Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 126 of 144
Found at i:30574243 original size:3 final size:3
Alignment explanation
Indices: 30574235--30574265 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30574225 TAAAGTATGC
30574235 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
30574266 AAGTACATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:30574672 original size:21 final size:22
Alignment explanation
Indices: 30574639--30574691 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
30574629 AAAATTTTCA
*
30574639 ATAAATAAATAAAATAAAATAAT
1 ATAAAT-ATTAAAATAAAATAAT
*
30574662 -TAAATATTAAATTAAAATAAT
1 ATAAATATTAAAATAAAATAAT
30574683 ATAAATATT
1 ATAAATATT
30574692 TTTTCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATATTAAAATAAAATAAT
Found at i:30574687 original size:22 final size:21
Alignment explanation
Indices: 30574638--30574691 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 21
30574628 AAAAATTTTC
30574638 AATAA-ATAAATA--AAATAA
1 AATAATATAAATATTAAATAA
30574656 AATAAT-TAAATATTAAATTAA
1 AATAATATAAATATTAAA-TAA
30574677 AATAATATAAATATT
1 AATAATATAAATATT
30574692 TTTTCAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.35
20 3 0.10
21 9 0.29
22 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATATAAATATTAAATAA
Found at i:30577986 original size:155 final size:152
Alignment explanation
Indices: 30577819--30578129 Score: 586
Period size: 155 Copynumber: 2.0 Consensus size: 152
30577809 GGAAACGTAA
30577819 TTTTTTTTTTGTTTATTGGATCCTTTTGGCGCTCAGGATAGATATAATATTTTATTCAGCTAAGG
1 TTTTTTTTTTGTTTATTGGATCCTTTTGGCGCTCAGGATAGATATAATATTTTATTCAGCTAAGG
*
30577884 AAAATAATTAGTCAAAATTATTGTTTAGAAGGCTGTGTTGAGTTAGAAGACGAAGATCAATTTTG
66 AAAATAATTAGTCAAAATTATTGTTTAGAAGGCTGTGTTGAGTTAGAAGACGAAG-T-AA-ATTG
30577949 AAACGTGATTTATATGTTTTAGTAT
128 AAACGTGATTTATATGTTTTAGTAT
30577974 TTTTTTTTTTGTTTATTGGATCCTTTTGGCGCTCAGGATAGATATAATATTTTATTCAGCTAAGG
1 TTTTTTTTTTGTTTATTGGATCCTTTTGGCGCTCAGGATAGATATAATATTTTATTCAGCTAAGG
30578039 AAAATAATTAGTCAAAATTATTGTTTAGAAGGCTGTGTTGAGTTAGAAGACGAAGTAAATTGAAA
66 AAAATAATTAGTCAAAATTATTGTTTAGAAGGCTGTGTTGAGTTAGAAGACGAAGTAAATTGAAA
30578104 CGTGATTTATATGTTTTAGTAT
131 CGTGATTTATATGTTTTAGTAT
30578126 TTTT
1 TTTT
30578130 CCGCCGCCAA
Statistics
Matches: 155, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
152 32 0.21
153 2 0.01
154 1 0.01
155 120 0.77
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.43
Consensus pattern (152 bp):
TTTTTTTTTTGTTTATTGGATCCTTTTGGCGCTCAGGATAGATATAATATTTTATTCAGCTAAGG
AAAATAATTAGTCAAAATTATTGTTTAGAAGGCTGTGTTGAGTTAGAAGACGAAGTAAATTGAAA
CGTGATTTATATGTTTTAGTAT
Found at i:30587746 original size:6 final size:6
Alignment explanation
Indices: 30587735--30587766 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
30587725 CGGATACGGG
30587735 CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CC
1 CCTTAC CCTTAC CCTTAC CCTTAC CCTTAC CC
30587767 GCCACCGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTTAC
Found at i:30597412 original size:29 final size:30
Alignment explanation
Indices: 30597366--30597445 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
30597356 GAATTTGATC
* *
30597366 AAATCAAAATTTCGTGTATAAAATTACACA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
30597396 AAATCAAAGTTCATGTATAAAATTACACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
* *
30597427 GAACCAAAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
30597446 GTTTTGAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 22 0.50
30 5 0.11
31 17 0.39
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:30597438 original size:31 final size:29
Alignment explanation
Indices: 30597380--30597445 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
30597370 CAAAATTTCG
*
30597380 TGTATAAAATTACACAAAATCAAAGTTCA
1 TGTATAAAATTACACAAAACCAAAGTTCA
*
30597409 TGTATAAAATTACACATTGAACCAAAGTTCA
1 TGTATAAAATTACACA--AAACCAAAGTTCA
30597440 TGTATA
1 TGTATA
30597446 GTTTTGAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (29 bp):
TGTATAAAATTACACAAAACCAAAGTTCA
Found at i:30599872 original size:17 final size:17
Alignment explanation
Indices: 30599841--30599889 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
30599831 TTTATATTTT
*
30599841 TAAAAATATTAATTATTA
1 TAAAAA-ATTAATTAGTA
*
30599859 TAAAAAATTTATTAGTA
1 TAAAAAATTAATTAGTA
*
30599876 TGAAAAAAATAATT
1 T-AAAAAATTAATT
30599890 TCTAAACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAAAAATTAATTAGTA
Found at i:30606213 original size:15 final size:15
Alignment explanation
Indices: 30606193--30606223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30606183 TATTTAAGGT
30606193 TTTTTTTTAATTTTC
1 TTTTTTTTAATTTTC
*
30606208 TTTTTTTTACTTTTC
1 TTTTTTTTAATTTTC
30606223 T
1 T
30606224 CATTCCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTAATTTTC
Found at i:30608912 original size:6 final size:6
Alignment explanation
Indices: 30608901--30608928 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30608891 CTTCACCTAC
30608901 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
30608929 TCCCTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:30614734 original size:14 final size:14
Alignment explanation
Indices: 30614715--30614748 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30614705 AAAATAAGTT
30614715 ATTTTTCAAAAATC
1 ATTTTTCAAAAATC
*
30614729 ATTTTTCAAAAGTC
1 ATTTTTCAAAAATC
30614743 ATTTTT
1 ATTTTT
30614749 AGTGAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTTTCAAAAATC
Found at i:30614739 original size:13 final size:15
Alignment explanation
Indices: 30614710--30614748 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
30614700 ACAAAAAAAT
*
30614710 AAGTTATTTTTCAAA
1 AAGTCATTTTTCAAA
30614725 AA-TCATTTTTC-AA
1 AAGTCATTTTTCAAA
30614738 AAGTCATTTTT
1 AAGTCATTTTT
30614749 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 16 0.73
15 2 0.09
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (15 bp):
AAGTCATTTTTCAAA
Found at i:30616062 original size:46 final size:47
Alignment explanation
Indices: 30615975--30616073 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 47
30615965 TTTTTATGAT
**
30615975 TAAAAATAAGAAAAAATATTAAAAATATTAAAAGTGATATAAACTTA
1 TAAAAATAAGAAAAAATATTAAAAATATTAAAAGTGATATAAAAATA
30616022 TAAAAATAA-AAAAAAT-TGTAAAAACT-TTATAAA-T-ATTATAAAAATA
1 TAAAAATAAGAAAAAATAT-TAAAAA-TATTA-AAAGTGA-TATAAAAATA
30616068 TAAAAA
1 TAAAAA
30616074 AATCTAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
45 2 0.04
46 31 0.67
47 13 0.28
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (47 bp):
TAAAAATAAGAAAAAATATTAAAAATATTAAAAGTGATATAAAAATA
Found at i:30616107 original size:9 final size:9
Alignment explanation
Indices: 30616019--30616221 Score: 71
Period size: 9 Copynumber: 22.0 Consensus size: 9
30616009 TGATATAAAC
30616019 TTATAAAAA
1 TTATAAAAA
* *
30616028 TAAAAAAAA
1 TTATAAAAA
*
30616037 TTGTAAAAA
1 TTATAAAAA
*
30616046 CTTTATAAATA
1 --TTATAAAAA
30616057 TTATAAAAA
1 TTATAAAAA
*
30616066 TATAAAAAAA
1 T-TATAAAAA
*
30616076 TCTA-ATAAA
1 T-TATAAAAA
* **
30616085 TTGTACTGAA
1 TTATA-AAAA
30616095 TTATAAAAA
1 TTATAAAAA
30616104 TTAT-AAAA
1 TTATAAAAA
30616112 TTAATAAAAA
1 TT-ATAAAAA
*
30616122 TTTATTTAAAA
1 -TTA-TAAAAA
**
30616133 -TATTTAAA
1 TTATAAAAA
30616141 --ATAAAAA
1 TTATAAAAA
* *
30616148 TGTATTATAAT
1 T-TA-TAAAAA
* *
30616159 TCTTTTAAAA
1 T-TATAAAAA
30616169 -TA-AAAAA
1 TTATAAAAA
*
30616176 TTGTAAAAA
1 TTATAAAAA
30616185 -TATTAAAAA
1 TTA-TAAAAA
*
30616194 TTATATAAAG
1 TTATA-AAAA
30616204 TTATAAAAA
1 TTATAAAAA
30616213 TTATAAAAA
1 TTATAAAAA
30616222 AAAATCATAA
Statistics
Matches: 143, Mismatches: 33, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
7 9 0.06
8 15 0.10
9 63 0.44
10 36 0.25
11 20 0.14
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:30616147 original size:27 final size:27
Alignment explanation
Indices: 30616114--30616174 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
30616104 TTATAAAATT
30616114 AATAAAAATTTATT-TAAAAT-ATTTAA
1 AATAAAAATTTATTAT-AAATCATTTAA
* * *
30616140 AATAAAAATGTATTATAATTCTTTTAA
1 AATAAAAATTTATTATAAATCATTTAA
30616167 AATAAAAA
1 AATAAAAA
30616175 ATTGTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AATAAAAATTTATTATAAATCATTTAA
Found at i:30619588 original size:2 final size:2
Alignment explanation
Indices: 30619583--30619616 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30619573 GTTGGGGGGG
30619583 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
30619617 TTCTACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30631745 original size:2 final size:2
Alignment explanation
Indices: 30631738--30631766 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30631728 TGCAAAACAT
30631738 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30631767 GCAGAAATGC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30632887 original size:40 final size:40
Alignment explanation
Indices: 30632833--30632910 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
30632823 TTTATCCCTC
30632833 AAAAAATTAAAATGATATTTTAACAAGTAAA-TAAATTTT
1 AAAAAATTAAAATGATATTTTAACAAGTAAATTAAATTTT
* * *
30632872 AAAATATTAAAAATGATATTTTAATAATTAAATTAAATT
1 AAAAAATT-AAAATGATATTTTAACAAGTAAATTAAATT
30632911 CTAATGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.21
40 21 0.62
41 6 0.18
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (40 bp):
AAAAAATTAAAATGATATTTTAACAAGTAAATTAAATTTT
Found at i:30633954 original size:1 final size:1
Alignment explanation
Indices: 30633948--30633975 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
30633938 AGGGAGGGAA
30633948 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
30633976 CACTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:30645068 original size:29 final size:28
Alignment explanation
Indices: 30645036--30645117 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
30645026 ACTATTAATT
30645036 TATAAAAATTAAATTAAATCAAAATATTA
1 TATAAAAATTAAATTAAATCAAAAT-TTA
* * ** *
30645065 TATAGAAATTATACAAAATTAAAATTTA
1 TATAAAAATTAAATTAAATCAAAATTTA
*
30645093 TATATTAAATTATATATTAAATCAA
1 TATA-AAAATTA-A-ATTAAATCAA
30645118 TGTTTATGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 7 0.17
29 26 0.65
31 7 0.17
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (28 bp):
TATAAAAATTAAATTAAATCAAAATTTA
Found at i:30645107 original size:12 final size:12
Alignment explanation
Indices: 30645090--30645114 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30645080 AAATTAAAAT
30645090 TTATATATTAAA
1 TTATATATTAAA
30645102 TTATATATTAAA
1 TTATATATTAAA
30645114 T
1 T
30645115 CAATGTTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATATATTAAA
Found at i:30649057 original size:14 final size:15
Alignment explanation
Indices: 30649024--30649056 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30649014 ATAATCTAAT
30649024 AAAAA-AATATGTTG
1 AAAAATAATATGTTG
*
30649038 AAAAATAATATGTTC
1 AAAAATAATATGTTG
30649053 AAAA
1 AAAA
30649057 TGGTTGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (15 bp):
AAAAATAATATGTTG
Found at i:30649441 original size:25 final size:24
Alignment explanation
Indices: 30649413--30649473 Score: 88
Period size: 23 Copynumber: 2.5 Consensus size: 24
30649403 CTCATCAATT
30649413 ATTATTATTTTGTAACTCTCTTGCC
1 ATTATT-TTTTGTAACTCTCTTGCC
*
30649438 ATTA-TGTTTGTAACTCTCTTGCC
1 ATTATTTTTTGTAACTCTCTTGCC
30649461 ATTATGTTTTTGT
1 ATTAT-TTTTTGT
30649474 TTTAAATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.54
Consensus pattern (24 bp):
ATTATTTTTTGTAACTCTCTTGCC
Found at i:30649451 original size:23 final size:23
Alignment explanation
Indices: 30649416--30649469 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
30649406 ATCAATTATT
30649416 ATTAT-TTTGTAACTCTCTTGCC
1 ATTATGTTTGTAACTCTCTTGCC
30649438 ATTATGTTTGTAACTCTCTTGCC
1 ATTATGTTTGTAACTCTCTTGCC
30649461 ATTATGTTT
1 ATTATGTTT
30649470 TTGTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCTTGCC
Found at i:30652082 original size:27 final size:27
Alignment explanation
Indices: 30652051--30652107 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
30652041 TAATTCCAGA
30652051 TGTCTTCGTCAACTCGTATTCCTGAAG
1 TGTCTTCGTCAACTCGTATTCCTGAAG
30652078 TGTCTTCGTCAACTCGTATTCCTGAAG
1 TGTCTTCGTCAACTCGTATTCCTGAAG
30652105 TGT
1 TGT
30652108 TTTACTCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (27 bp):
TGTCTTCGTCAACTCGTATTCCTGAAG
Found at i:30655837 original size:15 final size:14
Alignment explanation
Indices: 30655808--30655842 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
30655798 TAAAATTCAG
*
30655808 AAAATACATAAATT
1 AAAATAAATAAATT
30655822 AAAATAAATCAAATT
1 AAAATAAAT-AAATT
30655837 AAAATA
1 AAAATA
30655843 TAAAAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:30670363 original size:23 final size:23
Alignment explanation
Indices: 30670289--30670502 Score: 151
Period size: 23 Copynumber: 9.5 Consensus size: 23
30670279 TAAACGGAAC
* * *
30670289 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
30670311 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
30670333 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
30670359 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
30670379 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30670398 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
30670421 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30670444 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
30670469 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
30670492 AATCAGAGAGC
1 AAACAGAGAGC
30670503 GAGCTAGTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 78 0.52
24 2 0.01
25 28 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:30670397 original size:39 final size:39
Alignment explanation
Indices: 30670343--30670417 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
30670333 GGGCAACAGA
*
30670343 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
30670382 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
30670418 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:30670456 original size:48 final size:46
Alignment explanation
Indices: 30670382--30670502 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
30670372 ACAAAGTACT
* * *
30670382 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
30670428 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
30670476 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
30670503 GAGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:30672852 original size:31 final size:34
Alignment explanation
Indices: 30672805--30672876 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 34
30672795 TTGGTGTAGT
*
30672805 TATACATATGAAATTTTGCTTGT-GGTTCAAAT-A
1 TATACATATGAAATTTTGATTGTGGGTTC-AATCA
30672838 TATACA-A-GAAATTTTGATTGTGGGTTCAATCA
1 TATACATATGAAATTTTGATTGTGGGTTCAATCA
30672870 TATACAT
1 TATACAT
30672877 TTAAAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 16 0.46
32 13 0.37
33 6 0.17
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (34 bp):
TATACATATGAAATTTTGATTGTGGGTTCAATCA
Found at i:30678166 original size:59 final size:59
Alignment explanation
Indices: 30678100--30678245 Score: 269
Period size: 59 Copynumber: 2.5 Consensus size: 59
30678090 GCTTGATCTA
30678100 ATATTTAATATTTACTTTTCTTTAAAGAGTCATTGACTTCTTATTCTTTGGTTTATTTT
1 ATATTTAATATTTACTTTTCTTTAAAGAGTCATTGACTTCTTATTCTTTGGTTTATTTT
30678159 ATATTTAATATTTACTTTTCTTTAAAGAGTCATTGACTTCTTATTCTTTGGTTTATTTT
1 ATATTTAATATTTACTTTTCTTTAAAGAGTCATTGACTTCTTATTCTTTGGTTTATTTT
*
30678218 ATATTTAATATTTA-TTTT-TTAAAAGAGT
1 ATATTTAATATTTACTTTTCTTTAAAGAGT
30678246 AAAATAAACA
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
57 9 0.10
58 4 0.05
59 73 0.85
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (59 bp):
ATATTTAATATTTACTTTTCTTTAAAGAGTCATTGACTTCTTATTCTTTGGTTTATTTT
Found at i:30686723 original size:2 final size:2
Alignment explanation
Indices: 30686716--30686766 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
30686706 GTACCGTAAA
30686716 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
30686758 AT AT AT AT A
1 AT AT AT AT A
30686767 ATTCTAATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30690362 original size:29 final size:30
Alignment explanation
Indices: 30690297--30690369 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
30690287 GTTTTTGATT
* *
30690297 CCTTAAAAATTAGAGAAAAAAAATTTAAGTC
1 CCTTAAAAGTTA-AGAAAAAAAATTTAAGGC
* * *
30690328 CTTTAAAAGTTAATAAAAAAAATTT-GGGC
1 CCTTAAAAGTTAAGAAAAAAAATTTAAGGC
30690357 CCTTAAAAGTTAA
1 CCTTAAAAGTTAA
30690370 AAGAATTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 12 0.33
31 10 0.28
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (30 bp):
CCTTAAAAGTTAAGAAAAAAAATTTAAGGC
Found at i:30690435 original size:56 final size:56
Alignment explanation
Indices: 30690342--30690467 Score: 137
Period size: 57 Copynumber: 2.2 Consensus size: 56
30690332 AAAAGTTAAT
* * *
30690342 AAAAAAAATTTGGGCCCTTAAAAGTTAAAAGAATTTTGAGCCCCTTAAAAATTGGTA
1 AAAAAAAATTTTGGCCCTTAAAAGTTAAAAGAATTTTGAACCCCTTAAAAACTGG-A
* * *** *
30690399 AAAAAAAATTTTGGTCTTTAAAAGTT-AAATTTTTTTGAACCTCTTAAAAACTGGA
1 AAAAAAAATTTTGGCCCTTAAAAGTTAAAAGAATTTTGAACCCCTTAAAAACTGGA
* *
30690454 AAATAATATTTTGG
1 AAAAAAAATTTTGG
30690468 ACTCCTTTCA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 13 0.22
56 22 0.38
57 23 0.40
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (56 bp):
AAAAAAAATTTTGGCCCTTAAAAGTTAAAAGAATTTTGAACCCCTTAAAAACTGGA
Found at i:30692042 original size:45 final size:45
Alignment explanation
Indices: 30691968--30692060 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
30691958 ATGAGTGTTA
30691968 TTTAGGAATAAAATTATATTTGGATTTAAAAATATTTGCG-TTTAG
1 TTTAGGAATAAAATTATATTTGGATTTAAAAATATTTG-GATTTAG
* * *
30692013 TTTATGAATGAAATTATATTTGGGTTTAAAAATATTTGGATTTAG
1 TTTAGGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTAG
30692058 TTT
1 TTT
30692061 GTTGATGAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.47
Consensus pattern (45 bp):
TTTAGGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTAG
Found at i:30702727 original size:29 final size:29
Alignment explanation
Indices: 30702685--30702742 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30702675 TATCTCTTTA
*
30702685 ATGTTCACAACGTTAGATAGAAATGAAAT
1 ATGTTCACAACGTTAGATAGAAAAGAAAT
* * *
30702714 ATGTTGACAACGTTGGATGGAAAAGAAAT
1 ATGTTCACAACGTTAGATAGAAAAGAAAT
30702743 GAGAAAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (29 bp):
ATGTTCACAACGTTAGATAGAAAAGAAAT
Found at i:30717327 original size:21 final size:22
Alignment explanation
Indices: 30717289--30717329 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
30717279 TAAAATTTTT
* *
30717289 AATATTTTGATATTTATAAAAG
1 AATATTGTGATATGTATAAAAG
30717311 AATATTGT-ATATGTATAAA
1 AATATTGTGATATGTATAAA
30717330 GGGGTTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (22 bp):
AATATTGTGATATGTATAAAAG
Found at i:30717590 original size:27 final size:27
Alignment explanation
Indices: 30717540--30717592 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
30717530 TTGATTCAAA
*
30717540 ATTTCTCACTCTACATGTATATGTTAG
1 ATTTCTCACTCTACATGTAAATGTTAG
*
30717567 ATTTCTCTCTCTACA-GATAAATGTTA
1 ATTTCTCACTCTACATG-TAAATGTTA
30717593 ATCTTCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.43
Consensus pattern (27 bp):
ATTTCTCACTCTACATGTAAATGTTAG
Found at i:30721124 original size:16 final size:15
Alignment explanation
Indices: 30721087--30721115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30721077 ATAAATTATG
30721087 TAATTTAATTTTTTA
1 TAATTTAATTTTTTA
30721102 TAATTTAATTTTTT
1 TAATTTAATTTTTT
30721116 TCTAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTAATTTTTTA
Found at i:30722534 original size:22 final size:23
Alignment explanation
Indices: 30722495--30722539 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
30722485 ATTACTTCAT
30722495 TTCTCTCACATGTTTTTTTATTAA
1 TTCTCTCACATG-TTTTTTATTAA
30722519 TTCTCTCACATG-TTTTTATTA
1 TTCTCTCACATGTTTTTTATTA
30722540 CCAGTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (23 bp):
TTCTCTCACATGTTTTTTATTAA
Found at i:30723430 original size:29 final size:29
Alignment explanation
Indices: 30723388--30723445 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30723378 TATCTCTTTA
*
30723388 ATGTTCACAACGTTAGATAGAAATGAAAT
1 ATGTTCACAACGTTAGATAGAAAAGAAAT
* * *
30723417 ATGTTGACAACGTTGGATGGAAAAGAAAT
1 ATGTTCACAACGTTAGATAGAAAAGAAAT
30723446 GAGGAAATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (29 bp):
ATGTTCACAACGTTAGATAGAAAAGAAAT
Found at i:30729163 original size:24 final size:24
Alignment explanation
Indices: 30729136--30729198 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
30729126 AAAAATAATC
* *
30729136 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
30729160 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
30729184 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
30729199 TATTAATCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:30736838 original size:17 final size:17
Alignment explanation
Indices: 30736812--30736845 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30736802 ACGAAACTGG
*
30736812 GGAAAGAGAAAAGGGAA
1 GGAAAAAGAAAAGGGAA
*
30736829 GGAAAAAGAAAGGGGAA
1 GGAAAAAGAAAAGGGAA
30736846 AACTAGGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (17 bp):
GGAAAAAGAAAAGGGAA
Found at i:30739576 original size:24 final size:23
Alignment explanation
Indices: 30739543--30739591 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
30739533 ATTTGAGAAA
* * *
30739543 TAATTTTTCAGTTAATCTTTGTT
1 TAATTTTTCAATTAAACTCTGTT
30739566 TAATTGTTTCAATTAAACTCTGTT
1 TAATT-TTTCAATTAAACTCTGTT
30739590 TA
1 TA
30739592 TTTATTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (23 bp):
TAATTTTTCAATTAAACTCTGTT
Found at i:30743075 original size:3 final size:3
Alignment explanation
Indices: 30743063--30743096 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
30743053 TATATATAAC
30743063 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
30743097 AAATTATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30743523 original size:28 final size:27
Alignment explanation
Indices: 30743492--30743578 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
30743482 TGTCATATAA
30743492 TAATAAATTTTATATACAATAAATGCTT
1 TAATAAATTTTATATACAATAAAT-CTT
* * * * *
30743520 TAAT-TATTTCATATA-AAAAACATATAA
1 TAATAAATTTTATATACAATAA-ATCT-T
*
30743547 TAATAAATTTTATATACAATAAACACTT
1 TAATAAATTTTATATACAATAAA-TCTT
30743575 TAAT
1 TAAT
30743579 TATTTATTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
26 5 0.12
27 15 0.35
28 18 0.42
29 5 0.12
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (27 bp):
TAATAAATTTTATATACAATAAATCTT
Found at i:30746780 original size:18 final size:17
Alignment explanation
Indices: 30746757--30746790 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30746747 AGAAGTTATG
*
30746757 ATAATTATATATTTAAAA
1 ATAATTA-AAATTTAAAA
30746775 ATAATTAAAATTTAAA
1 ATAATTAAAATTTAAA
30746791 TTACATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATTTAAAA
Found at i:30756104 original size:18 final size:18
Alignment explanation
Indices: 30756065--30756106 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30756055 TACCGTATTG
30756065 ATAATTTTTTATAATAAT
1 ATAATTTTTTATAATAAT
30756083 -TAATCTTTTTATAA-AAT
1 ATAAT-TTTTTATAATAAT
30756100 ATAATTT
1 ATAATTT
30756107 ATATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTTTTTATAATAAT
Found at i:30767838 original size:31 final size:31
Alignment explanation
Indices: 30767803--30767861 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30767793 CTGATCTTGA
30767803 CAATTG-TTCTCACATTAGAACCTGAATTAGG
1 CAATTGTTTC-CACATTAGAACCTGAATTAGG
* *
30767834 CAATTGTTTCCACATTGGGACCTGAATT
1 CAATTGTTTCCACATTAGAACCTGAATT
30767862 TTCTTTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (31 bp):
CAATTGTTTCCACATTAGAACCTGAATTAGG
Found at i:30769595 original size:32 final size:32
Alignment explanation
Indices: 30769552--30769614 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
30769542 CAATAAAGTG
* *
30769552 CCATCCTAAATCCCCGAGGAAACAGAACTTTT
1 CCATCCAAAATCCCCAAGGAAACAGAACTTTT
30769584 CCATCCAAAATCCCCAAGGAAACAGAACTTT
1 CCATCCAAAATCCCCAAGGAAACAGAACTTT
30769615 CTAGGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (32 bp):
CCATCCAAAATCCCCAAGGAAACAGAACTTTT
Found at i:30774389 original size:22 final size:20
Alignment explanation
Indices: 30774352--30774391 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
30774342 GAATTGGAGT
30774352 AAAAAAACTGGAATGTTGAA
1 AAAAAAACTGGAATGTTGAA
*
30774372 AAAATAAAGCTGGCATGTTG
1 AAAA-AAA-CTGGAATGTTG
30774392 GGAAAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (20 bp):
AAAAAAACTGGAATGTTGAA
Found at i:30775958 original size:30 final size:32
Alignment explanation
Indices: 30775886--30775966 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 32
30775876 ATTTTAAATT
30775886 AATAATAGTAAAATTATAATTTAACCCTCTCAAA
1 AATAATA--AAAATTATAATTTAACCCTCTCAAA
* *
30775920 AATGATAAAAATT-TAATTTAACCCT-TTAAA
1 AATAATAAAAATTATAATTTAACCCTCTCAAA
*
30775950 AATAATAAAGA-TATAAT
1 AATAATAAAAATTATAAT
30775967 CTATTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 17 0.40
31 12 0.29
32 6 0.14
34 6 0.14
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (32 bp):
AATAATAAAAATTATAATTTAACCCTCTCAAA
Found at i:30791337 original size:23 final size:23
Alignment explanation
Indices: 30791306--30791349 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30791296 TGATAGTCTA
*
30791306 AATACTAAAATAAAATAAATTTT
1 AATACTAAAATAAAAGAAATTTT
* *
30791329 AATATTAAAGTAAAAGAAATT
1 AATACTAAAATAAAAGAAATT
30791350 ATAAAGTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
AATACTAAAATAAAAGAAATTTT
Found at i:30795631 original size:16 final size:15
Alignment explanation
Indices: 30795605--30795647 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
30795595 ATTTTTATTT
*
30795605 ATATTTA-TTTGTTT
1 ATATTTAGTTTGTTC
*
30795619 ATTTTTAAGTTTGTTC
1 ATATTT-AGTTTGTTC
30795635 ATATTTAGTTTGT
1 ATATTTAGTTTGT
30795648 GTTCGTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (15 bp):
ATATTTAGTTTGTTC
Found at i:30797449 original size:47 final size:47
Alignment explanation
Indices: 30797380--30797473 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
30797370 TTATTTGGGT
*
30797380 GTTTGAAAGCTTAGGGGCTAAAGTGAATAATGAAGGAAAATATAAGG
1 GTTTGAAAGCTTAGCGGCTAAAGTGAATAATGAAGGAAAATATAAGG
30797427 GTTTGAAAGCTTAGCGGCTAAAGTGAATAATGAAGGAAAATATAAGG
1 GTTTGAAAGCTTAGCGGCTAAAGTGAATAATGAAGGAAAATATAAGG
30797474 TTTTATTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.23
Consensus pattern (47 bp):
GTTTGAAAGCTTAGCGGCTAAAGTGAATAATGAAGGAAAATATAAGG
Found at i:30799162 original size:30 final size:30
Alignment explanation
Indices: 30799108--30799165 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
30799098 CCGTCCAATC
*
30799108 ACTTAAATAAAAGGTTTTGAATAGTTTAGTG
1 ACTTAAATAAAA-GTTTGGAATAGTTTAGTG
30799139 ACTTAAATGAAAA-TTTGGAATAGTTTA
1 ACTTAAAT-AAAAGTTTGGAATAGTTTA
30799166 ATGATCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 8 0.32
32 4 0.16
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.38
Consensus pattern (30 bp):
ACTTAAATAAAAGTTTGGAATAGTTTAGTG
Found at i:30805282 original size:48 final size:48
Alignment explanation
Indices: 30805230--30805324 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
30805220 TATTTACTTA
* * * *
30805230 TCTTGATTCTAATACGTTTGATTTCATTAATGAATTGATAATAATTTG
1 TCTTGATTCTAACACGCTCGATCTCATTAATGAATTGATAATAATTTG
*
30805278 TCTTGATTCTAACACGCTCGATCTCATTAATGAGTTGATAATAATTT
1 TCTTGATTCTAACACGCTCGATCTCATTAATGAATTGATAATAATTT
30805325 TCACGATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (48 bp):
TCTTGATTCTAACACGCTCGATCTCATTAATGAATTGATAATAATTTG
Found at i:30805492 original size:11 final size:10
Alignment explanation
Indices: 30805474--30805508 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
30805464 AATAAATAAG
30805474 TTATTAAAAA
1 TTATTAAAAA
30805484 TTCATTAAAAA
1 TT-ATTAAAAA
*
30805495 ATATTAAAAA
1 TTATTAAAAA
30805505 TTAT
1 TTAT
30805509 AATACTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:30811113 original size:16 final size:16
Alignment explanation
Indices: 30811053--30811114 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
30811043 AAATATATAA
*
30811053 AAAATTTAGAAAATAT
1 AAAATTTAGAAAAAAT
*
30811069 AAAATCTAGAAAAAA-
1 AAAATTTAGAAAAAAT
* *
30811084 AATAAATTA-TAAAAAT
1 AA-AATTTAGAAAAAAT
*
30811100 AAAATTTACAAAAAA
1 AAAATTTAGAAAAAA
30811115 ATACGATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATTTAGAAAAAAT
Found at i:30818963 original size:54 final size:54
Alignment explanation
Indices: 30818899--30819048 Score: 178
Period size: 54 Copynumber: 2.7 Consensus size: 54
30818889 TTTAAAGGCG
* * *
30818899 AAATTATATTATCATATTTGAAAAGTAAATTGATCGGTTGATCTTTAAAAGACA
1 AAATGATATTATCATATTTGAAAAGTAAATTGATCGGTCGATCTTTAAAAAACA
*
30818953 AAATGATATTATCATATTT-ATAAAGTAAATTAATCGACATGTCGATCTTTAAAAAACA
1 AAATGATATTATCATATTTGA-AAAGTAAATTGATCG----GTCGATCTTTAAAAAACA
* * *
30819011 AAATGATATTATCGTA-TTGCAAAGTAAATTGGTCGGTC
1 AAATGATATTATCATATTTGAAAAGTAAATTGATCGGTC
30819049 TTTTAAAGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
53 4 0.05
54 32 0.39
57 15 0.18
58 31 0.38
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (54 bp):
AAATGATATTATCATATTTGAAAAGTAAATTGATCGGTCGATCTTTAAAAAACA
Found at i:30833936 original size:6 final size:6
Alignment explanation
Indices: 30833925--30833949 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30833915 TTCTTGTCAT
30833925 TGCTAG TGCTAG TGCTAG TGCTAG T
1 TGCTAG TGCTAG TGCTAG TGCTAG T
30833950 TTTGCAAGCG
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:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TGCTAG
Found at i:30834435 original size:27 final size:27
Alignment explanation
Indices: 30834405--30834496 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 27
30834395 TTGGTCGATC
30834405 TTTAAAAGACAAAATGATATTATCATA
1 TTTAAAAGACAAAATGATATTATCATA
* * *
30834432 TTTATAAAGTA-AATTGATCGATCATT-TGATC
1 TTTA-AAAG-ACAA--AAT-GAT-ATTATCATA
*
30834463 TTTAAAAGACAAAATGATATTATCGTA
1 TTTAAAAGACAAAATGATATTATCATA
30834490 TTGTAAA
1 TT-TAAA
30834497 GTAAATTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 17
0.67 0.10 0.23
Matches are distributed among these distances:
26 3 0.06
27 11 0.22
28 12 0.24
29 2 0.04
30 8 0.16
31 10 0.20
32 3 0.06
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (27 bp):
TTTAAAAGACAAAATGATATTATCATA
Found at i:30834481 original size:58 final size:61
Alignment explanation
Indices: 30834347--30834508 Score: 226
Period size: 62 Copynumber: 2.7 Consensus size: 61
30834337 GTCAATTTTT
* * *
30834347 AAAGACAAAATTATATTATTATATTTGA-AAAGTAAATTGATCGGTCGATTGGTCGATCTTTA
1 AAAGACAAAATGATATTATCATATTT-ATAAAGTAAATTGATCGATCGATT-GTCGATCTTTA
30834409 AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCGATC-ATT-T-GATCTTTA
1 AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCGATCGATTGTCGATCTTTA
* *
30834467 AAAGACAAAATGATATTATCGTA-TTGTAAAGTAAATTGATCG
1 AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCG
30834509 GTCTTTTAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
57 18 0.19
58 30 0.32
59 1 0.01
61 4 0.04
62 41 0.44
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (61 bp):
AAAGACAAAATGATATTATCATATTTATAAAGTAAATTGATCGATCGATTGTCGATCTTTA
Found at i:30835220 original size:30 final size:30
Alignment explanation
Indices: 30835186--30835261 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
30835176 GAAAATTGAG
* *
30835186 TTCCATATATAAAATTCTTGTTTTGACCAT
1 TTCCATATATAGAATTCTTATTTTGACCAT
* *
30835216 TTCCATATGTAGATTTCTTATTTTGACCAT
1 TTCCATATATAGAATTCTTATTTTGACCAT
30835246 TTCCATATATAGAATT
1 TTCCATATATAGAATT
30835262 GAGAGTTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (30 bp):
TTCCATATATAGAATTCTTATTTTGACCAT
Found at i:30838591 original size:58 final size:57
Alignment explanation
Indices: 30838439--30838618 Score: 210
Period size: 54 Copynumber: 3.2 Consensus size: 57
30838429 CTTAAAAAAT
* * * * *
30838439 GTAAATTCATAGATGCGTCAAT-TTTTAAAGACAAAATTATATTATTATATTTGA-AAA
1 GTAAATTGATCGAT-CGTCGATCTTTAAAAGACAAAATGATATTATTATATTT-ATAAA
*
30838496 GTAAATTGATCG---GTCGATCTTTAAAAGACAAAATGATATTATCATATTTATAAA
1 GTAAATTGATCGATCGTCGATCTTTAAAAGACAAAATGATATTATTATATTTATAAA
* *
30838550 GTAAATTGATCGATCCGTCGATCTTTAAAAGACAAAATGATATTATTGTA-TTGTAAA
1 GTAAATTGATCGAT-CGTCGATCTTTAAAAGACAAAATGATATTATTATATTTATAAA
*
30838607 GGAAATTGATCG
1 GTAAATTGATCG
30838619 GTCTTTTAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
53 6 0.06
54 42 0.39
57 27 0.25
58 32 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (57 bp):
GTAAATTGATCGATCGTCGATCTTTAAAAGACAAAATGATATTATTATATTTATAAA
Found at i:30838665 original size:107 final size:110
Alignment explanation
Indices: 30838465--30838670 Score: 242
Period size: 107 Copynumber: 1.9 Consensus size: 110
30838455 GTCAATTTTT
* *
30838465 AAAGACAAAATTATATTATTATATTTGAAAAGTAAATTGATCGGTCGATCTTTAAAAGACAAAAT
1 AAAGACAAAATGATATTATTATATTTGAAAAGGAAATTGATCGGTC-ATCTTTAAAAGACAAAAT
* * *
30838530 GATATTATCATATTTATAAAGTAAATTGATCGATCCGTCGATCTTTA
65 GATATTATCATA-TAATAAAGGAAATTGACCGATCCGTCGATCTTTA
* * * *
30838577 AAAGACAAAATGATATTATTGTA-TTGTAAAGGAAATTGATCGGTC-T-TTT-AAAGATAAAATT
1 AAAGACAAAATGATATTATTATATTTGAAAAGGAAATTGATCGGTCATCTTTAAAAGACAAAATG
* *
30838638 ATGTTATCATA-AATGAAATGGAGATTGACCGAT
66 ATATTATCATATAAT-AAA-GGAAATTGACCGAT
30838671 ATTTAATTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
105 2 0.02
106 3 0.04
107 31 0.38
108 3 0.04
109 1 0.01
111 20 0.25
112 21 0.26
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (110 bp):
AAAGACAAAATGATATTATTATATTTGAAAAGGAAATTGATCGGTCATCTTTAAAAGACAAAATG
ATATTATCATATAATAAAGGAAATTGACCGATCCGTCGATCTTTA
Found at i:30839329 original size:30 final size:29
Alignment explanation
Indices: 30839258--30839329 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
30839248 AGTTGAGTTC
* *
30839258 CATATATAGAATTCTTGTTTTAATCATTT
1 CATATATAGAATTCTTATTTTAACCATTT
* *
30839287 CATATGTAGAATTCTTATTTTGACCATTT
1 CATATATAGAATTCTTATTTTAACCATTT
30839316 CTATATATAGAATT
1 C-ATATATAGAATT
30839330 GAGAGTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (29 bp):
CATATATAGAATTCTTATTTTAACCATTT
Found at i:30845886 original size:17 final size:16
Alignment explanation
Indices: 30845864--30845906 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
30845854 AATTTCTAAT
30845864 ATTTAAATTTTTTATCA
1 ATTTAAATTTTTT-TCA
* *
30845881 ATTTAACTTTTTTTTA
1 ATTTAAATTTTTTTCA
*
30845897 AGTTAAATTT
1 ATTTAAATTT
30845907 AGCTTTCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAAATTTTTTTCA
Found at i:30848761 original size:30 final size:29
Alignment explanation
Indices: 30848698--30848764 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
30848688 ATTTCAAAAG
*
30848698 CAAAAAGAACAATCTTTAAGTATGTATTT
1 CAAAAAGAACAATCTTTAAGCATGTATTT
* *
30848727 CAAAAATAACAATCTTTTAAGCGTGT-TTT
1 CAAAAAGAACAATC-TTTAAGCATGTATTT
*
30848756 CCAAAAGAA
1 CAAAAAGAA
30848765 AATTATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (29 bp):
CAAAAAGAACAATCTTTAAGCATGTATTT
Found at i:30849091 original size:12 final size:12
Alignment explanation
Indices: 30849074--30849098 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30849064 ATGGAGATTA
30849074 GCTTAGTTGCTT
1 GCTTAGTTGCTT
30849086 GCTTAGTTGCTT
1 GCTTAGTTGCTT
30849098 G
1 G
30849099 AATTAAATTT
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:0.16, G:0.28, T:0.48
Consensus pattern (12 bp):
GCTTAGTTGCTT
Found at i:30859313 original size:13 final size:13
Alignment explanation
Indices: 30859297--30859329 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
30859287 GAGTTATTTT
30859297 TTCGAATTTCGAG
1 TTCGAATTTCGAG
30859310 TTCGAATTTCGAG
1 TTCGAATTTCGAG
*
30859323 TTTGAAT
1 TTCGAAT
30859330 CGAGTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (13 bp):
TTCGAATTTCGAG
Found at i:30859593 original size:42 final size:42
Alignment explanation
Indices: 30859541--30859624 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
30859531 CAAATATTTT
* * *
30859541 TAAACTCAAATATAATTTCATTCTTAAAAAACACTTATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
* *
30859583 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
30859625 AACTTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
Found at i:30860218 original size:22 final size:21
Alignment explanation
Indices: 30860193--30860233 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
30860183 GTTGTCATTG
*
30860193 TTTACTTGAATGTTTTCATTTA
1 TTTACTTCAAT-TTTTCATTTA
*
30860215 TTTATTTCAATTTTTCATT
1 TTTACTTCAATTTTTCATT
30860234 GTATAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTACTTCAATTTTTCATTTA
Found at i:30865130 original size:196 final size:196
Alignment explanation
Indices: 30864796--30865190 Score: 738
Period size: 196 Copynumber: 2.0 Consensus size: 196
30864786 CACTTTATGA
*
30864796 ATAACAGTTACTAAATGAGAAGATAAGAAACCAAATTTAAGTGCATGGATCTCGGAGGGAATTCA
1 ATAACAGTTACTAAATGAGAAGATAAGAAACCAAATTTAAGTGCATGGAACTCGGAGGGAATTCA
30864861 GAGTGCTATCGGAAGCATGAATGATACATATGTTTCAAGGAACATAAACCTTCATTTATCAGACT
66 GAGTGCTATCGGAAGCATGAATGATACATATGTTTCAAGGAACATAAACCTTCATTTATCAGACT
*
30864926 TCAGTTTAAAGCAAACAATGTCGCAACTTGCAAGTCTAAGCAATTCCAGCATAGTTTGTAGAAAC
131 TCAGTTTAAAGCAAACAATGTCACAACTTGCAAGTCTAAGCAATTCCAGCATAGTTTGTAGAAAC
30864991 T
196 T
*
30864992 ATAACAGTTACTAAATGAGAAGATTAGAAACCAAATTTAAGTGCATGGAACTCGGAGGGAATTCA
1 ATAACAGTTACTAAATGAGAAGATAAGAAACCAAATTTAAGTGCATGGAACTCGGAGGGAATTCA
30865057 GAGTGCTATCGGAAGCATGAATGATACATCA-GTTTCAAGGAACATAAACCTTCATTTATCAGAC
66 GAGTGCTATCGGAAGCATGAATGATACAT-ATGTTTCAAGGAACATAAACCTTCATTTATCAGAC
*
30865121 TTCAGTTTAAAGCAAACAATGTCACAACTTGCAAGTCTAAGCAATTCCGGCATAGTTTGTAGAAA
130 TTCAGTTTAAAGCAAACAATGTCACAACTTGCAAGTCTAAGCAATTCCAGCATAGTTTGTAGAAA
30865186 CT
195 CT
30865188 ATA
1 ATA
30865191 GCAGGCACTC
Statistics
Matches: 194, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
196 193 0.99
197 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (196 bp):
ATAACAGTTACTAAATGAGAAGATAAGAAACCAAATTTAAGTGCATGGAACTCGGAGGGAATTCA
GAGTGCTATCGGAAGCATGAATGATACATATGTTTCAAGGAACATAAACCTTCATTTATCAGACT
TCAGTTTAAAGCAAACAATGTCACAACTTGCAAGTCTAAGCAATTCCAGCATAGTTTGTAGAAAC
T
Found at i:30871225 original size:5 final size:5
Alignment explanation
Indices: 30871210--30871242 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
30871200 TATATGATTT
*
30871210 TATAA -ATAA TATAA TATAA TATAA TACAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
30871243 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:30871335 original size:14 final size:14
Alignment explanation
Indices: 30871313--30871343 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30871303 CTCGTATTTA
*
30871313 TATATATTATAGAC
1 TATAAATTATAGAC
30871327 TATAAATTATAGAC
1 TATAAATTATAGAC
30871341 TAT
1 TAT
30871344 GAGTTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
TATAAATTATAGAC
Found at i:30878113 original size:11 final size:11
Alignment explanation
Indices: 30878097--30878154 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
30878087 CCACATCAAC
30878097 AAATTATTTTA
1 AAATTATTTTA
30878108 AAATTATTTTTA
1 AAATTA-TTTTA
*
30878120 AAA--A-TATA
1 AAATTATTTTA
30878128 AAATTA--TTA
1 AAATTATTTTA
30878137 AAATTATTTTA
1 AAATTATTTTA
30878148 AAATTAT
1 AAATTAT
30878155 AACTATCATC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 6 0.15
9 8 0.20
10 2 0.05
11 16 0.40
12 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:30879135 original size:26 final size:26
Alignment explanation
Indices: 30879104--30879153 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
30879094 TGATTATAAT
*
30879104 TTTTAAATAAATTTAATAATTTTATA
1 TTTTAAAAAAATTTAATAATTTTATA
30879130 TTTTAAAAAAATTTAATAATTTTA
1 TTTTAAAAAAATTTAATAATTTTA
30879154 AAATCATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTAAAAAAATTTAATAATTTTATA
Found at i:30882036 original size:23 final size:24
Alignment explanation
Indices: 30882006--30882060 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
30881996 AGCGTTCACT
30882006 AACATGTTCATCTA-ACATTCGCG
1 AACATGTTCATCTATACATTCGCG
* * **
30882029 AACATGTTCGTTTATATGTTCGCG
1 AACATGTTCATCTATACATTCGCG
30882053 AACATGTT
1 AACATGTT
30882061 TGTTTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
AACATGTTCATCTATACATTCGCG
Found at i:30882110 original size:19 final size:20
Alignment explanation
Indices: 30882083--30882124 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
30882073 CTAAACAAAC
*
30882083 AAACAAAAAATAAATAAATA
1 AAACAAAAAACAAATAAATA
* *
30882103 AAAC-AAAACCAACTAAATA
1 AAACAAAAAACAAATAAATA
30882122 AAA
1 AAA
30882125 AATCAAGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (20 bp):
AAACAAAAAACAAATAAATA
Found at i:30883532 original size:12 final size:12
Alignment explanation
Indices: 30883514--30883548 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30883504 ATTATTAATA
30883514 AATAAACGAGCT
1 AATAAACGAGCT
*
30883526 TATAAACGAGCT
1 AATAAACGAGCT
*
30883538 AATAAGCGAGC
1 AATAAACGAGC
30883549 CATAAATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:30909639 original size:24 final size:24
Alignment explanation
Indices: 30909612--30909675 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
30909602 TTTTATGATA
30909612 ATTAAAATATAATTTTAT-TATTAT
1 ATTAAAATATAATTTTATATATT-T
*
30909636 ATT-AATTAATAATTTTATATATTT
1 ATTAAAAT-ATAATTTTATATATTT
*
30909660 -TTAAAGATATATTTTT
1 ATTAAA-ATATAATTTT
30909676 TGAGAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 5 0.15
24 23 0.70
25 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTAAAATATAATTTTATATATTT
Found at i:30927347 original size:60 final size:60
Alignment explanation
Indices: 30927278--30927398 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
30927268 CCATCAACAA
*
30927278 ACTAAACCCAAATATTTTT-AAACCCAAATATAATTTCATTCTTCAAA-AACACTTATAAAC
1 ACTAAACCC-AATATTTTTAAAACCCAAATATAATTTCATTCTT-AAATAACACTCATAAAC
* *
30927338 ACTACACCCAATATTTTTAAAACCCAAATATAATTTTATTCTTAAATAACACTCATAAAC
1 ACTAAACCCAATATTTTTAAAACCCAAATATAATTTCATTCTTAAATAACACTCATAAAC
30927398 A
1 A
30927399 ACTCCTTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 12 0.21
60 44 0.79
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (60 bp):
ACTAAACCCAATATTTTTAAAACCCAAATATAATTTCATTCTTAAATAACACTCATAAAC
Found at i:30943503 original size:51 final size:51
Alignment explanation
Indices: 30943427--30943529 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
30943417 CAGTCCCACT
30943427 AAAGCCAACAGGCCTGGAAACAAAACCTGGACTAACCTTAGGGTTATTGCC
1 AAAGCCAACAGGCCTGGAAACAAAACCTGGACTAACCTTAGGGTTATTGCC
30943478 AAAGCCAACAGGCCTGGAAACAAAACCTGGACTAACCTTAGGGTTATTGCC
1 AAAGCCAACAGGCCTGGAAACAAAACCTGGACTAACCTTAGGGTTATTGCC
30943529 A
1 A
30943530 GTCTGATACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (51 bp):
AAAGCCAACAGGCCTGGAAACAAAACCTGGACTAACCTTAGGGTTATTGCC
Found at i:30951266 original size:22 final size:22
Alignment explanation
Indices: 30951238--30951295 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
30951228 TATGCACTAA
*
30951238 TGAACGGAGAGCACCGAGGTGT
1 TGAACGGAGAGCACCGAGGTGC
30951260 TGAACGGAGAGCACCGAGGTGC
1 TGAACGGAGAGCACCGAGGTGC
*
30951282 TAAACGGAGAGCAC
1 TGAACGGAGAGCAC
30951296 TACACGTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.38, T:0.10
Consensus pattern (22 bp):
TGAACGGAGAGCACCGAGGTGC
Found at i:30959148 original size:26 final size:26
Alignment explanation
Indices: 30959101--30959151 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
30959091 TTTTAAGAAA
*
30959101 ATTGTAAGAATTATTATAATTTTTAG
1 ATTGTAAAAATTATTATAATTTTTAG
30959127 ATTGTAAAAAATTATTAT-ATTTTTA
1 ATTGT-AAAAATTATTATAATTTTTA
30959152 CAATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
ATTGTAAAAATTATTATAATTTTTAG
Found at i:30959768 original size:21 final size:23
Alignment explanation
Indices: 30959744--30959788 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
30959734 TTTTACCAGC
30959744 TTTTTAC-A-TTTTAAAATATTT
1 TTTTTACAATTTTTAAAATATTT
30959765 TTTTTACAATTTTTAAAATATTT
1 TTTTTACAATTTTTAAAATATTT
30959788 T
1 T
30959789 AATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTACAATTTTTAAAATATTT
Found at i:30962363 original size:17 final size:17
Alignment explanation
Indices: 30962322--30962398 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
30962312 GCCAATGAGA
*
30962322 TAAATTTAGTTTTAAAAT
1 TAAATTTA-TTTTAAATT
* *
30962340 TAGATTTATTTTGAATT
1 TAAATTTATTTTAAATT
*** *
30962357 TAAATTTGCATAAAATT
1 TAAATTTATTTTAAATT
*
30962374 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
30962391 TAAATTTA
1 TAAATTTA
30962399 AAATTAAATT
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 38 0.84
18 7 0.16
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:30962383 original size:34 final size:33
Alignment explanation
Indices: 30962334--30962397 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
30962324 AATTTAGTTT
* * *
30962334 TAAAATTAGATTTATTTTGAATTTAAATTTGCA
1 TAAAATTAAATTTATTATAAATTTAAATTTGCA
30962367 TAAAATTTAAATTTATTATAAATTTAAATTT
1 TAAAA-TTAAATTTATTATAAATTTAAATTT
30962398 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (33 bp):
TAAAATTAAATTTATTATAAATTTAAATTTGCA
Found at i:30962411 original size:34 final size:33
Alignment explanation
Indices: 30962334--30962412 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
30962324 AATTTAGTTT
* * * **
30962334 TAAAATTAGATTTATTTTGAATTTAAATTTGCA
1 TAAAATTAAATTTATTATAAATTTAAATTTAAA
30962367 TAAAATTTAAATTTATTATAAATTTAAATTTAAAA
1 TAAAA-TTAAATTTATTATAAATTTAAATTT-AAA
*
30962402 TTAAATTAAAT
1 TAAAATTAAAT
30962413 GTTCAAAGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 5 0.13
34 28 0.74
35 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (33 bp):
TAAAATTAAATTTATTATAAATTTAAATTTAAA
Found at i:30962796 original size:26 final size:26
Alignment explanation
Indices: 30962757--30962824 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
30962747 ACAAAAGGTT
30962757 ACAAACCCAGTTCTTGGATTCAATAG
1 ACAAACCCAGTTCTTGGATTCAATAG
*
30962783 ACGAACCCAGTTCTTGGATTCAATAG
1 ACAAACCCAGTTCTTGGATTCAATAG
30962809 ACAAACCCAGTTCTTG
1 ACAAACCCAGTTCTTG
30962825 AAAAAGAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (26 bp):
ACAAACCCAGTTCTTGGATTCAATAG
Found at i:30963402 original size:28 final size:27
Alignment explanation
Indices: 30963341--30963439 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 27
30963331 AAATTATTCA
* *
30963341 AAAATTATATTTGTGATCTCAAAACTT-C
1 AAAATTACATTT-TGACCTC-AAACTTCC
30963369 AGAAATTACATTTTGACCTCGAAACTTCC
1 A-AAATTACATTTTGACCTC-AAACTTCC
30963398 AAAATTACCATTTT-ACCCTCAAACTTTCC
1 AAAATTA-CATTTTGA-CCTCAAAC-TTCC
*
30963427 AAAATTCCATTTT
1 AAAATTACATTTT
30963440 TAACCCCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
28 30 0.48
29 32 0.52
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (27 bp):
AAAATTACATTTTGACCTCAAACTTCC
Found at i:30963486 original size:58 final size:59
Alignment explanation
Indices: 30963398--30963679 Score: 374
Period size: 59 Copynumber: 4.8 Consensus size: 59
30963388 CGAAACTTCC
* * *
30963398 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTCCACCA
* * * * *
30963457 AAAATTACCA-CTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCTCGATTCCATCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTCCACCA
* * * * *
30963515 AAAATTACCATTTTACCCCCAAACTTTCCAAACTTTCATTCTTAATCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTCCACCA
* * * *
30963574 AAAATTACCATTTTACCCTCGAACCTTT-CAAAATTCCATTTTTAACCACGATTCCATCA
1 AAAATTACCATTTTACCC-CCAAACTTTCCAAAATTCCATTTTTAACCCCGATTCCACCA
30963633 AAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCA-TTTTAACCCC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC
30963680 AAATTTTCCC
Statistics
Matches: 190, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
57 9 0.05
58 65 0.34
59 109 0.57
60 7 0.04
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTCCACCA
Found at i:30963641 original size:118 final size:117
Alignment explanation
Indices: 30963398--30963679 Score: 451
Period size: 118 Copynumber: 2.4 Consensus size: 117
30963388 CGAAACTTCC
* * *
30963398 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTCTTAACCCCGATTTCACCAAAAATT
*
30963463 ACCACTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCTCGATTCCATCA
66 ACCACTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCACGATTCCATCA
* * *
30963515 AAAATTACCATTTTACCCCCAAACTTTCCAAACTTTCATTCTTAATCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTCTTAACCCCGATTTCACCAAAAATT
* * *
30963580 ACCATTTTACCCTCGAACCTTTCAAAATTCCATTTTTAACCACGATTCCATCA
66 ACCA-CTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCACGATTCCATCA
30963633 AAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATT-TTAACCCC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTCTTAACCCC
30963680 AAATTTTCCC
Statistics
Matches: 151, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
116 7 0.05
117 71 0.47
118 73 0.48
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.33
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTCTTAACCCCGATTTCACCAAAAATT
ACCACTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCACGATTCCATCA
Found at i:30963671 original size:27 final size:29
Alignment explanation
Indices: 30963634--30963711 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 29
30963624 ATTCCATCAA
30963634 AAATTACCATTTTACCCCCAAACTTT-CC-
1 AAATT-CCATTTTACCCCCAAACTTTCCCG
* *
30963662 AAATTCCATTTTAACCCCAAATTTTCCCG
1 AAATTCCATTTTACCCCCAAACTTTCCCG
* *
30963691 AAATTACATTTTTGCCCCCAA
1 AAATTCCA-TTTTACCCCCAA
30963712 GAGTCAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.43
28 7 0.17
29 7 0.17
30 10 0.24
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (29 bp):
AAATTCCATTTTACCCCCAAACTTTCCCG
Found at i:30967819 original size:7 final size:7
Alignment explanation
Indices: 30967809--30967840 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
30967799 TGCACATTGC
30967809 TCAGCAT
1 TCAGCAT
30967816 TCAGCAT
1 TCAGCAT
30967823 TCAGCAT
1 TCAGCAT
*
30967830 TCAGCAC
1 TCAGCAT
30967837 TCAG
1 TCAG
30967841 GATCCAGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (7 bp):
TCAGCAT
Found at i:30972399 original size:2 final size:2
Alignment explanation
Indices: 30972392--30972422 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30972382 CAAGTCGAGG
30972392 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30972423 CAGAAGTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30976287 original size:9 final size:9
Alignment explanation
Indices: 30976248--30976299 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
30976238 AAAGTTCAAG
30976248 AAAATTATA
1 AAAATTATA
30976257 TAAAATT-TA
1 -AAAATTATA
*
30976266 ATAAAATATTA
1 A-AAATTA-TA
30976277 AAAATTATA
1 AAAATTATA
*
30976286 AAACTTATA
1 AAAATTATA
30976295 AAAAT
1 AAAAT
30976300 AGGGTGAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 1 0.03
9 20 0.57
10 11 0.31
11 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:30988111 original size:1 final size:1
Alignment explanation
Indices: 30988105--30988129 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30988095 TTCAAATGTC
30988105 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
30988130 GGTTTCCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:30988878 original size:16 final size:17
Alignment explanation
Indices: 30988841--30988886 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
30988831 TATTTTTTAA
*
30988841 AAAATGATTTTTTTGTT
1 AAAATAATTTTTTTGTT
*
30988858 CAAATAATTTTTTTG-T
1 AAAATAATTTTTTTGTT
*
30988874 AAAATTATTTTTT
1 AAAATAATTTTTT
30988887 CGAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (17 bp):
AAAATAATTTTTTTGTT
Found at i:30988910 original size:13 final size:13
Alignment explanation
Indices: 30988892--30988923 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30988882 TTTTTCGAAT
30988892 AAAATATTTTGAA
1 AAAATATTTTGAA
*
30988905 AAAATATTTTTAA
1 AAAATATTTTGAA
30988918 AAAATA
1 AAAATA
30988924 AATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAATATTTTGAA
Found at i:30995018 original size:16 final size:16
Alignment explanation
Indices: 30994999--30995064 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
30994989 TAAAATAAGA
30994999 AATAAATTATTTTTTT
1 AATAAATTATTTTTTT
* **
30995015 AATATATTATTGTAATT
1 AATAAATTATT-TTTTT
**
30995032 ACATGGTATTATTTTTTT
1 A-AT-AAATTATTTTTTT
*
30995050 AACAAATTATTTTTT
1 AATAAATTATTTTTT
30995065 AGTATATATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 20 0.53
17 5 0.13
18 6 0.16
19 7 0.18
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (16 bp):
AATAAATTATTTTTTT
Found at i:31000737 original size:23 final size:23
Alignment explanation
Indices: 31000711--31000755 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31000701 TTTTTCGAAT
**
31000711 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
31000734 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
31000756 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:31001040 original size:58 final size:58
Alignment explanation
Indices: 31000974--31001093 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 58
31000964 ACCTATTAAC
*
31000974 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAACAACACTCAT
*
31001032 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAACAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAACAACACTCAT
31001090 AAAC
1 AAAC
31001094 AACTACTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 3 0.05
58 56 0.95
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAACAACACTCAT
Found at i:31003540 original size:27 final size:25
Alignment explanation
Indices: 31003494--31003546 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
31003484 TAAAAATCAG
31003494 TTTATATATAAATAATTTTATAATT
1 TTTATATATAAATAATTTTATAATT
* *
31003519 TTTATTTATAAAATTATATTTATAATT
1 TTTATATAT-AAATAAT-TTTATAATT
31003546 T
1 T
31003547 ACAAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 6 0.25
27 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATATATAAATAATTTTATAATT
Found at i:31009300 original size:29 final size:29
Alignment explanation
Indices: 31009245--31009300 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
31009235 TATTTAGTGT
*
31009245 TTTTAATTTAATATATTAATATATTTAAA
1 TTTTAATTTAATATAGTAATATATTTAAA
* *
31009274 TTTTATTTTAATATCGTACATAT-TTTA
1 TTTTAATTTAATATAGTA-ATATATTTA
31009301 TGTGTTGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTAATTTAATATAGTAATATATTTAAA
Found at i:31009401 original size:79 final size:79
Alignment explanation
Indices: 31009317--31009475 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
31009307 GTTATTGATT
31009317 TGTTTCAAATCATATATATGTGGTTATCACACGAATATGCGTGTGATAAAATTTCTTATTAATAA
1 TGTTTCAAATCATATATATGTGGTTATCACACGAATATGCGTGTGATAAAATTTCTTATTAATAA
31009382 TATTATTATTTGAG
66 TATTATTATTTGAG
*
31009396 TGTTTCAAATCATATATATGTGGTTATCACACGAATATGCGTGTGATAAAATTTTTTATTAATAA
1 TGTTTCAAATCATATATATGTGGTTATCACACGAATATGCGTGTGATAAAATTTCTTATTAATAA
31009461 TATTATTATTTGAG
66 TATTATTATTTGAG
31009475 T
1 T
31009476 TGGTATCATA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (79 bp):
TGTTTCAAATCATATATATGTGGTTATCACACGAATATGCGTGTGATAAAATTTCTTATTAATAA
TATTATTATTTGAG
Found at i:31041551 original size:9 final size:10
Alignment explanation
Indices: 31041517--31041583 Score: 75
Period size: 10 Copynumber: 6.8 Consensus size: 10
31041507 TTTGACAATT
31041517 ATTTTTTATTA
1 ATTTTTTA-TA
*
31041528 A-ATTTTATA
1 ATTTTTTATA
*
31041537 ATTTTTTATG
1 ATTTTTTATA
31041547 ATTTTTTATA
1 ATTTTTTATA
31041557 A-TTTTTATA
1 ATTTTTTATA
* *
31041566 ATTTTTTGTG
1 ATTTTTTATA
31041576 ATTTTTTA
1 ATTTTTTA
31041584 AAAAATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 12 0.26
10 34 0.72
11 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:31041552 original size:29 final size:29
Alignment explanation
Indices: 31041517--31041583 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
31041507 TTTGACAATT
31041517 ATTTTTTATTAAATTTTATAATTTTTTATG
1 ATTTTTTA-TAAATTTTATAATTTTTTATG
* *
31041547 ATTTTTTATAATTTTTATAATTTTTTGTG
1 ATTTTTTATAAATTTTATAATTTTTTATG
31041576 ATTTTTTA
1 ATTTTTTA
31041584 AAAAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (29 bp):
ATTTTTTATAAATTTTATAATTTTTTATG
Found at i:31041630 original size:29 final size:29
Alignment explanation
Indices: 31041517--31041669 Score: 89
Period size: 29 Copynumber: 5.1 Consensus size: 29
31041507 TTTGACAATT
* * *
31041517 ATTTTTTATTAAATTTTATAATTTTTTATG
1 ATTTTTTATTAATTTTTATAA-TATTTATA
* * *
31041547 ATTTTTTA-TAATTTTTATAATTTTTTGTG
1 ATTTTTTATTAATTTTTATAA-TATTTATA
* ** * *
31041576 ATTTTTTA-AAAAATATATCAA-CTTTATA
1 ATTTTTTATTAATTTTTAT-AATATTTATA
*
31041604 ATTTTTTATGAATTTTTATAATATTTAATAA
1 ATTTTTTATTAATTTTTATAATATTT-AT-A
*
31041635 ATTTTATTAGTTTATTTTT-TAATATTTTATA
1 ATTTT-TTA-TTAATTTTTATAATA-TTTATA
31041666 ATTT
1 ATTT
31041670 CTATTAAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
28 14 0.14
29 42 0.42
30 12 0.12
31 11 0.11
32 10 0.10
33 10 0.10
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTTTTATTAATTTTTATAATATTTATA
Found at i:31042600 original size:19 final size:18
Alignment explanation
Indices: 31042576--31042614 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31042566 CATTATTTAC
31042576 TTTTAAACACATATTTATA
1 TTTTAAACA-ATATTTATA
* *
31042595 TTTTAAATAATTTTTATA
1 TTTTAAACAATATTTATA
31042613 TT
1 TT
31042615 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAACAATATTTATA
Found at i:31044255 original size:31 final size:31
Alignment explanation
Indices: 31044192--31044255 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
31044182 ACTAGGGTAA
* * *
31044192 TTTGGGTAACGGAGTATAATTTATGTATCAC
1 TTTGGGTAACGAAGTATAATTTAGGTACCAC
* *
31044223 TTTGGGTAACGAAGTATGATTTAGGTGCCAC
1 TTTGGGTAACGAAGTATAATTTAGGTACCAC
31044254 TT
1 TT
31044256 CTAACAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (31 bp):
TTTGGGTAACGAAGTATAATTTAGGTACCAC
Found at i:31044410 original size:22 final size:22
Alignment explanation
Indices: 31044385--31044436 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
31044375 GCATGAGATC
31044385 TTGGCATATACGTGTTGTTTGA
1 TTGGCATATACGTGTTGTTTGA
*
31044407 TTGGCATATCCGTGTTGTTTGA
1 TTGGCATATACGTGTTGTTTGA
31044429 TTGGCATA
1 TTGGCATA
31044437 AGCTCATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (22 bp):
TTGGCATATACGTGTTGTTTGA
Found at i:31046659 original size:19 final size:17
Alignment explanation
Indices: 31046625--31046663 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31046615 TTTAAATAAT
31046625 TTTTGGGTAAAATAAATA
1 TTTTGGGTAAAATAAA-A
*
31046643 TTTTGGGTCAAATTAAAA
1 TTTTGGGT-AAAATAAAA
31046661 TTT
1 TTT
31046664 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TTTTGGGTAAAATAAAA
Found at i:31047788 original size:20 final size:20
Alignment explanation
Indices: 31047763--31047801 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31047753 TGGTGTTTTG
* *
31047763 AATTGTGTTTCTAGTGATTC
1 AATTGTATTTCAAGTGATTC
31047783 AATTGTATTTCAAGTGATT
1 AATTGTATTTCAAGTGATT
31047802 TAGATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.49
Consensus pattern (20 bp):
AATTGTATTTCAAGTGATTC
Found at i:31059284 original size:40 final size:41
Alignment explanation
Indices: 31059240--31059334 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 41
31059230 TATTATATTG
*
31059240 ATAATTATTTTTATTTTT-AAA-ATTATTAAAACATTA-ATAT
1 ATAATTATTTATATTTTTCAAATATTATT-AAACA-TACATAT
31059280 ATAA-TA-TTATATTTTTCAAATATTATTAAACATACATAT
1 ATAATTATTTATATTTTTCAAATATTATTAAACATACATAT
*
31059319 TTAATTATTTATATTT
1 ATAATTATTTATATTT
31059335 AGTCATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
38 11 0.23
39 17 0.35
40 12 0.25
41 8 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (41 bp):
ATAATTATTTATATTTTTCAAATATTATTAAACATACATAT
Found at i:31059927 original size:19 final size:19
Alignment explanation
Indices: 31059894--31059944 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
31059884 ATCCAAGCAT
*
31059894 AAAAAAATATTAATTTTTTTC
1 AAAAAAATA--AATTATTTTC
31059915 AAAAAAATAAATTATTTTC
1 AAAAAAATAAATTATTTTC
* *
31059934 TATAAAATAAA
1 AAAAAAATAAA
31059945 CATAACCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 18 0.67
21 9 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAAATAAATTATTTTC
Found at i:31060376 original size:15 final size:16
Alignment explanation
Indices: 31060352--31060390 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
31060342 AGTAGAGAGT
31060352 TTATAATA-TTTTATA
1 TTATAATATTTTTATA
*
31060367 TTATATTATTTTTATA
1 TTATAATATTTTTATA
31060383 -TATAATAT
1 TTATAATAT
31060391 AATTCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATAATATTTTTATA
Found at i:31060501 original size:16 final size:16
Alignment explanation
Indices: 31060473--31060505 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31060463 AGATTACTGT
31060473 ATAAAATATTATAATAA
1 ATAAAATATTAT-ATAA
31060490 ATAAAA-ATTATATAA
1 ATAAAATATTATATAA
31060505 A
1 A
31060506 AGTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAATATTATATAA
Found at i:31061884 original size:39 final size:39
Alignment explanation
Indices: 31061830--31061910 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
31061820 AAACCCGGAT
31061830 CTCCTAAGATTAATATCAATCTCTTTTCCACTAGAATCA
1 CTCCTAAGATTAATATCAATCTCTTTTCCACTAGAATCA
31061869 CTCCTAAGATTAATATCAATCTCTTTTCCACTAGAATCA
1 CTCCTAAGATTAATATCAATCTCTTTTCCACTAGAATCA
31061908 CTC
1 CTC
31061911 ATTAGGTTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (39 bp):
CTCCTAAGATTAATATCAATCTCTTTTCCACTAGAATCA
Done.