Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 11 of 16
Found at i:1699482 original size:16 final size:18
Alignment explanation
Indices: 1699463--1699501 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1699453 AATAATGACT
1699463 ATTTTTATTA-ATTTA-A
1 ATTTTTATTACATTTATA
*
1699479 ATTTTTTTTACATTTATA
1 ATTTTTATTACATTTATA
1699497 ATTTT
1 ATTTT
1699502 ATATATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATTACATTTATA
Found at i:1700134 original size:18 final size:17
Alignment explanation
Indices: 1700102--1700135 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1700092 TTTAAAAAAA
*
1700102 TTAAATTAAATTTTAAC
1 TTAAATTAAAATTTAAC
1700119 TTAAATATAAAATTTAA
1 TTAAAT-TAAAATTTAA
1700136 AAAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTAAAATTTAAC
Found at i:1700303 original size:24 final size:24
Alignment explanation
Indices: 1700271--1700345 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
1700261 GGTTTTTTAA
1700271 CTTAAAATAGATAGTTAATTTCGG
1 CTTAAAATAGATAGTTAATTTCGG
1700295 CTTAAAATA-A-ACGTTTAA------
1 CTTAAAATAGATA-G-TTAATTTCGG
1700313 CTTAAAATAGATAGTTAATTTCGG
1 CTTAAAATAGATAGTTAATTTCGG
1700337 CTTAAAATA
1 CTTAAAATA
1700346 AACGTTTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 20
0.67 0.00 0.33
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 1 0.02
22 1 0.02
23 2 0.05
24 22 0.54
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (24 bp):
CTTAAAATAGATAGTTAATTTCGG
Found at i:1700325 original size:42 final size:42
Alignment explanation
Indices: 1700266--1700355 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
1700256 AAATGGGTTT
1700266 TTTAACTTAAAATAGATAGTTAATTTCGGCTTAAAATAAACG
1 TTTAACTTAAAATAGATAGTTAATTTCGGCTTAAAATAAACG
1700308 TTTAACTTAAAATAGATAGTTAATTTCGGCTTAAAATAAACG
1 TTTAACTTAAAATAGATAGTTAATTTCGGCTTAAAATAAACG
1700350 TTTAAC
1 TTTAAC
1700356 CTATCAATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (42 bp):
TTTAACTTAAAATAGATAGTTAATTTCGGCTTAAAATAAACG
Found at i:1700354 original size:24 final size:24
Alignment explanation
Indices: 1700285--1700354 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1700275 AAATAGATAG
1700285 TTAATTTCGGCTTAAAATAAACGT
1 TTAATTTCGGCTTAAAATAAACGT
1700309 TTAA------CTTAAAATAGATA-G-
1 TTAATTTCGGCTTAAAATA-A-ACGT
1700327 TTAATTTCGGCTTAAAATAAACGT
1 TTAATTTCGGCTTAAAATAAACGT
1700351 TTAA
1 TTAA
1700355 CCTATCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 20
0.64 0.00 0.36
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
20 1 0.03
22 1 0.03
23 2 0.06
24 17 0.47
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (24 bp):
TTAATTTCGGCTTAAAATAAACGT
Found at i:1703024 original size:31 final size:30
Alignment explanation
Indices: 1702989--1703048 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1702979 AATACAAAAT
*
1702989 AATAACA-AAAATTTAATATATAATATTTAAA
1 AATAACATAAAA-ATAATAT-TAATATTTAAA
*
1703020 AATAATATAAAAATAATATTAATATTTAA
1 AATAACATAAAAATAATATTAATATTTAA
1703049 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 12 0.46
32 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
AATAACATAAAAATAATATTAATATTTAAA
Found at i:1703026 original size:13 final size:13
Alignment explanation
Indices: 1703008--1703039 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1702998 AATTTAATAT
1703008 ATAATATTTAAAA
1 ATAATATTTAAAA
1703021 ATAATA--TAAAA
1 ATAATATTTAAAA
1703032 ATAATATT
1 ATAATATT
1703040 AATATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATTTAAAA
Found at i:1703050 original size:37 final size:36
Alignment explanation
Indices: 1702984--1703067 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 36
1702974 GATATAATAC
*
1702984 AAAATAATA-ACAAAAATTTAATATATAATA-TTTA
1 AAAATAATATAAAAAAATTTAATATATAATATTTTA
*
1703018 AAAATAATATAAAAATAATATTAATATTTAATATTTTA
1 AAAATAATATAAAAA-AAT-TTAATATATAATATTTTA
**
1703056 AATTTAATATAA
1 AAAATAATATAA
1703068 TATACAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 9 0.21
35 4 0.10
36 3 0.07
37 12 0.29
38 14 0.33
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (36 bp):
AAAATAATATAAAAAAATTTAATATATAATATTTTA
Found at i:1703111 original size:15 final size:15
Alignment explanation
Indices: 1703088--1703153 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
1703078 TAACGTATCA
*
1703088 AAATTATATAAATAT
1 AAATAATATAAATAT
1703103 AAATAATATTAAAT-T
1 AAATAATA-TAAATAT
1703118 AATTATAATAT-AATA-
1 AA--ATAATATAAATAT
1703133 AAAT-ATATAAATAT
1 AAATAATATAAATAT
1703147 AATATAA
1 AA-ATAA
1703154 ATATCAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
12 4 0.10
13 6 0.14
14 2 0.05
15 17 0.40
16 7 0.17
17 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATATAAATAT
Found at i:1703115 original size:10 final size:9
Alignment explanation
Indices: 1703098--1703156 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 9
1703088 AAATTATATA
1703098 AATATAAAT
1 AATATAAAT
1703107 AATATTAAATT
1 AATA-TAAA-T
1703118 AATTATAATAT
1 AA-TATAA-AT
1703129 AATA-AAAT
1 AATATAAAT
1703137 -ATATAAATAT
1 AATAT-AA-AT
1703147 AATATAAAT
1 AATATAAAT
1703156 A
1 A
1703157 TCAATTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
7 3 0.07
8 2 0.05
9 11 0.26
10 10 0.24
11 13 0.31
12 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATATAAAT
Found at i:1703121 original size:29 final size:26
Alignment explanation
Indices: 1703089--1703185 Score: 72
Period size: 28 Copynumber: 3.5 Consensus size: 26
1703079 AACGTATCAA
1703089 AATTATATAAATATAAATAATATTAAATT
1 AATTATATAAATATAAAT-ATA-TAAA-T
1703118 AATTATAATATAATA-AAATATATAAAT
1 AATTAT-ATA-AATATAAATATATAAAT
* * * *
1703145 -ATAATATAAATATCAATTTAATTAAAA
1 AATTATATAAATATAAATAT-A-TAAAT
*
1703172 AATTAAATAAATAT
1 AATTATATAAATAT
1703186 TATAATAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
24 4 0.07
25 7 0.12
26 5 0.09
27 5 0.09
28 15 0.27
29 9 0.16
30 7 0.12
31 4 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTATATAAATATAAATATATAAAT
Found at i:1707274 original size:163 final size:163
Alignment explanation
Indices: 1707004--1707298 Score: 358
Period size: 163 Copynumber: 1.8 Consensus size: 163
1706994 CCTAAGGGGC
* * * * **
1707004 TTCTTAGAATTCTGCATCATAAATAAGAAAACCTTGTTTTTATATTTACAAAGTTTGGAGCATTC
1 TTCTTAGAATTCTGCATCATAAATAAGAAAACATTGCTTTTAAATTGACAAAGTTCAGAGCATTC
* ** * ***
1707069 CTGCCATTTTGAGTTCTCATGACTTGCACACGTGTGAAGTTTCACTTCTCAATATTGTGGCTGAC
66 CTGCCATTGTGACATCTCATGACTTGCACACATACAAAGTTTCACTTCTCAATATTGTGGCTGAC
1707134 AGACATGAAGAGTTAAGTTTATGCGACTTGAAT
131 AGACATGAAGAGTTAAGTTTATGCGACTTGAAT
* * * *
1707167 TTCTTAGATTTTTGCATCATAAATAAGAAAGCATTGCTTTTACAATTGA-ACAGTTCAGAGCATT
1 TTCTTAGAATTCTGCATCATAAATAAGAAAACATTGCTTTTA-AATTGACAAAGTTCAGAGCATT
** * * * * *
1707231 CCTGCCATTGTGACATCTCATGGGTTGCACGCATACAAAGTTTCACTTTTGAATGTTGTGGTTGA
65 CCTGCCATTGTGACATCTCATGACTTGCACACATACAAAGTTTCACTTCTCAATATTGTGGCTGA
1707296 CAG
130 CAG
1707299 GAAGAATTAA
Statistics
Matches: 107, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
163 103 0.96
164 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (163 bp):
TTCTTAGAATTCTGCATCATAAATAAGAAAACATTGCTTTTAAATTGACAAAGTTCAGAGCATTC
CTGCCATTGTGACATCTCATGACTTGCACACATACAAAGTTTCACTTCTCAATATTGTGGCTGAC
AGACATGAAGAGTTAAGTTTATGCGACTTGAAT
Found at i:1713941 original size:2 final size:2
Alignment explanation
Indices: 1713932--1713970 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1713922 TTTTTTTTTC
1713932 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1713971 TGTTATGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1714397 original size:17 final size:17
Alignment explanation
Indices: 1714360--1714412 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1714350 TTTTTTGAAA
*
1714360 AAAAACAATTATTATAATT
1 AAAAA-AATT-TTATATTT
1714379 AAAAAAATTTTATATTT
1 AAAAAAATTTTATATTT
* *
1714396 -AAAATATTATATATTT
1 AAAAAAATTTTATATTT
1714412 A
1 A
1714413 TGTAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 14 0.47
17 7 0.23
18 4 0.13
19 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAAAATTTTATATTT
Found at i:1714870 original size:16 final size:17
Alignment explanation
Indices: 1714813--1714872 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
1714803 ATAAATTATA
* * *
1714813 AAATTTTTAATTTTATT
1 AAATTATTAATATAATT
1714830 AAATTATATAATATAATTT
1 AAATTAT-TAATATAA-TT
**
1714849 TTATTATTAATA-AATT
1 AAATTATTAATATAATT
1714865 AAATTATT
1 AAATTATT
1714873 TATTTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 8 0.24
17 8 0.24
18 11 0.32
19 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTATTAATATAATT
Found at i:1715223 original size:15 final size:15
Alignment explanation
Indices: 1715198--1715282 Score: 70
Period size: 15 Copynumber: 5.6 Consensus size: 15
1715188 GTTATATAAT
1715198 TTTTATATTTATGTAT-
1 TTTTAT-TTTAT-TATA
1715214 TTTTATTTTATTTATA
1 TTTTATTTTA-TTATA
1715230 TTATT-TTTTATTATA
1 TT-TTATTTTATTATA
* *
1715245 TTATATTTTA-AATA
1 TTTTATTTTATTATA
*
1715259 TTTTA-TATATTATA
1 TTTTATTTTATTATA
1715273 TTTATATTTT
1 TTT-TATTTT
1715283 TATAATTATA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
13 3 0.05
14 14 0.25
15 21 0.38
16 16 0.29
17 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:1715236 original size:36 final size:37
Alignment explanation
Indices: 1715189--1715286 Score: 98
Period size: 36 Copynumber: 2.7 Consensus size: 37
1715179 ATAATTTGTG
*
1715189 TTATATAATTTTTATATTTATGTAT-TTTT-AT-TTTAT
1 TTATATTATTTTTATATTTAT-TATATTTTAATATTT-T
1715225 TTATATTATTTTT-TATTATATTATATTTTAAATATTTT
1 TTATATTATTTTTATATT-TATTATATTTT-AATATTTT
* *
1715263 ATATATTATATTTATATTT-TTATA
1 TTATATTATTTTTATATTTATTATA
1715287 ATTATATCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
35 7 0.13
36 19 0.36
37 5 0.09
38 15 0.28
39 7 0.13
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (37 bp):
TTATATTATTTTTATATTTATTATATTTTAATATTTT
Found at i:1715271 original size:23 final size:22
Alignment explanation
Indices: 1715234--1715293 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
1715224 TTTATATTAT
1715234 TTTTTATTATATTATATTTTAAA
1 TTTTTA-TATATTATATTTTAAA
*
1715257 TATTTTATATATTATA-TTTATA
1 T-TTTTATATATTATATTTTAAA
1715279 TTTTTATA-ATTATAT
1 TTTTTATATATTATAT
1715294 CACGTCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 6 0.18
21 7 0.21
22 6 0.18
23 10 0.29
24 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATATATTATATTTTAAA
Found at i:1715273 original size:14 final size:14
Alignment explanation
Indices: 1715226--1715293 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 14
1715216 TTATTTTATT
*
1715226 TATATTATTTTTTA
1 TATATTATATTTTA
1715240 TTATATTATATTTTAAA
1 -TATATTATATTTT--A
* *
1715257 TATTTTATATATTA
1 TATATTATATTTTA
1715271 TAT-TTATATTTT-
1 TATATTATATTTTA
1715283 TATAATTATAT
1 TAT-ATTATAT
1715294 CACGTCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
12 3 0.07
13 8 0.18
14 10 0.22
15 12 0.27
16 11 0.24
17 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATTATATTTTA
Found at i:1715281 original size:20 final size:20
Alignment explanation
Indices: 1715196--1715293 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
1715186 GTGTTATATA
*
1715196 ATTTT-TATATT-TATGTAT
1 ATTTTATATATTATATTTAT
*
1715214 -TTTTATTTTATT-TATATTAT
1 ATTTTA-TATATTATAT-TTAT
*
1715234 TTTTTATTATATTATATTTTAAAT
1 ATTTTA-TATATTATA-TTT--AT
1715258 ATTTTATATATTATATTTAT
1 ATTTTATATATTATATTTAT
1715278 ATTTT-TATAATTATAT
1 ATTTTATAT-ATTATAT
1715294 CACGTCAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.06
19 11 0.16
20 17 0.25
21 11 0.16
22 7 0.10
23 10 0.15
24 7 0.10
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (20 bp):
ATTTTATATATTATATTTAT
Found at i:1715320 original size:16 final size:17
Alignment explanation
Indices: 1715286--1715322 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1715276 ATATTTTTAT
1715286 AATTATATCACGTCAAA
1 AATTATATCACGTCAAA
1715303 AATTATCAT-ACG-CAAA
1 AATTAT-ATCACGTCAAA
1715319 AATT
1 AATT
1715323 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 9 0.47
18 2 0.11
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (17 bp):
AATTATATCACGTCAAA
Found at i:1724143 original size:12 final size:12
Alignment explanation
Indices: 1724126--1724153 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1724116 TTGACTTTGG
1724126 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1724138 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1724150 AAAA
1 AAAA
1724154 GCATTAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1724712 original size:2 final size:2
Alignment explanation
Indices: 1724705--1724732 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1724695 CAATAATTAA
1724705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1724733 CAATGAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1725189 original size:20 final size:20
Alignment explanation
Indices: 1725147--1725186 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1725137 TGCATATTTT
*
1725147 ATTAATTATTTAATATATTA
1 ATTAATTATTTAATATATAA
*
1725167 ATTATTTATTTAATA-ATAA
1 ATTAATTATTTAATATATAA
1725186 A
1 A
1725187 ATTTTAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATTATTTAATATATAA
Found at i:1725281 original size:17 final size:18
Alignment explanation
Indices: 1725214--1725301 Score: 71
Period size: 18 Copynumber: 5.1 Consensus size: 18
1725204 AATATGTGAT
1725214 TAAAA-AAATAATTTTTTA
1 TAAAATAAATAA-TTTTTA
1725232 TAAAATATAGATAA--TTTA
1 TAAAATA-A-ATAATTTTTA
*
1725250 -AAAA-AAATAACTTTTA
1 TAAAATAAATAATTTTTA
** *
1725266 T-ATGTAAATAATTTTTT
1 TAAAATAAATAATTTTTA
1725283 TAAAATAAATAATTTTTA
1 TAAAATAAATAATTTTTA
1725301 T
1 T
1725302 TATTTAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 6 0.11
17 15 0.27
18 23 0.42
19 1 0.02
20 1 0.02
21 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAATAAATAATTTTTA
Found at i:1725313 original size:23 final size:23
Alignment explanation
Indices: 1725281--1725347 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
1725271 AAATAATTTT
*
1725281 TTTAAAATAAATAATTTTTATTA
1 TTTAATATAAATAATTTTTATTA
* *
1725304 TTTAATATAATATAAATTTAATTA
1 TTTAATATAA-ATAATTTTTATTA
*
1725328 TTT-GTATAAATTAATATTTT
1 TTTAATATAAA-TAAT-TTTT
1725348 TTTAATTCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.03
23 17 0.49
24 17 0.49
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTAATATAAATAATTTTTATTA
Found at i:1725327 original size:24 final size:23
Alignment explanation
Indices: 1725281--1725330 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1725271 AAATAATTTT
* *
1725281 TTTAAAATAAATAATTTTTATTA
1 TTTAAAATAAATAAATTTAATTA
*
1725304 TTTAATATAATATAAATTTAATTA
1 TTTAAAATAA-ATAAATTTAATTA
1725328 TTT
1 TTT
1725331 GTATAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAAATAAATAAATTTAATTA
Found at i:1725346 original size:24 final size:23
Alignment explanation
Indices: 1725286--1725346 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 23
1725276 ATTTTTTTAA
*
1725286 AATAAA-TAAT-TTTTATTATTT
1 AATAAATTAATATTTAATTATTT
1725307 AATATAATATAA-ATTTAATTATTT
1 AATA-AAT-TAATATTTAATTATTT
*
1725331 GTATAAATTAATATTT
1 -AATAAATTAATATTT
1725347 TTTTAATTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 3 0.09
24 20 0.62
25 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATAAATTAATATTTAATTATTT
Found at i:1725376 original size:29 final size:29
Alignment explanation
Indices: 1725342--1725403 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1725332 TATAAATTAA
*
1725342 TATTTTTTTA-ATTCG--TAATATTAAATT
1 TATTTTTTTATAATCGAATAAT-TTAAATT
1725369 TATTTTTTTATAATCGAATAAATTTAAATT
1 TATTTTTTTATAATCGAAT-AATTTAAATT
1725399 TATTT
1 TATTT
1725404 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.33
28 4 0.13
30 13 0.43
31 3 0.10
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TATTTTTTTATAATCGAATAATTTAAATT
Found at i:1725388 original size:27 final size:29
Alignment explanation
Indices: 1725342--1725403 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
1725332 TATAAATTAA
*
1725342 TATTTTTTTAATTCGTAAT-A-TTAAATT
1 TATTTTTTTAAATCGTAATAATTTAAATT
1725369 TATTTTTTTATAATCG-AATAAATTTAAATT
1 TATTTTTTTA-AATCGTAAT-AATTTAAATT
1725399 TATTT
1 TATTT
1725404 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 13 0.43
28 4 0.13
29 1 0.03
30 12 0.40
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TATTTTTTTAAATCGTAATAATTTAAATT
Found at i:1728098 original size:18 final size:20
Alignment explanation
Indices: 1728070--1728113 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1728060 AAGTAAACAA
*
1728070 ATATAATAAAAGATA-AAAT
1 ATATTATAAAAGATATAAAT
*
1728089 A-ATTATAAAATATATAAAT
1 ATATTATAAAAGATATAAAT
1728108 ATATTA
1 ATATTA
1728114 AAATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 11 0.52
19 6 0.29
20 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATTATAAAAGATATAAAT
Found at i:1728105 original size:20 final size:19
Alignment explanation
Indices: 1728082--1728193 Score: 60
Period size: 20 Copynumber: 6.1 Consensus size: 19
1728072 ATAATAAAAG
1728082 ATAAAATAATTATAAAATAT
1 ATAAAAT-ATTATAAAATAT
*
1728102 ATAAATATATTA-AAATTTAT
1 ATAAA-ATATTATAAA-ATAT
* *
1728122 ATAAATAAATTAT-TAATAT
1 ATAAA-ATATTATAAAATAT
* * *
1728141 ATTAAATTTTATATAATAT
1 ATAAAATATTATAAAATAT
*
1728160 AT--ATTA-T-TAAAATAT
1 ATAAAATATTATAAAATAT
1728175 -TAAAAT-TTATATAAATAT
1 ATAAAATATTATA-AAATAT
1728193 A
1 A
1728194 ATTTTTTTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 1 0.01
15 7 0.10
16 4 0.06
17 4 0.06
18 11 0.15
19 18 0.25
20 24 0.34
21 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATATTATAAAATAT
Found at i:1728143 original size:31 final size:31
Alignment explanation
Indices: 1728096--1728196 Score: 139
Period size: 32 Copynumber: 3.2 Consensus size: 31
1728086 AATAATTATA
*
1728096 AAATATATAAATATATTAAAATTTATATAAAT
1 AAAT-TATTAATATATTAAAATTTATATAAAT
*
1728128 AAATTATTAATATATTAAATTTTATATAATAT
1 AAATTATTAATATATTAAAATTTATATAA-AT
* *
1728160 ATATTATTAAAATATTAAAATTTATATAAAT
1 AAATTATTAATATATTAAAATTTATATAAAT
1728191 ATAATT
1 A-AATT
1728197 TTTTTTAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 26 0.43
32 35 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATTATTAATATATTAAAATTTATATAAAT
Found at i:1728233 original size:63 final size:62
Alignment explanation
Indices: 1728082--1728236 Score: 160
Period size: 63 Copynumber: 2.5 Consensus size: 62
1728072 ATAATAAAAG
*
1728082 ATAAA-ATAAT-TAT-AAAATATATAAATATATTAAAATTTATATAAATAAATTATTAATAT
1 ATAAATATAATATATAAAAATATTTAAATATATTAAAATTTATATAAATAAATTATTAATAT
* * * **
1728141 ATTAAAT-T-TTATATAATATATATTATTAAA-ATATTAAAATTTATATAAATATAATTTTTTTT
1 A-TAAATATAATATATAA-AAATA-T-TTAAATATATTAAAATTTATATAAATA-AATTATTAAT
1728203 AAT
61 -AT
1728206 ATAAATATAATATATAAAAATATTTAAATAT
1 ATAAATATAATATATAAAAATATTTAAATAT
1728237 GATAAATAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
59 2 0.03
60 8 0.11
61 1 0.01
62 4 0.05
63 27 0.36
64 19 0.25
65 8 0.11
66 7 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (62 bp):
ATAAATATAATATATAAAAATATTTAAATATATTAAAATTTATATAAATAAATTATTAATAT
Found at i:1728791 original size:18 final size:19
Alignment explanation
Indices: 1728762--1728870 Score: 71
Period size: 18 Copynumber: 6.3 Consensus size: 19
1728752 TTTATGTTAA
*
1728762 ATATATATATTAAATATATT
1 ATATAAATATT-AATATATT
1728782 A-A-AAATATT-ATATATT
1 ATATAAATATTAATATATT
*
1728798 ATATAAATTTTAATATATT
1 ATATAAATATTAATATATT
*
1728817 -TAT-AAT-TT--T-TGTT
1 ATATAAATATTAATATATT
*
1728830 ATATAAATTTTAATATATT
1 ATATAAATATTAATATATT
*
1728849 -TAT--ATATTATTTATATT
1 ATATAAATATTA-ATATATT
1728866 ATATA
1 ATATA
1728871 TTATATTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
13 3 0.04
14 4 0.06
15 3 0.04
16 17 0.24
17 10 0.14
18 22 0.31
19 11 0.15
20 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
ATATAAATATTAATATATT
Found at i:1728870 original size:7 final size:7
Alignment explanation
Indices: 1728842--1728886 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
1728832 ATAAATTTTA
1728842 ATATATTT
1 ATATA-TT
1728850 ATATATT
1 ATATATT
1728857 ATTTATATT
1 A--TATATT
1728866 ATATATT
1 ATATATT
*
1728873 ATATTTT
1 ATATATT
1728880 ATATATT
1 ATATATT
1728887 TAAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 21 0.64
8 5 0.15
9 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATATATT
Found at i:1728898 original size:36 final size:34
Alignment explanation
Indices: 1728774--1728899 Score: 132
Period size: 32 Copynumber: 3.6 Consensus size: 34
1728764 ATATATATTA
* *
1728774 AATATATTAAAAATATTATATATTATATAAATTTT
1 AATATATT-TAAATATTTTATATTATATAAATTTT
* *
1728809 AATATATTTATA-ATTTT-TGTTATATAAATTTT
1 AATATATTTAAATATTTTATATTATATAAATTTT
*
1728841 AATATATTTATATATTATTTATATTATATATTATATTTT
1 AATATATTTAAATA-T-TTTATATTATATA--A-ATTTT
1728880 -ATATATTTAAATATTTTATA
1 AATATATTTAAATATTTTATA
1728900 CTTTGTTTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
32 26 0.33
33 5 0.06
34 3 0.04
35 11 0.14
36 14 0.18
37 1 0.01
38 13 0.17
39 5 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
AATATATTTAAATATTTTATATTATATAAATTTT
Found at i:1729183 original size:24 final size:25
Alignment explanation
Indices: 1729154--1729241 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 25
1729144 TATAAAAATA
1729154 ATTAAATT-TTAAATAAAATATAAT
1 ATTAAATTATTAAATAAAATATAAT
* * **
1729178 ATTAAA-AAATAAATTTAATATAAAT
1 ATTAAATTATTAAATAAAATAT-AAT
1729203 ATATAAATATATTAAA-AAATATATAAT
1 AT-TAAAT-TATTAAATAAA-ATATAAT
1729230 A-TAAATTATTAA
1 ATTAAATTATTAA
1729242 TATATTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
24 22 0.44
25 10 0.20
26 4 0.08
27 5 0.10
28 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTAAATTATTAAATAAAATATAAT
Found at i:1729196 original size:19 final size:18
Alignment explanation
Indices: 1729164--1729223 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
1729154 ATTAAATTTT
1729164 AAATAAAATATAATATTAAA
1 AAAT-AAAT-TAATATTAAA
1729184 AAATAAATTTAATA-TAAA
1 AAATAAA-TTAATATTAAA
*
1729202 TATATAAA-T-ATATTAAA
1 -AAATAAATTAATATTAAA
1729219 AAATA
1 AAATA
1729224 TATAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 4 0.11
19 14 0.40
20 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATTAATATTAAA
Found at i:1729249 original size:32 final size:33
Alignment explanation
Indices: 1729176--1729267 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 33
1729166 ATAAAATATA
*
1729176 ATATTAAAAAATAAATTTAATATAAATATATAAAT
1 ATATTAAAAAAT--ATATAATATAAATATATAAAT
*
1729211 ATATTAAAAAATATATAATATAAAT-TATTAAT
1 ATATTAAAAAATATATAATATAAATATATAAAT
**
1729243 ATATTAAAATTTATATAA-ATAAATA
1 ATATTAAAAAATATATAATATAAATA
1729268 ATATTTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 6 0.12
32 22 0.42
33 12 0.23
35 12 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
ATATTAAAAAATATATAATATAAATATATAAAT
Found at i:1729258 original size:27 final size:28
Alignment explanation
Indices: 1729188--1729277 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 28
1729178 ATTAAAAAAT
*
1729188 AAATTTAATATAAATATATAAATATATTAAA
1 AAATTTAATATAAAT-TATTAATATATT--A
1729219 AAATATATAATATAAATTATTAATATATTA
1 AAAT-T-TAATATAAATTATTAATATATTA
* * *
1729249 AAATTT-ATATAAATAAATAATATTTTA
1 AAATTTAATATAAATTATTAATATATTA
1729276 AA
1 AA
1729278 TATAATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 20 0.38
28 1 0.02
29 1 0.02
30 5 0.09
31 4 0.08
32 12 0.23
33 10 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATTTAATATAAATTATTAATATATTA
Found at i:1729263 original size:20 final size:20
Alignment explanation
Indices: 1729188--1729263 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 20
1729178 ATTAAAAAAT
1729188 AAATTTAATATAAATATA-TA
1 AAATTT-ATATAAATATATTA
*
1729208 AATATATTA-AAAAATATATAATA
1 AA-AT-TTATATAAATATAT--TA
1729231 TAAA-TTAT-T-AATATATTA
1 -AAATTTATATAAATATATTA
1729249 AAATTTATATAAATA
1 AAATTTATATAAATA
1729264 AATAATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 1 0.02
20 21 0.48
21 6 0.14
22 2 0.05
23 3 0.07
24 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTTATATAAATATATTA
Found at i:1729292 original size:15 final size:16
Alignment explanation
Indices: 1729186--1729297 Score: 50
Period size: 14 Copynumber: 7.6 Consensus size: 16
1729176 ATATTAAAAA
* *
1729186 ATAAATTTAATATA-A
1 ATAAATATAATATATT
*
1729201 ATATATA-AATATATT
1 ATAAATATAATATATT
* *
1729216 A-AAAAAT-ATATAAT
1 ATAAATATAATATATT
1729230 ATAAATTATTAATATATT
1 ATAAA-TA-TAATATATT
* *
1729248 A-AAAT-TTATATA-A
1 ATAAATATAATATATT
1729261 AT-AA-ATAATAT-TT
1 ATAAATATAATATATT
1729274 -TAAATATAAT-TATT
1 ATAAATATAATATATT
*
1729288 ATAAAAATAA
1 ATAAATATAA
1729298 AATAAAATGA
Statistics
Matches: 71, Mismatches: 13, Indels: 26
0.65 0.12 0.24
Matches are distributed among these distances:
12 1 0.01
13 11 0.15
14 29 0.41
15 17 0.24
16 2 0.03
17 4 0.06
18 7 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATATAATATATT
Found at i:1729804 original size:6 final size:6
Alignment explanation
Indices: 1729793--1729817 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1729783 TATTTTTATC
1729793 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
1729818 GTACTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:1730188 original size:16 final size:17
Alignment explanation
Indices: 1730151--1730198 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1730141 GAACATGATG
1730151 AAAAA-ATAATAAATAA
1 AAAAATATAATAAATAA
*
1730167 ATAAAATATAATAAA-AT
1 A-AAAATATAATAAATAA
1730184 AAAAATATAA-AAATA
1 AAAAATATAATAAATA
1730199 TTTTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 6 0.21
18 8 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATATAATAAATAA
Found at i:1731953 original size:16 final size:16
Alignment explanation
Indices: 1731917--1731958 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1731907 AGGAGATATT
*
1731917 AATATTAAATAAAATA
1 AATATTTAATAAAATA
*
1731933 AATATTTAATAAAATG
1 AATATTTAATAAAATA
*
1731949 TATATTTAAT
1 AATATTTAAT
1731959 TTAATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATTTAATAAAATA
Found at i:1732088 original size:2 final size:2
Alignment explanation
Indices: 1732066--1732102 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1732056 CCTCACCAAA
1732066 AT AT A- AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1732103 TTAAATCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1732793 original size:20 final size:20
Alignment explanation
Indices: 1732770--1732809 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1732760 TATTTTTGAT
*
1732770 ATAAAAATTAAAATAAATAA
1 ATAAAAATAAAAATAAATAA
1732790 ATAAAAATAAAAATAAATAA
1 ATAAAAATAAAAATAAATAA
1732810 TTATATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAAAAATAAAAATAAATAA
Found at i:1733421 original size:2 final size:2
Alignment explanation
Indices: 1733410--1733447 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1733400 GCTAATAGCC
* *
1733410 TA TA -A TA TA TA TG TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1733448 CTGCACACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1735398 original size:54 final size:53
Alignment explanation
Indices: 1735336--1735442 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 53
1735326 AGTTAATAAA
*
1735336 TTACCATAATATTTTATTAAAAGCAATGATTGATAAATGAATTTTTTTTTGTAT
1 TTACCATAATATTTTATTAAAAGCAATGATTGATAAATGAA-ATTTTTTTGTAT
*
1735390 TTACCATAATATTTTATTAAAAGCAATGGTTGATAAATGAAATTTTTTTGTAT
1 TTACCATAATATTTTATTAAAAGCAATGATTGATAAATGAAATTTTTTTGTAT
1735443 AAGTATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 11 0.22
54 40 0.78
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (53 bp):
TTACCATAATATTTTATTAAAAGCAATGATTGATAAATGAAATTTTTTTGTAT
Found at i:1737850 original size:3 final size:3
Alignment explanation
Indices: 1737842--1737879 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1737832 AGGAGTTGAG
1737842 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1737880 AACGCATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1739702 original size:2 final size:2
Alignment explanation
Indices: 1739697--1739731 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1739687 ATTCACCCCC
*
1739697 CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1739732 TTACTGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1745020 original size:2 final size:2
Alignment explanation
Indices: 1745013--1745049 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1745003 TTTTTGCAGG
*
1745013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1745050 AAGGAACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1745223 original size:17 final size:17
Alignment explanation
Indices: 1745198--1745236 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1745188 AAAATGTATA
1745198 TATTAAATATAAATATT
1 TATTAAATATAAATATT
*
1745215 TATTTAATATAAATATT
1 TATTAAATATAAATATT
1745232 T-TTAA
1 TATTAA
1745237 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAATATAAATATT
Found at i:1745249 original size:8 final size:9
Alignment explanation
Indices: 1745230--1745255 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1745220 AATATAAATA
1745230 TTTTTAATT
1 TTTTTAATT
1745239 TTTTTAATT
1 TTTTTAATT
1745248 TTTTTAAT
1 TTTTTAAT
1745256 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTAATT
Found at i:1745382 original size:29 final size:28
Alignment explanation
Indices: 1745336--1745395 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
1745326 TTTTATGAAA
1745336 AATAAAAAATTAAAATAATATAATTTAT
1 AATAAAAAATTAAAATAATATAATTTAT
** *
1745364 AATATAAAAATTAGGATAATATGATTTAT
1 AATA-AAAAATTAAAATAATATAATTTAT
1745393 AAT
1 AAT
1745396 TTAATCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (28 bp):
AATAAAAAATTAAAATAATATAATTTAT
Found at i:1745791 original size:2 final size:2
Alignment explanation
Indices: 1745784--1745819 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1745774 TCTACTACTT
1745784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1745820 ATCTTATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1747896 original size:17 final size:19
Alignment explanation
Indices: 1747860--1747901 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1747850 TTAATTAAAT
1747860 AAAAATTAATAAATTATTA
1 AAAAATTAATAAATTATTA
*
1747879 ATAAATTAA-AAA-TATTA
1 AAAAATTAATAAATTATTA
1747896 AAAAAT
1 AAAAAT
1747902 AATTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
18 3 0.14
19 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTAATAAATTATTA
Found at i:1749996 original size:5 final size:5
Alignment explanation
Indices: 1749980--1750009 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1749970 GAAGAGTGAT
1749980 TGGGG TTGGGG TGGGG TGGGG TGGGG TGGG
1 TGGGG -TGGGG TGGGG TGGGG TGGGG TGGG
1750010 CTGGCCACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.00, G:0.77, T:0.23
Consensus pattern (5 bp):
TGGGG
Found at i:1750413 original size:2 final size:2
Alignment explanation
Indices: 1750406--1750430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1750396 AGCCCAAATC
1750406 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 C
1750431 CCCCCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1755235 original size:27 final size:29
Alignment explanation
Indices: 1755180--1755236 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1755170 GAAGATTTAT
*
1755180 TTGTCTCCATCCAAGCAAGTCATTGATTGAA
1 TTGTCTCCATCCAAGCAAG-CA-TCATTGAA
1755211 TTGTCTCCATCCAAGCAAG-A-CATTGA
1 TTGTCTCCATCCAAGCAAGCATCATTGA
1755237 TGAGCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
29 1 0.04
31 19 0.76
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (29 bp):
TTGTCTCCATCCAAGCAAGCATCATTGAA
Found at i:1756568 original size:27 final size:25
Alignment explanation
Indices: 1756529--1756578 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
1756519 TTTCATTCAT
*
1756529 ATTTTATATTATTTAAAGTATTATAA
1 ATTTTATAATATTTAAAG-ATTATAA
*
1756555 ATTTATATAATATTTATAGATTAT
1 ATTT-TATAATATTTAAAGATTAT
1756579 TTTTAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTTATAATATTTAAAGATTATAA
Found at i:1756730 original size:14 final size:15
Alignment explanation
Indices: 1756708--1756745 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1756698 AAGGAGAGAG
*
1756708 AAAGGAAAAGAAAGA
1 AAAGAAAAAGAAAGA
*
1756723 AAA-AAAAAGAAGGA
1 AAAGAAAAAGAAAGA
1756737 AAAGAAAAA
1 AAAGAAAAA
1756746 AGAACTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:1757620 original size:11 final size:11
Alignment explanation
Indices: 1757606--1757652 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1757596 AATACGTTTA
1757606 TATATT-TATAT
1 TATATTATAT-T
1757617 TATATTATATT
1 TATATTATATT
*
1757628 T-TAATTATTTT
1 TAT-ATTATATT
1757639 TATATTATATT
1 TATATTATATT
1757650 TAT
1 TAT
1757653 GTTGTGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 1 0.03
11 26 0.84
12 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTATATT
Found at i:1757683 original size:10 final size:10
Alignment explanation
Indices: 1757665--1757699 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1757655 TGTGTTTTAA
1757665 TTTTT-TAAT
1 TTTTTATAAT
1757674 TTTTTATAAT
1 TTTTTATAAT
1757684 TTTTTATAAT
1 TTTTTATAAT
*
1757694 TATTTA
1 TTTTTA
1757700 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1757685 original size:18 final size:17
Alignment explanation
Indices: 1757659--1757704 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1757649 TTATGTTGTG
*
1757659 TTTTAATTTTTTAATTT
1 TTTTAATTTTTTAAATT
1757676 TTTATAATTTTTTATAATT
1 TTT-TAATTTTTTA-AATT
*
1757695 ATTTAATTTT
1 TTTTAATTTT
1757705 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTAATTTTTTAAATT
Found at i:1757864 original size:3 final size:3
Alignment explanation
Indices: 1757850--1757922 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
1757840 GAAATTTTAG
* *
1757850 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1757898 TGA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1757923 TATGCAAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1766390 original size:2 final size:2
Alignment explanation
Indices: 1766383--1766446 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1766373 ATCAGTTGCC
1766383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1766425 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1766447 GGATATGGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1769539 original size:45 final size:44
Alignment explanation
Indices: 1769483--1769598 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 44
1769473 ACCGTCACCG
* * ** *
1769483 GGGGTTTTACAATTGGAGGGACGGTAACCGGTGGCAAGTTGATT
1 GGGGCTTTACAATAGGAGGGACAATAACCGGTGGCAAGTTGATC
*
1769527 GGTGGCTTTACAACAGGAGGGACAATAACCGGTGGCAAGTTGATC
1 GG-GGCTTTACAATAGGAGGGACAATAACCGGTGGCAAGTTGATC
* * *
1769572 GGGGGTTTAACAATGGGAGGGATAATA
1 GGGGCTTT-ACAATAGGAGGGACAATA
1769599 GTAATGGGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 7 0.12
45 53 0.88
ACGTcount: A:0.28, C:0.12, G:0.37, T:0.23
Consensus pattern (44 bp):
GGGGCTTTACAATAGGAGGGACAATAACCGGTGGCAAGTTGATC
Found at i:1773753 original size:2 final size:2
Alignment explanation
Indices: 1773746--1773771 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1773736 AAATTGATGG
1773746 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1773772 TTCCTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1775777 original size:16 final size:16
Alignment explanation
Indices: 1775711--1775780 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
1775701 TATATTTTAA
*
1775711 TTATATTACA-AATATT
1 TTATATTATATAA-ATT
* **
1775727 TTTTATTATATGTATT
1 TTATATTATATAAATT
1775743 TTA-A-TATATAAATAAT
1 TTATATTATATAAAT--T
1775759 TTATATTATATAAATT
1 TTATATTATATAAATT
1775775 TTATAT
1 TTATAT
1775781 ATTAATATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 7 0.17
15 1 0.02
16 24 0.57
17 1 0.02
18 9 0.21
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:1775781 original size:18 final size:17
Alignment explanation
Indices: 1775711--1775796 Score: 58
Period size: 18 Copynumber: 5.2 Consensus size: 17
1775701 TATATTTTAA
*
1775711 TTATATTACA-AATATTT
1 TTATATTATATAA-ATTT
**
1775728 TT-TATTATATGTA-TT
1 TTATATTATATAAATTT
*
1775743 TTA-A-TATATAAATAAT
1 TTATATTATATAAAT-TT
1775759 TTATATTATATAAATTT
1 TTATATTATATAAATTT
*
1775776 TATATATTA-ATATATTT
1 T-TATATTATATAAATTT
1775793 TTAT
1 TTAT
1775797 TATTTTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
14 6 0.11
15 5 0.09
16 14 0.26
17 13 0.24
18 16 0.30
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTATATTATATAAATTT
Found at i:1775815 original size:32 final size:33
Alignment explanation
Indices: 1775691--1775815 Score: 121
Period size: 32 Copynumber: 3.8 Consensus size: 33
1775681 TGTATTTACG
* *
1775691 TTTATTTTAATATATTTTAATTATATTACAAATATTT
1 TTTATTAT-ATATATTTT-ATTATATTA-ATATA-TT
* * *
1775728 TTTATTATATGTATTTTAATATATAAATA-ATT
1 TTTATTATATATATTTTATTATATTAATATATT
* *
1775760 TATATTATATAAATTTTA-TATATTAATATATT
1 TTTATTATATATATTTTATTATATTAATATATT
*
1775792 TTTATTAT-TTTATTTTATTATATT
1 TTTATTATATATATTTTATTATATT
1775816 TAATTAATTA
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
31 16 0.22
32 33 0.45
33 1 0.01
34 2 0.03
35 7 0.09
36 8 0.11
37 7 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTATTATATATATTTTATTATATTAATATATT
Found at i:1782610 original size:12 final size:12
Alignment explanation
Indices: 1782593--1782620 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1782583 TTGTATATAA
1782593 TTAATAAAAATT
1 TTAATAAAAATT
1782605 TTAATAAAAATT
1 TTAATAAAAATT
1782617 TTAA
1 TTAA
1782621 ATTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAATAAAAATT
Found at i:1784344 original size:2 final size:2
Alignment explanation
Indices: 1784337--1784368 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1784327 TGTAAATAGA
1784337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1784369 TAAACCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1787708 original size:26 final size:25
Alignment explanation
Indices: 1787649--1787713 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 25
1787639 TGTTTTTGAT
*
1787649 AAATATTTATTTTATCTTT-TTTTTA
1 AAATATTTATATTAT-TTTATTTTTA
1787674 AAA-A--T-TATTATTTTATCTTTTA
1 AAATATTTATATTATTTTAT-TTTTA
1787696 AAATATTTATATT-TTTTA
1 AAATATTTATATTATTTTA
1787714 ATATATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
20 3 0.09
21 6 0.18
22 9 0.27
23 1 0.03
24 1 0.03
25 9 0.27
26 4 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
AAATATTTATATTATTTTATTTTTA
Found at i:1787714 original size:18 final size:18
Alignment explanation
Indices: 1787682--1787722 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1787672 TAAAAATTAT
1787682 TATTT-TATCTTTTAAAA
1 TATTTATATCTTTTAAAA
* *
1787699 TATTTATATTTTTTAATA
1 TATTTATATCTTTTAAAA
1787717 TATTTA
1 TATTTA
1787723 ATATATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATATCTTTTAAAA
Found at i:1788358 original size:17 final size:17
Alignment explanation
Indices: 1788309--1788359 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1788299 TATAAATTTT
1788309 AATTATTATT-AATAA-A
1 AATT-TTATTAAATAATA
*
1788325 AATTTAATTATAA-AATA
1 AATTTTATTA-AATAATA
1788342 AATTTTATTAAATAATA
1 AATTTTATTAAATAATA
1788359 A
1 A
1788360 TTATGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
17 17 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTATTAAATAATA
Found at i:1788884 original size:16 final size:16
Alignment explanation
Indices: 1788863--1788895 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1788853 TATATATTTC
1788863 TTTTCTTTATTTTCTT
1 TTTTCTTTATTTTCTT
*
1788879 TTTTCTTTTTTTTCTT
1 TTTTCTTTATTTTCTT
1788895 T
1 T
1788896 GCATCTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTATTTTCTT
Found at i:1789255 original size:30 final size:30
Alignment explanation
Indices: 1789221--1789277 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1789211 CATTTAATTA
*
1789221 CATTAAAGTGTTAAAATTTACATAAATAAT
1 CATTAAAGTGTAAAAATTTACATAAATAAT
* *
1789251 CATTAATGTGTAAAAATTTATATAAAT
1 CATTAAAGTGTAAAAATTTACATAAAT
1789278 TTATACTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (30 bp):
CATTAAAGTGTAAAAATTTACATAAATAAT
Found at i:1789500 original size:22 final size:23
Alignment explanation
Indices: 1789464--1789510 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
1789454 AACACATTAA
1789464 ATTTTCTTTTATTTC-CTTTTTC
1 ATTTTCTTTTATTTCACTTTTTC
1789486 ATTTTCTTTCT-TTTCATCTTTTTC
1 ATTTTCTTT-TATTTCA-CTTTTTC
1789510 A
1 A
1789511 GTCCCTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTCTTTTATTTCACTTTTTC
Found at i:1789880 original size:22 final size:23
Alignment explanation
Indices: 1789853--1789906 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1789843 AATTATTAAT
*
1789853 ATATAAAAATTTTATAT-AAACA
1 ATATAAAAATTTTAAATAAAACA
* *
1789875 ATAT-AATATTTTAAATAAAATA
1 ATATAAAAATTTTAAATAAAACA
1789897 ATATAAAAAT
1 ATATAAAAAT
1789907 AAGCTTGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.38
22 12 0.46
23 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAAAAATTTTAAATAAAACA
Found at i:1790600 original size:23 final size:23
Alignment explanation
Indices: 1790552--1790617 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1790542 TAATAAAATA
* * *
1790552 TAAATTTAAACT-TAAACCTATT
1 TAAATTTAAACTAAAAACCCATC
1790574 TAAATTTAAACTAAAAACCCATC
1 TAAATTTAAACTAAAAACCCATC
* *
1790597 TAAACTTAAATTAAAAACCCA
1 TAAATTTAAACTAAAAACCCA
1790618 ATTACAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 12 0.32
23 26 0.68
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATTTAAACTAAAAACCCATC
Found at i:1791532 original size:2 final size:2
Alignment explanation
Indices: 1791525--1791554 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1791515 CTGTCAAACT
*
1791525 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1791555 ATTTATCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1794392 original size:21 final size:20
Alignment explanation
Indices: 1794355--1794395 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1794345 TTTTACTTTA
*
1794355 ATTTTTTTTAAGATTATATT
1 ATTTTTTTAAAGATTATATT
*
1794375 ATTTTTTTAATAGTTTATATT
1 ATTTTTTTAA-AGATTATATT
1794396 TACTGCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTTTTAAAGATTATATT
Found at i:1795931 original size:19 final size:19
Alignment explanation
Indices: 1795894--1795931 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1795884 CAAAAAAAAA
*
1795894 AATTAATAATTAATATTTT
1 AATTAATAAATAATATTTT
1795913 AATTAATAAAATAAT-TTTT
1 AATTAAT-AAATAATATTTT
1795932 TTCAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAATAAATAATATTTT
Found at i:1796725 original size:22 final size:23
Alignment explanation
Indices: 1796700--1796746 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1796690 TTATATATTT
1796700 TATA-ATTAAATTTAATTTA-AAA
1 TATATATT-AATTTAATTTATAAA
*
1796722 TATATATTATTTTAATTTATAAA
1 TATATATTAATTTAATTTATAAA
1796745 TA
1 TA
1796747 GTTACTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATATTAATTTAATTTATAAA
Found at i:1796728 original size:33 final size:34
Alignment explanation
Indices: 1796668--1796735 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 34
1796658 TAAAATATTA
*
1796668 ATAATTAATTTTATATTAATAATTATA-TATTTT
1 ATAATTAATTTAATATTAATAATTATATTATTTT
1796701 ATAATTAAATTTAAT-TTAA-AATATATATTATTTT
1 ATAATT-AATTTAATATTAATAAT-TATATTATTTT
1796735 A
1 A
1796736 ATTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 3 0.10
33 14 0.45
34 14 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATAATTAATTTAATATTAATAATTATATTATTTT
Found at i:1796865 original size:34 final size:33
Alignment explanation
Indices: 1796827--1796893 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
1796817 GATAAAATAT
1796827 TAATTAAATAA-TTAAAATATAATATAATATAAAA
1 TAATTAAA-AATTTAAAAT-TAATATAATATAAAA
*
1796861 TAATTAAAAATTTTAAAATTTATATAATATAAA
1 TAATTAAAAA-TTTAAAATTAATATAATATAAA
1796894 TTATTATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 21 0.70
35 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATTAAAAATTTAAAATTAATATAATATAAAA
Found at i:1796894 original size:15 final size:16
Alignment explanation
Indices: 1796876--1796926 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
1796866 AAAAATTTTA
1796876 AAATTTA-TATAATAT
1 AAATTTATTATAATAT
*
1796891 AAA-TTATTATCATAT
1 AAATTTATTATAATAT
*
1796906 CAAAATTTATTAAAATAT
1 --AAATTTATTATAATAT
1796924 AAA
1 AAA
1796927 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 3 0.10
17 3 0.10
18 10 0.34
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTATTATAATAT
Found at i:1796917 original size:18 final size:17
Alignment explanation
Indices: 1796834--1796928 Score: 65
Period size: 17 Copynumber: 5.7 Consensus size: 17
1796824 TATTAATTAA
* *
1796834 ATAAT-TAAAATATAAT
1 ATAATATAAAATTTATT
*
1796850 ATAATATAAAA-TAATT
1 ATAATATAAAATTTATT
* *
1796866 AAAAATTTTAAAATTTA-T
1 -ATAA-TATAAAATTTATT
1796884 ATAATAT-AAA-TTATT
1 ATAATATAAAATTTATT
*
1796899 ATCATATCAAAATTTATT
1 ATAATAT-AAAATTTATT
*
1796917 AAAATATAAAAT
1 ATAATATAAAAT
1796929 ATTTTAAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.05
15 10 0.17
16 9 0.15
17 19 0.32
18 17 0.28
19 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATATAAAATTTATT
Found at i:1797402 original size:17 final size:16
Alignment explanation
Indices: 1797365--1797411 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1797355 TGTTCTGTTA
* *
1797365 ATTTTATTAATTATGT
1 ATTTTATTTATTATCT
1797381 ATTTTATTTATTATACT
1 ATTTTATTTATTAT-CT
1797398 ATTTTTATTT-TTAT
1 A-TTTTATTTATTAT
1797412 TAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 13 0.48
17 6 0.22
18 8 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTTATTTATTATCT
Found at i:1797433 original size:21 final size:20
Alignment explanation
Indices: 1797365--1797446 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
1797355 TGTTCTGTTA
*
1797365 ATTTTATTAATTATGTATTT-T
1 ATTTTATTAAATAT-T-TTTAT
*
1797386 A-TTTATTATACTATTTTTAT
1 ATTTTATTA-AATATTTTTAT
1797406 -TTTTATTAAATATTTTTAT
1 ATTTTATTAAATATTTTTAT
* *
1797425 ATTTATATTATATTTTTTTAT
1 ATTT-TATTAAATATTTTTAT
1797446 A
1 A
1797447 ATATTTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.25
20 19 0.37
21 20 0.38
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (20 bp):
ATTTTATTAAATATTTTTAT
Found at i:1797614 original size:32 final size:30
Alignment explanation
Indices: 1797540--1797636 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 30
1797530 TAATAATTTT
1797540 AAATATAATATTAACATAATATTAAA-AAAATA
1 AAATATAATATTAA-AT-ATA-TAAATAAAATA
*
1797572 AAATAAAATATTAAATATAGTACAATAAAA-A
1 AAATATAATATTAAATATA-TA-AATAAAATA
*
1797603 AATATATAATA-TAAATATATAAATAAATTA
1 AA-ATATAATATTAAATATATAAATAAAATA
1797633 AAAT
1 AAAT
1797637 TTATTAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
29 8 0.14
30 10 0.18
31 15 0.26
32 24 0.42
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (30 bp):
AAATATAATATTAAATATATAAATAAAATA
Found at i:1797620 original size:13 final size:12
Alignment explanation
Indices: 1797539--1797630 Score: 54
Period size: 12 Copynumber: 7.8 Consensus size: 12
1797529 TTAATAATTT
1797539 TAAATATAATAT-
1 TAAATA-AATATA
1797551 TAACAT-AATAT-
1 TAA-ATAAATATA
1797562 TAAA-AAA-ATA
1 TAAATAAATATA
1797572 -AAATAAA-ATA
1 TAAATAAATATA
* *
1797582 TTAAATATAGTACAA
1 -TAAATA-AATA-TA
*
1797597 TAAAAAAATATA
1 TAAATAAATATA
1797609 TAATATAAATATA
1 TAA-ATAAATATA
1797622 TAAATAAAT
1 TAAATAAAT
1797631 TAAAATTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
9 5 0.08
10 9 0.14
11 8 0.12
12 18 0.28
13 17 0.27
14 6 0.09
15 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (12 bp):
TAAATAAATATA
Found at i:1797634 original size:17 final size:16
Alignment explanation
Indices: 1797557--1797630 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 16
1797547 ATATTAACAT
*
1797557 AATAT-TAAAAAAATA
1 AATATATAAATAAATA
*
1797572 AA-ATA-AAAT-ATTA
1 AATATATAAATAAATA
*
1797585 AATATAGTACAATAAAAA
1 AATATA-TA-AATAAATA
1797603 AATATAT-AAT--ATA
1 AATATATAAATAAATA
1797616 AATATATAAATAAAT
1 AATATATAAATAAAT
1797631 TAAAATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 17
0.67 0.07 0.25
Matches are distributed among these distances:
13 14 0.31
14 11 0.24
15 5 0.11
16 3 0.07
17 4 0.09
18 8 0.18
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (16 bp):
AATATATAAATAAATA
Found at i:1799809 original size:2 final size:2
Alignment explanation
Indices: 1799804--1799831 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1799794 TTGTTTTTTC
1799804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1799832 ATTAGACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1803932 original size:24 final size:24
Alignment explanation
Indices: 1803889--1803936 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1803879 TTATATATAT
*
1803889 AATATAAATTATTAATATATTAAA
1 AATATAAATTATTAACATATTAAA
1803913 AATATAAA-TATATAACATATTAAA
1 AATATAAATTAT-TAACATATTAAA
1803937 TATGATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATAAATTATTAACATATTAAA
Found at i:1805971 original size:15 final size:14
Alignment explanation
Indices: 1805935--1805975 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1805925 TATAATCAAT
*
1805935 TTATTAAGAATTGG
1 TTATTAAGAATTGA
1805949 TTATTAAGAATTGA
1 TTATTAAGAATTGA
1805963 TTAATTAAGAATT
1 TT-ATTAAGAATT
1805976 TATGCAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
TTATTAAGAATTGA
Found at i:1808975 original size:9 final size:9
Alignment explanation
Indices: 1808951--1808984 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
1808941 TCATTTAATC
1808951 ATATTTAAA
1 ATATTTAAA
1808960 ATA-TTAAA
1 ATATTTAAA
1808968 ATATTTAAA
1 ATATTTAAA
1808977 A-ATTTAAA
1 ATATTTAAA
1808985 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.62
9 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATTTAAA
Found at i:1809025 original size:11 final size:11
Alignment explanation
Indices: 1808993--1809027 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1808983 AATTAAATTA
*
1808993 ATTTAAATATT
1 ATTTAAATTTT
1809004 ATTTAATATTTT
1 ATTTAA-ATTTT
1809016 ATTTAAATTTT
1 ATTTAAATTTT
1809027 A
1 A
1809028 AATTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:1809607 original size:34 final size:33
Alignment explanation
Indices: 1809569--1809635 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
1809559 AATAAAATAT
1809569 TAATTAAATAA-TTAAAATATAATATAATATAAAA
1 TAATTAAA-AATTTAAAAT-TAATATAATATAAAA
*
1809603 TAATTAAAAATTTTAAAATTTATATAATATAAA
1 TAATTAAAAA-TTTAAAATTAATATAATATAAA
1809636 TTATTTTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.07
34 21 0.70
35 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATTAAAAATTTAAAATTAATATAATATAAAA
Found at i:1809693 original size:11 final size:10
Alignment explanation
Indices: 1809674--1809711 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
1809664 ATAAAATATT
1809674 TTAAATATAA
1 TTAAATATAA
1809684 TTATAATATAA
1 TTA-AATATAA
1809695 TTAAATAT-A
1 TTAAATATAA
1809704 -TAAATATA
1 TTAAATATA
1809712 TTTAGAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.27
9 1 0.04
10 8 0.31
11 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAATATAA
Found at i:1809890 original size:28 final size:27
Alignment explanation
Indices: 1809832--1809921 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
1809822 TACCCATTTG
* *
1809832 TTTGTAAAAAATGGTGGTTATTTTATG
1 TTTGTCAAAAATGGTGGTTATTTTATA
*
1809859 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
1809887 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
1809912 TTTGTCAAAA
1 TTTGTCAAAA
1809922 TTTGTGGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.21
26 3 0.06
27 18 0.34
28 21 0.40
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:1812521 original size:21 final size:22
Alignment explanation
Indices: 1812492--1812537 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1812482 AGTTCAGACA
** *
1812492 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1812514 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
1812535 AGT
1 AGT
1812538 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:1814482 original size:28 final size:27
Alignment explanation
Indices: 1814423--1814512 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
1814413 CACCCTTTTG
* * *
1814423 TTTGTCAAAAATAGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
1814450 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
1814478 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
1814503 TTTGTCAAAA
1 TTTGTCAAAA
1814513 TTTGTGGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.21
26 3 0.06
27 18 0.34
28 21 0.40
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:1815040 original size:17 final size:17
Alignment explanation
Indices: 1814999--1815078 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
1814989 ATGTGTTTTG
*
1814999 TTAATTTTATTAATTATA
1 TTAATTTTATT-TTTATA
1815017 -T-ATTTTATTTTTATA
1 TTAATTTTATTTTTATA
*
1815032 TTAATTTTATATTTATTAA
1 TTAATTTTATTTTTA-T-A
* * *
1815051 ATATTTTTATATTTATA
1 TTAATTTTATTTTTATA
1815068 TT-ATTTT-TTTT
1 TTAATTTTATTTT
1815079 ATACAATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
15 8 0.16
16 13 0.25
17 14 0.27
18 2 0.04
19 14 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATTTTATTTTTATA
Found at i:1815077 original size:19 final size:18
Alignment explanation
Indices: 1815019--1815076 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
1815009 TAATTATATA
* *
1815019 TTTTATTTTTATATTA-A
1 TTTTATATTTATATTATT
*
1815036 TTTTATATTTAT-TAAATAT
1 TTTTATATTTATAT-TAT-T
1815055 TTTTATATTTATATTATT
1 TTTTATATTTATATTATT
1815073 TTTT
1 TTTT
1815077 TTATACAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 12 0.36
18 5 0.15
19 14 0.42
20 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATATTTATATTATT
Found at i:1815283 original size:33 final size:30
Alignment explanation
Indices: 1815246--1815317 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 30
1815236 AAAAAAATAA
1815246 ATATAATATAAATATATCAATAAATTAAAATTT
1 ATATAATATAAAT-TATCAATAAATTAAAA--T
* * *
1815279 ATATAATATAAATTATTAATATATTTAAAT
1 ATATAATATAAATTATCAATAAATTAAAAT
1815309 ATATAATAT
1 ATATAATAT
1815318 TTTAAACTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.28
32 13 0.36
33 13 0.36
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATATAAATTATCAATAAATTAAAAT
Found at i:1815315 original size:17 final size:17
Alignment explanation
Indices: 1815254--1815323 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
1815244 AAATATAATA
*
1815254 TAAATATATCAATAAATT
1 TAAATATAT-AATATATT
* * *
1815272 AAAATTTAT-ATA-ATA
1 TAAATATATAATATATT
1815287 TAAAT-TATTAATATATT
1 TAAATATA-TAATATATT
1815304 TAAATATATAATAT-TT
1 TAAATATATAATATATT
1815320 TAAA
1 TAAA
1815324 CTCTGGCACG
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.05
15 7 0.16
16 12 0.28
17 13 0.30
18 9 0.21
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATATAATATATT
Found at i:1817135 original size:11 final size:11
Alignment explanation
Indices: 1817121--1817145 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1817111 TAGAAAACCA
1817121 AAAAAAAAAAG
1 AAAAAAAAAAG
1817132 AAAAAAAAAAG
1 AAAAAAAAAAG
1817143 AAA
1 AAA
1817146 GATTCCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1817951 original size:33 final size:30
Alignment explanation
Indices: 1817903--1817982 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 30
1817893 TAGTAAAATT
* *
1817903 GAATTTTTTATTTTTTGTTTTTAGATTTTTAAA
1 GAATTTTTTA-TTTTTATTTTTAAATTTTT--A
1817936 GAATTTATTTATTTTTATTTTTAAATTTTTA
1 GAATTT-TTTATTTTTATTTTTAAATTTTTA
*
1817967 GATTTTTTTTATTTTT
1 GA-ATTTTTTATTTTT
1817983 TAAGTTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.29
32 3 0.07
33 23 0.55
34 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (30 bp):
GAATTTTTTATTTTTATTTTTAAATTTTTA
Found at i:1817975 original size:25 final size:27
Alignment explanation
Indices: 1817942--1818009 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
1817932 TAAAGAATTT
1817942 ATTTATTTTTA-TTTTTAAATTTTTAG
1 ATTTATTTTTATTTTTTAAATTTTTAG
*
1817968 ATTT-TTTTTATTTTTTAAGTTTTTA-
1 ATTTATTTTTATTTTTTAAATTTTTAG
*
1817993 A-TTACTTTTTGTTTTTT
1 ATTTA-TTTTTATTTTTT
1818010 TGATTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 2 0.05
25 7 0.19
26 28 0.76
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.74
Consensus pattern (27 bp):
ATTTATTTTTATTTTTTAAATTTTTAG
Found at i:1818008 original size:18 final size:17
Alignment explanation
Indices: 1817947--1818033 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 17
1817937 AATTTATTTA
1817947 TTTTTATTTTTAA--AT
1 TTTTTATTTTTAATTAT
* *
1817962 TTTTAGATTTTT-TTTAT
1 TTTT-TATTTTTAATTAT
1817979 TTTTTAAGTTTTTAATTACT
1 TTTTT-A-TTTTTAATTA-T
* *
1817999 TTTTGTTTTTTTGATTA-
1 TTTT-TATTTTTAATTAT
1818016 TTTTTATTTTTAATTAT
1 TTTTTATTTTTAATTAT
1818033 T
1 T
1818034 CAATATCAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
15 4 0.07
16 16 0.29
17 12 0.22
18 5 0.09
19 12 0.22
20 5 0.09
21 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTATTTTTAATTAT
Found at i:1818974 original size:34 final size:34
Alignment explanation
Indices: 1818935--1819086 Score: 250
Period size: 34 Copynumber: 4.4 Consensus size: 34
1818925 TATGGGAAAT
* *
1818935 CCTAACATTCTCACCAGATACATCACCTAATACA
1 CCTAACATTCTCACCAAATACATCACCTAACACA
*
1818969 CCTAACATTCTCACCAAATACATTACCTAACACA
1 CCTAACATTCTCACCAAATACATCACCTAACACA
*
1819003 CCTAACATTCTCACCAAATACATTACCTAACACA
1 CCTAACATTCTCACCAAATACATCACCTAACACA
*
1819037 CCTAACATTCTTACCAAATACATCACCTAACACA
1 CCTAACATTCTCACCAAATACATCACCTAACACA
1819071 CCTAACATTCTTCACC
1 CCTAACATTC-TCACC
1819087 TAACACACTT
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
34 107 0.96
35 4 0.04
ACGTcount: A:0.39, C:0.36, G:0.01, T:0.24
Consensus pattern (34 bp):
CCTAACATTCTCACCAAATACATCACCTAACACA
Found at i:1823844 original size:34 final size:34
Alignment explanation
Indices: 1823801--1823987 Score: 329
Period size: 34 Copynumber: 5.5 Consensus size: 34
1823791 TATAAAATAA
1823801 CTAACACACCTAACATTCTCACCAAATACATCAC
1 CTAACACACCTAACATTCTCACCAAATACATCAC
1823835 CTAACACACCTAACATTCTCACCAAATACATCAC
1 CTAACACACCTAACATTCTCACCAAATACATCAC
* *
1823869 CTAATACACCTAACATTCTCACCAAATACATTAC
1 CTAACACACCTAACATTCTCACCAAATACATCAC
*
1823903 CTAACACACCTAACATTCTCACCAAATACATTAC
1 CTAACACACCTAACATTCTCACCAAATACATCAC
* *
1823937 TTAACACACCTAACATTCTTACCAAATACATCAC
1 CTAACACACCTAACATTCTCACCAAATACATCAC
1823971 CTAACACACCTAACATT
1 CTAACACACCTAACATT
1823988 TTTCACCTAA
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 146 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (34 bp):
CTAACACACCTAACATTCTCACCAAATACATCAC
Found at i:1827225 original size:34 final size:32
Alignment explanation
Indices: 1827152--1827226 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
1827142 ATTATTTTAC
* * *
1827152 TTTAAATTATTATTTAATATTTATATTTAAAT
1 TTTAAAATATTATTTAATATTTATAATTAAAA
* *
1827184 TTATAAAATATTTTTTATTAATTTATAATTAATAA
1 TT-TAAAATATTATTTAAT-ATTTATAATTAA-AA
1827219 TTTAAAAT
1 TTTAAAAT
1827227 TTCAGATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 2 0.06
33 13 0.37
34 17 0.49
35 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTAAAATATTATTTAATATTTATAATTAAAA
Found at i:1827528 original size:25 final size:26
Alignment explanation
Indices: 1827495--1827543 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1827485 TAAAGAATTT
1827495 ATTTATTTTTATTTTTAAATTTTTAG
1 ATTTATTTTTATTTTTAAATTTTTAG
*
1827521 ATTT-TTTTTATTTTTTAATTTTT
1 ATTTATTTTTATTTTTAAATTTTT
1827544 TAATTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (26 bp):
ATTTATTTTTATTTTTAAATTTTTAG
Found at i:1827534 original size:8 final size:8
Alignment explanation
Indices: 1827500--1827579 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
1827490 AATTTATTTA
1827500 TTTTTATT
1 TTTTTATT
**
1827508 TTTAAATT
1 TTTTTATT
**
1827516 TTTAGATTT
1 TTTTTA-TT
1827525 TTTTTATT
1 TTTTTATT
*
1827533 TTTTAATT
1 TTTTTATT
*
1827541 TTTTAATT
1 TTTTTATT
*
1827549 ACTTTTTGTT
1 --TTTTTATT
1827559 TTTTTGATT
1 TTTTT-ATT
1827568 ATTTTTATT
1 -TTTTTATT
1827577 TTT
1 TTT
1827580 AATTATTCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
8 36 0.62
9 11 0.19
10 11 0.19
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.76
Consensus pattern (8 bp):
TTTTTATT
Found at i:1827542 original size:33 final size:33
Alignment explanation
Indices: 1827459--1827548 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 33
1827449 TAAAATTGAA
* *
1827459 TTTTTTATTTTTTGTTTTTAGATTTTTAAAGAAT
1 TTTTTTATTTTTTATTTTTAAATTTTT-AAGAAT
* *
1827493 TTATTTA-TTTTTATTTTTAAATTTTT-AGATT
1 TTTTTTATTTTTTATTTTTAAATTTTTAAGAAT
*
1827524 TTTTTTATTTTTTAATTTTTTAATT
1 TTTTTTATTTTTT-ATTTTTAAATT
1827549 ACTTTTTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
31 10 0.21
32 5 0.10
33 27 0.56
34 6 0.12
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (33 bp):
TTTTTTATTTTTTATTTTTAAATTTTTAAGAAT
Done.