Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 16 of 85
Found at i:5249243 original size:3 final size:3
Alignment explanation
Indices: 5249237--5249280 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
5249227 CAACAACAAC
*
5249237 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
5249281 CTTTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5249350 original size:19 final size:21
Alignment explanation
Indices: 5249326--5249364 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5249316 ACTAAAACAA
*
5249326 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
5249345 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
5249365 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:5249408 original size:11 final size:11
Alignment explanation
Indices: 5249392--5249428 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5249382 AAAAAACCTC
5249392 CTTTTTCTCCT
1 CTTTTTCTCCT
5249403 CTTTTTCT-CT
1 CTTTTTCTCCT
*
5249413 CTTTTTCTCTT
1 CTTTTTCTCCT
5249424 CTTTT
1 CTTTT
5249429 CCGCGCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTTTTCTCCT
Found at i:5249583 original size:27 final size:27
Alignment explanation
Indices: 5249527--5249584 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5249517 CCAGTTAGTA
***
5249527 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGCCAT
* *
5249554 TGGCACCTTTGGTGCCGCCAATTCCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
5249581 TGGC
1 TGGC
5249585 GTGACCAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.29
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGCCAT
Found at i:5249667 original size:27 final size:27
Alignment explanation
Indices: 5249624--5249678 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5249614 TTTTTTTTTG
*
5249624 ATTTTTTTGATATATTTTGGTAAATAA
1 ATTTTTTTGATACATTTTGGTAAATAA
*
5249651 ATTTTTTTTATACATTTTGGTAAATAA
1 ATTTTTTTGATACATTTTGGTAAATAA
5249678 A
1 A
5249679 AAAATTATAA
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:0.35, C:0.02, G:0.09, T:0.55
Consensus pattern (27 bp):
ATTTTTTTGATACATTTTGGTAAATAA
Found at i:5251244 original size:88 final size:86
Alignment explanation
Indices: 5251143--5251365 Score: 295
Period size: 89 Copynumber: 2.5 Consensus size: 86
5251133 TTTAAGGGTG
* * *
5251143 CAAAAAG-CCCTCAAACTTAAAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCATTTGG
1 CAAAAAGACCCTCAAACTTTAAAAAAAAA--AATTAAGCCCCTACTTTTTTTTGCACTCAATTAG
*
5251207 GTACTTAAACTTTCAAAATGCAT
64 ATACTTAAACTTTCAAAATGCAT
* *
5251230 CAAAAAGACCCTCAAACCTTTTCAAAATAAAAATTAAGCCCCTACTGTTTTTTTGCACTCAATTA
1 CAAAAAGACCCTCAAA-C-TTTAAAAAAAAAAATTAAGCCCCTACT-TTTTTTTGCACTCAATTA
* *
5251295 GATACTTGAACTTTTAAAATGCAT
63 GATACTTAAACTTTCAAAATGCAT
* * *
5251319 CAAAAAGACTCTCAAACTTTAAAAAAAAAATTTAAGCCCCTTCTTTT
1 CAAAAAGACCCTCAAACTTTAAAAAAAAAAATTAAGCCCCTACTTTT
5251366 ATTAAAAATT
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
86 3 0.03
87 30 0.25
88 24 0.20
89 53 0.45
90 9 0.08
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (86 bp):
CAAAAAGACCCTCAAACTTTAAAAAAAAAAATTAAGCCCCTACTTTTTTTTGCACTCAATTAGAT
ACTTAAACTTTCAAAATGCAT
Found at i:5251611 original size:18 final size:19
Alignment explanation
Indices: 5251585--5251672 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 19
5251575 AAAAAAATTC
*
5251585 TAATCTTTAATAAATTT-T
1 TAATTTTTAATAAATTTAT
*
5251603 TAATTTTTATTAAAATTTAGT
1 TAATTTTTAAT-AAATTTA-T
*
5251624 AAATTTTCT-A-AAATTTAT
1 TAATTTT-TAATAAATTTAT
* *
5251642 TAATTATTAAT-TATTT-T
1 TAATTTTTAATAAATTTAT
5251659 CTAATTTTTAATAA
1 -TAATTTTTAATAA
5251673 GAGTAGGGGC
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
17 2 0.04
18 30 0.57
19 13 0.25
21 7 0.13
22 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (19 bp):
TAATTTTTAATAAATTTAT
Found at i:5251837 original size:88 final size:88
Alignment explanation
Indices: 5251677--5251849 Score: 249
Period size: 88 Copynumber: 2.0 Consensus size: 88
5251667 TAATAAGAGT
* *
5251677 AGGGGCTTAATTGTTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTA
1 AGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTA
5251742 CCCAATTGAATG-AAAAAAAGAC
66 CCCAATTGAATGCAAAAAAAGAC
* * *
5251764 AGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGTTTTTTTAATGCATTTTGAAAGTTCAAGT
1 AGGGGCTTAATTG-TTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGT
* ** *
5251829 GCTTAATTGAGTGCAAAAAAA
65 ACCCAATTGAATGCAAAAAAA
5251850 AAAGAGAGAG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
87 13 0.17
88 55 0.73
89 7 0.09
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.38
Consensus pattern (88 bp):
AGGGGCTTAATTGTTTTTTTGAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTTCAAGTA
CCCAATTGAATGCAAAAAAAGAC
Found at i:5253912 original size:18 final size:18
Alignment explanation
Indices: 5253889--5253926 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5253879 AGATCAGCAG
5253889 TGGTTTAACACCAGTCGA
1 TGGTTTAACACCAGTCGA
5253907 TGGTTTAACACCAGTCGA
1 TGGTTTAACACCAGTCGA
5253925 TG
1 TG
5253927 TTCCGGCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (18 bp):
TGGTTTAACACCAGTCGA
Found at i:5259974 original size:14 final size:14
Alignment explanation
Indices: 5259955--5259988 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5259945 AAATTTAAGT
5259955 TTTTCAAATT-TTAA
1 TTTTCAAATTATT-A
5259969 TTTTCAAATTATTA
1 TTTTCAAATTATTA
5259983 TTTTCA
1 TTTTCA
5259989 TAAACTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTCAAATTATTA
Found at i:5260535 original size:31 final size:29
Alignment explanation
Indices: 5260465--5260538 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
5260455 GGTTCAAGTT
* *
5260465 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* *
5260494 ACGTTTTAGTCACTTATGTTATCATGATGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
5260525 ACATTTTAGTCACT
1 ACATTTTAGTCACT
5260539 GAGCCGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 2 0.05
31 17 0.45
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:5265168 original size:16 final size:16
Alignment explanation
Indices: 5265147--5265177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5265137 AAAGACACCG
5265147 AGTAAAAGAAATAATC
1 AGTAAAAGAAATAATC
*
5265163 AGTAAAAGAGATAAT
1 AGTAAAAGAAATAAT
5265178 TGAAAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.19
Consensus pattern (16 bp):
AGTAAAAGAAATAATC
Found at i:5266072 original size:15 final size:16
Alignment explanation
Indices: 5266054--5266086 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5266044 TGGTAAGCAA
5266054 TGAAATG-AATTAAGT
1 TGAAATGTAATTAAGT
5266069 TGAAATGTTAATTAAGT
1 TGAAATG-TAATTAAGT
5266086 T
1 T
5266087 AAAGGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (16 bp):
TGAAATGTAATTAAGT
Found at i:5273418 original size:12 final size:12
Alignment explanation
Indices: 5273401--5273427 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5273391 AGTCTAGAAG
5273401 AAAATTTATTTT
1 AAAATTTATTTT
5273413 AAAATTTATTTT
1 AAAATTTATTTT
5273425 AAA
1 AAA
5273428 GTTTTTACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAAATTTATTTT
Found at i:5279944 original size:24 final size:24
Alignment explanation
Indices: 5279832--5279958 Score: 68
Period size: 24 Copynumber: 5.3 Consensus size: 24
5279822 TCTTTGTGAT
* *
5279832 CTTCCCGA-TATGGCTCACTTGAA
1 CTTCCCGATTATGGCTCACATGAG
*
5279855 CTTCCCGATATATGGCT-ATTC-GGAG
1 CTTCCCGAT-TATGGCTCA--CATGAG
* * *
5279880 CTTCCC-ATTAATGACTCTTCA-AAG
1 CTTCCCGATT-ATGGCTC-ACATGAG
* *
5279904 CTACCC-ATTATTAGCTCACATGAG
1 CTTCCCGATTA-TGGCTCACATGAG
**
5279928 CTTCCCGATTATGGCTCTTATGAG
1 CTTCCCGATTATGGCTCACATGAG
5279952 CTTCCCG
1 CTTCCCG
5279959 TAGTTGTAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 21
0.69 0.12 0.18
Matches are distributed among these distances:
23 12 0.15
24 47 0.59
25 19 0.24
26 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (24 bp):
CTTCCCGATTATGGCTCACATGAG
Found at i:5295491 original size:26 final size:26
Alignment explanation
Indices: 5295461--5295531 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
5295451 ATCTCACCAT
*
5295461 AGCTCGTATGAGCTTACCGATATAAC
1 AGCTCTTATGAGCTTACCGATATAAC
5295487 AGCTCTTATGAGCTTACCGATATAAC
1 AGCTCTTATGAGCTTACCGATATAAC
5295513 AGCTCTTATGAGCTTACCG
1 AGCTCTTATGAGCTTACCG
5295532 TTTCAACTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (26 bp):
AGCTCTTATGAGCTTACCGATATAAC
Found at i:5300453 original size:14 final size:14
Alignment explanation
Indices: 5300434--5300464 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5300424 AGGTTAACAA
5300434 TTTAATAAATGATT
1 TTTAATAAATGATT
5300448 TTTAATAAATGATT
1 TTTAATAAATGATT
5300462 TTT
1 TTT
5300465 GATGATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTAATAAATGATT
Found at i:5302959 original size:30 final size:31
Alignment explanation
Indices: 5302925--5302984 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
5302915 AAACCTTTTA
5302925 TTTTCCC-TCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCAT-AAAATTTTTACTCCCTTCCCAC
*
5302955 TTTTCCCATAAAATTTTTATTCCCTTCCCA
1 TTTTCCCATAAAATTTTTACTCCCTTCCCA
5302985 TCCCACCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCATAAAATTTTTACTCCCTTCCCAC
Found at i:5303161 original size:17 final size:17
Alignment explanation
Indices: 5303107--5303187 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
5303097 TTTTTTCTAC
5303107 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
5303124 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
5303143 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
*
5303160 TATTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
5303177 TATTTATATTA
1 TATTTATATTA
5303188 AAATTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 7 0.13
19 11 0.21
20 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:5306716 original size:13 final size:13
Alignment explanation
Indices: 5306695--5306732 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5306685 ACACTCAAAT
5306695 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
5306708 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
5306721 ATCTCAAAAGCA
1 TTCTCAAAAGCA
5306733 ATGAAGAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:5313683 original size:49 final size:50
Alignment explanation
Indices: 5313608--5313705 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 50
5313598 ACAATATGAA
*
5313608 CATATTGAAAGATAGCAAATAAGCTTTAGCACTAGTGAGTGAAATCACAG
1 CATATTGAAAGATAGCAAATAAGCTTTAGCACTACTGAGTGAAATCACAG
5313658 CATATTGAAAGAT-GCAAATAAGCTTTAGCACTACTGAGTGAAATCACA
1 CATATTGAAAGATAGCAAATAAGCTTTAGCACTACTGAGTGAAATCACA
5313706 TGCCTTGTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 34 0.72
50 13 0.28
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (50 bp):
CATATTGAAAGATAGCAAATAAGCTTTAGCACTACTGAGTGAAATCACAG
Found at i:5316400 original size:4 final size:4
Alignment explanation
Indices: 5316391--5316443 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
5316381 TCCTCAGCCA
5316391 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5316439 AATG T
1 TATG T
5316444 GTTTAGGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:5324662 original size:43 final size:44
Alignment explanation
Indices: 5324555--5324671 Score: 143
Period size: 44 Copynumber: 2.7 Consensus size: 44
5324545 TATGAGTTAT
*
5324555 CATGTAAGACCACGTCTGGGACGTTGGCATGGATTTGAGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTA
* * *
5324599 CGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATGTT-TGA-TTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TTGAGATTTA
5324642 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
5324672 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 1 0.02
43 28 0.45
44 30 0.48
45 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTA
Found at i:5327025 original size:506 final size:507
Alignment explanation
Indices: 5326073--5327085 Score: 2019
Period size: 506 Copynumber: 2.0 Consensus size: 507
5326063 TTACGTGTTC
5326073 CATGTGTATAAAAATGATAAATGACTACTGATCTATATTTTGTCCGGTAATGCCTTGTAACCCTA
1 CATGTGTATAAAAATGATAAATGACTACTGATCTATATTTTGTCCGGTAATGCCTTGTAACCCTA
5326138 ATTCGGTGACAGATACGGGTTAGGGGTGTTACAACACGTGCATCATGCTAACGTGTCAAAATGCC
66 ATTCGGTGACAGATACGGGTTAGGGGTGTTACAACACGTGCATCATGCTAACGTGTCAAAATGCC
5326203 ACATCAACAAATATTTTTAAAAAATAAAAAATCCAAAAAATAATTATTTAAAAAATCACATCTAA
131 ACATCAACAAATATTTTTAAAAAATAAAAAATCCAAAAAATAATTATTTAAAAAATCACATCTAA
5326268 GATGCACGTCAACATGATATACACGTGGCTGCCACGTGTTGCTATACGATTGGTCTATCAACCAC
196 GATGCACGTCAACATGATATACACGTGGCTGCCACGTGTTGCTATACGATTGGTCTATCAACCAC
5326333 ATCAACGAAACATAATGGTCAAACCTAGTGAACATTAAAAGAGGGGCTTAATTGATTTATTTTTC
261 ATCAACGAAACATAATGGTCAAACCTAGTGAACATTAAAAGAGGGGCTTAATTGATTTATTTTTC
5326398 ATCCTTTAGGAGCTCAATTGGGTGCTAAATTTTGATAAGGGCTTAATTGATTTTTTGATCTTTCA
326 ATCCTTTAGGAGCTCAATTGGGTGCTAAATTTTGATAAGGGCTTAATTGATTTTTTGATCTTTCA
5326463 CGAATGGCTTTTTTTTACTAATAAGCCTTTAAATTAGTTTCTAACAAATTTTATAAATTTTGTTT
391 CGAATGGCTTTTTTTTACTAATAAGCCTTTAAATTAGTTTCTAACAAATTTTATAAATTTTGTTT
5326528 CTAATTTTTTATGGTTTTTAATAAATTTATTTTTTATAAAA-TTATAAAAAA
456 CTAATTTTTTATGGTTTTTAATAAATTTATTTTTTATAAAATTTATAAAAAA
5326579 CATGTGTATAAAAATGATAAATGACTACTGATCTATATTTTGTCCGGTAATGCCTTGTAACCCTA
1 CATGTGTATAAAAATGATAAATGACTACTGATCTATATTTTGTCCGGTAATGCCTTGTAACCCTA
5326644 ATTCGGTGACAGATACGGGTTAGGGGTGTTACAACACGTGCATCATGCTAACGTGTCAAAATGCC
66 ATTCGGTGACAGATACGGGTTAGGGGTGTTACAACACGTGCATCATGCTAACGTGTCAAAATGCC
5326709 ACATCAACAAATATTTTTAAAAAATAAAAAATCCAAAAAATAATTATTTAAAAAATCACATCTAA
131 ACATCAACAAATATTTTTAAAAAATAAAAAATCCAAAAAATAATTATTTAAAAAATCACATCTAA
5326774 GATGCACGTCAACATGATATACACGTGGCTGCCACGTGTTGCTATACGATTGGTCTATCAACCAC
196 GATGCACGTCAACATGATATACACGTGGCTGCCACGTGTTGCTATACGATTGGTCTATCAACCAC
5326839 ATCAACGAAACATAATGGTCAAACCTAGTGAACATTAAAAGAGGGGCTTAATTGATTTATTTTTC
261 ATCAACGAAACATAATGGTCAAACCTAGTGAACATTAAAAGAGGGGCTTAATTGATTTATTTTTC
5326904 ATCCTTTAGGAGCTCAATTGGGTGCTAAATTTTGATAAGGGCTTAATTGATTTTTTGATCTTTCA
326 ATCCTTTAGGAGCTCAATTGGGTGCTAAATTTTGATAAGGGCTTAATTGATTTTTTGATCTTTCA
5326969 CGAATGGCTTTTTTTTACTAATAAGCCTTTAAATTAGTTTCTAACAAATTTTATAAATTTTGTTT
391 CGAATGGCTTTTTTTTACTAATAAGCCTTTAAATTAGTTTCTAACAAATTTTATAAATTTTGTTT
5327034 CTAATTTTTTATGGTTTTTAATAAATTTATTTTTTATAAAATTTATAAAAAA
456 CTAATTTTTTATGGTTTTTAATAAATTTATTTTTTATAAAATTTATAAAAAA
5327086 AATTGTTTTG
Statistics
Matches: 506, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
506 496 0.98
507 10 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (507 bp):
CATGTGTATAAAAATGATAAATGACTACTGATCTATATTTTGTCCGGTAATGCCTTGTAACCCTA
ATTCGGTGACAGATACGGGTTAGGGGTGTTACAACACGTGCATCATGCTAACGTGTCAAAATGCC
ACATCAACAAATATTTTTAAAAAATAAAAAATCCAAAAAATAATTATTTAAAAAATCACATCTAA
GATGCACGTCAACATGATATACACGTGGCTGCCACGTGTTGCTATACGATTGGTCTATCAACCAC
ATCAACGAAACATAATGGTCAAACCTAGTGAACATTAAAAGAGGGGCTTAATTGATTTATTTTTC
ATCCTTTAGGAGCTCAATTGGGTGCTAAATTTTGATAAGGGCTTAATTGATTTTTTGATCTTTCA
CGAATGGCTTTTTTTTACTAATAAGCCTTTAAATTAGTTTCTAACAAATTTTATAAATTTTGTTT
CTAATTTTTTATGGTTTTTAATAAATTTATTTTTTATAAAATTTATAAAAAA
Found at i:5330657 original size:31 final size:30
Alignment explanation
Indices: 5330622--5330683 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5330612 ATTTCTTTAA
*
5330622 ATGTATATAATCAAATCAAAATTAAAGTTTC
1 ATGTATAT-ATCAAATCAAAATTAAAATTTC
** *
5330653 ATGTATATATTGAATCACAATTAAAATTTC
1 ATGTATATATCAAATCAAAATTAAAATTTC
5330683 A
1 A
5330684 CACATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (30 bp):
ATGTATATATCAAATCAAAATTAAAATTTC
Found at i:5342875 original size:62 final size:63
Alignment explanation
Indices: 5342778--5342902 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 63
5342768 ACAAACGATC
5342778 GAAACTCGAACAGAAAAAGAAGAAATAGGATAGGCTCCAAGGTGTGTATCAA-CCACTATCTT
1 GAAACTCGAACAGAAAAAGAAGAAATAGGATAGGCTCCAAGGTGTGTATCAACCCACTATCTT
5342840 GAAACTCGAACAGAAAAAGAAGAAATAGGATAGGCTCCAAGGTGTGTATCAACCCACTATCTT
1 GAAACTCGAACAGAAAAAGAAGAAATAGGATAGGCTCCAAGGTGTGTATCAACCCACTATCTT
5342903 TAAGGTTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 52 0.84
63 10 0.16
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (63 bp):
GAAACTCGAACAGAAAAAGAAGAAATAGGATAGGCTCCAAGGTGTGTATCAACCCACTATCTT
Found at i:5348378 original size:3 final size:3
Alignment explanation
Indices: 5348352--5348435 Score: 104
Period size: 3 Copynumber: 28.3 Consensus size: 3
5348342 GTTTTTTAGT
*
5348352 TTA TT- TTA TTA GTA TTGA -TA TTA TTA TT- TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA TTA
5348396 TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
5348436 ACCTATATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
2 7 0.10
3 59 0.82
4 6 0.08
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5349021 original size:4 final size:4
Alignment explanation
Indices: 5349002--5349038 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
5348992 TTGATTTATT
* *
5349002 TTTA TTTG TTTG TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
5349039 GCTATTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5352428 original size:30 final size:30
Alignment explanation
Indices: 5352394--5352454 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5352384 GTGGTCCAGA
5352394 TTCGAGAAGTAGCTGATCACATACAGACTT
1 TTCGAGAAGTAGCTGATCACATACAGACTT
5352424 TTCGAGAAGTAGCTGATCACATACAGACTT
1 TTCGAGAAGTAGCTGATCACATACAGACTT
5352454 T
1 T
5352455 GGCAGTACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (30 bp):
TTCGAGAAGTAGCTGATCACATACAGACTT
Found at i:5356861 original size:20 final size:22
Alignment explanation
Indices: 5356823--5356862 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5356813 TACCGAAACG
5356823 GTAGCAAAATAACAACAAAATA
1 GTAGCAAAATAACAACAAAATA
*
5356845 GTAG-AAAA-AACAGCAAAA
1 GTAGCAAAATAACAACAAAA
5356863 CACAATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.10
Consensus pattern (22 bp):
GTAGCAAAATAACAACAAAATA
Found at i:5358851 original size:17 final size:17
Alignment explanation
Indices: 5358813--5358854 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5358803 ATTAAATGAA
5358813 TAGAAATGGTGAAAATG
1 TAGAAATGGTGAAAATG
* *
5358830 GAGAAATGG-GAAACATT
1 TAGAAATGGTGAAA-ATG
5358847 TAGAAATG
1 TAGAAATG
5358855 ATTATTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
TAGAAATGGTGAAAATG
Found at i:5359159 original size:61 final size:61
Alignment explanation
Indices: 5359083--5359210 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
5359073 AGTCATAATG
*
5359083 ATTTTAACAAAACTAGAACTAAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
1 ATTTTGACAAAACTAGAACTAAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
*
5359144 ATTTTGACAAAACTAGAACTGAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
1 ATTTTGACAAAACTAGAACTAAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
5359205 ATTTTG
1 ATTTTG
5359211 GGAAATAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (61 bp):
ATTTTGACAAAACTAGAACTAAGTTGAGAAGATTATTTAATGGAAAAATATTAAGATGTTT
Found at i:5361660 original size:6 final size:6
Alignment explanation
Indices: 5361649--5361677 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5361639 AGGACTTAAG
5361649 TCTGAA TCTGAA TCTGAA TCTGAA TCTGA
1 TCTGAA TCTGAA TCTGAA TCTGAA TCTGA
5361678 CTGCGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
TCTGAA
Found at i:5367594 original size:17 final size:17
Alignment explanation
Indices: 5367572--5367611 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5367562 TGTGGTTGGT
5367572 CGTGTGCGAGACACAAC
1 CGTGTGCGAGACACAAC
*
5367589 CGTGTGTGAGACACAAC
1 CGTGTGCGAGACACAAC
5367606 CGTGTG
1 CGTGTG
5367612 GTGGTGTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (17 bp):
CGTGTGCGAGACACAAC
Found at i:5371281 original size:20 final size:20
Alignment explanation
Indices: 5371256--5371309 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
5371246 TTGTACGGGA
5371256 TTGCACTTTGGTGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
5371276 TTGCACTTTGGTGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
5371296 TTGCACTTTGGTGC
1 TTGCACTTTGGTGC
5371310 TCCCTAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.06, C:0.24, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGT
Found at i:5371861 original size:19 final size:18
Alignment explanation
Indices: 5371832--5371869 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5371822 GGTTTCGAAG
*
5371832 TTGTTAAATTTGAAGTTC
1 TTGTTAAATTTAAAGTTC
5371850 TTGTTGAAATTTAAAGTTC
1 TTGTT-AAATTTAAAGTTC
5371869 T
1 T
5371870 ATATAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (18 bp):
TTGTTAAATTTAAAGTTC
Found at i:5373037 original size:22 final size:22
Alignment explanation
Indices: 5373010--5373060 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
5373000 CCACAAGAAA
5373010 CAAAGAAACTCATAATAATCTC
1 CAAAGAAACTCATAATAATCTC
5373032 CAAAGAAACTCATAATAATCTC
1 CAAAGAAACTCATAATAATCTC
5373054 CAAAGAA
1 CAAAGAA
5373061 GTCAAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.20
Consensus pattern (22 bp):
CAAAGAAACTCATAATAATCTC
Found at i:5375479 original size:22 final size:22
Alignment explanation
Indices: 5375451--5375494 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5375441 CAAAAGATAC
5375451 AATTGGCATGCCAATAGGGGTA
1 AATTGGCATGCCAATAGGGGTA
5375473 AATTGGCATGCCAATAGGGGTA
1 AATTGGCATGCCAATAGGGGTA
5375495 TTTTTTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (22 bp):
AATTGGCATGCCAATAGGGGTA
Found at i:5377133 original size:20 final size:19
Alignment explanation
Indices: 5377108--5377159 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
5377098 TTTAATTAGC
*
5377108 CTTAATTAATCATATTTTAT
1 CTTAATTAATCATAATTT-T
5377128 CTTAATTAAAT-ATAATTTT
1 CTTAATT-AATCATAATTTT
5377147 CTTAATTAATCAT
1 CTTAATTAATCAT
5377160 TAGGAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.10
19 10 0.34
20 13 0.45
21 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
CTTAATTAATCATAATTTT
Found at i:5377783 original size:33 final size:34
Alignment explanation
Indices: 5377727--5377803 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
5377717 CATTATCAAC
*
5377727 CATACCAAAACATCCTCGAAAAACATGTTCAAAT
1 CATACCTAAACATCCTCGAAAAACATGTTCAAAT
* * *
5377761 CATGCCTAAACATGCTC-AAAAACATGTTCCAAT
1 CATACCTAAACATCCTCGAAAAACATGTTCAAAT
5377794 CATACCTAAA
1 CATACCTAAA
5377804 TAATAACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.22
Consensus pattern (34 bp):
CATACCTAAACATCCTCGAAAAACATGTTCAAAT
Found at i:5380175 original size:26 final size:23
Alignment explanation
Indices: 5380110--5380165 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
5380100 ACGATATCCA
* * *
5380110 AACAATATTAAAAGTGGTAGCGG
1 AACAACATTAAAAGTAGCAGCGG
*
5380133 AACAAGATTAAAAGTAGCAGCGG
1 AACAACATTAAAAGTAGCAGCGG
5380156 AACAACATTA
1 AACAACATTA
5380166 CAAACGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (23 bp):
AACAACATTAAAAGTAGCAGCGG
Found at i:5382887 original size:188 final size:189
Alignment explanation
Indices: 5382570--5382946 Score: 747
Period size: 188 Copynumber: 2.0 Consensus size: 189
5382560 CTAAATCAAG
5382570 TTCTCAAGACATCAAAAACATAATATTACAAGAAAAAGACTAAATTAAACTAACCAATTGAAGGT
1 TTCTCAAGACATCAAAAACATAATATTACAAGAAAAAGACTAAATTAAACTAACCAATTGAAGGT
5382635 TTAAAACTTCCAACCCTAGGTTGACACTCTTCTCTCCTTCTTCTTTCTATATTCAATTTTCAAGA
66 TTAAAACTTCCAACCCTAGGTTGACACTCTTCTCTCCTTCTTCTTTCTATATTCAATTTTCAAGA
5382700 AATGAGAGATAAAATTTTCCTCTTTCTTTCCATTACATTGTTTTA-TTTATATATTTTA
131 AATGAGAGATAAAATTTTCCTCTTTCTTTCCATTACATTGTTTTATTTTATATATTTTA
5382758 TTCTCAAGACATCAAAAACATAATATTACAAGAAAAAGACTAAATTAAACTAACCAATTGAAGGT
1 TTCTCAAGACATCAAAAACATAATATTACAAGAAAAAGACTAAATTAAACTAACCAATTGAAGGT
5382823 TTAAAACTTCCAACCCTAGGTTGACACTCTTCTCTCCTTCTTCTTTCTATATTCAATTTTCAAGA
66 TTAAAACTTCCAACCCTAGGTTGACACTCTTCTCTCCTTCTTCTTTCTATATTCAATTTTCAAGA
5382888 AATGAGAGATAAAATTTTCCTCTTTCTTTCCATTACATTGTTTTATTTTATATATTTTA
131 AATGAGAGATAAAATTTTCCTCTTTCTTTCCATTACATTGTTTTATTTTATATATTTTA
5382947 CATTTTAATT
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 175 0.93
189 13 0.07
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (189 bp):
TTCTCAAGACATCAAAAACATAATATTACAAGAAAAAGACTAAATTAAACTAACCAATTGAAGGT
TTAAAACTTCCAACCCTAGGTTGACACTCTTCTCTCCTTCTTCTTTCTATATTCAATTTTCAAGA
AATGAGAGATAAAATTTTCCTCTTTCTTTCCATTACATTGTTTTATTTTATATATTTTA
Found at i:5382983 original size:22 final size:22
Alignment explanation
Indices: 5382941--5382986 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5382931 TATTTTATAT
5382941 ATTTTACATTTTAATTAATTTA
1 ATTTTACATTTTAATTAATTTA
*
5382963 ATTTTA-ATTTTAATATTATTTA
1 ATTTTACATTTTAAT-TAATTTA
5382985 AT
1 AT
5382987 CAAAACCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTACATTTTAATTAATTTA
Found at i:5393997 original size:30 final size:29
Alignment explanation
Indices: 5393925--5393997 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
5393915 AATAAACACC
5393925 AAAAAT-T-TATTTTAAAAATAAAAAATA
1 AAAAATATATATTTTAAAAATAAAAAATA
* * *
5393952 ACAAAAAAAAGTATTTTAAAATTAAAAAAATA
1 A-AAAATATA-TATTTTAAAAAT-AAAAAATA
5393984 AAAAATATATATTT
1 AAAAATATATATTT
5393998 ATTATATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
30 5 0.14
31 17 0.47
32 9 0.25
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAATATATATTTTAAAAATAAAAAATA
Found at i:5399209 original size:9 final size:9
Alignment explanation
Indices: 5399174--5399215 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
5399164 TGGTGAAGAG
*
5399174 AGAGAGAGGG
1 AGAG-GAGGA
5399184 AGAGGA-GA
1 AGAGGAGGA
5399192 GAGAGGAGGA
1 -AGAGGAGGA
5399202 AGAGGAGGA
1 AGAGGAGGA
5399211 AGAGG
1 AGAGG
5399216 GACATGTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 1 0.03
9 22 0.76
10 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (9 bp):
AGAGGAGGA
Found at i:5401497 original size:15 final size:15
Alignment explanation
Indices: 5401477--5401505 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5401467 CATGCAAATT
5401477 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
5401492 AGAAAAGAAAGAAA
1 AGAAAAGAAAGAAA
5401506 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:5405205 original size:42 final size:42
Alignment explanation
Indices: 5405158--5405320 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 42
5405148 GCACATAAGT
* * ***
5405158 GCTAAACAGAAACCCATAAGGGTTGAACGGAAGCTTGTAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
* * *
5405200 GCTAAACGGAAGCCTATAAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
* * * * * *
5405242 GCTGAACGGGAACCCATTAGGGTTGACCTGAAGCTCAAAAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
* *
5405284 GCTGAACGGAAACCCATTAA-GGTTAAACGGAAACTCA
1 GCTAAACGGAAACCCA-TAAGGGTTAAACGGAAGCTCA
5405321 TATAAGTTAA
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 97 0.98
43 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (42 bp):
GCTAAACGGAAACCCATAAGGGTTAAACGGAAGCTCAAAAGA
Found at i:5405219 original size:21 final size:21
Alignment explanation
Indices: 5405183--5405250 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
5405173 ATAAGGGTTG
* *
5405183 AACGGAAGCTTGTAAGAGCTA
1 AACGGAAGCCTATAAGAGCTA
* *
5405204 AACGGAAGCCTATAAGGGTTA
1 AACGGAAGCCTATAAGAGCTA
* * *
5405225 AACTGAAG-CTCAAAAGAGCTG
1 AACGGAAGCCT-ATAAGAGCTA
5405246 AACGG
1 AACGG
5405251 GAACCCATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (21 bp):
AACGGAAGCCTATAAGAGCTA
Found at i:5405314 original size:21 final size:21
Alignment explanation
Indices: 5405288--5405330 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5405278 AAAAGAGCTG
5405288 AACGGAAACCCAT-TAAGGTTA
1 AACGGAAACCCATATAA-GTTA
*
5405309 AACGGAAACTCATATAAGTTA
1 AACGGAAACCCATATAAGTTA
5405330 A
1 A
5405331 CAGAACCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (21 bp):
AACGGAAACCCATATAAGTTA
Found at i:5407719 original size:3 final size:3
Alignment explanation
Indices: 5407711--5407755 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
5407701 TATACTAAAT
5407711 ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA AT- ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5407754 AT
1 AT
5407756 TAAAAAACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 10 0.27
3 27 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:5407725 original size:5 final size:5
Alignment explanation
Indices: 5407708--5407755 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
5407698 TTATATACTA
5407708 AATAT AATAAT AATAT AATAT -A-AT AATAAT AATAT AATAT AATAT AAT
1 AATAT AAT-AT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AAT
5407756 TAAAAAACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 25 0.64
6 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:5407735 original size:19 final size:19
Alignment explanation
Indices: 5407711--5407755 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
5407701 TATACTAAAT
5407711 ATAATAATAATATAATATA
1 ATAATAATAATATAATATA
5407730 ATAATAATAATATAATATA
1 ATAATAATAATATAATATA
5407749 AT-ATAAT
1 ATAATAAT
5407756 TAAAAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATAATAATATAATATA
Found at i:5410858 original size:13 final size:13
Alignment explanation
Indices: 5410840--5410913 Score: 94
Period size: 13 Copynumber: 5.7 Consensus size: 13
5410830 CTCAAATTTT
5410840 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
5410853 TCAAAATCACTTC
1 TCAAAAGCACTTC
*
5410866 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
5410879 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
5410892 TCAAAAGTACTTT
1 TCAAAAGCACTTC
5410905 TCAAAAGCA
1 TCAAAAGCA
5410914 ATGAAGAACT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:5414868 original size:2 final size:2
Alignment explanation
Indices: 5414861--5414887 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5414851 CATTTTAACA
5414861 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 A
5414888 ACTTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5418893 original size:26 final size:26
Alignment explanation
Indices: 5418864--5418914 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5418854 TGTTCATTTC
5418864 TTCTCTTTTCTCT-T-TTCTATCTTCTA
1 TTCT-TTTTCTCTCTATTC-ATCTTCTA
5418890 TTCTTTTTCTCTCTATTCATCTTCT
1 TTCTTTTTCTCTCTATTCATCTTCT
5418915 TCTAGCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.35
26 12 0.52
27 3 0.13
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (26 bp):
TTCTTTTTCTCTCTATTCATCTTCTA
Found at i:5421258 original size:17 final size:19
Alignment explanation
Indices: 5421236--5421270 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5421226 ATATATACTT
5421236 TTATTTA-TATTT-TTTTA
1 TTATTTACTATTTATTTTA
5421253 TTATTTACTATTTATTTT
1 TTATTTACTATTTATTTT
5421271 TTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTACTATTTATTTTA
Found at i:5424119 original size:27 final size:27
Alignment explanation
Indices: 5424081--5424135 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5424071 TTTATTTAAT
5424081 CATCCAACTTACTCAAATGATCATATA
1 CATCCAACTTACTCAAATGATCATATA
5424108 CATCCAACTTACTCAAATGATCATATA
1 CATCCAACTTACTCAAATGATCATATA
5424135 C
1 C
5424136 TTACTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (27 bp):
CATCCAACTTACTCAAATGATCATATA
Found at i:5424906 original size:23 final size:25
Alignment explanation
Indices: 5424843--5424913 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
5424833 GCACTCTTTC
* * *
5424843 GAGCTATATAACAAGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCATCT
* *
5424868 GAGCCATGTAACAGGAAGCTTATCT
1 GAGCCATATAACAGGAAGCTCATCT
*
5424893 GAG-C-TATAACAGGAAACTCAT
1 GAGCCATATAACAGGAAGCTCAT
5424914 AAGAGTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 14 0.37
24 1 0.03
25 23 0.61
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATCT
Found at i:5424963 original size:45 final size:47
Alignment explanation
Indices: 5424877--5424965 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 47
5424867 TGAGCCATGT
* * *
5424877 AACAGGAAGCTTATCTGAGCTATAACAGGAAACTCATAAGAGTTTAA
1 AACAGGAAACTTATCTAAGCTATAACAGGAAACTCAGAAGAGTTTAA
* *
5424924 AACAGGAAACTTAT-TAAGCT-TAACAGGTAACTCCGAAGAGTT
1 AACAGGAAACTTATCTAAGCTATAACAGGAAACTCAGAAGAGTT
5424966 ATTATCAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 19 0.51
46 5 0.14
47 13 0.35
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.24
Consensus pattern (47 bp):
AACAGGAAACTTATCTAAGCTATAACAGGAAACTCAGAAGAGTTTAA
Found at i:5425044 original size:25 final size:24
Alignment explanation
Indices: 5425010--5425062 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
5425000 AAGTTCAAGC
5425010 GAGCCATATC-AGGAAACTCATAAA
1 GAGCCATATCGA-GAAACTCATAAA
**
5425034 GAGCCTATATCGAGATGCTCATAAA
1 GAGCC-ATATCGAGAAACTCATAAA
5425059 GAGC
1 GAGC
5425063 TACAGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 19 0.76
26 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (24 bp):
GAGCCATATCGAGAAACTCATAAA
Found at i:5431707 original size:17 final size:16
Alignment explanation
Indices: 5431657--5431707 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5431647 CCCAGTTTGA
*
5431657 TTTTAAATT-TATAAT
1 TTTTATATTATATAAT
* *
5431672 ATTTTATATTATGTTAT
1 -TTTTATATTATATAAT
5431689 TTTATATATTATATAAT
1 TTT-TATATTATATAAT
5431706 TT
1 TT
5431708 ATAACACGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTATATTATATAAT
Found at i:5434450 original size:42 final size:44
Alignment explanation
Indices: 5434391--5434472 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
5434381 CTGTTTAAGG
*
5434391 TCGTGATTTGTTTTTG-TT-ATAATTGTGTTTAAGGTATTATGA
1 TCGTGATTTGTTTTTGTTTCATAATTGCGTTTAAGGTATTATGA
*
5434433 TCGTG-TTGTGTTTTTGTTTCATAATTGCGTTTGAGGTATT
1 TCGTGATT-TGTTTTTGTTTCATAATTGCGTTTAAGGTATT
5434473 CATGTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 13 0.37
43 2 0.06
44 18 0.51
ACGTcount: A:0.17, C:0.05, G:0.23, T:0.55
Consensus pattern (44 bp):
TCGTGATTTGTTTTTGTTTCATAATTGCGTTTAAGGTATTATGA
Found at i:5437640 original size:18 final size:19
Alignment explanation
Indices: 5437605--5437645 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
5437595 TTAATTTTTA
*
5437605 AAAAAATATATAATACA-T
1 AAAAAATATATAAAACATT
5437623 AAAAAATACTA-AAAACATT
1 AAAAAATA-TATAAAACATT
5437642 AAAA
1 AAAA
5437646 TAAATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAAATATATAAAACATT
Found at i:5445794 original size:30 final size:30
Alignment explanation
Indices: 5445743--5445827 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 30
5445733 TGAAAAAGTA
5445743 AAAAG-TGATGGAGTCAAAGTGTGAATATTT-
1 AAAAGTTGATGGAGTCAAAGTGT-AA-ATTTG
* *
5445773 AAAAGTTGATGG-GTTATAGTGTAAATTTG
1 AAAAGTTGATGGAGTCAAAGTGTAAATTTG
* * * *
5445802 AAAAATTGAAGGACTAAAAGTGTAAA
1 AAAAGTTGATGGAGTCAAAGTGTAAA
5445828 AAACCAAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.09
29 12 0.27
30 23 0.51
31 6 0.13
ACGTcount: A:0.44, C:0.02, G:0.25, T:0.29
Consensus pattern (30 bp):
AAAAGTTGATGGAGTCAAAGTGTAAATTTG
Found at i:5448918 original size:35 final size:35
Alignment explanation
Indices: 5448862--5448964 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 35
5448852 TTCACTATTT
*
5448862 ATTCGTCGGTTTATCTTACTAGCGCTGGGCGCAAC
1 ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
* * * *
5448897 -TTCCGTCAGTTTATCTGACTAGTGCTGGACAC-AC
1 ATT-CGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
* *
5448931 ATTTGTCGGTTTATCTGACTAGCGCAGGGCGCAA
1 ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAA
5448965 ACTCTTTCGC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
34 27 0.50
35 27 0.50
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.31
Consensus pattern (35 bp):
ATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAC
Found at i:5448918 original size:74 final size:72
Alignment explanation
Indices: 5448783--5448965 Score: 169
Period size: 74 Copynumber: 2.6 Consensus size: 72
5448773 AATAAATAAA
* * * **
5448783 TATTTATTCGTCGGTTTATCTGACTAGCGTTGGGCTCAAATATTGTTGGTATATTCAACTAGAGC
1 TATTTATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAATATCGTCAGTATATTCAACTAGAGC
*
5448848 TGGGTTCAC
66 T-GG-ACAC
* * * * *
5448857 TATTTATTCGTCGGTTTATCTTACTAGCGCTGGGCGCAACT-TCCGTCAGTTTA-TCTGACTAGT
1 TATTTATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAATAT-CGTCAGTATATTC-AACTAGA
5448920 GCTGGACAC
64 GCTGGACAC
* * *
5448929 -A--CATTTGTCGGTTTATCTGACTAGCGCAGGGCGCAAA
1 TATTTATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAA
5448966 CTCTTTCGCA
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
69 31 0.34
71 1 0.01
72 3 0.03
73 5 0.05
74 51 0.56
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (72 bp):
TATTTATTCGTCGGTTTATCTGACTAGCGCTGGGCGCAAATATCGTCAGTATATTCAACTAGAGC
TGGACAC
Found at i:5451941 original size:21 final size:21
Alignment explanation
Indices: 5451917--5451958 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5451907 GAAATTAAAA
5451917 TGTTTTAATTT-CACTTTAATT
1 TGTTTTAATTTCCA-TTTAATT
5451938 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
5451959 ACAAAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:5461574 original size:25 final size:25
Alignment explanation
Indices: 5461546--5461600 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5461536 AGCTCTTTCG
* *
5461546 AGCCATGCAACGGGAAGCTCATGTA
1 AGCCATACAACGGGAAGCTCATGCA
* * *
5461571 AGCCATATAATGGGAAGCTCTTGCA
1 AGCCATACAACGGGAAGCTCATGCA
5461596 AGCCA
1 AGCCA
5461601 ATTATCAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (25 bp):
AGCCATACAACGGGAAGCTCATGCA
Found at i:5465967 original size:6 final size:6
Alignment explanation
Indices: 5465956--5466001 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
5465946 TAGCGGAAAA
*
5465956 AAATAT AAATAT AAATAT AAATA- AACATAT ATATAAT AAA-AT AAAT
1 AAATAT AAATAT AAATAT AAATAT AA-ATAT AAAT-AT AAATAT AAAT
5466002 TTAATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 7 0.21
6 22 0.65
7 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:5465989 original size:16 final size:15
Alignment explanation
Indices: 5465960--5466008 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
5465950 GGAAAAAAAT
*
5465960 ATAAATATAAATATAA
1 ATAAACATAAATAT-A
*
5465976 ATAAACATATATATA
1 ATAAACATAAATATA
*
5465991 ATAAA-ATAAATTTA
1 ATAAACATAAATATA
5466005 ATAA
1 ATAA
5466009 TTTATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.38
15 6 0.21
16 12 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAACATAAATATA
Found at i:5468561 original size:15 final size:15
Alignment explanation
Indices: 5468541--5468569 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5468531 TTATTATAAT
5468541 TGTGTATATATATTG
1 TGTGTATATATATTG
5468556 TGTGTATATATATT
1 TGTGTATATATATT
5468570 ATATGCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (15 bp):
TGTGTATATATATTG
Found at i:5469249 original size:110 final size:110
Alignment explanation
Indices: 5469056--5469276 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
5469046 GCCAAATGAA
5469056 GGTTAAAAATATCTGCTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
1 GGTTAAAAATATCTGCTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
*
5469121 AAAAAGCACTTACTTATAGTGTTTGGTTGTATGAACATAGACATT
66 AAAAAGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
*
5469166 GGTTAATAATATCTGCTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
1 GGTTAAAAATATCTGCTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
*
5469231 AAAAGGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
66 AAAAAGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
5469276 G
1 G
5469277 CACTAAGGGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (110 bp):
GGTTAAAAATATCTGCTAATATAAATTCTATACTTATGCTTAATGGGACTAATTTCAATGAATGA
AAAAAGCACTTACTTATAGTGTTTGGTTGTATGAACACAGACATT
Found at i:5481093 original size:118 final size:119
Alignment explanation
Indices: 5480959--5481195 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 119
5480949 AATTCTTTTT
5480959 ATATTATTATTTTTGCATAAAACAAGTTTAAAAAATATAATACATCAAATAGATTAAAAATATTA
1 ATATTATTATTTTTGCATAAAACAAGTTTAAAAAATATAATACATCAAATAGATTAAAAATATTA
5481024 AAATAAATATTTCCCAATAAATTGAAAATAAATTAAATATATTT-ATATTTATG
66 AAATAAATATTTCCCAATAAATTGAAAATAAATTAAATATATTTAATATTTATG
5481077 ATATTATTATTTTTGCATAAAACAAGTTTAAAAAATATAATACATCAAATAGATTAAAAATATTA
1 ATATTATTATTTTTGCATAAAACAAGTTTAAAAAATATAATACATCAAATAGATTAAAAATATTA
5481142 AAATAAATATTTCCCAATAAATTGAAAATAAATTAAATATATTTAATATTTATG
66 AAATAAATATTTCCCAATAAATTGAAAATAAATTAAATATATTTAATATTTATG
5481196 CTTAAATAAC
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 109 0.92
119 9 0.08
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (119 bp):
ATATTATTATTTTTGCATAAAACAAGTTTAAAAAATATAATACATCAAATAGATTAAAAATATTA
AAATAAATATTTCCCAATAAATTGAAAATAAATTAAATATATTTAATATTTATG
Found at i:5481335 original size:22 final size:23
Alignment explanation
Indices: 5481310--5481353 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5481300 AAAATAATTA
* *
5481310 CAAAACTGTGGCAA-AACAACAC
1 CAAAACAGTGGAAACAACAACAC
5481332 CAAAACAGTGGAAACAACAACA
1 CAAAACAGTGGAAACAACAACA
5481354 TTTTCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.55, C:0.25, G:0.14, T:0.07
Consensus pattern (23 bp):
CAAAACAGTGGAAACAACAACAC
Found at i:5483279 original size:22 final size:22
Alignment explanation
Indices: 5483230--5483279 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
5483220 ATTTATGTTG
*
5483230 TTTTATTTGTTTACTTTTAAAT
1 TTTTATTTGATTACTTTTAAAT
** * *
5483252 ACTTATTTGATTATTTTTTAAT
1 TTTTATTTGATTACTTTTAAAT
5483274 TTTTAT
1 TTTTAT
5483280 AGTTTTTGAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTATTTGATTACTTTTAAAT
Found at i:5488862 original size:16 final size:15
Alignment explanation
Indices: 5488825--5488867 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
5488815 CTCAAGAAAT
5488825 TATAAATAAATTAAA
1 TATAAATAAATTAAA
*
5488840 AATTAAATAAATTAATA
1 TA-TAAATAAATTAA-A
5488857 TATAAA-AAATT
1 TATAAATAAATT
5488868 TTAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 16 0.67
17 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAAATAAATTAAA
Found at i:5491313 original size:28 final size:28
Alignment explanation
Indices: 5491254--5491311 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
5491244 GATTTCCAGG
*
5491254 AAAATGGCCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* *
5491282 AAAAT-GCCCATTTCGGTAAAT-TTAAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
5491308 AAAA
1 AAAA
5491312 AACGGCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
27 15 0.56
28 5 0.19
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:5502009 original size:21 final size:21
Alignment explanation
Indices: 5501974--5502042 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
5501964 ATGAATGTTG
5501974 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
*
5501996 TTTAAGTTT-TCATATATTAT
1 TTTAAATTTATCATATATTAT
* *
5502016 TCTTCAAATTTATTATGTATTAT
1 T-TT-AAATTTATCATATATTAT
5502039 TTTA
1 TTTA
5502043 TACATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.15
21 9 0.22
22 15 0.38
23 10 0.25
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:5504750 original size:18 final size:17
Alignment explanation
Indices: 5504727--5504760 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5504717 GCCCCATAGC
5504727 TAGATACAAACATAATAT
1 TAGATA-AAACATAATAT
*
5504745 TAGATATAACATAATA
1 TAGATAAAACATAATA
5504761 ACAGATACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (17 bp):
TAGATAAAACATAATAT
Found at i:5510771 original size:67 final size:67
Alignment explanation
Indices: 5510658--5510792 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
5510648 TATGAGTTTA
* * *
5510658 TATTACAGGGGATTTTGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGCAGTAGTGTGC
1 TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGC
5510723 TC
66 TC
* * *
5510725 TATTGCAGGGGATTTAGCTTGGACTGGTGATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGC
1 TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGC
5510790 TC
66 TC
5510792 T
1 T
5510793 CTGAATTGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (67 bp):
TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGC
TC
Found at i:5511744 original size:77 final size:77
Alignment explanation
Indices: 5511659--5511811 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 77
5511649 GATTAAATTA
* * * *
5511659 CAATAGAAGTGAAAGTTTAATTATAGATTAAAATAAAATAA-AGGGGATTAAATAGGTAATTATG
1 CAATAGAAGTGAAAGTTTAATTATAGATTAAAAGAAAATAATA-GGGACTAAATAGGCAATGATG
*
5511723 CCAATTGTCAAAC
65 CCAATTGCCAAAC
*
5511736 CAATAGAAGTGAAAGTTTAATTATAGATTAAAGGAAAATAATAGGGACTAAATAGGCAATGATGC
1 CAATAGAAGTGAAAGTTTAATTATAGATTAAAAGAAAATAATAGGGACTAAATAGGCAATGATGC
5511801 CAATTGCCAAA
66 CAATTGCCAAA
5511812 TTTGAGGCGG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
77 68 0.99
78 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (77 bp):
CAATAGAAGTGAAAGTTTAATTATAGATTAAAAGAAAATAATAGGGACTAAATAGGCAATGATGC
CAATTGCCAAAC
Found at i:5513592 original size:16 final size:16
Alignment explanation
Indices: 5513571--5513607 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5513561 CGGTTGTACT
5513571 AGGTCATTAGGGTTCA
1 AGGTCATTAGGGTTCA
5513587 AGGTCATTAGGGTTCA
1 AGGTCATTAGGGTTCA
5513603 AGGTC
1 AGGTC
5513608 CAGTTCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (16 bp):
AGGTCATTAGGGTTCA
Found at i:5518774 original size:23 final size:23
Alignment explanation
Indices: 5518748--5518820 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5518738 AGTGCCACAG
5518748 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
* *
5518771 TGATACGTAGCCGTAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
5518794 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
5518817 TGAT
1 TGAT
5518821 CAATAACACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:5519445 original size:21 final size:21
Alignment explanation
Indices: 5519421--5519465 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5519411 CTTACTTATG
5519421 AACATTTTTCCCTTCTATGGT
1 AACATTTTTCCCTTCTATGGT
5519442 AACATTTTTCCCTTCTATGGT
1 AACATTTTTCCCTTCTATGGT
5519463 AAC
1 AAC
5519466 TCGTTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.44
Consensus pattern (21 bp):
AACATTTTTCCCTTCTATGGT
Found at i:5520471 original size:3 final size:3
Alignment explanation
Indices: 5520463--5520525 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
5520453 GCAAGAACAA
5520463 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
5520511 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
5520526 GAAAAGATAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5520764 original size:31 final size:32
Alignment explanation
Indices: 5520701--5520766 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 32
5520691 TAGTAAAAAT
*
5520701 TATAAATATATATAAGAAATATATGTGTGTGTATA
1 TATAAATATATAAAAGAAATATA---GTGTGTATA
*
5520736 TATATATATATAAAAGAAATATA-TGTGTATA
1 TATAAATATATAAAAGAAATATAGTGTGTATA
5520767 ACGAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.28
35 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (32 bp):
TATAAATATATAAAAGAAATATAGTGTGTATA
Found at i:5521699 original size:6 final size:6
Alignment explanation
Indices: 5521690--5521716 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5521680 TATATGCTAA
5521690 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
5521717 TCAGGAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:5522675 original size:45 final size:44
Alignment explanation
Indices: 5522529--5522693 Score: 215
Period size: 44 Copynumber: 3.7 Consensus size: 44
5522519 TCATCGTTTT
* *
5522529 AATCCGCTCCACTGCAACTTCAGGGAGAT-AGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGG-TTAGTATCTTC
* * *
5522573 AATTTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAGTATCTTC
* * *
5522617 AACCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAGT-ATCTTC
* *
5522662 AGTCTGTTCCACTGCAACTTCAGGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
5522694 ACTTATTATG
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
44 69 0.66
45 36 0.34
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTAGTATCTTC
Found at i:5523120 original size:129 final size:128
Alignment explanation
Indices: 5522856--5523100 Score: 316
Period size: 129 Copynumber: 1.9 Consensus size: 128
5522846 ATCTGATGTG
* * * *
5522856 ATCTGCTCTACTACAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCAATTTCA
1 ATCTGCTCTACTACAACTTCAGAGAGAAAAGATCCATCATTTTAATCCGCTCCACTACAACTTCA
* * *
5522921 GGAAGATAGAATTGGTTTCTTCAATCTACTCCGCTGCAACTTTAGGGAGATAAGACTAGATGCA
66 GGAAGATAGAATTGGTTTCTT-AATCTACTCCACTGCAAATTCAGGGAGATAAGACTAGATGCA
* * ** *
5522985 ATCTGCTCTACTGCAACTTCAGATAGAAAAGATCTGTGATTTTAATCCGCTCCACTACAACTTCA
1 ATCTGCTCTACTACAACTTCAGAGAGAAAAGATCCATCATTTTAATCCGCTCCACTACAACTTCA
* * *
5523050 -GAGAGATAGGATTGGTTT-TT-TTCTTCTCCACTGCAAATTCAGGGAGATAAG
66 GGA-AGATAGAATTGGTTTCTTAATCTACTCCACTGCAAATTCAGGGAGATAAG
5523101 GTTGGTGGCT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
126 26 0.26
128 4 0.04
129 70 0.70
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (128 bp):
ATCTGCTCTACTACAACTTCAGAGAGAAAAGATCCATCATTTTAATCCGCTCCACTACAACTTCA
GGAAGATAGAATTGGTTTCTTAATCTACTCCACTGCAAATTCAGGGAGATAAGACTAGATGCA
Found at i:5523144 original size:44 final size:44
Alignment explanation
Indices: 5523094--5523232 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 44
5523084 AAATTCAGGG
5523094 AGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGA
1 AGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGA
* **** ** ** *
5523138 AGATAAGATTCGCCATCTTCGATCTGCTTTACTACT-GCTTAGGG-
1 AGATAAGGTT-GGTGGCTTAAATCTGCTTCCCTACTACCTT-GGGA
*
5523182 AGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGA
1 AGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGA
5523226 AGATAAG
1 AGATAAG
5523233 ATTCATCGTC
Statistics
Matches: 70, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
43 20 0.29
44 30 0.43
45 20 0.29
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (44 bp):
AGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGA
Found at i:5523196 original size:88 final size:88
Alignment explanation
Indices: 5523090--5523276 Score: 302
Period size: 88 Copynumber: 2.1 Consensus size: 88
5523080 CTGCAAATTC
* *
5523090 AGGGAGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCATC
1 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATC
* * **
5523155 TTCGATCTGCTTTACTACTGCTT
66 TTCAATCTACTCCACTACTGCTT
* *
5523178 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCATCGTC
1 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATC
5523243 TTCAATCTACTCCACTACTGCTT
66 TTCAATCTACTCCACTACTGCTT
5523266 AGGGAGATAAG
1 AGGGAGATAAG
5523277 ATCTACAATC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (88 bp):
AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATC
TTCAATCTACTCCACTACTGCTT
Found at i:5523274 original size:44 final size:43
Alignment explanation
Indices: 5523226--5523410 Score: 153
Period size: 44 Copynumber: 4.2 Consensus size: 43
5523216 TACCTTGGGA
5523226 AGATAAGATTCATCGTCTTCAATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTC-TCGTCTTCAATCTACTCCACTACTGCTTAGGG
* * *
5523270 AGATAAGA-TCTACAATCTTCAACCTACTCCACTGCTGCTTAGGG
1 AGATAAGATTCT-C-GTCTTCAATCTACTCCACTACTGCTTAGGG
* * * * * *
5523314 AGATAAG--GCTGGTGGCTTAAATCTGCTTCC-CTACTACCTTAGGA
1 AGATAAGATTCTCGT--CTTCAATCTAC-TCCACTACT-GCTTAGGG
* * *
5523358 AGATAAGATTTTTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGA-TTCTCGTCTTCAATCTACTCCACTACTGCTTAGGG
*
5523402 AGATTAGAT
1 AGATAAGAT
5523411 CTGCAATCTT
Statistics
Matches: 111, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 18 0.16
44 74 0.67
45 14 0.13
47 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
AGATAAGATTCTCGTCTTCAATCTACTCCACTACTGCTTAGGG
Found at i:5523308 original size:132 final size:132
Alignment explanation
Indices: 5523172--5523474 Score: 473
Period size: 132 Copynumber: 2.3 Consensus size: 132
5523162 TGCTTTACTA
*
5523172 CTGCTTAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTC
1 CTGCTTAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTC
5523237 ATCGTCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCAC
66 ATCGTCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCAC
5523302 TG
131 TG
*
5523304 CTGCTTAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTT
1 CTGCTTAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTC
* * * * * * * *
5523369 TTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATTAGATCTGCAATCTTTAACCTATTCGAC
66 ATCGTCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCAC
5523434 TG
131 TG
* **
5523436 CTGCTCAGGGAGAT-AGGACTGGTGGCTTCGATCTGCTTC
1 CTGCTTAGGGAGATAAGG-CTGGTGGCTTAAATCTGCTTC
5523475 ACTGCCGGTA
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 3 0.02
132 154 0.98
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (132 bp):
CTGCTTAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTC
ATCGTCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCAC
TG
Found at i:5533318 original size:13 final size:12
Alignment explanation
Indices: 5533270--5533336 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 12
5533260 GAAAAAGAAT
5533270 AAAAAGAAGAAGA
1 AAAAAG-AGAAGA
*
5533283 ACAAAGTAGAACG-
1 AAAAAG-AGAA-GA
*
5533296 AAACAGAGAAGA
1 AAAAAGAGAAGA
5533308 AAAAGAGAGAAAGA
1 AAAA-AGAG-AAGA
5533322 AAAAAGAGAA-A
1 AAAAAGAGAAGA
5533333 AAAA
1 AAAA
5533337 TTAGGGTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.13
12 9 0.20
13 21 0.47
14 9 0.20
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.01
Consensus pattern (12 bp):
AAAAAGAGAAGA
Found at i:5533318 original size:25 final size:25
Alignment explanation
Indices: 5533270--5533336 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
5533260 GAAAAAGAAT
* *
5533270 AAAAAGAAGAAGAACAAAGTAGAACG-
1 AAAAAG-AGAAGAA-AAAGGAGAAAGA
*
5533296 AAACAGAGAAGAAAAAGAGAGAAAGA
1 AAAAAGAGAAGAAAAAG-GAGAAAGA
5533322 AAAAAGAGAA-AAAAA
1 AAAAAGAGAAGAAAAA
5533337 TTAGGGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.11
25 17 0.49
26 14 0.40
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.01
Consensus pattern (25 bp):
AAAAAGAGAAGAAAAAGGAGAAAGA
Found at i:5541307 original size:50 final size:50
Alignment explanation
Indices: 5541177--5541338 Score: 162
Period size: 50 Copynumber: 3.2 Consensus size: 50
5541167 TAACTCATAA
** * * *
5541177 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTATTGTAG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAG
* ** * ** * * *
5541227 CTTCAATCTGTTCCACTACACCGCCCGGGAAGTAAGATTCACTGTTGTAG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAG
* * * *
5541277 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGGTGTGG
1 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAG
5541327 CTTTAATCTGTT
1 CTTTAATCTGTT
5541339 CCACTGCATC
Statistics
Matches: 84, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (50 bp):
CTTTAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAG
Found at i:5541311 original size:100 final size:100
Alignment explanation
Indices: 5541177--5541363 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
5541167 TAACTCATAA
** * * *
5541177 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTATTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCAGTGTAGCTTCAATCTGTTCCA
5541242 CTACACCGCCCGGGAAGTAAGATTCACTGTTGTAG
66 CTACACCGCCCGGGAAGTAAGATTCACTGTTGTAG
* * * * *
5541277 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGGTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCAGTGTAGCTTCAATCTGTTCCA
* * * *
5541342 CTGCATCGCCTGGGGAGTAAGA
66 CTACACCGCCCGGGAAGTAAGA
5541364 ATTGATATTC
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCAGTGTAGCTTCAATCTGTTCCA
CTACACCGCCCGGGAAGTAAGATTCACTGTTGTAG
Found at i:5541424 original size:43 final size:45
Alignment explanation
Indices: 5541353--5541441 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 45
5541343 TGCATCGCCT
*
5541353 GGGGAGTAAGAATTGATATTCTCAGTCTGCCCCACTGTAACTTCA
1 GGGGAGTAAGAATTGATATTCTCAGTCTGCCCCACTGCAACTTCA
* * * * *
5541398 GGGG-GTAAGACTTG-TCTTCTTAGTCTGCTCTACTGCAACTTCA
1 GGGGAGTAAGAATTGATATTCTCAGTCTGCCCCACTGCAACTTCA
5541441 G
1 G
5541442 AGAGATAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 25 0.66
44 9 0.24
45 4 0.11
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (45 bp):
GGGGAGTAAGAATTGATATTCTCAGTCTGCCCCACTGCAACTTCA
Found at i:5541725 original size:132 final size:131
Alignment explanation
Indices: 5541526--5541948 Score: 632
Period size: 132 Copynumber: 3.2 Consensus size: 131
5541516 CACTGCAACC
* * * * * *
5541526 TTAGGGGGATAAGACCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTG
1 TTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG-TTGGTG
** *
5541591 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCTACTACT
65 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACT
5541656 GT
130 GT
* *
5541658 TTAGGGAGATAAGATCTACAATCTTCAACCTACTCTGCTGCTGCTTAGGGAGACAAGGTTCGGTG
1 TTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTT-GGTG
* *
5541723 GCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCGGCTCCACTACT
65 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACT
*
5541788 GC
130 GT
*
5541790 TTAAGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTGGGTG
1 TTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTT-GGTG
* *
5541855 GCTTAAATCTGCTTCCCACTATCATAGAAAGATAAGATTTACCGTCTTCT-ATCTGCTCCACTAC
65 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTT-TGATCTGCTCCACTAC
5541919 TGT
129 TGT
* *
5541922 TTAGGGAGATAAGATCTGCTATCTTCA
1 TTAGGGAGATAAGATCTACAATCTTCA
5541949 CTGATCTGTT
Statistics
Matches: 263, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 260 0.99
133 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (131 bp):
TTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTGGTGG
CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTG
T
Found at i:5544833 original size:8 final size:8
Alignment explanation
Indices: 5544820--5544883 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
5544810 ACCACATTTT
5544820 AATAAACA
1 AATAAACA
*
5544828 AATAAATGA
1 AATAAA-CA
* *
5544837 AACAGAATA
1 AATA-AACA
* *
5544846 ATTAAAGA
1 AATAAACA
5544854 AATAAACA
1 AATAAACA
*
5544862 AACAAACA
1 AATAAACA
5544870 AATAAACA
1 AATAAACA
5544878 AATAAA
1 AATAAA
5544884 TCAACCACAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 35 0.80
9 7 0.16
10 2 0.05
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (8 bp):
AATAAACA
Found at i:5544876 original size:12 final size:12
Alignment explanation
Indices: 5544820--5544884 Score: 76
Period size: 12 Copynumber: 5.2 Consensus size: 12
5544810 ACCACATTTT
5544820 AATAAACAAATA
1 AATAAACAAATA
5544832 AATGAAACAGAATA
1 AAT-AAACA-AATA
* *
5544846 ATTAAAGAAATA
1 AATAAACAAATA
* *
5544858 AACAAACAAACA
1 AATAAACAAATA
5544870 AATAAACAAATA
1 AATAAACAAATA
5544882 AAT
1 AAT
5544885 CAACCACACC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 28 0.65
13 9 0.21
14 6 0.14
ACGTcount: A:0.71, C:0.09, G:0.05, T:0.15
Consensus pattern (12 bp):
AATAAACAAATA
Found at i:5545090 original size:4 final size:4
Alignment explanation
Indices: 5545076--5545111 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
5545066 ACATAGTTTA
*
5545076 AAAT GAAT AAAT AAAT AAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAA
5545112 CACAAAACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5545096 original size:17 final size:17
Alignment explanation
Indices: 5545074--5545111 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5545064 TAACATAGTT
*
5545074 TAAAATGAATAAATAAA
1 TAAAATAAATAAATAAA
5545091 TAAAATAAATAAATAAA
1 TAAAATAAATAAATAAA
5545108 TAAA
1 TAAA
5545112 CACAAAACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TAAAATAAATAAATAAA
Found at i:5546359 original size:21 final size:19
Alignment explanation
Indices: 5546311--5546365 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
5546301 TACAAAAATC
* *
5546311 TTTTTTGTTCTCTTCTCTG
1 TTTTTTCTTCTGTTCTCTG
5546330 TTGTTTTCTTCTGTTCTCTTG
1 TT-TTTTCTTCTGTTCTC-TG
*
5546351 TCTTTTTCTTTTGTT
1 T-TTTTTCTTCTGTT
5546366 GTTTTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.43
21 14 0.47
22 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.71
Consensus pattern (19 bp):
TTTTTTCTTCTGTTCTCTG
Found at i:5556408 original size:18 final size:18
Alignment explanation
Indices: 5556373--5556408 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5556363 ACGAAGCGGT
* *
5556373 AATAATAATAGTAGTAAA
1 AATAATAATAATAATAAA
5556391 AATAATAATAATAATAAA
1 AATAATAATAATAATAAA
5556409 CAATCAGAAG
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:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AATAATAATAATAATAAA
Found at i:5564154 original size:93 final size:93
Alignment explanation
Indices: 5563995--5564181 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
5563985 TTAGAAGTGG
5563995 ATCGGGACTTATTCGAGTGCTCCGAAAATTTTTATTTAAAAAAAAAAACTCAATATAACCCCTTT
1 ATCGGGACTTATTCGAGTGCTCCGAAAATTTTTATTTAAAAAAAAAAACTCAATATAACCCCTTT
5564060 ATAATTATCTAACCTTCCCTGTAATTTT
66 ATAATTATCTAACCTTCCCTGTAATTTT
5564088 ATCGGGACTTATTCGAGTGCTCCGAAAATTTTTATTTAAAAAAAAAAACTCAATATAACCCCTTT
1 ATCGGGACTTATTCGAGTGCTCCGAAAATTTTTATTTAAAAAAAAAAACTCAATATAACCCCTTT
5564153 ATAATTATCTAACCTTCCCTGTAATTTT
66 ATAATTATCTAACCTTCCCTGTAATTTT
5564181 A
1 A
5564182 AACCATAACC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (93 bp):
ATCGGGACTTATTCGAGTGCTCCGAAAATTTTTATTTAAAAAAAAAAACTCAATATAACCCCTTT
ATAATTATCTAACCTTCCCTGTAATTTT
Found at i:5567285 original size:17 final size:18
Alignment explanation
Indices: 5567253--5567286 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5567243 AATTTCTTTT
5567253 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
5567271 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
5567287 AGCTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:5567810 original size:15 final size:13
Alignment explanation
Indices: 5567778--5567823 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
5567768 AACTAATAAT
5567778 ATTAATAA-TATA
1 ATTAATAATTATA
5567790 ATTAATAATTATA
1 ATTAATAATTATA
*
5567803 ATT-ATAATAATAA
1 ATTAATAATTAT-A
5567816 ATTAATAA
1 ATTAATAA
5567824 CAAAATCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 15 0.50
13 11 0.37
14 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAATAATTATA
Found at i:5568228 original size:17 final size:18
Alignment explanation
Indices: 5568200--5568243 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5568190 ATAATTGTTT
5568200 TAAAAGTAAAAC-AGAAAG
1 TAAAA-TAAAACTAGAAAG
5568218 TAAAATAAAACTAGAAAG
1 TAAAATAAAACTAGAAAG
5568236 --AAATAAAA
1 TAAAATAAAA
5568244 GTAAACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (18 bp):
TAAAATAAAACTAGAAAG
Found at i:5568330 original size:17 final size:16
Alignment explanation
Indices: 5568291--5568329 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5568281 TAAAACTAAT
5568291 ATTTTTTAAAAATTCA
1 ATTTTTTAAAAATTCA
*
5568307 ATTTTTTACAATATTC-
1 ATTTTTTA-AAAATTCA
5568323 ATTTTTT
1 ATTTTTT
5568330 TCCTTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTAAAAATTCA
Found at i:5569972 original size:12 final size:14
Alignment explanation
Indices: 5569954--5569995 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5569944 GAATTATCTA
5569954 ATATATAT-TAAAT
1 ATATATATATAAAT
*
5569967 -TATATATATATAT
1 ATATATATATAAAT
5569980 ATATATATATGAAAT
1 ATATATATAT-AAAT
5569995 A
1 A
5569996 GGAAATTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 9 0.38
15 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:5577736 original size:39 final size:39
Alignment explanation
Indices: 5577682--5577759 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
5577672 GCTTTATATA
5577682 GCCAAAACTAAAATGAAAATTACAAAACAAAAAAAATGT
1 GCCAAAACTAAAATGAAAATTACAAAACAAAAAAAATGT
5577721 GCCAAAACTAAAATGAAAATTACAAAACAAAAAAAATGT
1 GCCAAAACTAAAATGAAAATTACAAAACAAAAAAAATGT
5577760 CTTTTTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (39 bp):
GCCAAAACTAAAATGAAAATTACAAAACAAAAAAAATGT
Found at i:5577753 original size:20 final size:20
Alignment explanation
Indices: 5577684--5577752 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
5577674 TTTATATAGC
5577684 CAAAACTAAAATGAAAATTA
1 CAAAACTAAAATGAAAATTA
*
5577704 CAAAAC-AAAA--AAAATGTGC
1 CAAAACTAAAATGAAAAT-T-A
5577723 CAAAACTAAAATGAAAATTA
1 CAAAACTAAAATGAAAATTA
5577743 CAAAAC-AAAA
1 CAAAACTAAAA
5577753 AAAATGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.12
18 1 0.02
19 14 0.33
20 16 0.38
21 1 0.02
22 5 0.12
ACGTcount: A:0.67, C:0.13, G:0.06, T:0.14
Consensus pattern (20 bp):
CAAAACTAAAATGAAAATTA
Found at i:5587597 original size:21 final size:21
Alignment explanation
Indices: 5587573--5587623 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5587563 AAAATAGTAG
*
5587573 TAAAAGTGATATTA-ATTATTA
1 TAAAAGTGAGATTAGA-TATTA
*
5587594 TAAAAATGAGATTAGATATTA
1 TAAAAGTGAGATTAGATATTA
*
5587615 TAATAGTGA
1 TAAAAGTGA
5587624 AATCGATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (21 bp):
TAAAAGTGAGATTAGATATTA
Found at i:5590312 original size:9 final size:9
Alignment explanation
Indices: 5590298--5590382 Score: 89
Period size: 9 Copynumber: 9.4 Consensus size: 9
5590288 TTTGGTTAAA
5590298 AATTAACCG
1 AATTAACCG
*
5590307 AATTAACAG
1 AATTAACCG
* *
5590316 AATTATCCA
1 AATTAACCG
5590325 AATTAACCG
1 AATTAACCG
*
5590334 AATTACCCG
1 AATTAACCG
* *
5590343 AATTAATCA
1 AATTAACCG
*
5590352 AATTACCCG
1 AATTAACCG
**
5590361 AATTAATTG
1 AATTAACCG
5590370 AATTAACCG
1 AATTAACCG
5590379 AATT
1 AATT
5590383 GAATCACTAC
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:5590382 original size:27 final size:27
Alignment explanation
Indices: 5590297--5590382 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
5590287 TTTTGGTTAA
*
5590297 AAATTAACCGAATTAACAGAATTATCC
1 AAATTAACCGAATTAACAGAATTAACC
* * *
5590324 AAATTAACCGAATTACCCGAATTAATC
1 AAATTAACCGAATTAACAGAATTAACC
* **
5590351 AAATTACCCGAATTAATTGAATTAACC
1 AAATTAACCGAATTAACAGAATTAACC
*
5590378 GAATT
1 AAATT
5590383 GAATCACTAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATTAACCGAATTAACAGAATTAACC
Found at i:5590712 original size:18 final size:18
Alignment explanation
Indices: 5590686--5590728 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5590676 TTTATGATTG
* *
5590686 GGTTGGGTTGGGTAATTA
1 GGTTTGGTTGGATAATTA
* *
5590704 GGTTTGGTTGGATACTTG
1 GGTTTGGTTGGATAATTA
5590722 GGTTTGG
1 GGTTTGG
5590729 ACTGAGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (18 bp):
GGTTTGGTTGGATAATTA
Found at i:5595877 original size:20 final size:20
Alignment explanation
Indices: 5595836--5595883 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5595826 TTATAGTTAA
* *
5595836 TTAATTATTATTGTGCATTT
1 TTAATTATTATTGTGAAATT
5595856 TTAATTATTATT-TGAAAATT
1 TTAATTATTATTGTG-AAATT
*
5595876 TTTATTAT
1 TTAATTAT
5595884 AATATCTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (20 bp):
TTAATTATTATTGTGAAATT
Found at i:5595893 original size:22 final size:21
Alignment explanation
Indices: 5595852--5595894 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5595842 ATTATTGTGC
*
5595852 ATTTTTAATTATTATTTGAAA
1 ATTTTTAATTATTATCTGAAA
5595873 ATTTTT-ATTATAATATCTGAAA
1 ATTTTTAATTAT--TATCTGAAA
5595895 TAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTTTTAATTATTATCTGAAA
Found at i:5598491 original size:114 final size:115
Alignment explanation
Indices: 5598281--5598511 Score: 410
Period size: 114 Copynumber: 2.0 Consensus size: 115
5598271 TTTCAATTCT
* * *
5598281 TGGGTTCATCTCACTTAAGCTAATTCAATTAGGGTTTTTTTTTTTTTTTGTTTTTTTTTTTGCGG
1 TGGGTTCATCTCACTTAAGCTAATTCAATTAGGG-TTTTTTTTTTTTTTGCTTTTGTTTTTGCAG
*
5598346 TTGTTTTCTTCACATCTACCTCGTTGGCTTCAAGTTCTTCTTACTGAGAAA
65 CTGTTTTCTTCACATCTACCTCGTTGGCTTCAAGTTCTTCTTACTGAGAAA
5598397 TGGGTTCATCTCACTTAAGCTAATTCAATTAGGG-TTTTTTTTTTTTTGCTTTTGTTTTTGCAGC
1 TGGGTTCATCTCACTTAAGCTAATTCAATTAGGGTTTTTTTTTTTTTTGCTTTTGTTTTTGCAGC
5598461 TGTTTTCTTCACATCTACCTCGTTGGCTTCAAGTTCTTCTTACTGAGAAA
66 TGTTTTCTTCACATCTACCTCGTTGGCTTCAAGTTCTTCTTACTGAGAAA
5598511 T
1 T
5598512 TCTTCAACGC
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 77 0.69
116 34 0.31
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (115 bp):
TGGGTTCATCTCACTTAAGCTAATTCAATTAGGGTTTTTTTTTTTTTTGCTTTTGTTTTTGCAGC
TGTTTTCTTCACATCTACCTCGTTGGCTTCAAGTTCTTCTTACTGAGAAA
Done.