAATGAATCTCATAATGATTAAATTTGGAATCTCATGGGATCTTTAATATGATTGAGGCCA
* * * *
2358816 GTAAAAATGAATTTCATAATGATTAATTTTGGGAT-TGCATGGGATCTTTAGTATGATTGAGGCC
1 GTAAAAATGAATCTCATAATGATTAAATTTGGAATCT-CATGGGATCTTTAATATGATTGAGGCC
2358880 TCTCCGCTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 1 0.02
65 55 0.98
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (65 bp):
GTAAAAATGAATCTCATAATGATTAAATTTGGAATCTCATGGGATCTTTAATATGATTGAGGCCA
Found at i:2361907 original size:25 final size:25
Alignment explanation
Indices: 2361873--2361923 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2361863 CAATTTAAGG
2361873 TGCCAATTGTAATTGAGATTATGTT
1 TGCCAATTGTAATTGAGATTATGTT
2361898 TGCCAATTGTAATTGAGATTATGTT
1 TGCCAATTGTAATTGAGATTATGTT
2361923 T
1 T
2361924 TTACGGTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
TGCCAATTGTAATTGAGATTATGTT
Found at i:2368987 original size:22 final size:22
Alignment explanation
Indices: 2368962--2369004 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2368952 TTTTCTATCT
*
2368962 TTAATTCTAGGGATATAAATAC
1 TTAATTCTAGGGATAGAAATAC
*
2368984 TTAATTTTAGGGATAGAAATA
1 TTAATTCTAGGGATAGAAATA
2369005 TAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (22 bp):
TTAATTCTAGGGATAGAAATAC
Found at i:2375721 original size:41 final size:39
Alignment explanation
Indices: 2375607--2375713 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 39
2375597 ATTGATTGTC
2375607 TAGGATAATTTACCTTTTCTTTTTCTTTTGAATGGTTTACA
1 TAGGATAA-TTACCTTTT-TTTTTCTTTTGAATGGTTTACA
*
2375648 TAGGATAATTATCTTTTTTTTTTTCTTTTGAATGGTTTACA
1 TAGGATAATTA-C-CTTTTTTTTTCTTTTGAATGGTTTACA
2375689 TAGGATAATTACCTTTCTTTTTTCT
1 TAGGATAATTACCTTT-TTTTTTCT
2375714 GAATGAATCA
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
39 3 0.05
40 12 0.20
41 42 0.69
42 4 0.07
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.56
Consensus pattern (39 bp):
TAGGATAATTACCTTTTTTTTTCTTTTGAATGGTTTACA
Found at i:2375727 original size:37 final size:37
Alignment explanation
Indices: 2375607--2375736 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 37
2375597 ATTGATTGTC
*
2375607 TAGGATAATTTACCTTTTCTTTTTCTTTTGAATGGTTTACA
1 TAGGATAA-TTACC-TTTC-TTTT-TTCTGAATGGTTTACA
* *
2375648 TAGGATAATTATCTTTTTTTTTTTCTTTTGAATGGTTTACA
1 TAGGATAATTA-CCTTTCTTTTTTC---TGAATGGTTTACA
** *
2375689 TAGGATAATTACCTTTCTTTTTTCTGAATGAATCACA
1 TAGGATAATTACCTTTCTTTTTTCTGAATGGTTTACA
2375726 TAGGATAATTA
1 TAGGATAATTA
2375737 TATGGAAGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
37 21 0.27
38 2 0.03
39 4 0.05
40 17 0.22
41 33 0.43
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (37 bp):
TAGGATAATTACCTTTCTTTTTTCTGAATGGTTTACA
Found at i:2377399 original size:22 final size:24
Alignment explanation
Indices: 2377362--2377413 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 24
2377352 TCAAATTATT
2377362 AGTAATAATATATGTGAAAGAACA
1 AGTAATAATATATGTGAAAGAACA
2377386 AGTAA-AATA-ATGTGAAAGAACA
1 AGTAATAATATATGTGAAAGAACA
2377408 AG-AATA
1 AGTAATA
2377414 TCTGTGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.07
22 16 0.59
23 4 0.15
24 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (24 bp):
AGTAATAATATATGTGAAAGAACA
Found at i:2377698 original size:60 final size:59
Alignment explanation
Indices: 2377615--2377763 Score: 244
Period size: 60 Copynumber: 2.5 Consensus size: 59
2377605 TATTTTGGAG
* *
2377615 AACTCATCTCACCTATTGTTTCTCTACTTTTAAACTTATTAGTGCTAATAAATATAGGAT
1 AACTCATC-CACTTATTGTTTCTCTACTTTTAAACTTATTAGTACTAATAAATATAGGAT
*
2377675 AACTCATACCACTTATTGTTTCTCTACTTTTAAACTTATTAGTACTAATATATATAGGAT
1 AACTCAT-CCACTTATTGTTTCTCTACTTTTAAACTTATTAGTACTAATAAATATAGGAT
*
2377735 AACTCATCCACTTATTGTTTCTATACTTT
1 AACTCATCCACTTATTGTTTCTCTACTTT
2377764 CAAATTGGAC
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
59 21 0.25
60 62 0.74
61 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (59 bp):
AACTCATCCACTTATTGTTTCTCTACTTTTAAACTTATTAGTACTAATAAATATAGGAT
Found at i:2382173 original size:16 final size:16
Alignment explanation
Indices: 2382152--2382237 Score: 55
Period size: 16 Copynumber: 5.0 Consensus size: 16
2382142 ATAAAATTTT
*
2382152 TAAAAATTTTGAAAAA
1 TAAAAATTTTAAAAAA
* *
2382168 TAAAAAATATAAAAAA
1 TAAAAATTTTAAAAAA
* *
2382184 TTAAAATTTTAATAAA
1 TAAAAATTTTAAAAAA
*
2382200 TCCAAAAAAGCTTTAAAAAA
1 T---AAAAA-TTTTAAAAAA
*
2382220 TTAAGAAATATTAAAAAA
1 -TAA-AAATTTTAAAAAA
2382238 ATTAAATTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
16 26 0.50
18 10 0.19
19 7 0.13
20 8 0.15
21 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (16 bp):
TAAAAATTTTAAAAAA
Found at i:2382341 original size:25 final size:25
Alignment explanation
Indices: 2382280--2382361 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
2382270 TTTCTTTAAA
* *
2382280 TATTTTTTGAATTTTTAGATTTTTT
1 TATTTTTTAAATTTTAAGATTTTTT
* **
2382305 TATGTTCAAAATTTTAAG-TTTTTT
1 TATTTTTTAAATTTTAAGATTTTTT
**
2382329 GTATTTTTTAAATTTTAAGAAATTTT
1 -TATTTTTTAAATTTTAAGATTTTTT
2382355 TATTTTT
1 TATTTTT
2382362 ATTAAAATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 6 0.13
25 35 0.78
26 4 0.09
ACGTcount: A:0.27, C:0.01, G:0.07, T:0.65
Consensus pattern (25 bp):
TATTTTTTAAATTTTAAGATTTTTT
Found at i:2382493 original size:18 final size:17
Alignment explanation
Indices: 2382452--2382494 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2382442 TTTTTTAAAG
*
2382452 TTTTTATAATGTTTAAT
1 TTTTTAAAATGTTTAAT
*
2382469 TTCTTTAAAATGTTTTAGT
1 TT-TTTAAAATG-TTTAAT
2382488 TTTTTAA
1 TTTTTAA
2382495 TTTCTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (17 bp):
TTTTTAAAATGTTTAAT
Found at i:2384671 original size:31 final size:32
Alignment explanation
Indices: 2384633--2384700 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
2384623 AATATTATTT
*
2384633 TATTAAATTATT-TATAAAATATATTTAATAA
1 TATTAAATTATTATATAAAAAATATTTAATAA
**
2384664 TATTAAATTATTAATATAAAAAATATTTCTTAA
1 TATTAAATTATT-ATATAAAAAATATTTAATAA
2384697 TATT
1 TATT
2384701 TAGTAATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 12 0.38
33 20 0.62
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
TATTAAATTATTATATAAAAAATATTTAATAA
Found at i:2388129 original size:23 final size:23
Alignment explanation
Indices: 2388111--2388156 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2388101 TTAAAATATG
2388111 AATAAAATTAATACAAAAATTAA
1 AATAAAATTAATACAAAAATTAA
2388134 AATAAAATTAATACAAAAATTAA
1 AATAAAATTAATACAAAAATTAA
2388157 TTTTATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
AATAAAATTAATACAAAAATTAA
Found at i:2388131 original size:12 final size:12
Alignment explanation
Indices: 2388114--2388157 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2388104 AAATATGAAT
2388114 AAAATTAATACA
1 AAAATTAATACA
2388126 AAAATTAA-A-A
1 AAAATTAATACA
2388136 TAAAATTAATACA
1 -AAAATTAATACA
2388149 AAAATTAAT
1 AAAATTAAT
2388158 TTTATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 9 0.31
12 18 0.62
13 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATTAATACA
Found at i:2396033 original size:59 final size:59
Alignment explanation
Indices: 2395941--2396057 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
2395931 TCAGTACTAC
* *
2395941 GTTTGTGTGGTTTATTTCTTGTAGAGCTGATATATCATTGAGACTATGTAAAATAATCA
1 GTTTGTGTGGTTTATTTCTTGTAGAGCTGATATATCATTAAGACTATGTAAAACAATCA
*
2396000 GTTTGTGTGGTTTATTTCTTGTAGAGCTGATATATCGTTAAGACTATGTAAAACAATC
1 GTTTGTGTGGTTTATTTCTTGTAGAGCTGATATATCATTAAGACTATGTAAAACAATC
2396058 CGTGATATCC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (59 bp):
GTTTGTGTGGTTTATTTCTTGTAGAGCTGATATATCATTAAGACTATGTAAAACAATCA
Found at i:2397884 original size:19 final size:19
Alignment explanation
Indices: 2397856--2397895 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2397846 AATTGCCATC
2397856 CCTCAAGTCTTGCCCTGAA
1 CCTCAAGTCTTGCCCTGAA
* *
2397875 CCTCATGTCTTGCCTTGAA
1 CCTCAAGTCTTGCCCTGAA
2397894 CC
1 CC
2397896 ACGGGATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.38, G:0.15, T:0.30
Consensus pattern (19 bp):
CCTCAAGTCTTGCCCTGAA
Found at i:2399095 original size:19 final size:20
Alignment explanation
Indices: 2399073--2399115 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2399063 TTTTTTTGCT
2399073 ATTAAATTAATTTTTAT-TA
1 ATTAAATTAATTTTTATGTA
** *
2399092 ATTATTTTCATTTTTATGTA
1 ATTAAATTAATTTTTATGTA
2399112 ATTA
1 ATTA
2399116 TTTAATATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTAAATTAATTTTTATGTA
Found at i:2400397 original size:18 final size:18
Alignment explanation
Indices: 2400374--2400409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2400364 AAGAAGACTG
*
2400374 CAAAAGCAAAAATAAAAA
1 CAAAAGCAAAAAGAAAAA
*
2400392 CAAAAGCCAAAAGAAAAA
1 CAAAAGCAAAAAGAAAAA
2400410 AACCCTGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.14, G:0.08, T:0.03
Consensus pattern (18 bp):
CAAAAGCAAAAAGAAAAA
Found at i:2404520 original size:6 final size:6
Alignment explanation
Indices: 2404509--2404540 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2404499 TAAGTCTAGA
*
2404509 TGATGG TGATGG TGATGG TGATGG TGACGG TG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TG
2404541 CAAATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.03, G:0.50, T:0.31
Consensus pattern (6 bp):
TGATGG
Found at i:2404907 original size:18 final size:18
Alignment explanation
Indices: 2404884--2404936 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2404874 ATAGTTATTA
2404884 TCCACCACAAATGTATCC
1 TCCACCACAAATGTATCC
*
2404902 TCCACCTCAAATGTATCC
1 TCCACCACAAATGTATCC
* *
2404920 CCCACCACAAATATATC
1 TCCACCACAAATGTATC
2404937 ATCCTCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.40, G:0.04, T:0.23
Consensus pattern (18 bp):
TCCACCACAAATGTATCC
Found at i:2404962 original size:18 final size:18
Alignment explanation
Indices: 2404884--2404962 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 18
2404874 ATAGTTATTA
* *
2404884 TCCACCACAAATGTATCC
1 TCCACCTCAAATATATCC
*
2404902 TCCACCTCAAATGTATCC
1 TCCACCTCAAATATATCC
* * *
2404920 CCCACCACAAATATATCA
1 TCCACCTCAAATATATCC
*
2404938 T---CCTCAAATATATCT
1 TCCACCTCAAATATATCC
2404953 TCCACCTCAA
1 TCCACCTCAA
2404963 TTGCATCAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
15 13 0.26
18 37 0.74
ACGTcount: A:0.34, C:0.38, G:0.03, T:0.25
Consensus pattern (18 bp):
TCCACCTCAAATATATCC
Found at i:2407380 original size:14 final size:14
Alignment explanation
Indices: 2407361--2407391 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2407351 GGATAAAATT
2407361 AATTATTAAACTAA
1 AATTATTAAACTAA
*
2407375 AATTATTAAACTTA
1 AATTATTAAACTAA
2407389 AAT
1 AAT
2407392 ACTATGCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATTAAACTAA
Found at i:2409774 original size:90 final size:90
Alignment explanation
Indices: 2409675--2409857 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 90
2409665 TTGTATGGAT
* *
2409675 GAGATTGTTGCAGAAGATGATGTTGCAAGAGAAGATAAGGC-AAAGA-ATGAAGGAAGAGGGAGT
1 GAGATTGTTGCAGAAGATGATGGTGCAAGAGAAGATAA-GCTAAA-ACAGGAAGGAAGAGGGAGT
* * * *
2409738 GACGAATTAAAGGTTCAAGTTTTGGGG
64 AACGAATTAAAGGGTCAACTTTTGAGG
*
2409765 GAGATTGTTGCAGAAGATGATGGTGCAAGAGAAGATAAGCTAAAACAGGAAGGAAGAGGTAGTAA
1 GAGATTGTTGCAGAAGATGATGGTGCAAGAGAAGATAAGCTAAAACAGGAAGGAAGAGGGAGTAA
2409830 CGAATTAAAGGGTCAACTTTTGAGG
66 CGAATTAAAGGGTCAACTTTTGAGG
2409855 GAG
1 GAG
2409858 GAAATAGTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
89 3 0.04
90 81 0.96
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (90 bp):
GAGATTGTTGCAGAAGATGATGGTGCAAGAGAAGATAAGCTAAAACAGGAAGGAAGAGGGAGTAA
CGAATTAAAGGGTCAACTTTTGAGG
Found at i:2413245 original size:17 final size:18
Alignment explanation
Indices: 2413198--2413252 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
2413188 AAAATTGAAA
2413198 ATAAAATAAACAACTAAAAAT
1 ATAAAAT-AA-AA-TAAAAAT
*
2413219 ATCAAAT-AAATAAAAAT
1 ATAAAATAAAATAAAAAT
2413236 -TAAAATTAAAATAAAAA
1 ATAAAA-TAAAATAAAAA
2413253 AAAGACCTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 11 0.37
19 1 0.03
21 6 0.20
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAATAAAATAAAAAT
Found at i:2414788 original size:62 final size:63
Alignment explanation
Indices: 2414592--2414848 Score: 220
Period size: 64 Copynumber: 4.1 Consensus size: 63
2414582 TTTTTGACAG
* * * * * *
2414592 AAAAATGCCTTTAATAATCCATAGAA-AAAATATGGAACGGATTCTTGAAGGCATTTTTGGTC
1 AAAAATGCCTTTAATAATCCACACAATAAAATTTAGAACGGATTATTGAAGGTATTTTTGGTC
* * * * * *
2414654 GAAAGTGTCTTCAATAATCCA-ATCAATAAAATTTCATG-A-GTGATTATTAAAGGCGA-TTTTG
1 AAAAATGCCTTTAATAATCCACA-CAATAAAATTT-A-GAACG-GATTATTGAAGG-TATTTTTG
*
2414715 GTA
61 GTC
* * * *
2414718 AAAAATGCCTTAAATAATCCACACAA-AAAAGTTAGAACGGATTCTTGAAGGTATTTTTGGCC
1 AAAAATGCCTTTAATAATCCACACAATAAAATTTAGAACGGATTATTGAAGGTATTTTTGGTC
* * ** *
2414780 TAAAATGCCTTTAATAATCCACACAATAAATTTTTAGATGGGATTATTGAAGGTAGTTTTGGTC
1 AAAAATGCCTTTAATAATCCACACAATAAA-ATTTAGAACGGATTATTGAAGGTATTTTTGGTC
2414844 AAAAA
1 AAAAA
2414849 CACCTTCAAT
Statistics
Matches: 152, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
61 3 0.02
62 61 0.40
63 17 0.11
64 68 0.45
65 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (63 bp):
AAAAATGCCTTTAATAATCCACACAATAAAATTTAGAACGGATTATTGAAGGTATTTTTGGTC
Found at i:2414825 original size:126 final size:126
Alignment explanation
Indices: 2414592--2414832 Score: 308
Period size: 126 Copynumber: 1.9 Consensus size: 126
2414582 TTTTTGACAG
* * * * *
2414592 AAAAATGCCTTTAATAATCCATAGAAAAAATATGGAACGGATTCTTGAAGGCATTTTTGGTCGAA
1 AAAAATGCCTTAAATAATCCACACAAAAAATATAGAACGGATTCTTGAAGGCATTTTTGGCCGAA
* * *
2414657 AGTGTCTTCAATAATCCAATCAATAAAATTTCATGAGTGATTATTAAAGGCGATTTTGGTA
66 AATGCCTTCAATAATCCAATCAATAAAATTTCATGAGGGATTATTAAAGGCGATTTTGGTA
* *
2414718 AAAAATGCCTTAAATAATCCACACAAAAAAGT-TAGAACGGATTCTTGAAGGTATTTTTGGCCTA
1 AAAAATGCCTTAAATAATCCACACAAAAAA-TATAGAACGGATTCTTGAAGGCATTTTTGGCCGA
* * * *
2414782 AAATGCCTTTAATAATCCACA-CAATAAATTTTTA-GATGGGATTATTGAAGG
65 AAATGCCTTCAATAATCCA-ATCAATAAAATTTCATGA-GGGATTATTAAAGG
2414833 TAGTTTTGGT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
125 2 0.02
126 94 0.96
127 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (126 bp):
AAAAATGCCTTAAATAATCCACACAAAAAATATAGAACGGATTCTTGAAGGCATTTTTGGCCGAA
AATGCCTTCAATAATCCAATCAATAAAATTTCATGAGGGATTATTAAAGGCGATTTTGGTA
Found at i:2414860 original size:126 final size:126
Alignment explanation
Indices: 2414599--2414860 Score: 289
Period size: 126 Copynumber: 2.1 Consensus size: 126
2414589 CAGAAAAATG
* * * * * * *
2414599 CCTTTAATAATCCATAGAAAAAATATGGAACGGATTCTTGAAGGCATTTTTGGTCGAAAGTGTCT
1 CCTTAAATAATCCACACAAAAAATATAGAACGGATTCTTGAAGGCATTTTTGGCCGAAAATGCCT
* * **
2414664 TCAATAATCCAATCAATAAAATTTCATGAGTGATTATTAAAGGCGATTTTGGTAAAAAATG
66 TCAATAATCCAATCAATAAAATTTCATGAGGGATTATTAAAGGAGATTTTGGTAAAAAACA
* *
2414725 CCTTAAATAATCCACACAAAAAAGT-TAGAACGGATTCTTGAAGGTATTTTTGGCCTAAAATGCC
1 CCTTAAATAATCCACACAAAAAA-TATAGAACGGATTCTTGAAGGCATTTTTGGCCGAAAATGCC
* * * * *
2414789 TTTAATAATCCACA-CAATAAATTTTTA-GATGGGATTATTGAAGGTAG-TTTTGGTCAAAAACA
65 TTCAATAATCCA-ATCAATAAAATTTCATGA-GGGATTATTAAAGG-AGATTTTGGTAAAAAACA
*
2414851 CCTTCAATAA
1 CCTTAAATAA
2414861 CATTTTGTTA
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
125 2 0.02
126 108 0.96
127 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (126 bp):
CCTTAAATAATCCACACAAAAAATATAGAACGGATTCTTGAAGGCATTTTTGGCCGAAAATGCCT
TCAATAATCCAATCAATAAAATTTCATGAGGGATTATTAAAGGAGATTTTGGTAAAAAACA
Found at i:2418256 original size:25 final size:25
Alignment explanation
Indices: 2418228--2418276 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2418218 ATGTGTTTAG
2418228 AAACACCATTAAGCAAACCATTCAA
1 AAACACCATTAAGCAAACCATTCAA
* *
2418253 AAACACCATTTAGCAACCCATTCA
1 AAACACCATTAAGCAAACCATTCA
2418277 GCATACCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.31, G:0.04, T:0.18
Consensus pattern (25 bp):
AAACACCATTAAGCAAACCATTCAA
Found at i:2418315 original size:28 final size:28
Alignment explanation
Indices: 2418270--2418337 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
2418260 ATTTAGCAAC
* * * *
2418270 CCATTCAGCATACCAATATTATACAATA
1 CCATTCAGCAAAACAATATCACACAATA
*
2418298 CCATTCAGCAAAATAATATCACACAATA
1 CCATTCAGCAAAACAATATCACACAATA
*
2418326 CCATTTAGCAAA
1 CCATTCAGCAAA
2418338 CCGCAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (28 bp):
CCATTCAGCAAAACAATATCACACAATA
Found at i:2419664 original size:238 final size:238
Alignment explanation
Indices: 2419268--2420033 Score: 901
Period size: 238 Copynumber: 3.2 Consensus size: 238
2419258 AGAAAACGCT
* * * ** * * **
2419268 TTCAATAAATTTTTTAAAAAATTATAATGAATTAGTGAAGACATTTTTTTGGAATAAACGTCATC
1 TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGTGAAGGCATTTTTTTGGAATAAAAGTTTTC
** * * * *
2419333 AATAATGCCCTTAAAATTTTAGTAGTAGAATGTTGAATG-CGTTTCTACTAAAAGATGCCTTTAA
66 AATAACCCCCTTAAAATTTTAGTAGTGGAATATTGAATGCCTTTTCTACTAAAAGATACCTTTAA
* * * *
2419397 TAATCTCAAATAATTTTTTTAAA-AAAATTATT-AAAATCGTTTATTCTAAAAAAATACCTTTAA
131 TAATCTCAAATAA-TTTTTAAAAGAAAATTATTGAAAGT-ATTTTTTCTAAAAAAATACCTTTAA
*
2419460 TAATTCTGTATAAAAATTATTGAAGGCGTATAATGCAAAAAACCC
194 TAATTCTGTACAAAAATTATTGAAGGCGTATAATGCAAAAAACCC
** * * *
2419505 TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGAAAAGGCATTTTTCTAGAATAAATGTTTTC
1 TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGTGAAGGCATTTTTTTGGAATAAAAGTTTTC
* * * * * * * *
2419570 AATAACCCCCTTCAAATTCTAGTAATGGAATATTGAAGGCCTTTTCTTCTAAAAGACATCTGTAA
66 AATAACCCCCTTAAAATTTTAGTAGTGGAATATTGAATGCCTTTTCTACTAAAAGATACCTTTAA
* * * *
2419635 TAATCCCAAACAATTTTTAAAAGAAAATTATTGAAGGTATTTTTTCTCAAAAAATACCTTTAATA
131 TAATCTCAAATAATTTTTAAAAGAAAATTATTGAAAGTATTTTTTCTAAAAAAATACCTTTAATA
* ** *
2419700 ATTCTGTACAAAAATTATTGAAGGTGTATAATGCAAAACGCCT
196 ATTCTGTACAAAAATTATTGAAGGCGTATAATGCAAAAAACCC
* * *
2419743 TTCAATAAATTCTTTTAACAATTAGAACGAATTAGTGAAGGCATTTTTTTGGAATAAAAAGTCTT
1 TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGTGAAGGCATTTTTTTGGAAT-AAAAGT-TT
* * * * * *
2419808 T-AGTAACCCCCTTTAAATTTTGGTAGTGGAATATTGAATGCATTTTCTGCTAAAATATACCTTT
64 TCAATAACCCCCTTAAAATTTTAGTAGTGGAATATTGAATGCCTTTTCTACTAAAAGATACCTTT
* * * * *
2419872 AATAATCTCAAATAATTTTTAAAAGAAAACTATTGAAAGTTTTTTTTTTAAAAAAAATCCCTTCA
129 AATAATCTCAAATAATTTTTAAAAGAAAATTATTGAAAGTATTTTTTCT-AAAAAAATACCTTTA
* * *
2419937 ATAATTTTGTACAAAAATTATTGAAGGCATATAATGCAAAAAATGCC
193 ATAATTCTGTACAAAAATTATTGAAGGCGTATAATGCAAAAAA-CCC
* * *
2419984 TTCAATAAATACCTTCAAAAATTATAACAAATTAGTGAAGGCATTTTTTT
1 TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGTGAAGGCATTTTTTT
2420034 TTTTTGAAAA
Statistics
Matches: 440, Mismatches: 82, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
237 91 0.21
238 149 0.34
239 102 0.23
240 53 0.12
241 45 0.10
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (238 bp):
TTCAATAAATTCTTTCAAAAATTAGAACAAATTAGTGAAGGCATTTTTTTGGAATAAAAGTTTTC
AATAACCCCCTTAAAATTTTAGTAGTGGAATATTGAATGCCTTTTCTACTAAAAGATACCTTTAA
TAATCTCAAATAATTTTTAAAAGAAAATTATTGAAAGTATTTTTTCTAAAAAAATACCTTTAATA
ATTCTGTACAAAAATTATTGAAGGCGTATAATGCAAAAAACCC
Found at i:2426262 original size:140 final size:139
Alignment explanation
Indices: 2426024--2426281 Score: 358
Period size: 140 Copynumber: 1.8 Consensus size: 139
2426014 AAATTAACAA
* * *
2426024 TTATTATTCTATTTTAATAGTTTTGATAGTTTCAATACATGATATTAAACTTATTGAAAGTATTA
1 TTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAAACTTATTGAAAG-ATTA
* *
2426089 AACTTAGTTGCCATGGTTGATATGTATAAAAAAGTTATTGTTTATGTCTATTTAGGTAAAAATAC
65 AACTTAGTTGCCACGGTTGATATGTATAAAAAAGTTATCGTTTATGTCTATTTAGGTAAAAATAC
2426154 AAATTTGCTG
130 AAATTTGCTG
* *
2426164 TTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACTTGATATTAAACTTATTCGATTA-ATT
1 TTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAAACTTATT-GA-AAGATT
* * * * *
2426228 GAACTTTGTCT-CTACGGTTGATATGTGTGAAAAAGTTATCGTTTATGTCTATTT
64 AAACTTAGT-TGCCACGGTTGATATGTATAAAAAAGTTATCGTTTATGTCTATTT
2426282 GGGACTATTT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
140 99 0.96
141 3 0.03
142 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (139 bp):
TTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAAACTTATTGAAAGATTAA
ACTTAGTTGCCACGGTTGATATGTATAAAAAAGTTATCGTTTATGTCTATTTAGGTAAAAATACA
AATTTGCTG
Found at i:2428155 original size:3 final size:3
Alignment explanation
Indices: 2428149--2428342 Score: 150
Period size: 3 Copynumber: 69.0 Consensus size: 3
2428139 AAAAGAAGGA
2428149 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2428197 -AT GAT AAC AAT -AT AAT -AT ACT -AT GAGA- AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -A-AT AAT AAT AAT AAT AAT
* * * *
2428237 AAT AAT AAA AAT -AT AAT AAT -AT GAT AAT AAT -AC AAT -GT ACA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
2428278 AAT -AT AAT AAT -AT AGT -AT AGT -AT ACT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2428322 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
2428343 CACTGGTTAA
Statistics
Matches: 153, Mismatches: 19, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
2 25 0.16
3 127 0.83
5 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2428236 original size:52 final size:54
Alignment explanation
Indices: 2428174--2428286 Score: 142
Period size: 52 Copynumber: 2.1 Consensus size: 54
2428164 AATAATAATA
* * * *
2428174 ATAATAATAATAATAATAATAATATGATAACAAT-ATAAT-ATACTATG-AGAAAT
1 ATAAT-ATAATAATAATAAAAATATAATAA-AATGATAATAATACAATGTACAAAT
*
2428227 ATAATATAATAATAATAAAAATATAATAATATGATAATAATACAATGTACAAAT
1 ATAATATAATAATAATAAAAATATAATAAAATGATAATAATACAATGTACAAAT
2428281 ATAATA
1 ATAATA
2428287 ATATAGTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
51 2 0.04
52 27 0.52
53 12 0.23
54 11 0.21
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (54 bp):
ATAATATAATAATAATAAAAATATAATAAAATGATAATAATACAATGTACAAAT
Found at i:2429090 original size:6 final size:6
Alignment explanation
Indices: 2429079--2429106 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2429069 TTAACAAAAT
2429079 ATATTA ATATTA ATATTA ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATAT
2429107 ACTCTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:2435759 original size:6 final size:6
Alignment explanation
Indices: 2435748--2435779 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2435738 ACATCCTTCG
*
2435748 AAAATC AAAATC AAAATC AAAATC AAAGTC AA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AA
2435780 CTATATATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAATC
Found at i:2438214 original size:15 final size:14
Alignment explanation
Indices: 2438171--2438222 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
2438161 TCCGGTTTAG
2438171 TTTTT-TTTTAATT
1 TTTTTATTTTAATT
2438184 TTTTTATATATT-ATT
1 TTTTTAT-T-TTAATT
2438199 TTTGTTATTTTAATT
1 TTT-TTATTTTAATT
2438214 TTTATTATT
1 TTT-TTATT
2438223 AACATTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 5 0.15
14 3 0.09
15 19 0.58
16 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTAATT
Found at i:2441112 original size:9 final size:9
Alignment explanation
Indices: 2441098--2441125 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2441088 TTGAATGGAT
2441098 GATGCCTTG
1 GATGCCTTG
2441107 GATGCCTTG
1 GATGCCTTG
2441116 GATGCCTTG
1 GATGCCTTG
2441125 G
1 G
2441126 GTGTTCCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (9 bp):
GATGCCTTG
Found at i:2445048 original size:22 final size:22
Alignment explanation
Indices: 2445019--2445066 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2445009 AGTCACACCA
2445019 TAAT-GCTCTATTGAAAGTGCT
1 TAATCGCTCTATTGAAAGTGCT
2445040 TAATCGCTCTATTGAAAGTGCT
1 TAATCGCTCTATTGAAAGTGCT
2445062 TAATC
1 TAATC
2445067 AAGTATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (22 bp):
TAATCGCTCTATTGAAAGTGCT
Found at i:2449864 original size:11 final size:11
Alignment explanation
Indices: 2449848--2449879 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2449838 TATTTTACTT
2449848 AAAAAAAAAGA
1 AAAAAAAAAGA
2449859 AAAAAAAAAGA
1 AAAAAAAAAGA
2449870 AAAAAGAAAA
1 AAAAA-AAAA
2449880 ATGATGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:2450836 original size:50 final size:50
Alignment explanation
Indices: 2450702--2451051 Score: 302
Period size: 50 Copynumber: 7.0 Consensus size: 50
2450692 TTAAGAACAT
* * * * * *
2450702 ATGAATTTTTAAAGTTATTAAGCCTCTGCTTAGAGGAGCTATTT-CAAGATG
1 ATGAA-TTTTAAAATTGTTGAGCCTCTACTTAGAAGAG-TTTTTCCAAGATG
*
2450753 ATGAATTTTTAAAATTGTTGAGCCTCTACTTAGATGAGTTTTTCCAAGATG
1 ATGAA-TTTTAAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCCAAGATG
** * * * *
2450804 ATGAATTTTAAAATTGTTGAGCCTCTGTTTAGAACAACTTTTT-TAAGATT
1 ATGAATTTTAAAATTGTTGAGCCTCTACTTAGAA-GAGTTTTTCCAAGATG
* * * * * **
2450854 TTAAAGTTGTT--GATTGTTGAGCTTCTACTTAAAAGAGTTTTTTTAAGATG
1 ATGAA-TT-TTAAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCCAAGATG
* * **
2450904 A-GATTTTTAAAATTGTTGAGCCTCTACCTAGAAGAACTTTTCCAAGATG
1 ATGAATTTTAAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCCAAGATG
* * *
2450953 ATGAATTTTAAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTTCTAAGATG
1 ATGAATTTTAAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCCAAGATG
* * * *
2451003 A-GATTTTTAAAATTATTGAGCCTCTGCTTA-AAGAAGCTTTT-CAAGATG
1 ATGAATTTTAAAATTGTTGAGCCTCTACTTAGAAG-AGTTTTTCCAAGATG
2451051 A
1 A
2451052 ATTTTTTAAG
Statistics
Matches: 246, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.01
48 12 0.05
49 71 0.29
50 106 0.43
51 53 0.22
52 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (50 bp):
ATGAATTTTAAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCCAAGATG
Found at i:2450944 original size:99 final size:98
Alignment explanation
Indices: 2450746--2451074 Score: 333
Period size: 99 Copynumber: 3.3 Consensus size: 98
2450736 GGAGCTATTT
* * * *
2450746 CAAGATGATGAATTTTTAAAATTGTTGAGCCTCTACTTAGATGAGTTTTTCCAAGATGATGAATT
1 CAAGATGAT-AAATTTT-AAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCTAAGATGA-GATTT
*** *
2450811 TTAAAATTGTTGAGCCTCTGTTTAGAACAACTTTTT
63 TTAAAATTGTTGAGCCTCTACCTAGAACAACTTTTC
* ** * * * *
2450847 TAAGATTTTAAAGTTGTT-GATTGTTGAGCTTCTACTTAAAAGAGTTTTTTTAAGATGAGATTTT
1 CAAGATGATAAA-TT-TTAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCTAAGATGAGATTTT
*
2450911 TAAAATTGTTGAGCCTCTACCTAGAAGAACTTTTC
64 TAAAATTGTTGAGCCTCTACCTAGAACAACTTTTC
* *
2450946 CAAGATGATGAATTTTAAAGTTGTTGAGCCTCTACTTAGAAGAGCTTTTCTAAGATGAGATTTTT
1 CAAGATGATAAATTTTAAA-TTGTTGAGCCTCTACTTAGAAGAGTTTTTCTAAGATGAGATTTTT
* * * *
2451011 AAAATTATTGAGCCTCTGCTTA-AAGAAGCTTTT-
65 AAAATTGTTGAGCCTCTACCTAGAACAA-CTTTTC
** * *
2451044 CAAGATGA-ATTTTTTAAGTTATTGAGCCTCT
1 CAAGATGATAAATTTTAAATTGTTGAGCCTCT
2451075 TTTTAGAGGA
Statistics
Matches: 190, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
96 12 0.06
97 8 0.04
98 16 0.08
99 108 0.57
100 36 0.19
101 8 0.04
102 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (98 bp):
CAAGATGATAAATTTTAAATTGTTGAGCCTCTACTTAGAAGAGTTTTTCTAAGATGAGATTTTTA
AAATTGTTGAGCCTCTACCTAGAACAACTTTTC
Found at i:2451356 original size:11 final size:10
Alignment explanation
Indices: 2451329--2451363 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2451319 TATTATACTA
*
2451329 TTTTTTCTTC
1 TTTTTTTTTC
2451339 ATTTTTTTTTC
1 -TTTTTTTTTC
2451350 TTTTTTTTTC
1 TTTTTTTTTC
2451360 TTTT
1 TTTT
2451364 CTGGGTCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Done.