Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 161 of 279
Found at i:53196069 original size:154 final size:154
Alignment explanation
Indices: 53195885--53196193 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
53195875 TTCTATACAA
53195885 GCCATATAACAAACACAACAACATATTTGCTCAATTCTTTTCATTTGCTTACCTATAAACTTTTT
1 GCCATATAACAAACACAACAACATATTTGCTCAATTCTTTTCATTTGCTTACCTATAAACTTTTT
53195950 ACAATATATTCACAATTCATTTGTATTCACACTTTACTTCTTAACAATATACCATTTTAATTCAT
66 ACAATATATTCACAATTCATTTGTATTCACACTTTACTTCTTAACAATATACCATTTTAATTCAT
53196015 TCCAACATCAATCATCATCCATGT
131 TCCAACATCAATCATCATCCATGT
53196039 GCCATATAACAAACACAACAACATATTTGCTCAATTCTTTTCATTTGCTTACCTATAAACTTTTT
1 GCCATATAACAAACACAACAACATATTTGCTCAATTCTTTTCATTTGCTTACCTATAAACTTTTT
53196104 ACAATATATTCACAATTCATTTGTATTCACACTTTACTTCTTAACAATATACCATTTTAATTCAT
66 ACAATATATTCACAATTCATTTGTATTCACACTTTACTTCTTAACAATATACCATTTTAATTCAT
53196169 TCCAACATCAATCATCATCCATGT
131 TCCAACATCAATCATCATCCATGT
53196193 G
1 G
53196194 AACTTCACTC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (154 bp):
GCCATATAACAAACACAACAACATATTTGCTCAATTCTTTTCATTTGCTTACCTATAAACTTTTT
ACAATATATTCACAATTCATTTGTATTCACACTTTACTTCTTAACAATATACCATTTTAATTCAT
TCCAACATCAATCATCATCCATGT
Found at i:53196258 original size:13 final size:14
Alignment explanation
Indices: 53196242--53196277 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
53196232 CAATCTCATA
53196242 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
53196255 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
53196268 TCTC-ATTTCA
1 TCTCAATTTCA
53196278 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:53196267 original size:18 final size:19
Alignment explanation
Indices: 53196229--53196269 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
53196219 TGGTTCATGT
53196229 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
53196248 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
53196266 TTTC
1 TTTC
53196270 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:53197811 original size:38 final size:39
Alignment explanation
Indices: 53197751--53197847 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
53197741 CGGATAGATT
* *
53197751 CGATGAGGTACTGGGTACCAACT-TTACTTCG-ACTAGGC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTA-GC
* * * *
53197789 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
*
53197828 CAATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
53197848 TATTGGTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.52
40 4 0.08
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
Found at i:53198691 original size:15 final size:15
Alignment explanation
Indices: 53198671--53198717 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
53198661 TAATATATAT
53198671 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
53198686 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
53198701 TTCAATCAATATAAA
1 TTCAATCAATATAAA
53198716 TT
1 TT
53198718 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:53199040 original size:14 final size:14
Alignment explanation
Indices: 53199021--53199056 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53199011 TTTTTTTCTT
53199021 TTTCATTTCTTATA
1 TTTCATTTCTTATA
*
53199035 TTTCATTTCTTTTA
1 TTTCATTTCTTATA
53199049 TTTCATTT
1 TTTCATTT
53199057 ATTTCTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCATTTCTTATA
Found at i:53199072 original size:13 final size:13
Alignment explanation
Indices: 53199054--53199085 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53199044 TTTTATTTCA
53199054 TTTATTTCTTTAT
1 TTTATTTCTTTAT
53199067 TTTATTTCTTTAT
1 TTTATTTCTTTAT
53199080 TTTATT
1 TTTATT
53199086 ATTAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:53210520 original size:10 final size:11
Alignment explanation
Indices: 53210505--53210556 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 11
53210495 TAAAGTGATT
53210505 AAATTAAAA-A
1 AAATTAAAATA
53210515 AAATTAAAACT-
1 AAATTAAAA-TA
53210526 --ATTAAAATA
1 AAATTAAAATA
53210535 AAA-TAAAATA
1 AAATTAAAATA
53210545 AAA-TAAAATA
1 AAATTAAAATA
53210555 AA
1 AA
53210557 CTTTATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.03
9 7 0.19
10 28 0.76
11 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:53210529 original size:24 final size:24
Alignment explanation
Indices: 53210502--53210547 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53210492 ATTTAAAGTG
*
53210502 ATTAAATTAAAA-AAAATTAAAACT
1 ATTAAAATAAAATAAAA-TAAAACT
53210526 ATTAAAATAAAATAAAATAAAA
1 ATTAAAATAAAATAAAATAAAA
53210548 TAAAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
ATTAAAATAAAATAAAATAAAACT
Found at i:53210538 original size:5 final size:5
Alignment explanation
Indices: 53210528--53210556 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53210518 TTAAAACTAT
53210528 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
53210557 CTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:53211364 original size:20 final size:20
Alignment explanation
Indices: 53211339--53211381 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
53211329 ATTTATTTAT
* *
53211339 TAAAATAATAGTTTTATAAA
1 TAAAATAATAATCTTATAAA
53211359 TAAAATAATAATCTTATAAA
1 TAAAATAATAATCTTATAAA
53211379 TAA
1 TAA
53211382 GCAATTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATAATAATCTTATAAA
Found at i:53216068 original size:7 final size:7
Alignment explanation
Indices: 53216056--53216098 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
53216046 CATGTTGCCA
53216056 TAAACCC
1 TAAACCC
53216063 TAAACCC
1 TAAACCC
53216070 TAAACCC
1 TAAACCC
* *
53216077 TAAATCT
1 TAAACCC
*
53216084 TAAACCT
1 TAAACCC
53216091 TAAACCC
1 TAAACCC
53216098 T
1 T
53216099 CCTCATCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:53217260 original size:13 final size:14
Alignment explanation
Indices: 53217244--53217279 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
53217234 CAATCTCATA
53217244 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
53217257 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
53217270 TCTC-ATTTCA
1 TCTCAATTTCA
53217280 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:53217269 original size:18 final size:19
Alignment explanation
Indices: 53217231--53217271 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
53217221 TGGTTCATGT
53217231 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
53217250 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
53217268 TTTC
1 TTTC
53217272 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:53217461 original size:39 final size:38
Alignment explanation
Indices: 53217394--53217528 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
53217384 ACCAATATGG
* * *
53217394 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
53217433 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
53217471 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
53217512 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
53217529 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:53217794 original size:18 final size:19
Alignment explanation
Indices: 53217768--53217806 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
53217758 TTTCAATTCA
53217768 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
53217787 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
53217805 AT
1 AT
53217807 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:53219132 original size:5 final size:5
Alignment explanation
Indices: 53219122--53219178 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
53219112 TTACTTATTT
* *
53219122 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
53219170 ATAT- ATATA
1 ATATA ATATA
53219179 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:53219138 original size:12 final size:12
Alignment explanation
Indices: 53219121--53219176 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
53219111 TTTACTTATT
53219121 TATATAATATAA
1 TATATAATATAA
53219133 TATATAATATAATA
1 TATATAATAT-A-A
53219147 TACTATAATATAA
1 TA-TATAATATAA
*
53219160 TA-ATAATTTAA
1 TATATAATATAA
53219171 TATATA
1 TATATA
53219177 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:53219191 original size:26 final size:26
Alignment explanation
Indices: 53219123--53219178 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
53219113 TACTTATTTA
*
53219123 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
53219150 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
53219175 TATA
1 TATA
53219179 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:53223846 original size:13 final size:14
Alignment explanation
Indices: 53223830--53223865 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
53223820 CAATCTCATA
53223830 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
53223843 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
53223856 TCTC-ATTTCA
1 TCTCAATTTCA
53223866 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:53223855 original size:18 final size:19
Alignment explanation
Indices: 53223817--53223857 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
53223807 TGGTTCATGT
53223817 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
53223836 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
53223854 TTTC
1 TTTC
53223858 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:53224047 original size:39 final size:38
Alignment explanation
Indices: 53223980--53224114 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
53223970 ACCAATATGG
* * *
53223980 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
53224019 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
53224057 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
53224098 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
53224115 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:53224380 original size:18 final size:19
Alignment explanation
Indices: 53224354--53224392 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
53224344 TTTCAATTCA
53224354 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
53224373 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
53224391 AT
1 AT
53224393 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:53225724 original size:5 final size:5
Alignment explanation
Indices: 53225714--53225766 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
53225704 TTACTTATTT
* *
53225714 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
53225762 ATATA
1 ATATA
53225767 TATTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:53225730 original size:12 final size:12
Alignment explanation
Indices: 53225713--53225768 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
53225703 TTTACTTATT
53225713 TATATAATATAA
1 TATATAATATAA
53225725 TATATAATATAATA
1 TATATAATAT-A-A
53225739 TACTATAATATAA
1 TA-TATAATATAA
*
53225752 TA-ATAATTTAA
1 TATATAATATAA
53225763 TATATA
1 TATATA
53225769 TTTTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:53228612 original size:14 final size:14
Alignment explanation
Indices: 53228593--53228619 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53228583 GGTGACATCC
53228593 ATATGTGTATATAT
1 ATATGTGTATATAT
53228607 ATATGTGTATATA
1 ATATGTGTATATA
53228620 AATAAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
ATATGTGTATATAT
Found at i:53237486 original size:39 final size:39
Alignment explanation
Indices: 53237443--53237588 Score: 256
Period size: 39 Copynumber: 3.7 Consensus size: 39
53237433 TGTGTGAGAT
*
53237443 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53237482 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
53237521 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
53237560 CTATATCCGGGCTAAGACCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
53237589 TGTGTTGGAA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 102 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53240512 original size:132 final size:132
Alignment explanation
Indices: 53240275--53240534 Score: 475
Period size: 132 Copynumber: 2.0 Consensus size: 132
53240265 TTTGTTATGG
* *
53240275 AGGAAGAACCAGTTCTGGTGGCTGTGCTATATATTCTGATATAAGCAGCTTTGCTGCGGATTATA
1 AGGAAGAACCAGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTGCTGCGGATTATA
53240340 GTTAGTGCCCCAACCGGTGCTAACACTGTAAGTGTAGGGATGACGTGGGTGATTTATTCCCCATA
66 GTTAGTGCCCCAACCGGTGCTAACACTGTAAGTGTAGGGATGACGTGGGTGATTTATTCCCCATA
53240405 GA
131 GA
*
53240407 AGGAAGAACCCGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTGCTGCGGATTATA
1 AGGAAGAACCAGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTGCTGCGGATTATA
* *
53240472 GTTAGTGCCGCAACCGGTGCTAACACTGTAAGTGTAGGGATGGCGTGGGTGATTTATTCCCCA
66 GTTAGTGCCCCAACCGGTGCTAACACTGTAAGTGTAGGGATGACGTGGGTGATTTATTCCCCA
53240535 CAGGAAGTGT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 123 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (132 bp):
AGGAAGAACCAGTTCTGGTGGCTGTGCCACATATTCTGATATAAGCAGCTTTGCTGCGGATTATA
GTTAGTGCCCCAACCGGTGCTAACACTGTAAGTGTAGGGATGACGTGGGTGATTTATTCCCCATA
GA
Found at i:53240697 original size:59 final size:59
Alignment explanation
Indices: 53240633--53240768 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
53240623 AACTGTGTTG
*
53240633 ATATGGGCAAGGCCCAATATA-TCTCG-ACTTGTATA-GGGCTACGGCCCAGATTGATACTA
1 ATATGGGCAAGGCCCAATATACTCT-GTAC-TGTA-AGGGGCTACGGCCCAGATTAATACTA
* * * * *
53240692 ATATGGGCTAGGCCCAGTATACTCTGTTACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCAAGGCCCAATATACTCTG-TACTGTAAGGGGCTACGGCCCAGATTAATACTA
53240752 ATATGGGCTAAGGCCCA
1 ATATGGGC-AAGGCCCA
53240769 GTTAACACTG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 21 0.32
60 35 0.54
61 9 0.14
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (59 bp):
ATATGGGCAAGGCCCAATATACTCTGTACTGTAAGGGGCTACGGCCCAGATTAATACTA
Found at i:53244335 original size:53 final size:53
Alignment explanation
Indices: 53244179--53244344 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
53244169 GACGAAAAAT
* **
53244179 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
53244231 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
53244284 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
53244338 TATGTGA
1 -ATGTGA
53244345 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:53248484 original size:60 final size:59
Alignment explanation
Indices: 53248356--53248494 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 59
53248346 CCCAACTGTG
* * *
53248356 TTGATATGGGCAAGGCCCAATATATCTCGACTTGTATAGGGCTACGGCCCAGATTGATA
1 TTGATATGGGCTAGGCCCAATATATCTCGACTTGTATAGGACTACGGCCCAGATTAATA
* * *
53248415 CTAATATGGGCTAGGCCCAATATA-CTCTGTTAC-TGTA-AGAGACTATGGCCCAGATTAATA
1 TTGATATGGGCTAGGCCCAATATATCTC-G--ACTTGTATAG-GACTACGGCCCAGATTAATA
53248475 TTGATATGGGCTAAGGCCCA
1 TTGATATGGGCT-AGGCCCA
53248495 GTTAACACTG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
58 3 0.04
59 24 0.36
60 31 0.46
61 9 0.13
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (59 bp):
TTGATATGGGCTAGGCCCAATATATCTCGACTTGTATAGGACTACGGCCCAGATTAATA
Found at i:53249185 original size:16 final size:17
Alignment explanation
Indices: 53249153--53249185 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53249143 CATCAAGAAG
53249153 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
53249171 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
53249186 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:53256169 original size:32 final size:32
Alignment explanation
Indices: 53256123--53256188 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
53256113 AAATCTCAAA
* ** *
53256123 TTTTCATAACAATTTTGGTTTAATATATAATT
1 TTTTCATAAAAATTTTAATTTAATATAAAATT
* *
53256155 TTTTTATAAAAATTTTAATTTTATATAAAATT
1 TTTTCATAAAAATTTTAATTTAATATAAAATT
53256187 TT
1 TT
53256189 AATTTAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTTCATAAAAATTTTAATTTAATATAAAATT
Found at i:53256178 original size:17 final size:18
Alignment explanation
Indices: 53256156--53256193 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
53256146 TATATAATTT
53256156 TTTTATA-AAAATTTTAA
1 TTTTATATAAAATTTTAA
53256173 TTTTATATAAAATTTTAA
1 TTTTATATAAAATTTTAA
53256191 TTT
1 TTT
53256194 AATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATAAAATTTTAA
Found at i:53256194 original size:17 final size:17
Alignment explanation
Indices: 53256145--53256194 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
53256135 TTTTGGTTTA
*
53256145 ATATATAATTTT--TTT
1 ATATAAAATTTTAATTT
53256160 ATA-AAAATTTTAATTTT
1 ATATAAAATTTTAA-TTT
53256177 ATATAAAATTTTAATTT
1 ATATAAAATTTTAATTT
53256194 A
1 A
53256195 ATTTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
17 10 0.33
18 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATAAAATTTTAATTT
Found at i:53256224 original size:27 final size:28
Alignment explanation
Indices: 53256168--53256250 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 28
53256158 TTATAAAAAT
* **
53256168 TTTAATTTTATATAAAATTTTAATTTAA
1 TTTAATTTTACATAAAATTTTAATACAA
53256196 TTTAATTTT-CAT-AAATTATTAATACAA
1 TTTAATTTTACATAAAATT-TTAATACAA
**
53256223 TTATTTTTTTACA-AAAA--TTAATACAA
1 TT-TAATTTTACATAAAATTTTAATACAA
53256249 TT
1 TT
53256251 ATTCACATGC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
26 16 0.35
27 11 0.24
28 14 0.30
29 5 0.11
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAATTTTACATAAAATTTTAATACAA
Found at i:53256863 original size:31 final size:31
Alignment explanation
Indices: 53256828--53256898 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
53256818 AAAAAATGAC
53256828 AATTTAACATT-TTTAAAAATA-TTAATAATCA
1 AATTTAAC-TTATTTAAAAATATTTAAT-ATCA
* *
53256859 AATTTGACTTATTTTAAAATATTTAATATCA
1 AATTTAACTTATTTAAAAATATTTAATATCA
*
53256890 AATTAAACT
1 AATTTAACT
53256899 ATAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 2 0.06
31 27 0.79
32 5 0.15
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (31 bp):
AATTTAACTTATTTAAAAATATTTAATATCA
Found at i:53259466 original size:21 final size:21
Alignment explanation
Indices: 53259426--53259487 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
53259416 TGAATACACC
*
53259426 AACAAAAGCTC-GAA-AGCTG
1 AACAAAAGCTCATAAGAGCTG
*
53259445 AACAGAAGCTCATAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
* *
53259466 AATAAAAGCTCGTAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
53259487 A
1 A
53259488 TCTACCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 10 0.28
20 2 0.06
21 24 0.67
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTG
Found at i:53260617 original size:10 final size:10
Alignment explanation
Indices: 53260602--53260638 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
53260592 CATAAATATT
53260602 TTTATAAATA
1 TTTATAAATA
53260612 TTTATAAATA
1 TTTATAAATA
53260622 TTTATATAAATA
1 -TT-TATAAATA
53260634 TTTAT
1 TTTAT
53260639 GGAGTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.52
11 4 0.16
12 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATAAATA
Found at i:53260621 original size:22 final size:22
Alignment explanation
Indices: 53260593--53260638 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
53260583 TAAACGAGCC
*
53260593 ATAAATATTTTTATAAATATTT
1 ATAAATATTTATATAAATATTT
53260615 ATAAATATTTATATAAATATTT
1 ATAAATATTTATATAAATATTT
53260637 AT
1 AT
53260639 GGAGTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAATATTTATATAAATATTT
Found at i:53260637 original size:12 final size:12
Alignment explanation
Indices: 53260593--53260638 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
53260583 TAAACGAGCC
*
53260593 ATAAATATTTTT
1 ATAAATATTTAT
53260605 ATAAATA-TT-T
1 ATAAATATTTAT
53260615 ATAAATATTTAT
1 ATAAATATTTAT
53260627 ATAAATATTTAT
1 ATAAATATTTAT
53260639 GGAGTGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.25
11 4 0.12
12 20 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATAAATATTTAT
Found at i:53262745 original size:28 final size:28
Alignment explanation
Indices: 53262692--53262775 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
53262682 CACTTTGTGC
53262692 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
53262721 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
53262749 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
53262776 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:53262787 original size:23 final size:24
Alignment explanation
Indices: 53262696--53262789 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
53262686 TTGTGCTATT
53262696 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
53262723 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
53262753 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
53262776 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
53262790 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:53263016 original size:21 final size:21
Alignment explanation
Indices: 53262992--53263065 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
53262982 AGGCACTTTA
53262992 TGTGTCGTATTTCAAGCACCTTG
1 TGTGTCGTA--TCAAGCACCTTG
*
53263015 TGTGTCGTATCAAGCACCTCG
1 TGTGTCGTATCAAGCACCTTG
* * *
53263036 TGTGTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAAGCACCTTG
*
53263056 TGTGCCGTAT
1 TGTGTCGTAT
53263066 ATTGATCAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.23
21 25 0.57
23 9 0.20
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.36
Consensus pattern (21 bp):
TGTGTCGTATCAAGCACCTTG
Found at i:53264302 original size:46 final size:48
Alignment explanation
Indices: 53264144--53264312 Score: 161
Period size: 46 Copynumber: 3.5 Consensus size: 48
53264134 TGGTTGGACC
53264144 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * * *
53264190 ATGGCATCAGAGATATGTGATTACGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
*
53264243 ATGGCATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* *
53264289 ATGGC-TACGGTGTGTGATATGTGA
1 ATGGCAT-CAGAGTGTGATATGTGA
53264313 CTATGTACAA
Statistics
Matches: 100, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
45 1 0.01
46 33 0.33
47 8 0.08
48 18 0.18
51 7 0.07
52 5 0.05
53 27 0.27
54 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.31
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:53267353 original size:19 final size:20
Alignment explanation
Indices: 53267308--53267355 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
53267298 TTAATATTTT
*
53267308 AATATAATAAAAATCTATTTA
1 AATA-AATAAAAATCTAATTA
**
53267329 CTTAAATAAAAAT-TAATTA
1 AATAAATAAAAATCTAATTA
53267348 AATAAATA
1 AATAAATA
53267356 TATTACAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAATAAAAATCTAATTA
Found at i:53268834 original size:12 final size:12
Alignment explanation
Indices: 53268817--53268841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53268807 ATAAAAATAC
53268817 CTACAATTTAGT
1 CTACAATTTAGT
53268829 CTACAATTTAGT
1 CTACAATTTAGT
53268841 C
1 C
53268842 AGGTAGTCAG
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:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (12 bp):
CTACAATTTAGT
Found at i:53285715 original size:30 final size:30
Alignment explanation
Indices: 53285679--53285735 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53285669 TTGAATATCT
53285679 TATGTTATAA-AA-AATATTATATTAATTATA
1 TATGTTA-AATAATAATATTATA-TAATTATA
53285709 TATGTTAAATAATAATATTATATAATT
1 TATGTTAAATAATAATATTATATAATT
53285736 GTAACGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 14 0.56
31 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TATGTTAAATAATAATATTATATAATTATA
Found at i:53286161 original size:18 final size:18
Alignment explanation
Indices: 53286125--53286161 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53286115 GGCACAAGTG
*
53286125 TTAAATAAATATTTGTTA
1 TTAAATAAATATTTATTA
*
53286143 TTAAATAAATTTTTATTA
1 TTAAATAAATATTTATTA
53286161 T
1 T
53286162 AGTTGTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATAAATATTTATTA
Found at i:53286207 original size:13 final size:13
Alignment explanation
Indices: 53286189--53286216 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53286179 TATATATATA
53286189 AAAGAAACAAAAG
1 AAAGAAACAAAAG
53286202 AAAGAAACAAAAG
1 AAAGAAACAAAAG
53286215 AA
1 AA
53286217 TAAAAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:53286762 original size:15 final size:15
Alignment explanation
Indices: 53286744--53286800 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
53286734 TATCTGTTTT
53286744 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
53286759 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
53286774 ATTGAATTTATATTG
1 ATTGAATTTATATTG
53286789 ATTGAA-TTATAT
1 ATTGAATTTATAT
53286801 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:53286779 original size:30 final size:28
Alignment explanation
Indices: 53286740--53286798 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
53286730 TGAATATCTG
53286740 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
53286769 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
53286798 T
1 T
53286799 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:53287219 original size:21 final size:22
Alignment explanation
Indices: 53287184--53287235 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
53287174 AGGCACTTTA
53287184 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
53287207 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
53287228 TGTGTCGT
1 TGTGTCGT
53287236 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 20 0.69
23 9 0.31
ACGTcount: A:0.12, C:0.25, G:0.29, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:53288162 original size:18 final size:18
Alignment explanation
Indices: 53288126--53288162 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53288116 GGCACAAGTG
*
53288126 TTAAATAAATATTTGTTA
1 TTAAATAAATATTTATTA
*
53288144 TTAAATAAATTTTTATTA
1 TTAAATAAATATTTATTA
53288162 T
1 T
53288163 AGTTGTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATAAATATTTATTA
Found at i:53288208 original size:13 final size:13
Alignment explanation
Indices: 53288190--53288217 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53288180 TATATATATA
53288190 AAAGAAACAAAAG
1 AAAGAAACAAAAG
53288203 AAAGAAACAAAAG
1 AAAGAAACAAAAG
53288216 AA
1 AA
53288218 TAAAAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:53290835 original size:39 final size:39
Alignment explanation
Indices: 53290789--53290928 Score: 244
Period size: 39 Copynumber: 3.6 Consensus size: 39
53290779 GCTCTGATGA
53290789 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
53290828 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
53290867 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
53290906 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
53290929 AGATCACGAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 96 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:53292656 original size:19 final size:20
Alignment explanation
Indices: 53292611--53292657 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
53292601 AAAATATAAA
53292611 AATATAAAATTTATATTTAAT
1 AATATAAAA-TTATATTTAAT
* **
53292632 ACTATAAAA-TATATTTTTT
1 AATATAAAATTATATTTAAT
53292651 AATATAA
1 AATATAA
53292658 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATAAAATTATATTTAAT
Found at i:53292662 original size:13 final size:12
Alignment explanation
Indices: 53292639--53292674 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
53292629 AATACTATAA
53292639 AATATATTTTTT
1 AATATATTTTTT
53292651 AATATAATTTTTT
1 AATAT-ATTTTTT
*
53292664 AATTTATTTTT
1 AATATATTTTT
53292675 AATGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
AATATATTTTTT
Found at i:53294473 original size:22 final size:22
Alignment explanation
Indices: 53294445--53294490 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
53294435 TACCTCAAGT
*
53294445 TAGTTGCAATTTCTCCATATTA
1 TAGTTGCAATTTATCCATATTA
53294467 TAGTTGCAATTTATCCATATTA
1 TAGTTGCAATTTATCCATATTA
53294489 TA
1 TA
53294491 AATCCAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (22 bp):
TAGTTGCAATTTATCCATATTA
Found at i:53297084 original size:122 final size:122
Alignment explanation
Indices: 53296922--53297170 Score: 408
Period size: 122 Copynumber: 2.0 Consensus size: 122
53296912 TGTGTTTTGC
* * *
53296922 TTTTGAATATGTAGAAGGCAGTACTATTGCTAGGTACAGGTAAGTTTCACTACTTCCAGGAACTG
1 TTTTTAATATGCAAAAGGCAGTACTATTGCTAGGTACAGGTAAGTTTCACTACTTCCAGGAACTG
* * *
53296987 AGATACCACTATGGTCTAGAGTATCTAATATATGACTAATAATATTTTTGTTAGTTT
66 AAATACCACTATAGTCTAGAGTATCTAATATATGACTAATAATATTTGTGTTAGTTT
* *
53297044 TTTTTAATATGCAAAAGGTAGTACTGTTGCTAGGTACAGGTAAGTTTCACTACTTCCAGGAACTG
1 TTTTTAATATGCAAAAGGCAGTACTATTGCTAGGTACAGGTAAGTTTCACTACTTCCAGGAACTG
* *
53297109 AAATACCACTGTAGTCTAGAGTATCTAATATATGACTACTAATATTTGTGTTAGTTT
66 AAATACCACTATAGTCTAGAGTATCTAATATATGACTAATAATATTTGTGTTAGTTT
53297166 TTTTT
1 TTTTT
53297171 TTGTATTTTT
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (122 bp):
TTTTTAATATGCAAAAGGCAGTACTATTGCTAGGTACAGGTAAGTTTCACTACTTCCAGGAACTG
AAATACCACTATAGTCTAGAGTATCTAATATATGACTAATAATATTTGTGTTAGTTT
Found at i:53301373 original size:27 final size:27
Alignment explanation
Indices: 53301310--53301377 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
53301300 AGTATTATTA
* *
53301310 TCAAGAGGTCCCGACATGAACCCTCTC
1 TCAATAGGACCCGACATGAACCCTCTC
* *
53301337 TCAATCGGACCCGACATGAACCCTCTT
1 TCAATAGGACCCGACATGAACCCTCTC
53301364 TCTAA-AGGACCCGA
1 TC-AATAGGACCCGA
53301378 ACCCGGAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (27 bp):
TCAATAGGACCCGACATGAACCCTCTC
Found at i:53306041 original size:22 final size:22
Alignment explanation
Indices: 53306006--53306047 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53305996 TGATATAATA
*
53306006 ATAATTTTAGTTATTAATTTTT
1 ATAATTTTAGTTATCAATTTTT
**
53306028 ATAATTTTTTTTATCAATTT
1 ATAATTTTAGTTATCAATTT
53306048 GGCCCTGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATAATTTTAGTTATCAATTTTT
Found at i:53315784 original size:17 final size:16
Alignment explanation
Indices: 53315762--53315872 Score: 59
Period size: 17 Copynumber: 6.5 Consensus size: 16
53315752 TTAAAATAGA
*
53315762 TATAAACTTATAAATAT
1 TATAAA-TTATAAAAAT
53315779 TATAAAAAGTTATAAAAAT
1 TAT--AAA-TTATAAAAAT
53315798 TAATAAATTATAAAAAAT
1 T-ATAAATTAT-AAAAAT
** *
53315816 TATATTTTTTATAAAAT
1 TATAAATTATA-AAAAT
53315833 TAATAAAATATATAAAAA-
1 T-AT-AAAT-TATAAAAAT
53315851 -AT--ATTATAAAAAT
1 TATAAATTATAAAAAT
53315864 GTATAAATT
1 -TATAAATT
53315873 TTTTTAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 26
0.68 0.07 0.24
Matches are distributed among these distances:
12 8 0.11
13 2 0.03
15 2 0.03
16 3 0.04
17 22 0.30
18 12 0.16
19 19 0.26
20 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (16 bp):
TATAAATTATAAAAAT
Found at i:53315797 original size:39 final size:38
Alignment explanation
Indices: 53315723--53315797 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
53315713 TAATTTAAAA
*
53315723 ATATAAAATATAAAACTATAAAAGAATTATTAAAATAG
1 ATATAAAATATAAAACTATAAAAGAATTATAAAAATAG
* * *
53315761 ATATAAACTTATAAATATTATAAAA-AGTTATAAAAAT
1 ATATAAA-ATATAAA-ACTATAAAAGAATTATAAAAAT
53315798 TAATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
38 7 0.23
39 16 0.52
40 8 0.26
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (38 bp):
ATATAAAATATAAAACTATAAAAGAATTATAAAAATAG
Found at i:53315897 original size:49 final size:49
Alignment explanation
Indices: 53315804--53315899 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
53315794 AAATTAATAA
* *
53315804 ATTATAAAAAATTATATTTTTTATAAAATTAATAAAATATATAAAAAAT
1 ATTATAAAAAATTATATTTTTTATAAAAATAATAAAATAAATAAAAAAT
*
53315853 ATTAT-AAAAATGTATAAATTTTTT-TAAAAATCATAAAA-AAATAAAAA
1 ATTATAAAAAAT-TAT--ATTTTTTATAAAAATAATAAAATAAATAAAAA
53315900 TTATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 6 0.15
49 16 0.39
50 12 0.29
51 7 0.17
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (49 bp):
ATTATAAAAAATTATATTTTTTATAAAAATAATAAAATAAATAAAAAAT
Found at i:53315910 original size:9 final size:9
Alignment explanation
Indices: 53315714--53315912 Score: 90
Period size: 10 Copynumber: 21.7 Consensus size: 9
53315704 TCCATAAAAT
53315714 AATT-TAAA
1 AATTATAAA
53315722 AA-TAT-AA
1 AATTATAAA
53315729 AA-TAT-AA
1 AATTATAAA
*
53315736 AACTATAAAA
1 AATTAT-AAA
*
53315746 GAATTATTAA
1 -AATTATAAA
*
53315756 AATAGATATAA
1 AAT-TATA-AA
*
53315767 ACTTATAAA
1 AATTATAAA
*
53315776 TATTATAAA
1 AATTATAAA
53315785 AAGTTATAAA
1 AA-TTATAAA
*
53315795 AATTA-ATA
1 AATTATAAA
53315803 AATTATAAAA
1 AATTAT-AAA
**
53315813 AATTATATT
1 AATTATAAA
**
53315822 TTTTAT-AA
1 AATTATAAA
53315830 AATTAATAAA
1 AATT-ATAAA
*
53315840 ATATATAAAAA
1 A-AT-TATAAA
53315851 ATATTATAAA
1 A-ATTATAAA
53315861 AATGTATAAA
1 AAT-TATAAA
** *
53315871 TTTTTTTAAA
1 -AATTATAAA
*
53315881 AATCATAAA
1 AATTATAAA
*
53315890 AA-AATAAA
1 AATTATAAA
53315898 AATTATAAA
1 AATTATAAA
53315907 AATTAT
1 AATTAT
53315913 CATAAAAGCT
Statistics
Matches: 144, Mismatches: 30, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
7 12 0.08
8 22 0.15
9 43 0.30
10 46 0.32
11 20 0.14
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
AATTATAAA
Found at i:53316389 original size:28 final size:27
Alignment explanation
Indices: 53316358--53316447 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 27
53316348 TTTTATAATC
53316358 TTTATAAGTTTATAGCAATTTTAATATT
1 TTTATAA-TTTATAGCAATTTTAATATT
* * *
53316386 TTTA-ACATTTTTAACATTTTTTAATATT
1 TTTATA-ATTTATAGCA-ATTTTAATATT
53316414 TTTCAT--TTTATAG-AATTTTAATATGAT
1 TTT-ATAATTTATAGCAATTTTAATAT--T
53316441 TTTATAA
1 TTTATAA
53316448 AATTTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
25 9 0.19
26 3 0.06
27 17 0.35
28 18 0.38
29 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTATAATTTATAGCAATTTTAATATT
Found at i:53316406 original size:10 final size:10
Alignment explanation
Indices: 53316384--53316416 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
53316374 AATTTTAATA
53316384 TTTTTAACA-
1 TTTTTAACAT
53316393 TTTTTAACAT
1 TTTTTAACAT
*
53316403 TTTTTAATAT
1 TTTTTAACAT
53316413 TTTT
1 TTTT
53316417 CATTTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTAACAT
Found at i:53316444 original size:21 final size:22
Alignment explanation
Indices: 53316418--53316460 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
53316408 AATATTTTTC
*
53316418 ATTTTATAGAATTTT-AATATG
1 ATTTTATAAAATTTTAAATATG
53316439 ATTTTATAAAATTTTAAATATG
1 ATTTTATAAAATTTTAAATATG
53316461 TTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATTTTATAAAATTTTAAATATG
Found at i:53316527 original size:9 final size:9
Alignment explanation
Indices: 53316376--53316519 Score: 71
Period size: 9 Copynumber: 15.6 Consensus size: 9
53316366 TTTATAGCAA
53316376 TTTTAATAT
1 TTTTAATAT
*
53316385 TTTTAACAT
1 TTTTAATAT
*
53316394 TTTTAACATT
1 TTTTAATA-T
53316404 TTTTAATAT
1 TTTTAATAT
*
53316413 TTTTCAT-T
1 TTTTAATAT
*
53316421 TTATAGA-AT
1 TTTTA-ATAT
*
53316430 TTTAATATGAT
1 TTTTA-AT-AT
*
53316441 TTTATAAAAT
1 TTT-TAATAT
*
53316451 TTTAAATAT
1 TTTTAATAT
* *
53316460 GTTTATTAAT
1 TTTTAAT-AT
53316470 TTTATAAT-T
1 TTT-TAATAT
* * *
53316479 TATTAGAAAA
1 TTTTA-ATAT
*
53316489 TATT-ATAT
1 TTTTAATAT
53316497 TTTTAATAT
1 TTTTAATAT
53316506 TTTTAATAT
1 TTTTAATAT
53316515 TTTTA
1 TTTTA
53316520 TCATTTTTCG
Statistics
Matches: 101, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
8 11 0.11
9 59 0.58
10 21 0.21
11 9 0.09
12 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTAATAT
Found at i:53332620 original size:3 final size:3
Alignment explanation
Indices: 53332612--53332638 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53332602 GAAAAATAAA
53332612 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
53332639 CTAAGCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53336841 original size:15 final size:15
Alignment explanation
Indices: 53336804--53336834 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53336794 CCATAGGCCC
53336804 AATGATTAGAACTTT
1 AATGATTAGAACTTT
53336819 AATGATTAGAACTTT
1 AATGATTAGAACTTT
53336834 A
1 A
53336835 CATATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (15 bp):
AATGATTAGAACTTT
Found at i:53340235 original size:24 final size:25
Alignment explanation
Indices: 53340208--53340268 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 25
53340198 GCTATTTGTT
*
53340208 ATTTGAGT-TTTATTTTAATGTTT-A
1 ATTTGAGTATTAATTTT-ATGTTTCA
*
53340232 ATTT-AGTATTAATTTTTTGTTTCA
1 ATTTGAGTATTAATTTTATGTTTCA
53340256 ATTTG-GTAATTAA
1 ATTTGAGT-ATTAA
53340269 ATAACTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 8 0.26
24 18 0.58
25 5 0.16
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (25 bp):
ATTTGAGTATTAATTTTATGTTTCA
Found at i:53342744 original size:3 final size:3
Alignment explanation
Indices: 53342736--53342763 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53342726 ATAATTAAGG
53342736 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
53342764 GAAAGGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53344570 original size:29 final size:30
Alignment explanation
Indices: 53344515--53344578 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
53344505 TTGGGTTTAT
* *
53344515 TTGAATCATTTTAATAATATAGAGATTAAA
1 TTGATTCATTTTAATAATAGAGAGATTAAA
* * *
53344545 TTGATTCA-TTTAATAATGGAGCGATTAAT
1 TTGATTCATTTTAATAATAGAGAGATTAAA
53344574 TTGAT
1 TTGAT
53344579 CTGGTCCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGATTCATTTTAATAATAGAGAGATTAAA
Found at i:53351270 original size:17 final size:17
Alignment explanation
Indices: 53351238--53351275 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53351228 ACATAAAATC
**
53351238 TAATTAATATTTTTACA
1 TAATTAATATAATTACA
53351255 TAATTAATATAATTACA
1 TAATTAATATAATTACA
53351272 -AATT
1 TAATT
53351276 TTGTTGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAATATAATTACA
Found at i:53351732 original size:11 final size:10
Alignment explanation
Indices: 53351712--53351736 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53351702 AAATTTATTG
53351712 TTTTTATTTT
1 TTTTTATTTT
53351722 TTTTTATTTT
1 TTTTTATTTT
53351732 TTTTT
1 TTTTT
53351737 GTTATGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:53354057 original size:21 final size:20
Alignment explanation
Indices: 53354006--53354058 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
53353996 GACTCTCATA
*
53354006 ATATAATTTTTTTAAAATTT
1 ATATATTTTTTTTAAAATTT
53354026 -TA-ATCTCTTTTTTGAAAATTT
1 ATATAT-T-TTTTTT-AAAATTT
53354047 ATATATTTTTTT
1 ATATATTTTTTT
53354059 CGATTTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 6 0.22
21 12 0.44
22 3 0.11
23 2 0.07
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATATTTTTTTTAAAATTT
Found at i:53355408 original size:66 final size:66
Alignment explanation
Indices: 53355260--53355416 Score: 181
Period size: 66 Copynumber: 2.4 Consensus size: 66
53355250 AAAAGAGCCT
* * * **
53355260 GCAAATGTTTTAGAACGACAAAGGGGGGAGAACGTTGAAGATCAAGCAGCTAAACGGAAAGGGGC
1 GCAAATGTTTTAGAACGACAAAGGGGAGAGAACGTTGAAGATCAAACAGCAAAACGGAAAGGGAA
53355325 G
66 G
* * * *
53355326 GCAAATCTTTTGGAACGACAAAGGGGAGAGAATGTTGAAGATCAAACGGCAAAAC-GACAAGGGA
1 GCAAATGTTTTAGAACGACAAAGGGGAGAGAACGTTGAAGATCAAACAGCAAAACGGA-AAGGGA
*
53355390 AT
65 AG
** *
53355392 GCTGATGTTTCAGAACGACAAAGGG
1 GCAAATGTTTTAGAACGACAAAGGG
53355417 AAGACAATCC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
65 2 0.03
66 73 0.97
ACGTcount: A:0.39, C:0.14, G:0.32, T:0.15
Consensus pattern (66 bp):
GCAAATGTTTTAGAACGACAAAGGGGAGAGAACGTTGAAGATCAAACAGCAAAACGGAAAGGGAA
G
Found at i:53358764 original size:86 final size:86
Alignment explanation
Indices: 53358619--53358790 Score: 283
Period size: 86 Copynumber: 2.0 Consensus size: 86
53358609 ACTAGGTTCC
* * * *
53358619 TGCTATATGCAGCGTCATACCATGAGCATACCTCATATCACAATATGGCATCTACATAACTTGTG
1 TGCTATATGCAGCGTCATACCATGAGCACACCGCATATCACAATATGACATCTACATAACTAGTG
53358684 AACTCACTT-AACTTGGTACAG
66 AACTCA-TTGAACTTGGTACAG
*
53358705 TGCTATATGCAGGGTCATACCATGAGCACACCGCATATCACAATATGACATCTACATAACTAGTG
1 TGCTATATGCAGCGTCATACCATGAGCACACCGCATATCACAATATGACATCTACATAACTAGTG
53358770 AACTCATTGAACTTGGTACAG
66 AACTCATTGAACTTGGTACAG
53358791 ATTGAACAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 2 0.03
86 78 0.98
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (86 bp):
TGCTATATGCAGCGTCATACCATGAGCACACCGCATATCACAATATGACATCTACATAACTAGTG
AACTCATTGAACTTGGTACAG
Found at i:53360597 original size:29 final size:29
Alignment explanation
Indices: 53360555--53360615 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
53360545 GGCAATCGGG
*
53360555 CAAATATAGCAGTACGTGCTCAACAGTTT
1 CAAATATAGCAGTACATGCTCAACAGTTT
53360584 CAAATATAGCAGTACATGCTCAACAGTTT
1 CAAATATAGCAGTACATGCTCAACAGTTT
53360613 CAA
1 CAA
53360616 CCGTTGTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (29 bp):
CAAATATAGCAGTACATGCTCAACAGTTT
Found at i:53365915 original size:2 final size:2
Alignment explanation
Indices: 53365908--53365936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53365898 GAGAAGAGCA
53365908 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
53365937 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:53371606 original size:29 final size:30
Alignment explanation
Indices: 53371564--53371625 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
53371554 GTGTGTAGAG
*
53371564 TTTAAAAATTCTAATATATA-AAAATATTT
1 TTTAAAAATCCTAATATATACAAAATATTT
*
53371593 TTTAAAAATCCTAATGTATACAAAATATTT
1 TTTAAAAATCCTAATATATACAAAATATTT
53371623 TTT
1 TTT
53371626 CTTATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTAAAAATCCTAATATATACAAAATATTT
Found at i:53384130 original size:12 final size:12
Alignment explanation
Indices: 53384113--53384156 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
53384103 TGTGCTAGAA
53384113 AAATATTAATAT
1 AAATATTAATAT
*
53384125 AAATATTATTAT
1 AAATATTAATAT
* *
53384137 ATATATTAAAAT
1 AAATATTAATAT
*
53384149 TAATATTA
1 AAATATTA
53384157 TTTCTAAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:53387210 original size:18 final size:17
Alignment explanation
Indices: 53387177--53387215 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
53387167 TTGTATAAAT
53387177 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
53387195 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
53387212 TGTG
1 TGTG
53387216 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:53387468 original size:23 final size:23
Alignment explanation
Indices: 53387441--53387538 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
53387431 AGTGTTATTG
53387441 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
53387464 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
53387487 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53387509 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53387532 ATCAGTG
1 ATCAGTG
53387539 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:53387507 original size:45 final size:45
Alignment explanation
Indices: 53387443--53387531 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
53387433 TGTTATTGAT
* *
53387443 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
53387488 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
53387532 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:53400360 original size:25 final size:25
Alignment explanation
Indices: 53400326--53400376 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
53400316 AACAAAAGTG
53400326 AACATGAAGAAGACTTAATTTCAAT
1 AACATGAAGAAGACTTAATTTCAAT
53400351 AACATGAAGAAGACTTAATTTCAAT
1 AACATGAAGAAGACTTAATTTCAAT
53400376 A
1 A
53400377 TTCTCAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (25 bp):
AACATGAAGAAGACTTAATTTCAAT
Found at i:53408154 original size:6 final size:6
Alignment explanation
Indices: 53408143--53408168 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53408133 TATAGATTCA
53408143 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
53408169 GGTTTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:53408847 original size:21 final size:21
Alignment explanation
Indices: 53408815--53408865 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
53408805 ATTTTACGAT
53408815 TTTTA-AAGAATTTT-AATATG
1 TTTTATAA-AATTTTAAATATG
53408835 CTTTTATAAAATTTTAAATATG
1 -TTTTATAAAATTTTAAATATG
53408857 TTTTATAAA
1 TTTTATAAA
53408866 TTATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTATAAAATTTTAAATATG
Found at i:53408874 original size:22 final size:20
Alignment explanation
Indices: 53408823--53408885 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
53408813 ATTTTTAAAG
53408823 AATTTT-AATATGCTTTTATAA
1 AATTTTAAATATG-TTTTAT-A
53408844 AATTTTAAATATGTTTTATA
1 AATTTTAAATATGTTTTATA
*
53408864 AATTATATAAAT-TATTTTATA
1 AATT-T-TAAATATGTTTTATA
53408885 A
1 A
53408886 TATATTAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 5 0.13
21 22 0.58
22 11 0.29
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (20 bp):
AATTTTAAATATGTTTTATA
Found at i:53408929 original size:20 final size:18
Alignment explanation
Indices: 53408896--53409031 Score: 67
Period size: 18 Copynumber: 7.7 Consensus size: 18
53408886 TATATTAGAA
53408896 TTTTATATTTTTAATATT
1 TTTTATATTTTTAATATT
53408914 TTTTATAATCTTTTAATATT
1 TTTTAT-AT-TTTTAATATT
* * *
53408934 TTATA-AGTTTATACA-AAT
1 TTTTATA-TTTTTA-ATATT
*
53408952 TTTCAT-TTTTTAATA--
1 TTTTATATTTTTAATATT
53408967 -TTTATATTTTCT-ATAATT
1 TTTTATATTTT-TAAT-ATT
* *
53408985 TTTT-TA-TATTAATAAT
1 TTTTATATTTTTAATATT
*
53409001 TTTTATATTTTT-TTATT
1 TTTTATATTTTTAATATT
*
53409018 TTTAATAATTTTTA
1 TTTTAT-ATTTTTA
53409032 TGTGTAAACC
Statistics
Matches: 88, Mismatches: 13, Indels: 33
0.66 0.10 0.25
Matches are distributed among these distances:
14 4 0.05
15 6 0.07
16 10 0.11
17 20 0.23
18 27 0.31
19 7 0.08
20 14 0.16
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (18 bp):
TTTTATATTTTTAATATT
Found at i:53408985 original size:26 final size:26
Alignment explanation
Indices: 53408956--53409032 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
53408946 ACAAATTTTC
*
53408956 ATTTTTTAATATTTAT-ATTTTCTATA
1 ATTTTTTAATATTAATAATTTT-TATA
*
53408982 ATTTTTTTATATTAATAATTTTTATA
1 ATTTTTTAATATTAATAATTTTTATA
* * *
53409008 TTTTTTTATTTTTAATAATTTTTAT
1 ATTTTTTAATATTAATAATTTTTAT
53409033 GTGTAAACCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 39 0.89
27 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTTTTAATATTAATAATTTTTATA
Found at i:53410706 original size:24 final size:24
Alignment explanation
Indices: 53410659--53410706 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
53410649 TATATTGTAT
* * *
53410659 ATGTATATGTATGGAAATTTAAAA
1 ATGTATATATATGGAAACTAAAAA
*
53410683 ATGTATATATATGGAAGCTAAAAA
1 ATGTATATATATGGAAACTAAAAA
53410707 TTTGAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (24 bp):
ATGTATATATATGGAAACTAAAAA
Found at i:53415054 original size:18 final size:18
Alignment explanation
Indices: 53415010--53415054 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
53415000 AAACCACTCC
*
53415010 CTTAAAAATTATGATTAT
1 CTTAAAAAATATGATTAT
* * *
53415028 CTTTAAAAATATTATTTT
1 CTTAAAAAATATGATTAT
53415046 CTTAAAAAA
1 CTTAAAAAA
53415055 ACTCAAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
CTTAAAAAATATGATTAT
Found at i:53418124 original size:24 final size:25
Alignment explanation
Indices: 53418090--53418138 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
53418080 CCTTGCAATG
53418090 TCAAGGGCATGTAACTATGCTTCTT
1 TCAAGGGCATGTAACTATGCTTCTT
*
53418115 TCAA-GGCATGTAACTATGTTTCTT
1 TCAAGGGCATGTAACTATGCTTCTT
53418139 AGCTTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (25 bp):
TCAAGGGCATGTAACTATGCTTCTT
Found at i:53424542 original size:13 final size:13
Alignment explanation
Indices: 53424524--53424563 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
53424514 CTACTCGGAT
53424524 TGGGAACTTAATA
1 TGGGAACTTAATA
53424537 TGGGAACTTAATA
1 TGGGAACTTAATA
53424550 TGGGAACTTAATA
1 TGGGAACTTAATA
53424563 T
1 T
53424564 CTTGGAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (13 bp):
TGGGAACTTAATA
Found at i:53432502 original size:12 final size:12
Alignment explanation
Indices: 53432485--53432509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53432475 AGCCACTATC
53432485 GCTGCTGGTACT
1 GCTGCTGGTACT
53432497 GCTGCTGGTACT
1 GCTGCTGGTACT
53432509 G
1 G
53432510 GGGCTACTGC
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:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (12 bp):
GCTGCTGGTACT
Found at i:53446050 original size:39 final size:37
Alignment explanation
Indices: 53445983--53446075 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
53445973 ACCAGAATGG
* *
53445983 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
53446022 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
53446059 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
53446076 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:53446438 original size:3 final size:3
Alignment explanation
Indices: 53446430--53446454 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53446420 ATTCCCACTC
53446430 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
53446455 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53458445 original size:24 final size:24
Alignment explanation
Indices: 53458418--53458469 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53458408 TTAGTAAGTC
*
53458418 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53458442 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53458466 AAAT
1 AAAT
53458470 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53458696 original size:12 final size:12
Alignment explanation
Indices: 53458679--53458703 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53458669 AATTCATACG
53458679 TCTTTGATCCTC
1 TCTTTGATCCTC
53458691 TCTTTGATCCTC
1 TCTTTGATCCTC
53458703 T
1 T
53458704 GATCAAATAT
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:0.08, C:0.32, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTTTGATCCTC
Found at i:53462820 original size:6 final size:6
Alignment explanation
Indices: 53462811--53462836 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53462801 ACCAGAATCA
53462811 CCACCT CCACCT CCACCT CCACCT CC
1 CCACCT CCACCT CCACCT CCACCT CC
53462837 TCCACCGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15
Consensus pattern (6 bp):
CCACCT
Found at i:53463813 original size:31 final size:29
Alignment explanation
Indices: 53463778--53463837 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
53463768 GCAACCGCTT
*
53463778 CGTAACAAAATGATAATATAAGTGACTAAAA
1 CGTAAC-AAATCA-AATATAAGTGACTAAAA
**
53463809 CGTAACATTTCAAATATAAGTGACTAAAA
1 CGTAACAAATCAAATATAAGTGACTAAAA
53463838 TGAAATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 3 0.12
31 6 0.23
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (29 bp):
CGTAACAAATCAAATATAAGTGACTAAAA
Found at i:53465287 original size:39 final size:39
Alignment explanation
Indices: 53465233--53465363 Score: 253
Period size: 39 Copynumber: 3.4 Consensus size: 39
53465223 GAAATCTCAG
53465233 AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
1 AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
53465272 AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
1 AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
*
53465311 AGGCTAACTGAAGCATATAAGTGCTAAACGGAAGCCCGA
1 AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
53465350 AGGCTAACTGAAGC
1 AGGCTAACTGAAGC
53465364 TCATCAGAGC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
AGGCTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGA
Found at i:53476578 original size:21 final size:21
Alignment explanation
Indices: 53476554--53476596 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
53476544 AATATTTAAA
53476554 TTCA-AAAAATTATTAAAAAAT
1 TTCATAAAAATT-TTAAAAAAT
*
53476575 TTCATAAAAGTTTTAAAAAAT
1 TTCATAAAAATTTTAAAAAAT
53476596 T
1 T
53476597 AGCATGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TTCATAAAAATTTTAAAAAAT
Found at i:53477082 original size:12 final size:12
Alignment explanation
Indices: 53477065--53477090 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53477055 CTTTATGCTA
53477065 TATTATCATTAT
1 TATTATCATTAT
53477077 TATTATCATTAT
1 TATTATCATTAT
53477089 TA
1 TA
53477091 AAGTTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:53488861 original size:20 final size:22
Alignment explanation
Indices: 53488818--53488871 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
53488808 CACCTTCCCT
*
53488818 TTTTATA-TATATATATATATA
1 TTTTATATTTTATATATATATA
53488839 TTTT-TAGTTTTATA-ATATA-A
1 TTTTATA-TTTTATATATATATA
53488859 TTTTATATTTTAT
1 TTTTATATTTTAT
53488872 TAGTTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 13 0.45
21 11 0.38
22 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTATATTTTATATATATATA
Found at i:53489386 original size:21 final size:21
Alignment explanation
Indices: 53489362--53489419 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
53489352 TTTATTAAAT
53489362 AAAATAAAATTATAAAACTA-C
1 AAAATAAAA-TATAAAACTAGC
53489383 AAAATATAAATATAAAACTAGC
1 AAAATA-AAATATAAAACTAGC
*
53489405 -TAATAAAATATAAAA
1 AAAATAAAATATAAAA
53489420 TTATATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.29
21 20 0.59
22 4 0.12
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAAAATATAAAACTAGC
Found at i:53489390 original size:15 final size:13
Alignment explanation
Indices: 53489360--53489447 Score: 52
Period size: 15 Copynumber: 6.5 Consensus size: 13
53489350 TTTTTATTAA
*
53489360 ATAAAATAAAATT
1 ATAAAATAAAAAT
53489373 ATAAAACTACAAAAT
1 ATAAAA-TA-AAAAT
*
53489388 ATAAATATAAAACT
1 ATAAA-ATAAAAAT
***
53489402 AGCTAAT-AAAAT
1 ATAAAATAAAAAT
* * *
53489414 ATAAAATTATATT
1 ATAAAATAAAAAT
53489427 ATAAAACTAGAAAAT
1 ATAAAA-TA-AAAAT
53489442 ATAAAA
1 ATAAAA
53489448 GGAGTGCCAC
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
12 8 0.15
13 17 0.31
14 9 0.16
15 20 0.36
16 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAAATAAAAAT
Found at i:53489616 original size:65 final size:66
Alignment explanation
Indices: 53489539--53489666 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 66
53489529 CTTTTAAATA
* *
53489539 ATACATTCTTGTAAACAACTTATTTTTATTTTATTTTCGTAATTA-ATTTTTTCATGTAAAAAAC
1 ATACATTATTGTAAACAACTTATTTTTATTTTATTTTAGTAATTACATTTTTTCATGTAAAAAAC
53489603 G
66 G
* * * *
53489604 ATACATTATTGTAAATAATTTGTTTTTATTTTATTTTAGTAATTACTTTTTTTCATGTAAAAA
1 ATACATTATTGTAAACAACTTATTTTTATTTTATTTTAGTAATTACATTTTTTCATGTAAAAA
53489667 CCGCTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
65 40 0.71
66 16 0.29
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (66 bp):
ATACATTATTGTAAACAACTTATTTTTATTTTATTTTAGTAATTACATTTTTTCATGTAAAAAAC
G
Found at i:53493468 original size:21 final size:22
Alignment explanation
Indices: 53493439--53493485 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
53493429 CAGAAGGAGT
*
53493439 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53493461 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53493482 GAGT
1 GAGT
53493486 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:53497496 original size:45 final size:45
Alignment explanation
Indices: 53497432--53497519 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
53497422 TCTAATTGCA
*
53497432 ATTGGCACACATAAACGACAG-CATTCCTAGG-TATATTATATATAT
1 ATTGGCACACATAAACGACAGTC-TCCCT-GGATATATTATATATAT
53497477 ATTGGCACACATAAACGACAGTCTCCCTGGATATATTATATAT
1 ATTGGCACACATAAACGACAGTCTCCCTGGATATATTATATAT
53497520 TTATATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 2 0.05
45 37 0.93
46 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (45 bp):
ATTGGCACACATAAACGACAGTCTCCCTGGATATATTATATATAT
Found at i:53498216 original size:7 final size:7
Alignment explanation
Indices: 53498204--53498233 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53498194 ATTTGGTAGG
53498204 AAGTCTC
1 AAGTCTC
53498211 AAGTCTC
1 AAGTCTC
53498218 AAGTCTC
1 AAGTCTC
53498225 AAGTCTC
1 AAGTCTC
53498232 AA
1 AA
53498234 TTTAATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (7 bp):
AAGTCTC
Found at i:53503132 original size:35 final size:35
Alignment explanation
Indices: 53503093--53503236 Score: 137
Period size: 35 Copynumber: 4.1 Consensus size: 35
53503083 TCACATTTCG
* * * *
53503093 GTATGGGAAATGTCATACCTATGTTTCTTAACTCA
1 GTATGGAAAATATCATACCTACGTTTCTCAACTCA
* *
53503128 GTAT-GAATAATACCATACTTACGTTTCTCAACTCA
1 GTATGGAA-AATATCATACCTACGTTTCTCAACTCA
* *** *
53503163 ATATGGTTGATATCATACCTACGTTTCACAACTCA
1 GTATGGAAAATATCATACCTACGTTTCTCAACTCA
** * *
53503198 GTATGGATGATACCATACCTACGTTTCACAACTCA
1 GTATGGAAAATATCATACCTACGTTTCTCAACTCA
53503233 GTAT
1 GTAT
53503237 AGTTAATATT
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.02
35 88 0.97
36 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (35 bp):
GTATGGAAAATATCATACCTACGTTTCTCAACTCA
Found at i:53503189 original size:70 final size:70
Alignment explanation
Indices: 53503105--53503263 Score: 201
Period size: 70 Copynumber: 2.3 Consensus size: 70
53503095 ATGGGAAATG
* ** * * *
53503105 TCATACCTATGTTTCTTAACTCAGTATGAATAATACCATACTTACGTTTCTCAACTCAATATGGT
1 TCATACCTACGTTTCACAACTCAGTATGAATAATACCATACCTACGTTTCACAACTCAATATAGT
*
53503170 TGATA
66 TAATA
* * *
53503175 TCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCAGTATAGT
1 TCATACCTACGTTTCACAACTCAGTATGAATAATACCATACCTACGTTTCACAACTCAATATAGT
53503240 TAATA
66 TAATA
* *
53503245 TTATACGTTACGTTTCACA
1 TCATAC-CTACGTTTCACA
53503264 CTTTGCTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
70 65 0.86
71 11 0.14
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (70 bp):
TCATACCTACGTTTCACAACTCAGTATGAATAATACCATACCTACGTTTCACAACTCAATATAGT
TAATA
Found at i:53503753 original size:22 final size:21
Alignment explanation
Indices: 53503713--53503780 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 21
53503703 CATATATTTG
*
53503713 TTATTA-AATAGATA-T-TTA
1 TTATTATAATTGATATTATTA
53503731 TTATTATAATT-ATTAATTATTA
1 TTATTATAATTGA-T-ATTATTA
53503753 TTATT-TAATTGATATTA-TA
1 TTATTATAATTGATATTATTA
53503772 TTATTATAA
1 TTATTATAA
53503781 AATAAATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
18 7 0.17
19 11 0.26
20 8 0.19
21 7 0.17
22 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATTATAATTGATATTATTA
Found at i:53503789 original size:40 final size:40
Alignment explanation
Indices: 53503713--53503789 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
53503703 CATATATTTG
* *
53503713 TTATTAAATAGATATTTATTATTATAATTATTAATTATTA
1 TTATTAAATAGATATTTATTATTATAATAATAAATTATTA
* *
53503753 TTATTTAATTGATATTATATTATTATAA-AATAAATTA
1 TTATTAAATAGATATT-TATTATTATAATAATAAATTA
53503790 AAATAAAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 21 0.66
41 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (40 bp):
TTATTAAATAGATATTTATTATTATAATAATAAATTATTA
Found at i:53530128 original size:34 final size:34
Alignment explanation
Indices: 53530085--53530152 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
53530075 GAAAACACGC
53530085 ACAAAAAATTATTTCACATTTGTGGAAGAGATAT
1 ACAAAAAATTATTTCACATTTGTGGAAGAGATAT
53530119 ACAAAAAATTATTTCACATTTGTGGAAGAGATAT
1 ACAAAAAATTATTTCACATTTGTGGAAGAGATAT
53530153 CATAGAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (34 bp):
ACAAAAAATTATTTCACATTTGTGGAAGAGATAT
Found at i:53532815 original size:21 final size:21
Alignment explanation
Indices: 53532791--53532891 Score: 57
Period size: 21 Copynumber: 5.0 Consensus size: 21
53532781 TTGGTGATGG
53532791 ATGAACTTGAGTAGGTGGCGT
1 ATGAACTTGAGTAGGTGGCGT
*
53532812 ATGACCTTGAGT--G-GGCG-
1 ATGAACTTGAGTAGGTGGCGT
* * * * * *
53532829 GTGAATGTTGCGTTGGTGGTGG
1 ATGAA-CTTGAGTAGGTGGCGT
* *
53532851 ATGAGCTTGAGTAGGTGGTGT
1 ATGAACTTGAGTAGGTGGCGT
* * *
53532872 ACGACCTTGAGTGGGTGGCG
1 ATGAACTTGAGTAGGTGGCG
53532892 AGTATTGGGA
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
17 3 0.05
18 9 0.15
19 1 0.02
20 1 0.02
21 42 0.71
22 3 0.05
ACGTcount: A:0.17, C:0.11, G:0.44, T:0.29
Consensus pattern (21 bp):
ATGAACTTGAGTAGGTGGCGT
Done.