Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 15 of 29
Found at i:5312068 original size:16 final size:17
Alignment explanation
Indices: 5312032--5312070 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5312022 AACTAAAGTA
5312032 TATAAATAATATTATAT
1 TATAAATAATATTATAT
5312049 TATAAAGTAATA-TA-AT
1 TATAAA-TAATATTATAT
5312065 TATAAA
1 TATAAA
5312071 ATTACATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAAATAATATTATAT
Found at i:5313241 original size:26 final size:26
Alignment explanation
Indices: 5313205--5313257 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
5313195 ACTTGTGAGA
5313205 AACATGAGTTTTTTAAAA-CGATTAGG
1 AACATGAG-TTTTTAAAAGCGATTAGG
5313231 AACATGAGTTTTTAAAAGCGATTAGG
1 AACATGAGTTTTTAAAAGCGATTAGG
5313257 A
1 A
5313258 TGATTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (26 bp):
AACATGAGTTTTTAAAAGCGATTAGG
Found at i:5318016 original size:8 final size:8
Alignment explanation
Indices: 5318005--5318052 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
5317995 AAAGGAAAAA
*
5318005 ATGTGTGT
1 ATGTATGT
*
5318013 ATGTGTGT
1 ATGTATGT
5318021 ACATGTATGT
1 A--TGTATGT
5318031 ATGTATGT
1 ATGTATGT
5318039 ATGTATGT
1 ATGTATGT
5318047 ATGTAT
1 ATGTAT
5318053 CAAATTCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 30 0.81
10 7 0.19
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (8 bp):
ATGTATGT
Found at i:5318032 original size:4 final size:4
Alignment explanation
Indices: 5318023--5318052 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
5318013 ATGTGTGTAC
5318023 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
5318053 CAAATTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5322549 original size:3 final size:3
Alignment explanation
Indices: 5322541--5322571 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5322531 CTCTGTTAGC
5322541 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5322572 TATTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5329161 original size:2 final size:2
Alignment explanation
Indices: 5329154--5329179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5329144 ATTGGAAGTA
5329154 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5329180 GTATGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5330227 original size:2 final size:2
Alignment explanation
Indices: 5330220--5330254 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5330210 TGTGTTCATC
5330220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5330255 AAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5338625 original size:2 final size:2
Alignment explanation
Indices: 5338607--5338645 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5338597 CGGATAAGAG
* *
5338607 TA TA AA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5338646 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5346889 original size:6 final size:6
Alignment explanation
Indices: 5346880--5346913 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5346870 AGAGAGATAG
5346880 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
5346914 AGAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:5347258 original size:6 final size:6
Alignment explanation
Indices: 5347239--5347272 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5347229 ATTTCCATAA
*
5347239 CCTTCT CCTCCT CCTTCT CCTTCT CCTTCT CCTT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTT
5347273 TTGGATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CCTTCT
Found at i:5353567 original size:13 final size:14
Alignment explanation
Indices: 5353549--5353606 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
5353539 AATAAAAAAT
5353549 TAAATTTTTTA-AA
1 TAAATTTTTTACAA
**
5353562 TAAATTTTACACAA
1 TAAATTTTTTACAA
* *
5353576 AAAATTTATTTATAA
1 TAAATTT-TTTACAA
5353591 TAAATTATTTTACAA
1 TAAATT-TTTTACAA
5353606 T
1 T
5353607 TATCAAATGG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 9 0.26
14 8 0.24
15 16 0.47
16 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTTTTACAA
Found at i:5360454 original size:333 final size:334
Alignment explanation
Indices: 5359712--5360707 Score: 1692
Period size: 333 Copynumber: 3.0 Consensus size: 334
5359702 ATTTCACAGG
*
5359712 ATTCTATGTTTGATTTCGATGTAAAGACTTAATTTCTTTATTCATAGTAGTAAGCCACTAAGAAG
1 ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTCTTTATTCATAGTAGTAAGCCACTAAGAAG
** *
5359777 ACTAGACACAAAGAATTACCTCACGATAAGAGTAAGGCTCATTAGTC-CTTTTACTTCTTCAACC
66 ACTAGACACATGGAATTGCCTCACGATAAGAGTAAGGCTCATTAGTCTC-TTTACTTCTTCAACC
**
5359841 ACTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATTGTCATATTGAGGTGT
130 ACTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGT
*
5359906 TTTTAAATTCTTTCTTGGTCTGTCTGTAGCAATGCTTCATTGTTGTATATGAAGTATTGATTCTT
195 TTTTAAATTCTTTCTTGGTCTGTCTGTAACAATGCTTCATTGTTGTATATGAAGTATTGATTCTT
** *
5359971 ACACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATT-TCTAGAGCTTTAACTTC
260 GTACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATTCT-TGGAGCTTTAACTTC
5360035 AAGCTCCACTT
324 AAGCTCCACTT
5360046 ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTCTTTATTCATAGTAGTAAGCCACTAAGAAG
1 ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTCTTTATTCATAGTAGTAAGCCACTAAGAAG
* *
5360111 ACTAGACACATGGAATTGCCTCATGATAAGAGTAAGGCTCATTAATCTCTTTACTTCTTCAACCA
66 ACTAGACACATGGAATTGCCTCACGATAAGAGTAAGGCTCATTAGTCTCTTTACTTCTTCAACCA
*
5360176 TTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGTT
131 CTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGTT
* * * * *
5360241 TTTAAATTCTTTCTTGGTCTGTCTATAACGATGC-TCATTGTTATATATGAAGCATTGATTTTTG
196 TTTAAATTCTTTCTTGGTCTGTCTGTAACAATGCTTCATTGTTGTATATGAAGTATTGATTCTTG
5360305 TACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATTCTTGGAGCTTTAACTTCAA
261 TACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATTCTTGGAGCTTTAACTTCAA
5360370 GCTCCACTT
326 GCTCCACTT
* * *
5360379 ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTATTTATTTATAATAGTAAGCCACTAAGAAG
1 ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTCTTTATTCATAGTAGTAAGCCACTAAGAAG
* *
5360444 ACCAGACACATGAAATTGCCTCACGATAAGAGTAAGGCTCATTAGTCTCTTTACTTCTTCAACCA
66 ACTAGACACATGGAATTGCCTCACGATAAGAGTAAGGCTCATTAGTCTCTTTACTTCTTCAACCA
*
5360509 CTGATAAAATTTAGGAATCATAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGTT
131 CTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGTT
5360574 TTTAAATTCTTTCTTGGTCTGTCTGTAACAATGCTTCATTGTTGTATATGAAGTATTGATTCTTG
196 TTTAAATTCTTTCTTGGTCTGTCTGTAACAATGCTTCATTGTTGTATATGAAGTATTGATTCTTG
* * * * *
5360639 TACCTCTTGTGATCCATTTTGAATTTCATTATCATTGTGCTCTATTCTCGAAGCTTTAACGTCAA
261 TACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATTCTTGGAGCTTTAACTTCAA
5360704 GCTC
326 GCTC
5360708 TATTAAATCT
Statistics
Matches: 622, Mismatches: 37, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
333 314 0.50
334 307 0.49
335 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (334 bp):
ATTCTATGTTTGATTTCGATGTAAAGACTTAATCTCTTTATTCATAGTAGTAAGCCACTAAGAAG
ACTAGACACATGGAATTGCCTCACGATAAGAGTAAGGCTCATTAGTCTCTTTACTTCTTCAACCA
CTGATAAAATTTAGGAATCAAAATCACCATTGACAAAAGTAATGAAATCATCATATTGAGGTGTT
TTTAAATTCTTTCTTGGTCTGTCTGTAACAATGCTTCATTGTTGTATATGAAGTATTGATTCTTG
TACCTCTTGTGATCCATTTTGAATTTCACTATCGTTGTGCTCTATTCTTGGAGCTTTAACTTCAA
GCTCCACTT
Found at i:5365437 original size:56 final size:57
Alignment explanation
Indices: 5365328--5365441 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 57
5365318 GACTAAAAGC
* *
5365328 ATTAACTACCCCAAAGTTTATTATTTCATGAAGGAAATAGCTAAAACTTGTTTTCCA
1 ATTAACTACCCCAAAGTCTATTATTTCATGAAGGAAATAGCTAAAACTAGTTTTCCA
* * **
5365385 ATTAATTACCCTAAAGTCT-TTATTTCATGAAGGGAAA-AGCTGGAACTAGTTTTCCA
1 ATTAACTACCCCAAAGTCTATTATTTCATGAA-GGAAATAGCTAAAACTAGTTTTCCA
5365441 A
1 A
5365442 AATTTTTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 29 0.58
57 21 0.42
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (57 bp):
ATTAACTACCCCAAAGTCTATTATTTCATGAAGGAAATAGCTAAAACTAGTTTTCCA
Found at i:5366667 original size:2 final size:2
Alignment explanation
Indices: 5366660--5366689 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5366650 TCACCCTAAT
*
5366660 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5366690 ACCAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5367623 original size:32 final size:31
Alignment explanation
Indices: 5367546--5367638 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
5367536 TATCATGTGT
* *
5367546 AATAATA--TTTTCTCAACATGGCGTGTAAC
1 AATAATATTTTTTTTCAACATGACGTGTAAC
5367575 AATAATATTTTTTTTCAACATGACGTGTAAC
1 AATAATATTTTTTTTCAACATGACGTGTAAC
5367606 AATAATATTTTTTTTTCAACATGACGTGTAAC
1 AATAATA-TTTTTTTTCAACATGACGTGTAAC
5367638 A
1 A
5367639 TCTTTTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 7 0.12
31 27 0.46
32 25 0.42
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (31 bp):
AATAATATTTTTTTTCAACATGACGTGTAAC
Found at i:5367903 original size:12 final size:13
Alignment explanation
Indices: 5367886--5367920 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5367876 AAAAATAATT
5367886 AAAATTATT-TTA
1 AAAATTATTATTA
5367898 AAAATTATTATTA
1 AAAATTATTATTA
5367911 AAAA-TATTAT
1 AAAATTATTAT
5367921 ATCTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTATTATTA
Found at i:5367909 original size:15 final size:14
Alignment explanation
Indices: 5367891--5367945 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
5367881 TAATTAAAAT
5367891 TATTTTAAAAATTA
1 TATTTTAAAAATTA
*
5367905 T-TATTAAAAATATTA
1 TAT-TTTAAAA-ATTA
*
5367920 TATCTTTAAAAGTTA
1 TAT-TTTAAAAATTA
5367935 T-TTTTAAAAAT
1 TATTTTAAAAAT
5367946 ACTTCATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 9 0.27
14 8 0.24
15 9 0.27
16 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
TATTTTAAAAATTA
Found at i:5371795 original size:27 final size:27
Alignment explanation
Indices: 5371735--5371810 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
5371725 TTATATTTAA
5371735 TTTTAATTATAAAATATTTTAAAATAT
1 TTTTAATTATAAAATATTTTAAAATAT
** *
5371762 TAATAATTTTAATATATATTTT-AAAT-T
1 TTTTAATTATAA-A-ATATTTTAAAATAT
* *
5371789 TTTTAATAATAAATATAGTTTA
1 TTTTAATTATAAA-ATATTTTA
5371811 GATAGGTAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
26 8 0.21
27 18 0.47
28 5 0.13
29 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TTTTAATTATAAAATATTTTAAAATAT
Found at i:5374410 original size:41 final size:41
Alignment explanation
Indices: 5374324--5374402 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
5374314 AGAAAATCCC
* * * *
5374324 AACATACACTATCATATGCCTTTTTAAAATCCACCTTTAAT
1 AACATAAACTATCATATGCCTTCTCAAAATCCACATTTAAT
5374365 AACATAAACTATCATATGCCTTCTCAAAATCCACATTT
1 AACATAAACTATCATATGCCTTCTCAAAATCCACATTT
5374403 CGTAACATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (41 bp):
AACATAAACTATCATATGCCTTCTCAAAATCCACATTTAAT
Found at i:5381159 original size:19 final size:19
Alignment explanation
Indices: 5381123--5381172 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
5381113 AATTTTGAAC
*
5381123 TTTTATT-TGTTATATTTG
1 TTTTATTATTTTATATTTG
5381141 ATTTTATTATTTTAT-TTTG
1 -TTTTATTATTTTATATTTG
*
5381160 TTATAATTATTTT
1 TT-TTATTATTTT
5381173 TATAACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 20 0.74
20 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTTATATTTG
Found at i:5392268 original size:2 final size:2
Alignment explanation
Indices: 5392261--5392285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5392251 CATAAATTCA
5392261 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5392286 TAAGGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5397065 original size:20 final size:21
Alignment explanation
Indices: 5397026--5397075 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
5397016 AATAAAAGAA
*
5397026 TAAAAATTTATTTAAAATTTTT
1 TAAAAA-TAATTTAAAATTTTT
5397048 TAAAAATAATTT-AAATTTTT
1 TAAAAATAATTTAAAATTTTT
5397068 TAAAAATA
1 TAAAAATA
5397076 TTATATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 16 0.59
21 5 0.19
22 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAATAATTTAAAATTTTT
Found at i:5397074 original size:11 final size:11
Alignment explanation
Indices: 5397026--5397074 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
5397016 AATAAAAGAA
5397026 TAAAAATTTATT
1 TAAAAATTT-TT
5397038 T-AAAATTTTT
1 TAAAAATTTTT
**
5397048 TAAAAATAATT
1 TAAAAATTTTT
5397059 T--AAATTTTT
1 TAAAAATTTTT
5397068 TAAAAAT
1 TAAAAAT
5397075 ATTATATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
9 7 0.23
10 3 0.10
11 19 0.63
12 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAAAAATTTTT
Found at i:5397319 original size:10 final size:10
Alignment explanation
Indices: 5397304--5397329 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5397294 ATTGTTTTGC
5397304 AATAAAGGAA
1 AATAAAGGAA
5397314 AATAAAGGAA
1 AATAAAGGAA
5397324 AATAAA
1 AATAAA
5397330 ACTTATGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (10 bp):
AATAAAGGAA
Found at i:5398406 original size:107 final size:107
Alignment explanation
Indices: 5398216--5398424 Score: 303
Period size: 107 Copynumber: 2.0 Consensus size: 107
5398206 TAAAATAATT
* * *
5398216 AAATATATTGATTTAGTTACAACTTTCACAATTTATAAATACACATTTTTTTGAAATTATTCAAT
1 AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACACTCTTTTGAAATTATTCAAT
* * **
5398281 TTTTACCTAATTTACTTTTTCTTGAAATTGACTCAAATTAGC
66 CTTTACCCAATTTACTTTTGATTGAAATTGACTCAAATTAGC
* *
5398323 AAATATGTTGATTTAGTTACAACTTTCACAATTTACAAATACACACTCTTTTGCAATTATTCAA-
1 AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACACTCTTTTGAAATTATTCAAT
* *
5398387 CTTTACCCAATTTACCTTTTGATTTAAATTTACTCAAA
66 CTTTACCCAATTTA-CTTTTGATTGAAATTGACTCAAA
5398425 ATTTCTTATA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 12 0.13
107 78 0.87
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (107 bp):
AAATATATTGATTTAGTTACAACTTTCACAATTTACAAATACACACTCTTTTGAAATTATTCAAT
CTTTACCCAATTTACTTTTGATTGAAATTGACTCAAATTAGC
Found at i:5409151 original size:8 final size:8
Alignment explanation
Indices: 5409140--5409175 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5409130 TGTATTAATA
5409140 AATTATAG
1 AATTATAG
5409148 AATTATAG
1 AATTATAG
*
5409156 AATTATTG
1 AATTATAG
*
5409164 ATTTATAG
1 AATTATAG
5409172 AATT
1 AATT
5409176 GTGAATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (8 bp):
AATTATAG
Found at i:5409920 original size:33 final size:32
Alignment explanation
Indices: 5409876--5409959 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
5409866 TTAAGATCAC
*
5409876 ATAT-TTTATTTTTATTTCTTATTATAATCTT
1 ATATATTTATTTTTATTTCTTAATATAATCTT
*
5409907 ATATATATTATTTTTATTTCTTAATATAATTTT
1 ATATAT-TTATTTTTATTTCTTAATATAATCTT
*
5409940 TTATATTATATATTTTATTT
1 ATATATT-TAT-TTTTATTT
5409960 TATTTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.09
32 2 0.04
33 32 0.70
34 8 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (32 bp):
ATATATTTATTTTTATTTCTTAATATAATCTT
Found at i:5409946 original size:22 final size:22
Alignment explanation
Indices: 5409903--5409964 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
5409893 CTTATTATAA
5409903 TCTTATATATATTATTTTTATT
1 TCTTATATATATTATTTTTATT
*
5409925 TCTTA-ATATA--ATTTTT-TA
1 TCTTATATATATTATTTTTATT
* *
5409943 TATTATATATTTTA-TTTTATT
1 TCTTATATATATTATTTTTATT
5409964 T
1 T
5409965 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
18 5 0.16
19 10 0.31
20 4 0.12
21 8 0.25
22 5 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (22 bp):
TCTTATATATATTATTTTTATT
Found at i:5410458 original size:2 final size:2
Alignment explanation
Indices: 5410451--5410479 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5410441 ATAAATAGTA
5410451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5410480 AAGTGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5426927 original size:34 final size:35
Alignment explanation
Indices: 5426884--5426949 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5426874 ACCTGTAATG
*
5426884 TTATTTAAGTT-AT-TGTTTAGATATTTATTTTTAA
1 TTATTTAAGTTGATAT-TTGAGATATTTATTTTTAA
5426918 TTATTTAAGTTGATATTTGAGATATTTATTTT
1 TTATTTAAGTTGATATTTGAGATATTTATTTT
5426950 CGACTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 11 0.38
35 17 0.59
36 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (35 bp):
TTATTTAAGTTGATATTTGAGATATTTATTTTTAA
Found at i:5426958 original size:35 final size:34
Alignment explanation
Indices: 5426885--5426960 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
5426875 CCTGTAATGT
* * *
5426885 TATTTAAGTTATTGTTTAGATATTTATTTTTAAT
1 TATTTAAGTTATTGTTGAGATATTTATTTTCAAC
*
5426919 TATTTAAGTTGATAT-TTGAGATATTTATTTTCGAC
1 TATTTAAGTT-AT-TGTTGAGATATTTATTTTCAAC
5426954 TATTTAA
1 TATTTAA
5426961 ATTTAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 10 0.28
35 25 0.69
36 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.57
Consensus pattern (34 bp):
TATTTAAGTTATTGTTGAGATATTTATTTTCAAC
Found at i:5431778 original size:16 final size:16
Alignment explanation
Indices: 5431757--5431789 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5431747 TAATTGAATT
5431757 TTTTTTAAAAACCATA
1 TTTTTTAAAAACCATA
*
5431773 TTTTTTAAAAACTATA
1 TTTTTTAAAAACCATA
5431789 T
1 T
5431790 CAATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTTAAAAACCATA
Found at i:5432457 original size:22 final size:20
Alignment explanation
Indices: 5432432--5432478 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
5432422 GATTTCAATG
*
5432432 TTTTCCCCTCAATCATTTTAGC
1 TTTTCCCCTCAA-CAATTT-GC
*
5432454 TTTTTCCCTCAACAATTTGC
1 TTTTCCCCTCAACAATTTGC
5432474 TTTTC
1 TTTTC
5432479 ATTTTCGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.17, C:0.30, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTCCCCTCAACAATTTGC
Found at i:5437648 original size:3 final size:3
Alignment explanation
Indices: 5437636--5437666 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5437626 CACACTACCC
5437636 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5437667 CTTTAATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5437969 original size:17 final size:17
Alignment explanation
Indices: 5437947--5437980 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5437937 CCTTTGAAAA
5437947 AAAAATAAAGATAGATT
1 AAAAATAAAGATAGATT
*
5437964 AAAAATAAGGATAGATT
1 AAAAATAAAGATAGATT
5437981 TAGGATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
AAAAATAAAGATAGATT
Found at i:5438629 original size:15 final size:15
Alignment explanation
Indices: 5438609--5438660 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
5438599 AGTTACTTTC
5438609 TCAATAATCATATTT
1 TCAATAATCATATTT
*
5438624 TCAATAATCACATTT
1 TCAATAATCATATTT
*
5438639 TCTATAATCATATTT
1 TCAATAATCATATTT
*
5438654 CCAATAA
1 TCAATAA
5438661 AATATCAAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (15 bp):
TCAATAATCATATTT
Found at i:5442173 original size:2 final size:2
Alignment explanation
Indices: 5442166--5442190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5442156 TTTACAGCAA
5442166 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5442191 AAAGAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5453018 original size:21 final size:20
Alignment explanation
Indices: 5452992--5453033 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5452982 TAATTTAAAA
5452992 TAAAATAACATAAAATTTAAC
1 TAAAATAAC-TAAAATTTAAC
*
5453013 TAAAATAACTTAAA-TTAAC
1 TAAAATAACTAAAATTTAAC
5453032 TA
1 TA
5453034 CTCAACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATAACTAAAATTTAAC
Found at i:5459408 original size:6 final size:5
Alignment explanation
Indices: 5459366--5459411 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
5459356 CTATTTTGTG
*
5459366 TTATT TTATT TTATT TCATT TT-TAT TTATT TTATT TTACTT TTATT
1 TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTA-TT TTATT
5459412 CTTTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 1 0.03
5 29 0.81
6 6 0.17
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:5459408 original size:20 final size:20
Alignment explanation
Indices: 5459370--5459411 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5459360 TTTGTGTTAT
*
5459370 TTTATTTTATTTCATTTTTA
1 TTTATTTTATTTCACTTTTA
*
5459390 TTTATTTTATTTTACTTTTA
1 TTTATTTTATTTCACTTTTA
5459410 TT
1 TT
5459412 CTTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTTATTTCACTTTTA
Found at i:5460659 original size:17 final size:17
Alignment explanation
Indices: 5460628--5460664 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5460618 ATATTAAGTG
5460628 AAATAAGAAAAAAATAT
1 AAATAAGAAAAAAATAT
*
5460645 AAAT-AGAAAATAA-AT
1 AAATAAGAAAAAAATAT
5460660 AAATA
1 AAATA
5460665 TTTAAGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAATAAGAAAAAAATAT
Found at i:5464161 original size:8 final size:10
Alignment explanation
Indices: 5464132--5464168 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5464122 TATTATTAAT
5464132 TATATTAAAAA
1 TATA-TAAAAA
5464143 TATATAAAAA
1 TATATAAAAA
5464153 T-TA-AAAAA
1 TATATAAAAA
5464161 TATATAAA
1 TATATAAA
5464169 GTCAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.25
9 4 0.17
10 10 0.42
11 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:5465024 original size:30 final size:30
Alignment explanation
Indices: 5464984--5465043 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5464974 CAAGAAGTTA
* *
5464984 ATGAAGAGATTCAAAATGATTATAGAAATC
1 ATGAAAAGATTCAAAATGATCATAGAAATC
5465014 ATGAAAAGATTCAAAATGATCATAGAAATC
1 ATGAAAAGATTCAAAATGATCATAGAAATC
5465044 CTGATGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (30 bp):
ATGAAAAGATTCAAAATGATCATAGAAATC
Found at i:5466353 original size:41 final size:41
Alignment explanation
Indices: 5466303--5466385 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
5466293 CAAACACATT
*
5466303 GGTAAAGTCGTATTCAAAGTGTTAAAGCAATAAGATTCCAA
1 GGTAAAGTCGTATTAAAAGTGTTAAAGCAATAAGATTCCAA
* *
5466344 GGTAGAGTCGTATTAAAAGTGTTAAAGTAATAAGATTCCAA
1 GGTAAAGTCGTATTAAAAGTGTTAAAGCAATAAGATTCCAA
5466385 G
1 G
5466386 CTCCACGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (41 bp):
GGTAAAGTCGTATTAAAAGTGTTAAAGCAATAAGATTCCAA
Found at i:5468966 original size:2 final size:2
Alignment explanation
Indices: 5468961--5468993 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5468951 TTAAATTCGT
*
5468961 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5468994 CACAGGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5486356 original size:21 final size:23
Alignment explanation
Indices: 5486317--5486360 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5486307 TAGATTTGAG
5486317 TTTAAATTGAGTATAAATTTATT
1 TTTAAATTGAGTATAAATTTATT
*
5486340 TTTAAA-T-AGTATTAATTTATT
1 TTTAAATTGAGTATAAATTTATT
5486361 AGTATATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTAAATTGAGTATAAATTTATT
Found at i:5488623 original size:19 final size:18
Alignment explanation
Indices: 5488597--5488634 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5488587 TTATAAAAAA
5488597 TTATAAATATCATAATAT
1 TTATAAATATCATAATAT
*
5488615 TTATCAAATATTATAATAT
1 TTAT-AAATATCATAATAT
5488634 T
1 T
5488635 CAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATAAATATCATAATAT
Found at i:5496993 original size:19 final size:20
Alignment explanation
Indices: 5496971--5497013 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
5496961 TTTATTTATT
*
5496971 TATTATTTTTTTAGTTTTA-
1 TATTATTTTGTTAGTTTTAC
*
5496990 TATT-TTTTGTTGGTTTTAC
1 TATTATTTTGTTAGTTTTAC
5497009 TATTA
1 TATTA
5497014 CCAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (20 bp):
TATTATTTTGTTAGTTTTAC
Found at i:5498995 original size:22 final size:22
Alignment explanation
Indices: 5498967--5499030 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
5498957 TCAGATCTCC
*
5498967 CACAAACTAGTAGCAAATCACT
1 CACAAACCAGTAGCAAATCACT
* * **
5498989 CACAAACCAATACCAAATTTCT
1 CACAAACCAGTAGCAAATCACT
5499011 CACAAACCAGTAGCAAATCA
1 CACAAACCAGTAGCAAATCA
5499031 ACAGTAGATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.30, G:0.06, T:0.17
Consensus pattern (22 bp):
CACAAACCAGTAGCAAATCACT
Found at i:5500050 original size:33 final size:33
Alignment explanation
Indices: 5500012--5500074 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
5500002 ATCATACCAC
* *
5500012 ATCAGTATGTTACATAATTATCAGTTATGATAT
1 ATCAGTATGTCACATAATTATCAATTATGATAT
*
5500045 ATCAGTATGTCACATCATTATCAATTATGA
1 ATCAGTATGTCACATAATTATCAATTATGA
5500075 CATTTCAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (33 bp):
ATCAGTATGTCACATAATTATCAATTATGATAT
Found at i:5501793 original size:34 final size:35
Alignment explanation
Indices: 5501741--5501821 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
5501731 TACCTATAAT
* *
5501741 GTTGTTTAAATTGTTATTT-GGATATTTGTTTTTA
1 GTTGTTTAAATTGATATTTAAGATATTTGTTTTTA
*
5501775 GTTGTTTAAGTTGATATTTAAGATATTTGTTTTT-
1 GTTGTTTAAATTGATATTTAAGATATTTGTTTTTA
*
5501809 GATTATTTAAATT
1 G-TTGTTTAAATT
5501822 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 18 0.45
35 22 0.55
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (35 bp):
GTTGTTTAAATTGATATTTAAGATATTTGTTTTTA
Found at i:5516420 original size:23 final size:23
Alignment explanation
Indices: 5516394--5516517 Score: 171
Period size: 23 Copynumber: 5.5 Consensus size: 23
5516384 ACAATACCTA
5516394 AGTCACACAATGCCTTACTAACT
1 AGTCACACAATGCCTTACTAACT
* *
5516417 AGTCACGCAATGCCTTACTAACA
1 AGTCACACAATGCCTTACTAACT
*
5516440 AGTCACACAATGCC-TACCAACT
1 AGTCACACAATGCCTTACTAACT
* *
5516462 AGTCACGCAATGCCTTACTAACA
1 AGTCACACAATGCCTTACTAACT
*
5516485 AGTCACACAATGCC-TACCAACT
1 AGTCACACAATGCCTTACTAACT
*
5516507 AGTCACGCAAT
1 AGTCACACAAT
5516518 ACCTAAAAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
22 35 0.40
23 53 0.60
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.21
Consensus pattern (23 bp):
AGTCACACAATGCCTTACTAACT
Found at i:5516472 original size:22 final size:22
Alignment explanation
Indices: 5516394--5516601 Score: 181
Period size: 22 Copynumber: 9.4 Consensus size: 22
5516384 ACAATACCTA
* *
5516394 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCC-TACAAACT
* *
5516417 AGTCACGCAATGCCTTACTAACA
1 AGTCACGCAATGCC-TACAAACT
* *
5516440 AGTCACACAATGCCTACCAACT
1 AGTCACGCAATGCCTACAAACT
* *
5516462 AGTCACGCAATGCCTTACTAACA
1 AGTCACGCAATGCC-TACAAACT
* *
5516485 AGTCACACAATGCCTACCAACT
1 AGTCACGCAATGCCTACAAACT
* * *
5516507 AGTCACGCAATACCTAAAAATT
1 AGTCACGCAATGCCTACAAACT
*
5516529 AGTCACGCAATGCC--CAAAGT
1 AGTCACGCAATGCCTACAAACT
** *
5516549 CAGTCACATAATG--TACAAAGT
1 -AGTCACGCAATGCCTACAAACT
*
5516570 AAGTCACGCAATGCCTAAAAACT
1 -AGTCACGCAATGCCTACAAACT
5516593 AGTCACGCA
1 AGTCACGCA
5516602 GTACCCAAAA
Statistics
Matches: 153, Mismatches: 26, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
20 4 0.03
21 26 0.17
22 64 0.42
23 59 0.39
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.20
Consensus pattern (22 bp):
AGTCACGCAATGCCTACAAACT
Found at i:5516473 original size:45 final size:45
Alignment explanation
Indices: 5516393--5516517 Score: 232
Period size: 45 Copynumber: 2.8 Consensus size: 45
5516383 AACAATACCT
*
5516393 AAGTCACACAATGCCTTACTAACTAGTCACGCAATGCCTTACTAAC
1 AAGTCACACAATGCC-TACCAACTAGTCACGCAATGCCTTACTAAC
5516439 AAGTCACACAATGCCTACCAACTAGTCACGCAATGCCTTACTAAC
1 AAGTCACACAATGCCTACCAACTAGTCACGCAATGCCTTACTAAC
5516484 AAGTCACACAATGCCTACCAACTAGTCACGCAAT
1 AAGTCACACAATGCCTACCAACTAGTCACGCAAT
5516518 ACCTAAAAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
45 63 0.81
46 15 0.19
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (45 bp):
AAGTCACACAATGCCTACCAACTAGTCACGCAATGCCTTACTAAC
Found at i:5516555 original size:21 final size:21
Alignment explanation
Indices: 5516529--5516584 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
5516519 CCTAAAAATT
*
5516529 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCCAAAGTA
** **
5516550 AGTCACATAATGTACAAAGTA
1 AGTCACGCAATGCCCAAAGTA
5516571 AGTCACGCAATGCC
1 AGTCACGCAATGCC
5516585 TAAAAACTAG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18
Consensus pattern (21 bp):
AGTCACGCAATGCCCAAAGTA
Found at i:5516780 original size:62 final size:60
Alignment explanation
Indices: 5516711--5516836 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
5516701 CTACTTGACA
* *
5516711 AAAAATACTCAAAATAATTAAAACAGTTTTCTTCATATATCAAAAA-TAATTCCAAAATGCCT
1 AAAAATACTCAAAAT-ACTAAAA-AGTTTTCTTCATATATCAAAAACT-ACTCCAAAATGCCT
* * * * *
5516773 AAAAATACTTAAAATGCTCAAAGGTTTTCTTCATATATCAAAAACTACTCCAAAATGCTT
1 AAAAATACTCAAAATACTAAAAAGTTTTCTTCATATATCAAAAACTACTCCAAAATGCCT
5516833 AAAA
1 AAAA
5516837 TGCTTAAACA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 37 0.66
61 5 0.09
62 14 0.25
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (60 bp):
AAAAATACTCAAAATACTAAAAAGTTTTCTTCATATATCAAAAACTACTCCAAAATGCCT
Found at i:5521562 original size:29 final size:28
Alignment explanation
Indices: 5521523--5521583 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
5521513 ATCATATTCA
* *
5521523 ATTTAGTGCCAAACATATGCACTATATC
1 ATTTAGTGCCAAACATATGCACAACATC
* *
5521551 ATTTATGTGCCAAGCATCTGCACAACATC
1 ATTTA-GTGCCAAACATATGCACAACATC
5521580 ATTT
1 ATTT
5521584 GAGTTTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (28 bp):
ATTTAGTGCCAAACATATGCACAACATC
Found at i:5522232 original size:404 final size:408
Alignment explanation
Indices: 5521450--5522269 Score: 1206
Period size: 404 Copynumber: 2.0 Consensus size: 408
5521440 CATATACACC
*
5521450 AATTCTTATTCATGTTCTATGTCACATAGTATATCAATTAAGCATTGCATAATTTACATACATAT
1 AATTCTTATTCATGTTCTATGTCACATAGTATATCAATTAAACATTGCATAATTTACATACATAT
* * * * *
5521515 CATATTCAATTTAGTGCCAAACATATGCACTATATCATTTATGTGCCAAGCATCTGCACAACATC
66 CATATTCAATTTAATGCCAAACATATGCACTATATCATTCAAGCGCCAAGCATATGCACAACATC
* * *
5521580 ATTTGAGTTTTTACACACTCATATATCATATTCATATTCATTACTCTATGGACATAAGCATACCC
131 ATTTGAGCTTTTACACAC-CACATATCA-ATTCATATTCATTACTCTATAGACATAAGCATACCC
*
5521645 TTAAGCTTTTAAACATATACACCAAAGATTCAATGTAGTTTATCAATTGACCTAGTTCACCTTAC
194 TTAAGCTCTTAAACATATACACCAAAGATTCAATGTAGTTTATCAATTGACCTAGTTCACCTTAC
** * * * * *
5521710 ATAGTTCATATCGAAAATAGGAGGTGTTATAGCGATTGACTTAATCATCAATGGGGAAACTTTTG
259 ATAGTTCATATAAAAAATAGGAGATGTTAAAGCGATTGACTCAATCATCAATGGAGAAACTTTTC
* * * * *
5521775 CTGCCAACACTGATTGAAGAACCCATTCTTTTTTTCTTTCTTTAACTTTTTATATACAAGAAAAA
324 CTGCCAACACCGATTGAAGAACCAATTCATTTTTTCTTTCTTAAACTTTTTATATACAAAAAAAA
*
5521840 TTACCTCTTTATCCCTCATT
389 TTACCTCTTTATCCCTCACT
* *
5521860 AATTCTTATTCATGTTCTATGTCACTTAGTATATCAATTAAACATTGCATAATTTACATACATCT
1 AATTCTTATTCATGTTCTATGTCACATAGTATATCAATTAAACATTGCATAATTTACATACATAT
5521925 CATATTCAATTTAATGCCAAACATATGCACTATATCATTCAAGCGCCAAGCATATGCACAACATC
66 CATATTCAATTTAATGCCAAACATATGCACTATATCATTCAAGCGCCAAGCATATGCACAACATC
5521990 ATTTGAGCTTTTACACA-CACATA-C-A-TCATATTCATTACTCTATAGACATAAGCATACCCTT
131 ATTTGAGCTTTTACACACCACATATCAATTCATATTCATTACTCTATAGACATAAGCATACCCTT
* * * * *
5522051 AAGCTCTTAAACATATACACTAAAGATTCAATTTAGTTTATCAATTGGCTTGGTTCACCTTACAT
196 AAGCTCTTAAACATATACACCAAAGATTCAATGTAGTTTATCAATTGACCTAGTTCACCTTACAT
**
5522116 AGTTCATATAAAAAATTA-GAGATGTTACAAG-GATTGACTCAATTGTCAATGGAGAAA-TTTTC
261 AGTTCATATAAAAAA-TAGGAGATGTTA-AAGCGATTGACTCAATCATCAATGGAGAAACTTTTC
**
5522178 CTTGCCAACACCGATTGAAGAACCAATTCATTTTTTCTTTTCTTAAAC-TTTTATATGTAAAAAA
324 C-TGCCAACACCGATTGAAGAACCAATTCATTTTTTC-TTTCTTAAACTTTTTATATACAAAAAA
* *
5522242 AATTATCTCTTTATCCTTCACT
387 AATTACCTCTTTATCCCTCACT
5522264 AATTCT
1 AATTCT
5522270 CTCCCCCCAC
Statistics
Matches: 370, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
403 5 0.01
404 207 0.56
405 14 0.04
407 1 0.00
408 5 0.01
410 138 0.37
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (408 bp):
AATTCTTATTCATGTTCTATGTCACATAGTATATCAATTAAACATTGCATAATTTACATACATAT
CATATTCAATTTAATGCCAAACATATGCACTATATCATTCAAGCGCCAAGCATATGCACAACATC
ATTTGAGCTTTTACACACCACATATCAATTCATATTCATTACTCTATAGACATAAGCATACCCTT
AAGCTCTTAAACATATACACCAAAGATTCAATGTAGTTTATCAATTGACCTAGTTCACCTTACAT
AGTTCATATAAAAAATAGGAGATGTTAAAGCGATTGACTCAATCATCAATGGAGAAACTTTTCCT
GCCAACACCGATTGAAGAACCAATTCATTTTTTCTTTCTTAAACTTTTTATATACAAAAAAAATT
ACCTCTTTATCCCTCACT
Found at i:5524580 original size:15 final size:15
Alignment explanation
Indices: 5524560--5524617 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
5524550 TCCCCACACA
5524560 TTTCCCTCCAAAAGT
1 TTTCCCTCCAAAAGT
*
5524575 TTTCCCTCC-AAAGCA
1 TTTCCCTCCAAAAG-T
*
5524590 TTTCCCTCAAAAAGT
1 TTTCCCTCCAAAAGT
5524605 TTTCCCTCCAAAA
1 TTTCCCTCCAAAA
5524618 CATTTGGGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.11
15 29 0.78
16 4 0.11
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.31
Consensus pattern (15 bp):
TTTCCCTCCAAAAGT
Found at i:5524592 original size:30 final size:30
Alignment explanation
Indices: 5524557--5524622 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
5524547 GGTTCCCCAC
*
5524557 ACATTTCCCTCCAAAAGTTTTCCCTCCAAA
1 ACATTTCCCTCAAAAAGTTTTCCCTCCAAA
*
5524587 GCATTTCCCTCAAAAAGTTTTCCCTCCAAA
1 ACATTTCCCTCAAAAAGTTTTCCCTCCAAA
5524617 ACATTT
1 ACATTT
5524623 GGGAGGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.32
Consensus pattern (30 bp):
ACATTTCCCTCAAAAAGTTTTCCCTCCAAA
Found at i:5524856 original size:15 final size:15
Alignment explanation
Indices: 5524836--5524892 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
5524826 GAGCCATTTT
*
5524836 GCGTGCCACGCATCC
1 GCGTGCCACGTATCC
*
5524851 GCGTGCCGCGTA-CC
1 GCGTGCCACGTATCC
5524865 TGCGTGCCACGTATCC
1 -GCGTGCCACGTATCC
5524881 GCGTGCCACGTA
1 GCGTGCCACGTA
5524893 CCTGCGCGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.40, G:0.30, T:0.18
Consensus pattern (15 bp):
GCGTGCCACGTATCC
Found at i:5524869 original size:30 final size:30
Alignment explanation
Indices: 5524835--5524898 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
5524825 CGAGCCATTT
*
5524835 TGCGTGCCACGCATCCGCGTGCCGCGTACC
1 TGCGTGCCACGCATCCGCGTGCCACGTACC
*
5524865 TGCGTGCCACGTATCCGCGTGCCACGTACC
1 TGCGTGCCACGCATCCGCGTGCCACGTACC
5524895 TGCG
1 TGCG
5524899 CGTCGCGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.41, G:0.30, T:0.19
Consensus pattern (30 bp):
TGCGTGCCACGCATCCGCGTGCCACGTACC
Found at i:5527627 original size:7 final size:7
Alignment explanation
Indices: 5527615--5527650 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
5527605 AGTTTTATAG
5527615 ACATTCA
1 ACATTCA
5527622 ACATTCA
1 ACATTCA
5527629 ACATTCA
1 ACATTCA
5527636 ACATTCA
1 ACATTCA
5527643 ACATTCA
1 ACATTCA
5527650 A
1 A
5527651 GCTTTTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATTCA
Found at i:5529102 original size:26 final size:26
Alignment explanation
Indices: 5529042--5529104 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
5529032 TCAAGTTCAC
5529042 GTGAAAAAAATACTGTTATATGTCAT
1 GTGAAAAAAATACTGTTATATGTCAT
* * *
5529068 GTCAGAAAAAAT-TTGTTATATGTTAT
1 GTGA-AAAAAATACTGTTATATGTCAT
5529094 GTTGAAAAAAA
1 G-TGAAAAAAA
5529105 AAGTTATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (26 bp):
GTGAAAAAAATACTGTTATATGTCAT
Found at i:5529190 original size:26 final size:26
Alignment explanation
Indices: 5529154--5529216 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
5529144 CACTATATTT
* * *
5529154 AAAAAGTTATTATGTATTATGATAAA
1 AAAAAATTATTATATATCATGATAAA
*
5529180 AAAAAATTATTATATATCATGTTAAA
1 AAAAAATTATTATATATCATGATAAA
5529206 AAAAAA-TATTA
1 AAAAAATTATTA
5529217 AACATCATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
AAAAAATTATTATATATCATGATAAA
Found at i:5529206 original size:25 final size:25
Alignment explanation
Indices: 5529154--5529239 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
5529144 CACTATATTT
* * * *
5529154 AAAAAGTTATTATGTATTATGATAAA
1 AAAAAATTATTATATATCATG-TTAA
5529180 AAAAAATTATTATATATCATGTTAA
1 AAAAAATTATTATATATCATGTTAA
* * * * *
5529205 AAAAAAATATTAAACATCATCTTGA
1 AAAAAATTATTATATATCATGTTAA
*
5529230 AAAATATTAT
1 AAAAAATTAT
5529240 AATCATCTCC
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 31 0.63
26 18 0.37
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (25 bp):
AAAAAATTATTATATATCATGTTAA
Found at i:5529244 original size:21 final size:22
Alignment explanation
Indices: 5529207--5529247 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5529197 CATGTTAAAA
5529207 AAAAATATTAAACATCATCTTG
1 AAAAATATTAAACATCATCTTG
*
5529229 AAAAATATTATA-ATCATCT
1 AAAAATATTAAACATCATCT
5529248 CCGAAAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATATTAAACATCATCTTG
Found at i:5529253 original size:22 final size:22
Alignment explanation
Indices: 5529207--5529253 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5529197 CATGTTAAAA
*
5529207 AAAAATATTAAACATCATCTTG
1 AAAAATATTAAACATCATCTCG
*
5529229 AAAAATATTATA-ATCATCTCCG
1 AAAAATATTAAACATCATCT-CG
5529251 AAA
1 AAA
5529254 GCCTTTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAATATTAAACATCATCTCG
Found at i:5536121 original size:14 final size:15
Alignment explanation
Indices: 5536102--5536132 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5536092 TTTTTTTGAT
5536102 AAAAACAA-ATAAGA
1 AAAAACAAGATAAGA
5536116 AAAAACAAGATAAGA
1 AAAAACAAGATAAGA
5536131 AA
1 AA
5536133 CAGTGCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.06
Consensus pattern (15 bp):
AAAAACAAGATAAGA
Found at i:5538461 original size:20 final size:21
Alignment explanation
Indices: 5538404--5538472 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
5538394 AAGCCCCCTA
* * *
5538404 CCTAAAACCAATTCACCCAAT
1 CCTAAAATCAATTCATCAAAT
5538425 CCTAAAATCAATTCATCAAAT
1 CCTAAAATCAATTCATCAAAT
* *
5538446 CCTCAAA-CAGTTCATCAAA-
1 CCTAAAATCAATTCATCAAAT
*
5538465 CCTTAAAT
1 CCTAAAAT
5538473 TGGTTTACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.15
20 11 0.27
21 24 0.59
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.25
Consensus pattern (21 bp):
CCTAAAATCAATTCATCAAAT
Found at i:5538526 original size:21 final size:21
Alignment explanation
Indices: 5538515--5538556 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5538505 CTCTAAAAGC
5538515 AATTCACCAAACCTTAAAACT
1 AATTCACCAAACCTTAAAACT
*
5538536 AATTCATCAAACCTTAAAACT
1 AATTCACCAAACCTTAAAACT
5538557 GGTTCCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTCACCAAACCTTAAAACT
Found at i:5538646 original size:20 final size:20
Alignment explanation
Indices: 5538565--5538658 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
5538555 CTGGTTCCCT
* *
5538565 AAATCCTAAACTAGGTTCAAG
1 AAATCCTAAA-TTGATTCAAG
* * *
5538586 AAATCCTAAAAATCAGCTCAA-
1 AAATCCT-AAATTGA-TTCAAG
* **
5538607 AAAGTCCTAACATTGTTTCACT
1 AAA-TCCTAA-ATTGATTCAAG
5538629 AAATCCTAAATTGATTCAAG
1 AAATCCTAAATTGATTCAAG
5538649 AAATCCTAAA
1 AAATCCTAAA
5538659 ACCAGTTCAA
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
20 18 0.33
21 21 0.38
22 16 0.29
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.27
Consensus pattern (20 bp):
AAATCCTAAATTGATTCAAG
Found at i:5538833 original size:21 final size:20
Alignment explanation
Indices: 5538809--5538853 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5538799 CCAATTTAAA
*
5538809 AAACCCCAAAACGAGTTCACC
1 AAACCACAAAACG-GTTCACC
* *
5538830 AAACCATAAAATGGTTCACC
1 AAACCACAAAACGGTTCACC
5538850 AAAC
1 AAAC
5538854 TCTAAGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.47, C:0.31, G:0.09, T:0.13
Consensus pattern (20 bp):
AAACCACAAAACGGTTCACC
Found at i:5548731 original size:28 final size:27
Alignment explanation
Indices: 5548699--5548752 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5548689 TTAATGTGTA
*
5548699 TTATAAATTTAA-TTATTTAATAATTTTT
1 TTATAAATATAACTT-TTTAAT-ATTTTT
5548727 TTATAAATATAACTTTTTAATATTTT
1 TTATAAATATAACTTTTTAATATTTT
5548753 ATTGATACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 17 0.71
29 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATAAATATAACTTTTTAATATTTTT
Found at i:5549243 original size:26 final size:26
Alignment explanation
Indices: 5549214--5549263 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5549204 TTTAAAAATG
5549214 TTAAA-ATTTTAATATAAAAATATATT
1 TTAAATATTTTAATA-AAAAATATATT
*
5549240 TTAAATATTTTAATAATAAATATA
1 TTAAATATTTTAATAAAAAATATA
5549264 CGGTTGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAATATTTTAATAAAAAATATATT
Found at i:5551424 original size:21 final size:21
Alignment explanation
Indices: 5551383--5551428 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5551373 TGAAGACATA
* *
5551383 ACCACCATGTATGACCGATTC
1 ACCACCATGTATAACCAATTC
*
5551404 ACCACCATGTATAATCAATTC
1 ACCACCATGTATAACCAATTC
5551425 ACCA
1 ACCA
5551429 ACATAGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (21 bp):
ACCACCATGTATAACCAATTC
Found at i:5551622 original size:3 final size:3
Alignment explanation
Indices: 5551614--5551656 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
5551604 CTAGAAATGA
* * *
5551614 AAG AAG AAG AAG AAT AAA AAG AAG ACG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5551657 GAATGAGGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:5551867 original size:27 final size:27
Alignment explanation
Indices: 5551835--5551889 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5551825 AGGATCAAGG
*
5551835 TTCCTTATGAAAGAATAAATACAAGAT
1 TTCCTTATGAAAGAATAAAGACAAGAT
*
5551862 TTCCTTATGAAAGAATATAGACAAGAT
1 TTCCTTATGAAAGAATAAAGACAAGAT
5551889 T
1 T
5551890 GACTTCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (27 bp):
TTCCTTATGAAAGAATAAAGACAAGAT
Found at i:5570985 original size:25 final size:26
Alignment explanation
Indices: 5570968--5571053 Score: 61
Period size: 30 Copynumber: 3.2 Consensus size: 26
5570958 ATATAAGAAT
5570968 AAAAATTAAA-ATAAAATAAAATATA
1 AAAAATTAAATATAAAATAAAATATA
* *
5570993 AAAAATTAATATTTATATAATATAGATA-A
1 AAAAATTAA-A--TATAAAATA-AAATATA
*
5571022 ACACAATTAAA-ATAAAATATATAATATA
1 A-AAAATTAAATATAAAATA-A-AATATA
5571050 AAAA
1 AAAA
5571054 TATATTAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 9 0.19
26 10 0.21
27 5 0.11
28 2 0.04
29 10 0.21
30 11 0.23
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (26 bp):
AAAAATTAAATATAAAATAAAATATA
Found at i:5571088 original size:8 final size:9
Alignment explanation
Indices: 5571033--5571335 Score: 71
Period size: 8 Copynumber: 34.2 Consensus size: 9
5571023 CACAATTAAA
5571033 ATAAAATAT
1 ATAAAATAT
5571042 AT--AATAT
1 ATAAAATAT
5571049 A-AAAATAT
1 ATAAAATAT
*
5571057 ATTAAAGAAAT
1 A-TAAA-ATAT
*
5571068 GAAAAAATAT
1 -ATAAAATAT
5571078 ATAAAAT-T
1 ATAAAATAT
*
5571086 ATAATAATAA
1 ATAA-AATAT
5571096 AT-AAA-A-
1 ATAAAATAT
5571102 ATAAAATAT
1 ATAAAATAT
* *
5571111 ATGACAT-T
1 ATAAAATAT
5571119 A-AAAATAT
1 ATAAAATAT
5571127 ATTTAAAATAT
1 A--TAAAATAT
**
5571138 GATATTATAT
1 -ATAAAATAT
5571148 A-AAAAT-T
1 ATAAAATAT
* *
5571155 AATAATATAA
1 -ATAAAATAT
5571165 ATATAAATAT
1 ATA-AAATAT
5571175 ATTAAAAATAAAT
1 A-T-AAAAT--AT
5571188 ATAAAATATT
1 ATAAAATA-T
*
5571198 ATAATAATAA
1 ATAA-AATAT
5571208 AT-AAA-A-
1 ATAAAATAT
5571214 ATAAAATAT
1 ATAAAATAT
* * *
5571223 AT-GACTTT
1 ATAAAATAT
5571231 A-AAAATAT
1 ATAAAATAT
*
5571239 ATTTAAATAT
1 A-TAAAATAT
**
5571249 GATATTATAT
1 -ATAAAATAT
5571259 A-AAAAT-T
1 ATAAAATAT
* *
5571266 AATAATATAA
1 -ATAAAATAT
5571276 ATATAAATAT
1 ATA-AAATAT
*
5571286 AT-TAA-A-
1 ATAAAATAT
5571292 ATAAAATAT
1 ATAAAATAT
5571301 A-AAAATAT
1 ATAAAATAT
*
5571309 ATAATAATAA
1 ATAA-AATAT
5571319 AT-AAA-A-
1 ATAAAATAT
5571325 ATAAAATAT
1 ATAAAATAT
5571334 AT
1 AT
5571336 GATATTAAAA
Statistics
Matches: 212, Mismatches: 37, Indels: 90
0.63 0.11 0.27
Matches are distributed among these distances:
6 8 0.04
7 26 0.12
8 51 0.24
9 43 0.20
10 49 0.23
11 28 0.13
12 4 0.02
13 3 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAATAT
Found at i:5571088 original size:10 final size:10
Alignment explanation
Indices: 5571045--5571439 Score: 66
Period size: 10 Copynumber: 39.1 Consensus size: 10
5571035 AAAATATATA
5571045 ATATAAAAAT
1 ATATAAAAAT
5571055 ATATTAAAGAA-
1 ATA-TAAA-AAT
5571066 ATGA-AAAAAT
1 AT-ATAAAAAT
5571076 ATAT-AAAAT
1 ATATAAAAAT
*
5571085 -TATAATAAT
1 ATATAAAAAT
*
5571094 AAATAAAAAT
1 ATATAAAAAT
*
5571104 A-A-AATATAT
1 ATATAA-AAAT
*
5571113 GACATTAAAAAT
1 -ATA-TAAAAAT
**
5571125 ATATTTAAA-
1 ATATAAAAAT
* * *
5571134 ATATGATATT
1 ATATAAAAAT
5571144 ATATAAAAAT
1 ATATAAAAAT
5571154 -TAATAATATAA-
1 AT-ATAA-A-AAT
*
5571165 ATATAAATAT
1 ATATAAAAAT
5571175 AT-TAAAAAT
1 ATATAAAAAT
*
5571184 AAATATAAAAT
1 ATATA-AAAAT
*
5571195 ATTATAATAAT
1 A-TATAAAAAT
*
5571206 AAATAAAAAT
1 ATATAAAAAT
*
5571216 A-A-AATATAT
1 ATATAA-AAAT
*
5571225 GACTTTAAAAAT
1 -A-TATAAAAAT
**
5571237 ATATTTAAAT
1 ATATAAAAAT
*
5571247 ATGAT---ATT
1 AT-ATAAAAAT
5571255 ATATAAAAAT
1 ATATAAAAAT
5571265 -TAATAATATAA-
1 AT-ATAA-A-AAT
*
5571276 ATATAAATAT
1 ATATAAAAAT
*
5571286 AT-TAAAATAAA
1 ATAT-AAA-AAT
5571297 ATATAAAAAT
1 ATATAAAAAT
*
5571307 ATATAATAAT
1 ATATAAAAAT
*
5571317 AAATAAAAAT
1 ATATAAAAAT
*
5571327 A-A-AATATAT
1 ATATAA-AAAT
5571336 GATATTAAAAAT
1 -ATA-TAAAAAT
* *
5571348 ATATTTAAGA-
1 ATA-TAAAAAT
* * *
5571358 A-ATGATATT
1 ATATAAAAAT
5571367 ATATAAAAAT
1 ATATAAAAAT
5571377 -TAATAATAAA-
1 AT-ATAA-AAAT
*
5571387 ATATAAATAT
1 ATATAAAAAT
5571397 AT-TAAAAAT
1 ATATAAAAAT
*
5571406 AAAATATAAAAT
1 -ATATA-AAAAT
*
5571418 ATTATAATAAT
1 A-TATAAAAAT
*
5571429 AAATAAAAAT
1 ATATAAAAAT
5571439 A
1 A
5571440 AAATATATGA
Statistics
Matches: 277, Mismatches: 55, Indels: 106
0.63 0.13 0.24
Matches are distributed among these distances:
7 2 0.01
8 15 0.05
9 52 0.19
10 112 0.40
11 60 0.22
12 30 0.11
13 6 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:5571101 original size:29 final size:32
Alignment explanation
Indices: 5571031--5571111 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
5571021 AACACAATTA
*
5571031 AAATAAAATATATAATATAAAAATATATTAAAG
1 AAATAAAA-ATATAATATAAAAATATAATAAAG
* *
5571064 AAATGAAAAA-AT-ATATAAAATTATAAT-AAT
1 AAAT-AAAAATATAATATAAAAATATAATAAAG
*
5571094 AAATAAAAATAAAATATA
1 AAATAAAAATATAATATA
5571112 TGACATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 5 0.12
30 7 0.17
31 18 0.44
32 2 0.05
33 5 0.12
34 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (32 bp):
AAATAAAAATATAATATAAAAATATAATAAAG
Found at i:5571134 original size:33 final size:31
Alignment explanation
Indices: 5571030--5571134 Score: 79
Period size: 33 Copynumber: 3.1 Consensus size: 31
5571020 AAACACAATT
*
5571030 AAAATAAAATATATAATATAAAAATATATTAA
1 AAAATAAAATATATAAT-TAAAAATATATTTA
*
5571062 AGAAATGAAAAAATATATAAAATTATAATAATA-A-ATA
1 A-AAAT---AAAATATAT--AATTA-AA-AATATATTTA
5571099 AAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATAT-A-ATTAAAAATATATTTA
5571132 AAA
1 AAA
5571135 TATGATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
31 4 0.07
32 5 0.09
33 22 0.38
36 13 0.22
37 4 0.07
38 6 0.10
39 4 0.07
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (31 bp):
AAAATAAAATATATAATTAAAAATATATTTA
Found at i:5571153 original size:69 final size:69
Alignment explanation
Indices: 5571030--5571496 Score: 188
Period size: 70 Copynumber: 6.9 Consensus size: 69
5571020 AAACACAATT
5571030 AAAATAAAATATATAATATAAAAATATATTAAAGAAATGAAAAAATATATAAAATT-ATAATAAT
1 AAAATAAAATATATAATATAAAAATATATTAAAGAAATGAAAAAATATATAAAATTAATAAT-AT
5571094 AAATA
65 AAATA
* * **
5571099 AAAATAAAATATATGACAT-TAAAAATATATTTAAA-ATATGATATTATATA-AAAATTAATAAT
1 AAAATAAAATATAT-A-ATATAAAAATATA-TTAAAGAAATGAAAAAATATATAAAATTAATAAT
5571161 ATAAATA
63 ATAAATA
* * * **
5571168 TAAATATATTAAAAATA-AATATAAAATATTATAATAATAAATAAA--AATAAAATATATGACTT
1 -AAA-ATA--AAATATATAATATAAAA-A-TAT-AT--TAAAGAAATGAA-AAAATATATAAAAT
* *
5571230 TAA-AA-ATATATT
56 TAATAATATAAATA
* ** * * *
5571242 TAAATATGATAT-T-ATATAAAAAT-TAATAATATAAAT--ATAAATATATTAAAA-TAA-AATA
1 AAAATAAAATATATAATATAAAAATATATTAA-AGAAATGAAAAAATATA-TAAAATTAATAATA
5571300 T-AA-A
64 TAAATA
* * * * * * * * * *
5571304 AATATATAATA-ATAA-ATAAAAATAAAATATATGATATTAAAAATATATTTAAGA--AATGATA
1 AAAATAAAATATATAATATAAAAATATATTA-AAGAAATGAAAAA-ATATATAAAATTAATAATA
*
5571365 TTATATA
64 -TAAATA
* * *
5571372 AAAAT-TAATA-ATAAAATATAAATATATT-AA-AAAT---AAAATATA-AAATATT-ATAATAA
1 AAAATAAAATATATAATATAAAAATATATTAAAGAAATGAAAAAATATATAAA-ATTAATAAT-A
5571428 TAAATA
64 TAAATA
* * * **
5571434 AAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATA-AAAATTAATAATA
1 AAAATAAAATATATAATA-TAAAAATATATTAAAGAAATGAAAAAATATATAAAATTAATAATA
5571497 AAAAATATAA
Statistics
Matches: 298, Mismatches: 53, Indels: 94
0.67 0.12 0.21
Matches are distributed among these distances:
60 2 0.01
61 5 0.02
62 34 0.11
63 29 0.10
64 17 0.06
65 25 0.08
66 9 0.03
67 15 0.05
68 16 0.05
69 39 0.13
70 49 0.16
71 16 0.05
72 4 0.01
73 12 0.04
74 7 0.02
75 12 0.04
76 7 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (69 bp):
AAAATAAAATATATAATATAAAAATATATTAAAGAAATGAAAAAATATATAAAATTAATAATATA
AATA
Found at i:5571169 original size:6 final size:6
Alignment explanation
Indices: 5571158--5571334 Score: 59
Period size: 6 Copynumber: 29.0 Consensus size: 6
5571148 AAAAATTAAT
*
5571158 AATATA AATATA AATAT- -AT-TA AAAATA AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
* * * * * * *
5571207 AATAAA AATA-A AATATA TGACTTTA AAAATA TATTTA AATAT- GATAT-
1 AATATA AATATA AATATA --AATATA AATATA AATATA AATATA AATATA
* * *
5571254 TATATA AAAATTAA TAATATA AATATA AATAT- ATTA-A AATA-A AATATAAA
1 AATATA AATA-T-A -AATATA AATATA AATATA AATATA AATATA AATAT--A
*
5571304 AATATA TAATAATA AATAAA AATA-A AATATA
1 AATATA -AAT-ATA AATATA AATATA AATATA
5571335 TGATATTAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 30 0.23
6 54 0.42
7 17 0.13
8 21 0.16
9 4 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:5571210 original size:112 final size:112
Alignment explanation
Indices: 5571071--5571516 Score: 758
Period size: 112 Copynumber: 4.0 Consensus size: 112
5571061 AAGAAATGAA
5571071 AAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAA-AA
1 AAAATATA-AAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
5571135 TATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
65 -ATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
* *
5571184 -AAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACTTTAAAAATATATTTAA-AT
1 AAAATATAAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
5571247 ATGATATTATATAAAAATTAATAATATAAATATAAATATATT-AAAAT
65 ATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
*
5571294 AAAATATAAAAATATATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA
1 AAAATATAAAAAT-TATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
5571359 ATGATATTATATAAAAATTAATAATA-AAATATAAATATATTAAAAAT
65 ATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
*
5571406 AAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA
1 AAAATATAAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
*
5571471 ATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
65 ATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTAAA
5571517 CTTATATTTT
Statistics
Matches: 320, Mismatches: 5, Indels: 15
0.94 0.01 0.04
Matches are distributed among these distances:
110 7 0.02
111 116 0.36
112 176 0.55
113 3 0.01
114 18 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (112 bp):
AAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAAA
TGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT
Found at i:5571325 original size:223 final size:225
Alignment explanation
Indices: 5571071--5571516 Score: 787
Period size: 223 Copynumber: 2.0 Consensus size: 225
5571061 AAGAAATGAA
5571071 AAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAA-AA
1 AAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
5571135 TATGATATTATATAAAAATTAATAATATAAATATAAATATATTAAAAAT-AAATATAAAATATTA
66 -ATGATATTATATAAAAATTAATAATA-AAATATAAATATATTAAAAATAAAATATAAAATATTA
*
5571199 TAATAATAAATAAAAATAAAATATATGACT-TTAAAAATATATTTAA-ATATGATATTATATAAA
129 TAATAATAAATAAAAATAAAATATATGA-TATTAAAAATATATTTAAGAAATGATATTATATAAA
*
5571262 AATTAATAAT-ATAAATATAAATATATTAAAAT
193 AATTAATAATAAAAAATATAAATATATTAAAAT
*
5571294 AAAATATA-AAAATATATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGA
1 AAAATATATAAAAT-TATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGA
5571358 AATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATATTAT
65 AATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATATTAT
5571423 AATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAA
130 AATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAA
5571488 TTAATAATAAAAAATATAAATATATTAAA
195 TTAATAATAAAAAATATAAATATATTAAA
5571517 CTTATATTTT
Statistics
Matches: 214, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
222 27 0.13
223 140 0.65
224 28 0.13
225 19 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (225 bp):
AAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAA
ATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATATTATA
ATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTATATAAAAAT
TAATAATAAAAAATATAAATATATTAAAAT
Found at i:5571488 original size:16 final size:15
Alignment explanation
Indices: 5571104--5571504 Score: 93
Period size: 13 Copynumber: 28.6 Consensus size: 15
5571094 AAATAAAAAT
* *
5571104 AAAATATATGACATTA
1 AAAATATATTATA-TA
5571120 AAAATATATT-TA-A
1 AAAATATATTATATA
*
5571133 AATATGATATTATATA
1 AAAAT-ATATTATATA
*
5571149 AAAAT-TAATA-ATA
1 AAAATATATTATATA
* *
5571162 TAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
5571179 AAAATA-A--ATAT-
1 AAAATATATTATATA
5571190 -AAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
5571204 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
* *
5571216 AAAATATATGACTTTA
1 AAAATATATTA-TATA
5571232 AAAATATA-T-T-TA
1 AAAATATATTATATA
*
5571244 AATATGATATTATATA
1 AAAAT-ATATTATATA
*
5571260 AAAAT-TAATA-ATA
1 AAAATATATTATATA
* * *
5571273 TAAATATAAATATATT
1 AAAATAT-ATTATATA
*
5571289 AAAATA-A-AATATA
1 AAAATATATTATATA
5571302 AAAATATA-TA-ATA
1 AAAATATATTATATA
*
5571315 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
5571327 AAAATATATGATATTA
1 AAAATATATTATA-TA
5571343 AAAATATATT-TA-A
1 AAAATATATTATATA
*
5571356 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
5571372 AAAAT-TAATA-AT-
1 AAAATATATTATATA
*
5571384 AAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
5571401 AAAATA-A--A-ATA
1 AAAATATATTATATA
*
5571412 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
5571427 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
5571439 AAAATATATGATATTA
1 AAAATATATTATA-TA
5571455 AAAATATATT-TA-A
1 AAAATATATTATATA
*
5571468 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
5571484 AAAAT-TAATA-ATA
1 AAAATATATTATATA
5571497 AAAA-ATAT
1 AAAATATAT
5571505 AAATATATTA
Statistics
Matches: 292, Mismatches: 34, Indels: 121
0.65 0.08 0.27
Matches are distributed among these distances:
9 1 0.00
10 5 0.02
11 21 0.07
12 22 0.08
13 73 0.25
14 53 0.18
15 29 0.10
16 73 0.25
17 15 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:5571515 original size:60 final size:60
Alignment explanation
Indices: 5571306--5571525 Score: 230
Period size: 60 Copynumber: 3.8 Consensus size: 60
5571296 AATATAAAAA
* * *
5571306 TATATAATAATAAATAAAAATAAA-ATATATGATATTAAAAATATATTTAAGAAATGATAT
1 TATATAAAAATTAATAAAAA-AAATATAAATGATATTAAAAATATATTTAAGAAATGATAT
* ** *
5571366 TATATAAAAATTAAT-AATAAAATATAAAT-ATATTAAAAATA-AAAT-ATAAA--ATAT
1 TATATAAAAATTAATAAAAAAAATATAAATGATATTAAAAATATATTTAAGAAATGATAT
*
5571420 TATAATAATAAA-TAA-AAATAAAATAT--ATGATATTAAAAATATATTTAAGAAATGATAT
1 TAT-ATAA-AAATTAATAAAAAAAATATAAATGATATTAAAAATATATTTAAGAAATGATAT
**
5571478 TATATAAAAATTAATAATAAAAAATATAAAT-ATATTAAACTTATATTT
1 TATATAAAAATTAATAA-AAAAAATATAAATGATATTAAAAATATATTT
5571526 TAATAATTAG
Statistics
Matches: 133, Mismatches: 13, Indels: 28
0.76 0.07 0.16
Matches are distributed among these distances:
53 2 0.02
54 19 0.14
55 19 0.14
56 14 0.11
57 9 0.07
58 24 0.18
59 16 0.12
60 28 0.21
61 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (60 bp):
TATATAAAAATTAATAAAAAAAATATAAATGATATTAAAAATATATTTAAGAAATGATAT
Found at i:5571714 original size:15 final size:15
Alignment explanation
Indices: 5571661--5571719 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
5571651 TGTTACTTTC
* *
5571661 CCTGCAATCAAATTG
1 CCTGCAATCACATTA
*
5571676 CTTGCAATCACATTA
1 CCTGCAATCACATTA
*
5571691 CTTGCAATCACATTA
1 CCTGCAATCACATTA
*
5571706 CCTGTAATCACATT
1 CCTGCAATCACATT
5571720 GCATTGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:5573243 original size:23 final size:23
Alignment explanation
Indices: 5573217--5573263 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5573207 GTTTTAAAAT
*
5573217 ATAATTTAAAAGAATAAATAAAG
1 ATAATTTAAAAGAACAAATAAAG
* *
5573240 ATAATTTGAAAGAACAATTAAAG
1 ATAATTTAAAAGAACAAATAAAG
5573263 A
1 A
5573264 AAGAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.26
Consensus pattern (23 bp):
ATAATTTAAAAGAACAAATAAAG
Found at i:5577197 original size:43 final size:43
Alignment explanation
Indices: 5577137--5577224 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
5577127 CTTTAGTCAA
*
5577137 AAAAAAAAAAACTTACAAGTAATGTACCTTATAAAAAAAAACC
1 AAAAAAAAAAACTTACAAGCAATGTACCTTATAAAAAAAAACC
5577180 AAAAAAAAAAACTTACAAGCAATGTACCTTATAAAAAAAAACC
1 AAAAAAAAAAACTTACAAGCAATGTACCTTATAAAAAAAAACC
5577223 AA
1 AA
5577225 GCCATTGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.17
Consensus pattern (43 bp):
AAAAAAAAAAACTTACAAGCAATGTACCTTATAAAAAAAAACC
Found at i:5587716 original size:28 final size:28
Alignment explanation
Indices: 5587681--5587750 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
5587671 ACATTGAAAT
5587681 TTTATTTATATTTGATGTAATGTATTTA
1 TTTATTTATATTTGATGTAATGTATTTA
*
5587709 TTTATTTATATTTGATGTAATTTATTTA
1 TTTATTTATATTTGATGTAATGTATTTA
*
5587737 TTTATAATATATTT
1 TTTAT-TTATATTT
5587751 TTATTATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 32 0.82
29 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTATTTATATTTGATGTAATGTATTTA
Found at i:5598745 original size:19 final size:20
Alignment explanation
Indices: 5598723--5598769 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5598713 AGTCTTGGAC
5598723 AAAATAAAAAGA-GAAATA-A
1 AAAATAAAAA-ATGAAATAGA
5598742 AAAATAAAAAATGAAATAGA
1 AAAATAAAAAATGAAATAGA
*
5598762 GAAATAAA
1 AAAATAAA
5598770 TAATAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAATAAAAAATGAAATAGA
Found at i:5598787 original size:27 final size:27
Alignment explanation
Indices: 5598723--5598776 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
5598713 AGTCTTGGAC
*
5598723 AAAAT-AAAAAGAGAAATAAAAAATAA
1 AAAATGAAATAGAGAAATAAAAAATAA
*
5598749 AAAATGAAATAGAGAAATAAATAATAA
1 AAAATGAAATAGAGAAATAAAAAATAA
5598776 A
1 A
5598777 GGAATACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (27 bp):
AAAATGAAATAGAGAAATAAAAAATAA
Found at i:5601478 original size:27 final size:28
Alignment explanation
Indices: 5601431--5601485 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
5601421 AATGGGATTA
*
5601431 TGTTTTATCTAAACTAGAATTTTGATAAT
1 TGTTTTATC-AAACTAAAATTTTGATAAT
5601460 TGTTTTATC-AACTAAAATTTTGATAA
1 TGTTTTATCAAACTAAAATTTTGATAA
5601486 CTATCTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
29 9 0.36
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (28 bp):
TGTTTTATCAAACTAAAATTTTGATAAT
Found at i:5601494 original size:27 final size:27
Alignment explanation
Indices: 5601442--5601495 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5601432 GTTTTATCTA
* * * *
5601442 AACTAGAATTTTGATAATTGTTTTATC
1 AACTAAAATTTTGATAACTATCTTATC
5601469 AACTAAAATTTTGATAACTATCTTATC
1 AACTAAAATTTTGATAACTATCTTATC
5601496 TTATTATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (27 bp):
AACTAAAATTTTGATAACTATCTTATC
Found at i:5606830 original size:11 final size:11
Alignment explanation
Indices: 5606811--5606866 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
5606801 TTCTCTCAAT
5606811 AAATTAAAATG
1 AAATTAAAATG
* *
5606822 AATTTAAAATT
1 AAATTAAAATG
*
5606833 AAAATAAAA--
1 AAATTAAAATG
5606842 AAATTAAAATG
1 AAATTAAAATG
*
5606853 AATTTAAAAT-
1 AAATTAAAATG
5606863 AAAT
1 AAAT
5606867 AGATTTAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 8 0.22
10 3 0.08
11 25 0.69
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (11 bp):
AAATTAAAATG
Found at i:5607413 original size:316 final size:315
Alignment explanation
Indices: 5606833--5607454 Score: 794
Period size: 316 Copynumber: 2.0 Consensus size: 315
5606823 ATTTAAAATT
* *
5606833 AAAATAAAAAAATTAAAATGAATTTAAAATAAATAGATTTAACTTTTAACTATAAATTAAAAAAA
1 AAAAGAAAAAAATTAAAATGAAGTTAAAATAAATAGATTTAACTTTTAACTATAAATTAAAAAAA
* * * *
5606898 ATTACTATTTTAAACTTGAAATTAAATAAAAATTTTAATTATAAATTTTTTATATTTTAATATAT
66 ATTAATATTTAAAACTTGAAAATAAATAAAAATTTTAATTATAAACTTTTTATATTTTAATATAT
** **
5606963 TAAAATAAAGAATAAAATAATCTAATAATGTTAACTTGTTAAGTATAACTTATTAATATTTTGAA
131 TAAAATAAAGAATAAAATAAAATAATAAAATTAACTTGTTAAGTATAACTTATTAATATTTTGAA
* **
5607028 TGATATATAAATTTTTAATATTATGTAAATTAAAATAAATAATCATATTAAAATTTAAATAAAAA
196 TGAAATATAAATAATTAATATTATGTAAATTAAAATAAATAATCATATTAAAATTTAAATAAAAA
* *
5607093 TTTATTAAT-TTTTTAA-AACATTTATTAAAATAATTAAATATTATAATAAAAAATAA
261 TTTATAAATATTTATAATAA-A-TTATTAAAATAA-TAAATATTATAATAAAAAATAA
* * *
5607149 AAAAGAAAAAAATTAAAATGAAGTTAAAATAGAA-AGGTTTAACTTTTAATTATAAATTACAAAA
1 AAAAGAAAAAAATTAAAATGAAGTTAAAATA-AATAGATTTAACTTTTAACTATAAATTAAAAAA
* * * *
5607213 ATTTAATATTTAAAAC-TGAAAATAAATTAATATTTTAATTATATACTTTTTATATTTTAATATT
65 AATTAATATTTAAAACTTGAAAATAAATAAAAATTTTAATTATAAACTTTTTATATTTTAATA-T
* * * *
5607277 TTTAAAATAACGAATAAAATAAAATTATAAAATTAA--TGATTTAATTATATA-TTATTAATA-T
129 ATTAAAATAAAGAATAAAATAAAATAATAAAATTAACTTG--TTAAGTATA-ACTTATTAATATT
* * * * *
5607338 TTGAAATGAAATATAAATAATTAAT-TTCTTGTAAATTAAAATAAATATTTATATTAACATTTAC
191 TTG-AATGAAATATAAATAATTAATATT-ATGTAAATTAAAATAAATAATCATATTAAAATTTAA
* *
5607402 ATAACAATTTATAAATATTTATAATAAATTATTAAAATAATAAATATTTTAAT
254 ATAAAAATTTATAAATATTTATAATAAATTATTAAAATAATAAATATTATAAT
5607455 TTAAAACTTA
Statistics
Matches: 264, Mismatches: 33, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
314 2 0.01
315 59 0.22
316 191 0.72
317 10 0.04
318 2 0.01
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (315 bp):
AAAAGAAAAAAATTAAAATGAAGTTAAAATAAATAGATTTAACTTTTAACTATAAATTAAAAAAA
ATTAATATTTAAAACTTGAAAATAAATAAAAATTTTAATTATAAACTTTTTATATTTTAATATAT
TAAAATAAAGAATAAAATAAAATAATAAAATTAACTTGTTAAGTATAACTTATTAATATTTTGAA
TGAAATATAAATAATTAATATTATGTAAATTAAAATAAATAATCATATTAAAATTTAAATAAAAA
TTTATAAATATTTATAATAAATTATTAAAATAATAAATATTATAATAAAAAATAA
Found at i:5614390 original size:20 final size:20
Alignment explanation
Indices: 5614364--5614416 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
5614354 TGCACCAAAA
*
5614364 CTATCGATACATTCTTAAAG
1 CTATCGATACATTCATAAAG
* * * *
5614384 GTATCGATACTTTCATACAT
1 CTATCGATACATTCATAAAG
5614404 CTATCGATACATT
1 CTATCGATACATT
5614417 AGTAAAATGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (20 bp):
CTATCGATACATTCATAAAG
Found at i:5616296 original size:16 final size:16
Alignment explanation
Indices: 5616271--5616305 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5616261 ATAAAAATAT
5616271 TAAAAAAATCAAAATC
1 TAAAAAAATCAAAATC
*
5616287 TAAAAGAATCAAAATC
1 TAAAAAAATCAAAATC
5616303 TAA
1 TAA
5616306 GTTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (16 bp):
TAAAAAAATCAAAATC
Found at i:5619246 original size:34 final size:34
Alignment explanation
Indices: 5619203--5619306 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 34
5619193 TGAAAAGTTA
* *
5619203 GTGTAGGTTGTGCTTGCTCCCAATAAAAGGCATT
1 GTGTGGGTTGTGCTTGATCCCAATAAAAGGCATT
* * **
5619237 GTGTGGGTTGTGCTTGTTTCCGTTAAAAGGCATT
1 GTGTGGGTTGTGCTTGATCCCAATAAAAGGCATT
* *
5619271 GTGAGGGTTGTGCTTGAACCCAGA-AAAAGGCATT
1 GTGTGGGTTGTGCTTGATCCCA-ATAAAAGGCATT
5619305 GT
1 GT
5619307 AAGGTTTTGC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (34 bp):
GTGTGGGTTGTGCTTGATCCCAATAAAAGGCATT
Found at i:5630639 original size:36 final size:36
Alignment explanation
Indices: 5630585--5630656 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
5630575 ATTGTAATCT
* * *
5630585 TTTGAGTGGCTATGCCTTAACCAAATTAAAATGTAG
1 TTTGAGTGGCTATACCTTAACCAAAGTAAAAGGTAG
* *
5630621 TTTGAGTGGTTATACCTTAACCCAAGTAAAAGGTAG
1 TTTGAGTGGCTATACCTTAACCAAAGTAAAAGGTAG
5630657 AAAGGTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (36 bp):
TTTGAGTGGCTATACCTTAACCAAAGTAAAAGGTAG
Found at i:5632061 original size:16 final size:15
Alignment explanation
Indices: 5632040--5632069 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5632030 CCAAAAATTA
5632040 GATTTTGATTCTTTTG
1 GATTTTGATT-TTTTG
5632056 GATTTTGATTTTTT
1 GATTTTGATTTTTT
5632070 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (15 bp):
GATTTTGATTTTTTG
Found at i:5634081 original size:20 final size:20
Alignment explanation
Indices: 5634043--5634081 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5634033 GAAATCAGGA
* *
5634043 TAAATGCATCGATATATTAC
1 TAAATGCATCAATACATTAC
*
5634063 TAAATGTATCAATACATTA
1 TAAATGCATCAATACATTA
5634082 GAAATGGAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAATGCATCAATACATTAC
Found at i:5651328 original size:78 final size:79
Alignment explanation
Indices: 5651180--5651328 Score: 219
Period size: 78 Copynumber: 1.9 Consensus size: 79
5651170 CAAGCAATAA
* *
5651180 AAAATTCACCTATTGGTCATCCAATTTATCTCTAAATAAATTAAAATAATTTAGAGATAATATTT
1 AAAATTCACCTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGATAATATTC
*
5651245 GAATTTAATCAATT
66 AAATTTAATCAATT
* * * * *
5651259 AAAATTTACTTATTGGTTATCCAATTTATC-CTAAATGAATCAAGATAATTTAGAGATAATATTC
1 AAAATTCACCTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGATAATATTC
5651323 AAATTT
66 AAATTT
5651329 GGTCATCCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
78 35 0.56
79 27 0.44
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (79 bp):
AAAATTCACCTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGAGATAATATTC
AAATTTAATCAATT
Found at i:5651343 original size:56 final size:57
Alignment explanation
Indices: 5651271--5651384 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
5651261 AATTTACTTA
* *
5651271 TTGGTTATCCAATTTATC-CTAAATGAATCAAGATAATTTAGAGATAATATTCAAAT
1 TTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAATATTCAAAT
* * *
5651327 TTGGTCATCCTATTTATCTCTAAATAAATTAAGATAATTTGGAGATAATATTCAAAT
1 TTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAATATTCAAAT
5651384 T
1 T
5651385 CAGCCAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
56 16 0.31
57 36 0.69
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (57 bp):
TTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAATATTCAAAT
Found at i:5658895 original size:20 final size:20
Alignment explanation
Indices: 5658870--5658910 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5658860 CGTTCAACAG
*
5658870 ATCCAAGAAAGTGTATCAGA
1 ATCCAAGAAAGAGTATCAGA
*
5658890 ATCCAAGAAAGAGTTTCAGA
1 ATCCAAGAAAGAGTATCAGA
5658910 A
1 A
5658911 ACATAGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCCAAGAAAGAGTATCAGA
Found at i:5676391 original size:39 final size:39
Alignment explanation
Indices: 5676337--5676424 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
5676327 CTTGGCACTA
5676337 GCCTCTCAGACGGAAAAGGACACACCAATAAAACAGATT
1 GCCTCTCAGACGGAAAAGGACACACCAATAAAACAGATT
* *
5676376 GCCTCTCAGACGGAAAAGGACACACTAATAAAATAGATT
1 GCCTCTCAGACGGAAAAGGACACACCAATAAAACAGATT
5676415 GCCATCTCAG
1 GCC-TCTCAG
5676425 CACTCCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 40 0.87
40 6 0.13
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (39 bp):
GCCTCTCAGACGGAAAAGGACACACCAATAAAACAGATT
Found at i:5678856 original size:2 final size:2
Alignment explanation
Indices: 5678802--5678839 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5678792 GCGTAACTTT
*
5678802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5678840 AAATTGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5685800 original size:40 final size:40
Alignment explanation
Indices: 5685743--5685830 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
5685733 TCTTTTCAAA
* *
5685743 ACAATAACAACACAAACATATTTGCAAATTTTATAACAAC
1 ACAATAACAACACAAACACATTTACAAATTTTATAACAAC
*
5685783 ATAATAACAACACAAACACATTTACAAATTTTATAACAAC
1 ACAATAACAACACAAACACATTTACAAATTTTATAACAAC
5685823 ACAATAAC
1 ACAATAAC
5685831 TATTTATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.55, C:0.20, G:0.01, T:0.24
Consensus pattern (40 bp):
ACAATAACAACACAAACACATTTACAAATTTTATAACAAC
Found at i:5688716 original size:31 final size:31
Alignment explanation
Indices: 5688660--5688831 Score: 134
Period size: 31 Copynumber: 5.3 Consensus size: 31
5688650 AATTAAGAGA
*
5688660 AAAAGAAAGAAAATGCATGTAGAGAGACTAGATTG
1 AAAAGAAAGAAAAT--AT-T-GAGAGACTAAATTG
*
5688695 AAAAGAAAGAAAGTATTGAGAGAACGACTAAATTG
1 AAAAGAAAGAAAATATT--GAG-A-GACTAAATTG
* * *
5688730 AAAAGAAAGAAAGTGTTG-GAAAACTAAATTG
1 AAAAGAAAGAAAATATTGAG-AGACTAAATTG
* *
5688761 AAAAGAAAAAAAATGTTG-GAGGACTAAATTG
1 AAAAGAAAGAAAATATTGAGA-GACTAAATTG
* *
5688792 AAAAGAAA-ACTAAATATTGAGGGACTAAATTA
1 AAAAGAAAGA--AAATATTGAGAGACTAAATTG
5688824 AAAAGAAA
1 AAAAGAAA
5688832 ACTAAGGAAG
Statistics
Matches: 120, Mismatches: 10, Indels: 17
0.82 0.07 0.12
Matches are distributed among these distances:
30 2 0.02
31 43 0.36
32 28 0.23
33 8 0.07
34 1 0.01
35 38 0.32
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.18
Consensus pattern (31 bp):
AAAAGAAAGAAAATATTGAGAGACTAAATTG
Found at i:5714411 original size:18 final size:19
Alignment explanation
Indices: 5714390--5714431 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
5714380 AAATTTTACT
* *
5714390 TATGTTGTATTTTTG-TTG
1 TATGTTATATGTTTGTTTG
*
5714408 TATGGTATATGTTTGTTTG
1 TATGTTATATGTTTGTTTG
5714427 TATGT
1 TATGT
5714432 GCAAAACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (19 bp):
TATGTTATATGTTTGTTTG
Found at i:5715584 original size:44 final size:44
Alignment explanation
Indices: 5715504--5715591 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
5715494 AAAGAAAATA
* * * *
5715504 ACTATTTGAAGAGTTATATTATAAAAAGAAATAAGTCATTTCAT
1 ACTATTTGAAAAGTCAGATTATAAAAAGAAACAAGTCATTTCAT
* * * *
5715548 ACTATTTGAAAAGTCAGATTATGAAAGGATACAAGTCTTTTCAT
1 ACTATTTGAAAAGTCAGATTATAAAAAGAAACAAGTCATTTCAT
5715592 TGAAAGACGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (44 bp):
ACTATTTGAAAAGTCAGATTATAAAAAGAAACAAGTCATTTCAT
Found at i:5723153 original size:27 final size:27
Alignment explanation
Indices: 5723122--5723175 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5723112 TTTATTTAAT
*
5723122 ACCTCATCAAATCATTTTTGATTTAGC
1 ACCTCATCAAATCATATTTGATTTAGC
5723149 ACCTCATCAAATCATATTTGATTTAGC
1 ACCTCATCAAATCATATTTGATTTAGC
5723176 CCAATACCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (27 bp):
ACCTCATCAAATCATATTTGATTTAGC
Found at i:5723332 original size:6 final size:6
Alignment explanation
Indices: 5723321--5723345 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5723311 TCAACTAAGA
5723321 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
5723346 GATTATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:5724733 original size:24 final size:22
Alignment explanation
Indices: 5724706--5724763 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
5724696 AACATTAAAT
5724706 ACATAATTAAAATGCATAATAAGA
1 ACATAATTAAAAT--ATAATAAGA
*
5724730 ACATATCATTTAAATATAATAAGA
1 ACATA--ATTAAAATATAATAAGA
5724754 ACAT-ATTAAA
1 ACATAATTAAA
5724764 GCATCTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.17
24 18 0.60
26 7 0.23
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (22 bp):
ACATAATTAAAATATAATAAGA
Found at i:5725161 original size:18 final size:18
Alignment explanation
Indices: 5725140--5725174 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5725130 TTATGACAAG
5725140 TTATCCATTTCTAGTGGA
1 TTATCCATTTCTAGTGGA
* *
5725158 TTATTCATTTTTAGTGG
1 TTATCCATTTCTAGTGG
5725175 GTTAGTGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (18 bp):
TTATCCATTTCTAGTGGA
Found at i:5736576 original size:6 final size:6
Alignment explanation
Indices: 5736567--5736597 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5736557 CAGATGCAGC
*
5736567 AGATTG AGATTG AGATTG CGATTG AGATTG A
1 AGATTG AGATTG AGATTG AGATTG AGATTG A
5736598 AATGATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (6 bp):
AGATTG
Found at i:5752480 original size:12 final size:12
Alignment explanation
Indices: 5752463--5752487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5752453 TGTCAAGGAT
5752463 AAGGGCACTTGA
1 AAGGGCACTTGA
5752475 AAGGGCACTTGA
1 AAGGGCACTTGA
5752487 A
1 A
5752488 TAGGAGATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AAGGGCACTTGA
Done.