Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 113 of 221
Found at i:34638329 original size:15 final size:16
Alignment explanation
Indices: 34638303--34638338 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
34638293 TATAAATGCC
34638303 ACAATAAATAAATACA
1 ACAATAAATAAATACA
*
34638319 ACAAT-AATAAATATA
1 ACAATAAATAAATACA
34638334 ACAAT
1 ACAAT
34638339 GGCATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (16 bp):
ACAATAAATAAATACA
Found at i:34638760 original size:21 final size:21
Alignment explanation
Indices: 34638729--34638782 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
34638719 TAAAAAATAT
34638729 AAAAATATACATATATAGATAA
1 AAAAAT-TACATATATAGATAA
*
34638751 AAAAATTACATATATATATAA
1 AAAAATTACATATATAGATAA
34638772 AAAAATTACAT
1 AAAAATTACAT
34638783 TATTAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAATTACATATATAGATAA
Found at i:34638765 original size:29 final size:29
Alignment explanation
Indices: 34638692--34638766 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
34638682 TAATTATTTT
* *
34638692 AAAAACATAAATATATACGTATAAATATA
1 AAAAATATAAATATATACATATAAATATA
*
34638721 AAAAATATAAAAATATACATATATAGATA-A
1 AAAAATATAAATATATACATATA-A-ATATA
*
34638751 AAAAAT-TACATATATA
1 AAAAATATAAATATATA
34638767 TATAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 28 0.72
30 8 0.21
31 3 0.08
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATATAAATATATACATATAAATATA
Found at i:34640552 original size:84 final size:84
Alignment explanation
Indices: 34640446--34640731 Score: 299
Period size: 84 Copynumber: 3.3 Consensus size: 84
34640436 TTAATCTGCC
* * *
34640446 CCACTGCAACCTCA-GAAGGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAAG
1 CCACTGCAACTTCAGGGA-GATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* *
34640510 ATCCGTGGTTTTAATCCACT
65 ATCTGTGATTTTAATCCACT
* * * * * *
34640530 CCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCTG-TCTGCCCCACTGCAACTTCAGGGGG
1 CCACTGCAACTTCAGGGAGATAAGATTAG--A--TGC-GATCTG-CTCTCTGCAACTTCAGAGAG
* * * ***
34640594 ATAAGA-CTTTGCTTACTTAGTTTGCT
60 ATAAGATCTGTGATT--TTAATCCACT
* *
34640620 CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
34640685 TCTGTGATTTTAATCCACT
66 TCTGTGATTTTAATCCACT
34640704 CCACTGCAACTTCAGGGAGATAAGATTA
1 CCACTGCAACTTCAGGGAGATAAGATTA
34640732 ATGGCTTTAA
Statistics
Matches: 159, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
84 55 0.35
85 25 0.16
86 13 0.08
88 12 0.08
89 22 0.14
90 32 0.20
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (84 bp):
CCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
TCTGTGATTTTAATCCACT
Found at i:34640726 original size:44 final size:44
Alignment explanation
Indices: 34640480--34640943 Score: 217
Period size: 44 Copynumber: 10.7 Consensus size: 44
34640470 ATTAGATGCG
* ** * *
34640480 ATCTGCT-CTCTGCAACTTCAGAAAGATAAGATCCGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
** **
34640523 ATCCACTCCACTGCAACTTCAGGGAGATAAGAT-TCGCCATCTTCT-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGAT-TT-TA
* * * * *
34640568 GTCTGCCCCACTGCAACTTCAGGGGGATAAGA-CTTTGCTTACTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATT--TTA
* * * * ***
34640613 GTTTGCTCCACTGCAACTTCAGAGAGATAAGA-CT-AGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
* *
34640654 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
** * **
34640697 ATCCACTCCACTGCAACTTCAGGGAGATAAGAT-TAATGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGATTTTA
* * * * * *
34640741 ATCTGCTCCACTACAACTTCAAGGAGATAATATTTGCCG-TCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TGAT-TTTA
* * * * * *
34640786 GTATGC-CTCACTGTAGCTTCA-GGAGGATAAGA-CT-TGCTTGCTCA
1 ATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGATT--TTA
* * ***
34640830 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
** * ** *
34640871 ATCTGCT-CTTTGAAACTTCAAAGATATAAGATCTGTGATTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGA-TTTTA
*
34640915 ATCCGCTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
34640944 GGATTACGGT
Statistics
Matches: 310, Mismatches: 83, Indels: 54
0.69 0.19 0.12
Matches are distributed among these distances:
40 41 0.13
41 16 0.05
42 6 0.02
43 16 0.05
44 125 0.40
45 105 0.34
46 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTTA
Found at i:34640808 original size:218 final size:218
Alignment explanation
Indices: 34640489--34640949 Score: 645
Period size: 218 Copynumber: 2.1 Consensus size: 218
34640479 GATCTGCTCT
** *** * * *
34640489 CTGCAACTTCAGAAAGATAAGATCCGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCCACTCCACTACAACTTCAAGGAGATAAG
* * * * *
34640554 ATTCGCCATCTTCTGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTTGCTTACTTAGTTTGC
66 ATTCGCCATCTTCAGTATGCCCCACTGCAACTTCAGGAGGATAAGAC-TTGCTTACTCAGTCTGC
* *
34640619 TCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
130 TCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGAAACTTCAAAGAGATAAG
34640684 ATCTGTGA-TTTTAATCCACTCCA
195 ATCTGTGATTTTTAATCCACTCCA
** *
34640707 CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCTGCTCCACTACAACTTCAAGGAGATAAT
1 CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCCACTCCACTACAACTTCAAGGAGATAAG
* * * * * *
34640772 ATTTGCCGTCTTCAGTATGCCTCACTGTAGCTTCAGGAGGATAAGACTTGCTTGCTCAGTCTGCT
66 ATTCGCCATCTTCAGTATGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAGTCTGCT
* * *
34640837 CCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTTTGAAACTTCAAAGATATAAGA
131 CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGAAACTTCAAAGAGATAAGA
*
34640902 TCTGTGATTTTTAATCCGCTCCA
196 TCTGTGATTTTTAATCCACTCCA
*
34640925 CTGCAACTTCAGGGAGATAGGATTA
1 CTGCAACTTCAGGGAGATAAGATTA
34640950 CGGTTTCACT
Statistics
Matches: 213, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
217 82 0.38
218 131 0.62
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (218 bp):
CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCCACTCCACTACAACTTCAAGGAGATAAG
ATTCGCCATCTTCAGTATGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAGTCTGCT
CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGAAACTTCAAAGAGATAAGA
TCTGTGATTTTTAATCCACTCCA
Found at i:34652927 original size:15 final size:16
Alignment explanation
Indices: 34652901--34652936 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
34652891 TATAAATGCC
34652901 ACAATAAATAAATACA
1 ACAATAAATAAATACA
*
34652917 ACAAT-AATAAATATA
1 ACAATAAATAAATACA
34652932 ACAAT
1 ACAAT
34652937 GGCATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (16 bp):
ACAATAAATAAATACA
Found at i:34653087 original size:24 final size:24
Alignment explanation
Indices: 34653038--34653090 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
34653028 TAAAAATAAT
*
34653038 ATAAATGAAAACACAAATTAATAA
1 ATAAATGAAAACACAAATTAAAAA
34653062 ATAAATGAAAGA-ACTAAA-TAAAAA
1 ATAAATGAAA-ACAC-AAATTAAAAA
34653086 ATAAA
1 ATAAA
34653091 GAATAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.19
Consensus pattern (24 bp):
ATAAATGAAAACACAAATTAAAAA
Found at i:34653322 original size:23 final size:23
Alignment explanation
Indices: 34653295--34653338 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34653285 TTAAAAACAT
* *
34653295 AAATATATATGTATAAATATAAA
1 AAATATAAATATATAAATATAAA
*
34653318 AAATATAAATATATACATATA
1 AAATATAAATATATAAATATA
34653339 TAGATAAAAA
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:0.02, T:0.34
Consensus pattern (23 bp):
AAATATAAATATATAAATATAAA
Found at i:34653338 original size:29 final size:30
Alignment explanation
Indices: 34653287--34653361 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
34653277 TAATTATTTT
* * *
34653287 AAAAACATAAATATAT--ATGTATAAATATA
1 AAAAATATAAATATATACATATATAGATA-A
34653316 AAAAATATAAATATATACATATATAGATAA
1 AAAAATATAAATATATACATATATAGATAA
*
34653346 AAAAAT-TACATATATA
1 AAAAATATAAATATATA
34653362 TAAATTACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 24 0.60
30 7 0.17
31 9 0.22
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATATAAATATATACATATATAGATAA
Found at i:34659477 original size:25 final size:26
Alignment explanation
Indices: 34659445--34659499 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
34659435 TTATTAAATT
*
34659445 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
34659470 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
34659495 A-ATAT
1 ATATAT
34659500 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:34659686 original size:44 final size:45
Alignment explanation
Indices: 34659637--34659731 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
34659627 TTACACCTCT
* *
34659637 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
34659681 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
34659726 ATTACA
1 ATTACA
34659732 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:34659731 original size:16 final size:16
Alignment explanation
Indices: 34659712--34659779 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
34659702 GATTTGCTAT
* *
34659712 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
34659728 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34659744 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34659760 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34659776 TACA
1 TACA
34659780 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:34661904 original size:22 final size:22
Alignment explanation
Indices: 34661849--34661904 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
34661839 ATACAACTAT
34661849 TAGTACAATTGAAACACATGTTA
1 TAGTA-AATTGAAACACATGTTA
*
34661872 TAGT--ATTGAAACACATGTTG
1 TAGTAAATTGAAACACATGTTA
34661892 TAGTAAATTGAAA
1 TAGTAAATTGAAA
34661905 GTTTACAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 19 0.63
22 7 0.23
23 4 0.13
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (22 bp):
TAGTAAATTGAAACACATGTTA
Found at i:34674239 original size:14 final size:14
Alignment explanation
Indices: 34674220--34674246 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34674210 GTGCTTCCTT
34674220 TGTAACAACCCATA
1 TGTAACAACCCATA
34674234 TGTAACAACCCAT
1 TGTAACAACCCAT
34674247 TTTTCAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (14 bp):
TGTAACAACCCATA
Found at i:34677104 original size:42 final size:42
Alignment explanation
Indices: 34677040--34677148 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
34677030 ACGGCCAAGC
* *
34677040 CACATGCCTGTGTGCTAGGCCGTGTAACTTTCGAAATGGCCT
1 CACATGCCTGTGTGCCAAGCCGTGTAACTTTCGAAATGGCCT
*
34677082 CACACGCCTGTGTGCCAAGCCGTGTAACTTTCGAAATGGCCT
1 CACATGCCTGTGTGCCAAGCCGTGTAACTTTCGAAATGGCCT
34677124 CACATGCCTGTGTGCCAAGCCGTGT
1 CACATGCCTGTGTGCCAAGCCGTGT
34677149 GCTAGGCTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (42 bp):
CACATGCCTGTGTGCCAAGCCGTGTAACTTTCGAAATGGCCT
Found at i:34694519 original size:117 final size:118
Alignment explanation
Indices: 34694372--34694606 Score: 348
Period size: 117 Copynumber: 2.0 Consensus size: 118
34694362 CAACCACTAA
* *
34694372 AAAGAATTCAGAGATAATAAAGAGGCATATAAAAATTCAATACCATACACAA-ATCATGGCCAGA
1 AAAGAATACAGAGATAATAAAGAGGCATATAAAAATTCAATACCATACACAAGA-CATGACCAGA
* * * *
34694436 TTTGAATCTTGAAATTTCTTTTTACAACCTATCTAG-CCAAGAATAATTAGCAG
65 TTTGAACCTAGAAATTTCTGTTTACAACCTATCTAGTCCAAGAATAACTAGCAG
* * *
34694489 AAAGAATACAGAGATAATAATGATGCATATAAAAATTCAATACCATACACAAGACATGACTAGAT
1 AAAGAATACAGAGATAATAAAGAGGCATATAAAAATTCAATACCATACACAAGACATGACCAGAT
* *
34694554 TTGAACCTAGAAATTTCTGTTTACAGCCTATGTAGTCCAAGAATAACTAGCAG
66 TTGAACCTAGAAATTTCTGTTTACAACCTATCTAGTCCAAGAATAACTAGCAG
34694607 TGCACAGTGA
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 88 0.84
118 17 0.16
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (118 bp):
AAAGAATACAGAGATAATAAAGAGGCATATAAAAATTCAATACCATACACAAGACATGACCAGAT
TTGAACCTAGAAATTTCTGTTTACAACCTATCTAGTCCAAGAATAACTAGCAG
Found at i:34694690 original size:27 final size:27
Alignment explanation
Indices: 34694660--34694713 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
34694650 TTCTTAAAGA
*
34694660 AAATTTATTTTTGACATGAAATGAGTT
1 AAATTTATTTTTAACATGAAATGAGTT
*
34694687 AAATTTATTTTTAACATGAATTGAGTT
1 AAATTTATTTTTAACATGAAATGAGTT
34694714 CTGTTCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (27 bp):
AAATTTATTTTTAACATGAAATGAGTT
Found at i:34717035 original size:10 final size:11
Alignment explanation
Indices: 34717023--34717059 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
34717013 ATTTTTTTAA
*
34717023 TTTTAAAATAT
1 TTTTAAAATAC
34717034 TTTTAAAATAC
1 TTTTAAAATAC
34717045 TTTTAAAATAC
1 TTTTAAAATAC
34717056 TTTT
1 TTTT
34717060 TTTAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:34717056 original size:51 final size:52
Alignment explanation
Indices: 34716983--34717084 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 52
34716973 TTTTTTTTAA
* * * **
34716983 TTTTAAAATATTTTTTACATACTTTTTTTAATTTTT-TTAATTTTAAAATAT
1 TTTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATAT
34717034 TTTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATA
1 TTTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATA
34717085 AAAATAGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 33 0.73
52 12 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (52 bp):
TTTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATAT
Found at i:34717060 original size:40 final size:41
Alignment explanation
Indices: 34716975--34717084 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 41
34716965 TAAATATATT
* * **
34716975 TTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAAT-
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAATC
34717015 TTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAAT-C
34717056 TTTTTTTAATTTTTAAAA-A-TTTTAAAATA
1 -TTTTTTAA-TTTTAAAATATTTTTAAAATA
34717085 AAAATAGGCC
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.11
40 28 0.45
41 10 0.16
42 9 0.15
43 8 0.13
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAATC
Found at i:34717074 original size:22 final size:20
Alignment explanation
Indices: 34716974--34717078 Score: 76
Period size: 22 Copynumber: 5.2 Consensus size: 20
34716964 ATAAATATAT
34716974 TTTTTTTAA-TTTTAAAATA
1 TTTTTTTAATTTTTAAAATA
***
34716993 -TTTTTTACATACTTTTTTTA-A
1 TTTTTTTA-AT--TTTTAAAATA
34717014 TTTTTTTAA-TTTTAAAATA
1 TTTTTTTAATTTTTAAAATA
**
34717033 TTTTTAAAATACTTTTAAAATA
1 TTTTTTTAAT--TTTTAAAATA
34717055 CTTTTTTTAATTTTTAAAA-A
1 -TTTTTTTAATTTTTAAAATA
34717075 TTTT
1 TTTT
34717079 AAAATAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
18 12 0.18
19 13 0.20
20 1 0.02
21 10 0.15
22 22 0.33
23 8 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTAATTTTTAAAATA
Found at i:34717076 original size:10 final size:11
Alignment explanation
Indices: 34717023--34717084 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
34717013 ATTTTTTTAA
34717023 TTTTAAAATAT
1 TTTTAAAATAT
*
34717034 TTTTAAAATAC
1 TTTTAAAATAT
34717045 TTTTAAAATACT
1 TTTTAAAATA-T
**
34717057 TTTT-TTA-AT
1 TTTTAAAATAT
34717066 TTTTAAAA-A-
1 TTTTAAAATAT
34717075 TTTTAAAATA
1 TTTTAAAATA
34717085 AAAATAGGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
9 13 0.31
10 4 0.10
11 21 0.50
12 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:34717777 original size:11 final size:11
Alignment explanation
Indices: 34717761--34717798 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
34717751 TGATGTCTTT
34717761 TGTTTATAATC
1 TGTTTATAATC
34717772 TGTTTATAATC
1 TGTTTATAATC
*
34717783 TTCTTTATAATC
1 -TGTTTATAATC
34717795 TGTT
1 TGTT
34717799 GATGTTGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.58
Consensus pattern (11 bp):
TGTTTATAATC
Found at i:34717791 original size:12 final size:12
Alignment explanation
Indices: 34717763--34717795 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34717753 ATGTCTTTTG
*
34717763 TTTATAATC-TG
1 TTTATAATCTTC
34717774 TTTATAATCTTC
1 TTTATAATCTTC
34717786 TTTATAATCT
1 TTTATAATCT
34717796 GTTGATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTATAATCTTC
Found at i:34717817 original size:14 final size:14
Alignment explanation
Indices: 34717798--34717825 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34717788 TATAATCTGT
34717798 TGATGTTGCCTTAC
1 TGATGTTGCCTTAC
34717812 TGATGTTGCCTTAC
1 TGATGTTGCCTTAC
34717826 AGTTCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
TGATGTTGCCTTAC
Found at i:34717888 original size:58 final size:59
Alignment explanation
Indices: 34717786--34717897 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 59
34717776 TATAATCTTC
* *
34717786 TTTATAATCTGTTGATGTTGCCTTACTGATGTTGCCTTACAGTTCCCTTTGTTTAGCTG
1 TTTATAATCTGTCGATGTTGCCTTACTGATGTTGCCTTACAGTTCCATTTGTTTAGCTG
* *
34717845 TTTATAATTTGTCGTTGTTGCC-TACT-ATTGTTGCCTTACAGTTCCATTTGTTT
1 TTTATAATCTGTCGATGTTGCCTTACTGA-TGTTGCCTTACAGTTCCATTTGTTT
34717898 CGTTGTTGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 1 0.02
58 28 0.58
59 19 0.40
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.50
Consensus pattern (59 bp):
TTTATAATCTGTCGATGTTGCCTTACTGATGTTGCCTTACAGTTCCATTTGTTTAGCTG
Found at i:34718410 original size:12 final size:12
Alignment explanation
Indices: 34718395--34718437 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
34718385 TATTTGGAAT
34718395 TTTATACTCTGG
1 TTTATACTCTGG
*
34718407 TTTATATTCTGG
1 TTTATACTCTGG
*
34718419 TTTATAATCTGG
1 TTTATACTCTGG
34718431 TTTATAC
1 TTTATAC
34718438 CTTGTTGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (12 bp):
TTTATACTCTGG
Found at i:34718483 original size:12 final size:12
Alignment explanation
Indices: 34718466--34718495 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34718456 TATCTGAAAT
*
34718466 TTTATATTCTGG
1 TTTATAATCTGG
34718478 TTTATAATCTGG
1 TTTATAATCTGG
34718490 TTTATA
1 TTTATA
34718496 CCTTGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:34718541 original size:12 final size:12
Alignment explanation
Indices: 34718526--34718555 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34718516 TATATGAAAT
*
34718526 TTTATATTCTGG
1 TTTATAATCTGG
34718538 TTTATAATCTGG
1 TTTATAATCTGG
34718550 TTTATA
1 TTTATA
34718556 CCTTGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:34718542 original size:60 final size:59
Alignment explanation
Indices: 34718407--34718577 Score: 315
Period size: 60 Copynumber: 2.9 Consensus size: 59
34718397 TATACTCTGG
*
34718407 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATCTGAAAT
1 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATATGAAAT
34718466 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTTATATATGAAAT
1 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTC-TTTTTTATATATGAAAT
*
34718526 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGATGCTTCTTTTTTATAT
1 TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATAT
34718578 TTGTGACATT
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 52 0.48
60 57 0.52
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.57
Consensus pattern (59 bp):
TTTATATTCTGGTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTATATATGAAAT
Found at i:34723496 original size:3 final size:3
Alignment explanation
Indices: 34723488--34723537 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
34723478 TAAGAAAGAT
34723488 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34723536 TT
1 TT
34723538 CAAGTTGCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34724134 original size:17 final size:17
Alignment explanation
Indices: 34724103--34724135 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34724093 TGTATAATAC
34724103 TTGTTTTATTCTTAAAT
1 TTGTTTTATTCTTAAAT
34724120 TTGTTATTATT-TTAAA
1 TTGTT-TTATTCTTAAA
34724136 GGCATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TTGTTTTATTCTTAAAT
Found at i:34724580 original size:7 final size:7
Alignment explanation
Indices: 34724570--34724659 Score: 83
Period size: 7 Copynumber: 12.9 Consensus size: 7
34724560 AACTCAATAC
34724570 TCAATTT
1 TCAATTT
34724577 TCAATTT
1 TCAATTT
*
34724584 TCAATTC
1 TCAATTT
*
34724591 TCAATCCT
1 TCAAT-TT
34724599 T-AATTT
1 TCAATTT
* **
34724605 TTAATCC
1 TCAATTT
34724612 TCAATTT
1 TCAATTT
*
34724619 TCAATTC
1 TCAATTT
34724626 TCAATTT
1 TCAATTT
*
34724633 CCAATTT
1 TCAATTT
*
34724640 CCAATTT
1 TCAATTT
*
34724647 CCAATTT
1 TCAATTT
34724654 TCAATT
1 TCAATT
34724660 CTCGATCGTC
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
6 2 0.03
7 65 0.96
8 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (7 bp):
TCAATTT
Found at i:34724587 original size:21 final size:21
Alignment explanation
Indices: 34724563--34724630 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
34724553 TCTTTTTAAC
34724563 TCAATACTCAATTTTCAATTT
1 TCAATACTCAATTTTCAATTT
* *
34724584 TCAATTCTCAATCCTT-AATTT
1 TCAATACTCAAT-TTTCAATTT
* * *
34724605 TTAATCCTCAATTTTCAATTC
1 TCAATACTCAATTTTCAATTT
34724626 TCAAT
1 TCAAT
34724631 TTCCAATTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (21 bp):
TCAATACTCAATTTTCAATTT
Found at i:34724687 original size:35 final size:34
Alignment explanation
Indices: 34724562--34724696 Score: 94
Period size: 35 Copynumber: 3.9 Consensus size: 34
34724552 TTCTTTTTAA
**
34724562 CTCAATACTCAATTTTCAATTTTCAATTCTCAATC
1 CTCAAT-CTCAATCCTCAATTTTCAATTCTCAATC
* * *
34724597 CTTAATTTTTAATCCTCAATTTTCAATTCTCAAT-
1 CTCAA-TCTCAATCCTCAATTTTCAATTCTCAATC
* * * *
34724631 TTCCAATTTCCAAT-TTCCAATTTTCAATTCTCGATC
1 CT-CAATCT-CAATCCT-CAATTTTCAATTCTCAATC
* * *
34724667 GTCAATCCTCAATCCTCAATTCTAAATTCT
1 CTCAAT-CTCAATCCTCAATTTTCAATTCT
34724697 AAATTCTAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
34 5 0.06
35 69 0.88
36 4 0.05
ACGTcount: A:0.29, C:0.26, G:0.01, T:0.44
Consensus pattern (34 bp):
CTCAATCTCAATCCTCAATTTTCAATTCTCAATC
Found at i:34724694 original size:7 final size:7
Alignment explanation
Indices: 34724684--34724708 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34724674 CTCAATCCTC
34724684 AATTCTA
1 AATTCTA
34724691 AATTCTA
1 AATTCTA
34724698 AATTCTA
1 AATTCTA
34724705 AATT
1 AATT
34724709 ATTCTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTCTA
Found at i:34727006 original size:25 final size:25
Alignment explanation
Indices: 34726964--34727032 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
34726954 TATTTGTAAT
*
34726964 TTTCCTAAATTGTATACTTTATTTT-
1 TTTCCCAAA-TGTATACTTTATTTTA
*
34726989 TCTTCCCAAATGTATACTTTGTTTTA
1 T-TTCCCAAATGTATACTTTATTTTA
* *
34727015 TATCCCAAATGTACACTT
1 TTTCCCAAATGTATACTT
34727033 ACTTACATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 30 0.79
26 8 0.21
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (25 bp):
TTTCCCAAATGTATACTTTATTTTA
Found at i:34732884 original size:15 final size:15
Alignment explanation
Indices: 34732864--34732895 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34732854 TTAAGTTATA
34732864 TTATGTATAATTTTT
1 TTATGTATAATTTTT
34732879 TTATGTATAATTTTT
1 TTATGTATAATTTTT
34732894 TT
1 TT
34732896 TTGTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATAATTTTT
Found at i:34736714 original size:29 final size:29
Alignment explanation
Indices: 34736672--34736731 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
34736662 GAAGTACTTC
34736672 AATGATTGTACGATCATTAGATGTGAATA
1 AATGATTGTACGATCATTAGATGTGAATA
34736701 AATGATTGTACGATCATTAGATGTGAATA
1 AATGATTGTACGATCATTAGATGTGAATA
34736730 AA
1 AA
34736732 GATCAATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (29 bp):
AATGATTGTACGATCATTAGATGTGAATA
Found at i:34739637 original size:24 final size:24
Alignment explanation
Indices: 34739597--34739652 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
34739587 ACATGCCATC
*
34739597 TTGATTTTGAAATTGAAATGTT-AGT
1 TTGA-TTTGAAATTGAAAT-TTCACT
34739622 TTGATTTGATAA-TGAAATTTCACT
1 TTGATTTGA-AATTGAAATTTCACT
34739646 TTGATTT
1 TTGATTT
34739653 TGATTAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 20 0.71
25 6 0.21
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (24 bp):
TTGATTTGAAATTGAAATTTCACT
Found at i:34739684 original size:27 final size:27
Alignment explanation
Indices: 34739651--34739739 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
34739641 TCACTTTGAT
34739651 TTTGATTAATCGAATGCCATTTGAGAC
1 TTTGATTAATCGAATGCCATTTGAGAC
34739678 TTTGATTAATCGAATGCCATTTGAGAC
1 TTTGATTAATCGAATGCCATTTGAGAC
*
34739705 TTTGATTAATCGAATGCCATTTGAGAT
1 TTTGATTAATCGAATGCCATTTGAGAC
34739732 TTTGATTA
1 TTTGATTA
34739740 TGAAAGCTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (27 bp):
TTTGATTAATCGAATGCCATTTGAGAC
Found at i:34740108 original size:21 final size:19
Alignment explanation
Indices: 34740084--34740122 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
34740074 CATGTATCTA
34740084 AGTCATTAGTAAGTATTTTGG
1 AGTCATTA-TAA-TATTTTGG
*
34740105 AGTCTTTATAATATTTTG
1 AGTCATTATAATATTTTG
34740123 ATTTGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (19 bp):
AGTCATTATAATATTTTGG
Found at i:34741178 original size:28 final size:28
Alignment explanation
Indices: 34741145--34741207 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
34741135 AATTCAATGG
34741145 CCATATTGCAACGGTCAGATTCCAACAA
1 CCATATTGCAACGGTCAGATTCCAACAA
* * * *
34741173 TCATATTGTAACGGTTAGATTCTAACAA
1 CCATATTGCAACGGTCAGATTCCAACAA
34741201 CCATATT
1 CCATATT
34741208 TGTAATACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (28 bp):
CCATATTGCAACGGTCAGATTCCAACAA
Found at i:34742798 original size:16 final size:16
Alignment explanation
Indices: 34742777--34742807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34742767 TAATTGAAAG
*
34742777 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
34742793 TGAAAAAGTAAAATT
1 TGAAAAAGTAAAATT
34742808 GGCAACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:34757406 original size:18 final size:18
Alignment explanation
Indices: 34757365--34757406 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
34757355 TATAAATATG
*
34757365 ATAAAAATTAAAATAATA
1 ATAACAATTAAAATAATA
*
34757383 AAAACAATTAAAATCAA-A
1 ATAACAATTAAAAT-AATA
34757401 ATAACA
1 ATAACA
34757407 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAACAATTAAAATAATA
Found at i:34758745 original size:18 final size:19
Alignment explanation
Indices: 34758724--34758761 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34758714 ATCCTAAAAT
34758724 AAAAAGA-AATAAGCTTTA
1 AAAAAGACAATAAGCTTTA
* *
34758742 AAAAATACAATAAGTTTTA
1 AAAAAGACAATAAGCTTTA
34758761 A
1 A
34758762 TAGAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAAAGACAATAAGCTTTA
Found at i:34759263 original size:30 final size:30
Alignment explanation
Indices: 34759229--34759296 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
34759219 TAGTAAATGT
* *
34759229 AAAATTATACTTTGACCCTCTAAAAA-TATA
1 AAAATT-TAATTTAACCCTCTAAAAATTATA
* *
34759259 AAAATTTAATTTAATCCTTTAAAAATTATA
1 AAAATTTAATTTAACCCTCTAAAAATTATA
*
34759289 AAGATTTA
1 AAAATTTA
34759297 GGTTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTTAATTTAACCCTCTAAAAATTATA
Found at i:34760642 original size:30 final size:30
Alignment explanation
Indices: 34760586--34760642 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
34760576 ATTGCATGAG
* *
34760586 AAATATTTAAATTTTATATTTCATATATCA
1 AAATATTAAAATATTATATTTCATATATCA
*
34760616 AAATATTAATAATATTAT-TTTTATATA
1 AAATATTAA-AATATTATATTTCATATA
34760643 GTAGCATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATTAAAATATTATATTTCATATATCA
Found at i:34764951 original size:6 final size:6
Alignment explanation
Indices: 34764942--34764971 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
34764932 TGTTTATAAG
34764942 TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA
34764972 GGCATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:34767448 original size:83 final size:82
Alignment explanation
Indices: 34767315--34767518 Score: 320
Period size: 83 Copynumber: 2.5 Consensus size: 82
34767305 TGTATACATC
* * *
34767315 TTTCAACAAAACATTTCAAAAAATAAACAAAAA-ATGTTATACTAACAAAATAATCCTATAGCAG
1 TTTCAACAAATCATTTCAAAAAACAAA-AAAAATATGTTATACTAACAAAATAATCCTATAGAAG
*
34767379 TAAGATGTTAACCAACCA
65 TAAGATGTTAAACAACCA
* *
34767397 TTTCAACAAATCATTTCAAAAAACAAAAAGAAATATGTTATGCTAACAAAATGATCCTATAGAAG
1 TTTCAACAAATCATTTCAAAAAACAAAAA-AAATATGTTATACTAACAAAATAATCCTATAGAAG
34767462 TAAGATGTTAAACAACCA
65 TAAGATGTTAAACAACCA
*
34767480 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTA
1 TTTCAACAAATCATTTCAAAAAACAAAAAAAATATGTTA
34767519 ACCATCTCAA
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
81 2 0.02
82 38 0.34
83 73 0.65
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (82 bp):
TTTCAACAAATCATTTCAAAAAACAAAAAAAATATGTTATACTAACAAAATAATCCTATAGAAGT
AAGATGTTAAACAACCA
Found at i:34768063 original size:157 final size:154
Alignment explanation
Indices: 34767595--34768051 Score: 508
Period size: 159 Copynumber: 2.9 Consensus size: 154
34767585 TATGCTACCC
*
34767595 TTTTTTGGCTTCTAGTTCCCATACTTGTACCAGACTAA-G-AACAAAAATCAGAACCCCAAATTA
1 TTTTTTGGCTTCTAGTT-CTATACTTGTACCAGACTAAGGCAA-AAAAATCAGAACCCCAAATTA
* * *
34767658 GATTTAAATAATTTGGAATAGAAATTAAAAAAGTG-TTACGATATACCCGTGATCCAGTTGTGTT
64 GATTTAAAT-ATTTAGAATTGAAA-TAAAAAAGTGTTTACGATATACCTGTGATCCAGTTGTGTT
* * *
34767722 AGGCTGAATGGATGGTGTTCTGTTGTTC
127 AGGCTGAATGCATGGTGTTATGTTGTTA
* * * *
34767750 TTTTTTTGCTTCTAGTTCGTGTACTTGTACCAGACTAAGACAAAAAAAAATTAGAACCCCAAATT
1 TTTTTTGGCTTCTAGTTC-TATACTTGTACCAGACTAAGGC--AAAAAAATCAGAACCCCAAATT
* * * * * * * *
34767815 AGATTAAAATATTTTTGAATTGAAATTAAAATAGTGTATAGGATATACCTATGATCCAATTGTAT
63 AGATTTAAATA-TTTAGAATTGAAA-TAAAAAAGTGTTTACGATATACCTGTGATCCAGTTGTGT
34767880 TAGGCTGAATGCATGGTGTTATGTTGTTA
126 TAGGCTGAATGCATGGTGTTATGTTGTTA
** *
34767909 TTTTTTAGGCTTCTAGTTCTATACTCATACCAGACAAAGGCCAAAAAAATCAGAA-CCCAAATTA
1 TTTTTT-GGCTTCTAGTTCTATACTTGTACCAGACTAAGG-CAAAAAAATCAGAACCCCAAATTA
* * * * * *
34767973 GATTTTAATATTCTAGAATTGACAATGAAAAAGTGTTTATGATATACCTGTGTTCCCGTTATGTT
64 GATTTAAATATT-TAGAATTGA-AATAAAAAAGTGTTTACGATATACCTGTGATCCAGTTGTGTT
*
34768038 AGGCTGAATTCATG
127 AGGCTGAATGCATG
34768052 ATCTTTTGTT
Statistics
Matches: 252, Mismatches: 39, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
154 1 0.00
155 33 0.13
156 2 0.01
157 69 0.27
158 63 0.25
159 72 0.29
160 12 0.05
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (154 bp):
TTTTTTGGCTTCTAGTTCTATACTTGTACCAGACTAAGGCAAAAAAATCAGAACCCCAAATTAGA
TTTAAATATTTAGAATTGAAATAAAAAAGTGTTTACGATATACCTGTGATCCAGTTGTGTTAGGC
TGAATGCATGGTGTTATGTTGTTA
Found at i:34773115 original size:41 final size:41
Alignment explanation
Indices: 34773060--34773374 Score: 468
Period size: 41 Copynumber: 7.7 Consensus size: 41
34773050 TTAATTTAAA
* * * *
34773060 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * *
34773102 TAGATCAGCGGCACTTAGCCTGCTAGGCTTATAGCCTAATC
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
34773143 CAGTTCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
34773184 CAAATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
34773225 CAAATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
34773266 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
34773307 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
34773348 TAGATCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
34773375 TTTTAAAACC
Statistics
Matches: 251, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
41 248 0.99
42 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:34780936 original size:19 final size:21
Alignment explanation
Indices: 34780912--34780950 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
34780902 AATATGCCAG
*
34780912 CAGAAGGTCG-AA-AGCTGAA
1 CAGAAGCTCGTAAGAGCTGAA
34780931 CAGAAGCTCGTAAGAGCTGA
1 CAGAAGCTCGTAAGAGCTGA
34780951 TCCACCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.13
Consensus pattern (21 bp):
CAGAAGCTCGTAAGAGCTGAA
Found at i:34781475 original size:17 final size:16
Alignment explanation
Indices: 34781455--34781498 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
34781445 CTTAATTAGT
*
34781455 TAATCTATCAAATTAA
1 TAATATATCAAATTAA
*
34781471 CTAATTTATC-AATTAA
1 -TAATATATCAAATTAA
34781487 TAATATATCAAA
1 TAATATATCAAA
34781499 ATATTCTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATATCAAATTAA
Found at i:34787892 original size:34 final size:34
Alignment explanation
Indices: 34787848--34787915 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
34787838 CTACTCTCTG
*
34787848 TTATTTGAGATGAATTTACTTAGTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
* *
34787882 TTATTCGAGATTAATTTACTTGGTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
34787916 ACATAGGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (34 bp):
TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
Found at i:34788346 original size:127 final size:126
Alignment explanation
Indices: 34788121--34788373 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 126
34788111 GAAAGATAAA
*
34788121 AACTTTCAGTTCATGTTCTTATATAAAAGCTTTAACTATTTTAGATTTTTTTTAAAAATCATCTT
1 AACTTCCAGTTCATGTTCTTATATAAAAGCTTTAACTATTTTAGATTTTTTTTAAAAATCATCTT
34788186 TCTTACCAAACAAGTCTAAGCAGTCGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGC
66 TCTTACCAAACAAGTCTAAGCAGTCGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGC
34788247 AACTTCCAGTTCATGTTCTTATATAAAAGCTTTAACTATTTTAGATTTTTTTTTAAAAATCATCT
1 AACTTCCAGTTCATGTTCTTATATAAAAGCTTTAACTATTTTAGA-TTTTTTTTAAAAATCATCT
34788312 TTCTTACCAAACAAGTCTAAGCAGTCGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGC
65 TTCTTACCAAACAAGTCTAAGCAGTCGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGC
34788374 TCATAAGGAA
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 44 0.35
127 81 0.65
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (126 bp):
AACTTCCAGTTCATGTTCTTATATAAAAGCTTTAACTATTTTAGATTTTTTTTAAAAATCATCTT
TCTTACCAAACAAGTCTAAGCAGTCGTCAATGAGTGGATTGAAAGAAGGAATTATTTTTGC
Found at i:34793669 original size:29 final size:29
Alignment explanation
Indices: 34793627--34793688 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
34793617 CTATTAACGA
*
34793627 TGCTCCTTTCAAATCTCAAGCTTGCTAGG
1 TGCTCCTTTCAAATCTCAAGCTCGCTAGG
* *
34793656 TGCTCTTTTTAAATCTCAAGCTCGCTAGG
1 TGCTCCTTTCAAATCTCAAGCTCGCTAGG
34793685 TGCT
1 TGCT
34793689 TGGCAACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (29 bp):
TGCTCCTTTCAAATCTCAAGCTCGCTAGG
Found at i:34800974 original size:27 final size:27
Alignment explanation
Indices: 34800930--34800996 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
34800920 GGTGTGGTGC
* * *
34800930 CTATTTGATAGACTGCACCAGTGACCCT
1 CTATCTGATAGGCGGCACCAGTG-CCCT
** *
34800958 -TATCTGATAGGCGGCACTGGTGGCCT
1 CTATCTGATAGGCGGCACCAGTGCCCT
34800984 CTATCTGATAGGC
1 CTATCTGATAGGC
34800997 AACATCAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (27 bp):
CTATCTGATAGGCGGCACCAGTGCCCT
Found at i:34805006 original size:48 final size:48
Alignment explanation
Indices: 34804938--34805094 Score: 219
Period size: 48 Copynumber: 3.3 Consensus size: 48
34804928 TATGTAACCC
* *
34804938 AATGTACCTAATTTATATTACAAAGTTTAAT-CATCGTTTTAATGTTGT
1 AATGTATCTAATTTATATTACAAAGTTTAATCCA-AGTTTTAATGTTGT
**
34804986 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATATTACAAAGTTTAATCCAAGTTTTAATGTTGT
** *
34805034 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGA
1 AATGTATCTAATTTATATTACAAAGTTTAATCCAAGTTTTAATGTTGT
34805082 AAT-TGATCTAATT
1 AATGT-ATCTAATT
34805095 AAATAAATAC
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
47 1 0.01
48 99 0.97
49 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (48 bp):
AATGTATCTAATTTATATTACAAAGTTTAATCCAAGTTTTAATGTTGT
Found at i:34815464 original size:17 final size:17
Alignment explanation
Indices: 34815442--34815475 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34815432 TTTAAATAAA
34815442 TAAATAAATTTCCCAAT
1 TAAATAAATTTCCCAAT
* *
34815459 TAAATAATTTTCTCAAT
1 TAAATAAATTTCCCAAT
34815476 CCAATTTTAA
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAAATTTCCCAAT
Found at i:34818907 original size:46 final size:46
Alignment explanation
Indices: 34818840--34819024 Score: 343
Period size: 46 Copynumber: 4.0 Consensus size: 46
34818830 ACATTGCTAT
* *
34818840 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
34818886 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
34818932 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
34818978 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
34819024 A
1 A
34819025 CTTTGCCATG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 135 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:34819817 original size:16 final size:16
Alignment explanation
Indices: 34819777--34819818 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
34819767 TTTTAAATCG
34819777 CAAAAATTCACTAAAT
1 CAAAAATTCACTAAAT
*
34819793 CACAAAATTCACTAATT
1 CA-AAAATTCACTAAAT
*
34819810 TAAAAATTC
1 CAAAAATTC
34819819 TTCTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (16 bp):
CAAAAATTCACTAAAT
Found at i:34827529 original size:26 final size:24
Alignment explanation
Indices: 34827496--34827549 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
34827486 TATATGAGCT
34827496 GTAT-TTGGATGAATTATAATTGAAAA
1 GTATGTTGGATGAA--ATAATT-AAAA
*
34827522 -TATGTTGGTTGAAATAATTAAAA
1 GTATGTTGGATGAAATAATTAAAA
34827545 GTATG
1 GTATG
34827550 AGTGAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.16
24 10 0.40
25 3 0.12
26 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (24 bp):
GTATGTTGGATGAAATAATTAAAA
Found at i:34828340 original size:41 final size:41
Alignment explanation
Indices: 34828283--34828397 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
34828273 TTTATTGTCA
* *
34828283 ATGAAATAATTCAGACTTTACGTCTAGCAGGCTTGATGCCG
1 ATGAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCG
*
34828324 ATGAAATTATTCAGACTATACGTCTAGCAGGCTTAATGCCG
1 ATGAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCG
* * * *
34828365 GTGATACAATTCAGACTATAAGTCTAGCAGGCT
1 ATGAAATAATTCAGACTATACGTCTAGCAGGCT
34828398 AAAAGCTGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
ATGAAATAATTCAGACTATACGTCTAGCAGGCTTAATGCCG
Found at i:34835252 original size:37 final size:37
Alignment explanation
Indices: 34835210--34835286 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
34835200 CCTTAGGGAT
34835210 TTTAGACCAAATTGTAAAAGAAACAAAAGAACTTTCC
1 TTTAGACCAAATTGTAAAAGAAACAAAAGAACTTTCC
*
34835247 TTTAGACCAAATTGTAAAAGAAACAAAAGAATTTTCC
1 TTTAGACCAAATTGTAAAAGAAACAAAAGAACTTTCC
34835284 TTT
1 TTT
34835287 CCTTTTTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (37 bp):
TTTAGACCAAATTGTAAAAGAAACAAAAGAACTTTCC
Found at i:34840536 original size:7 final size:7
Alignment explanation
Indices: 34840526--34840550 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34840516 ATAGTCAATA
34840526 ATAAATT
1 ATAAATT
34840533 ATAAATT
1 ATAAATT
34840540 ATAAATT
1 ATAAATT
34840547 ATAA
1 ATAA
34840551 TACCAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:34851099 original size:33 final size:33
Alignment explanation
Indices: 34851057--34851123 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
34851047 GTAATGGTAA
34851057 TGCCCATAGCAC-TCCTAAAAGGAAAACATAAGT
1 TGCCCATAGCACTTCC-AAAAGGAAAACATAAGT
34851090 TGCCCATAGCACTTCCAAAAGGAAAACATAAGT
1 TGCCCATAGCACTTCCAAAAGGAAAACATAAGT
34851123 T
1 T
34851124 TGAACCTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (33 bp):
TGCCCATAGCACTTCCAAAAGGAAAACATAAGT
Found at i:34853212 original size:15 final size:15
Alignment explanation
Indices: 34853189--34853221 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34853179 AATCGCTGAG
34853189 CCTCCTAGGATTTCA
1 CCTCCTAGGATTTCA
*
34853204 CCTCTTAGGATTTCA
1 CCTCCTAGGATTTCA
34853219 CCT
1 CCT
34853222 AAAAGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.12, T:0.36
Consensus pattern (15 bp):
CCTCCTAGGATTTCA
Found at i:34873060 original size:28 final size:28
Alignment explanation
Indices: 34873007--34873087 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
34872997 TTTTTGGGCT
***
34873007 AATTTACCAAAAAAAGCCATTTTTTTCAA
1 AATTTACCAAAATGGGCCA-TTTTTTCAA
* *
34873036 AATTTACCAAAATGGGCCGATTTTTTTAT
1 AATTTACCAAAATGGGCC-ATTTTTTCAA
* *
34873065 TATTTACCGAAATGGGCCATTTT
1 AATTTACCAAAATGGGCCATTTT
34873088 CCAGAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.11
29 38 0.86
30 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (28 bp):
AATTTACCAAAATGGGCCATTTTTTCAA
Found at i:34876667 original size:56 final size:56
Alignment explanation
Indices: 34876605--34876729 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
34876595 TATGTAAAAC
* * *
34876605 TATGTAAAATTATTAAG-CCTAAAAACTTTTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAA-ATGTGTTAATGGTTAGTAAAATTATCAAAT
*
34876661 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAAATTATCAAAT
*
34876717 TAGGTAAAATTAT
1 TATGTAAAATTAT
34876730 GTTAGGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 56 0.89
57 7 0.11
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCCAAAAAATGTGTTAATGGTTAGTAAAATTATCAAAT
Found at i:34876756 original size:23 final size:23
Alignment explanation
Indices: 34876723--34876785 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
34876713 AAATTAGGTA
34876723 AAATTATGTTAGGGTTTTTACA-T
1 AAATTATGTTAGGGTTTTTA-ATT
*
34876746 AAATTAGGTTAGGGTTTTTAATT
1 AAATTATGTTAGGGTTTTTAATT
*
34876769 AAAATATGTTAGGGTTT
1 AAATTATGTTAGGGTTT
34876786 AGGGTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (23 bp):
AAATTATGTTAGGGTTTTTAATT
Found at i:34876802 original size:29 final size:29
Alignment explanation
Indices: 34876752--34877384 Score: 708
Period size: 29 Copynumber: 21.1 Consensus size: 29
34876742 ACATAAATTA
* *
34876752 GGTTAGGGTTTTTAATTAAAATATGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34876781 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
34876811 AGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
* * *
34876845 GGTTAGGGTTTTCAATTAAAATAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
34876874 GGTTAGAGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAG-G-GTTT--TT-AATTAAATTAGGTTAG
*
34876908 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34876937 GGTTAGGGTTTTAAATTAAATTAAATTAGGTTAG
1 GGTTAGGG-TTT---TT-AATTAAATTAGGTTAG
34876971 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * **
34877000 AGTTAGGGTTTTTAAATAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
34877028 GGTTA-GGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34877056 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
34877085 GGTTAGGGTTTTTAATTAAATTAGGCTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
34877114 GGTTACGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
34877143 GGTTAGGGTTTTTAATTAAATTAAATTAGGCTAAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGG-TTAG
*
34877178 GGTTAGGGTTTTTAATTAAATTAAATTAGGCTAG
1 GGTTAGGG--TTT--TT-AATTAAATTAGGTTAG
34877212 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* **
34877241 GGTTAGGGTTTTTAAATAAATTAAATT-G
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* **
34877269 GGTTAGGATTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34877297 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34877326 GGTTTAGGG-TTTT--TT--ATTACGGTTAGG
1 GG-TTAGGGTTTTTAATTAAATTA-GGTTA-G
*
34877353 GGTTAGGGTTTTTAAATAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
34877382 GGT
1 GGT
34877385 ATCAAATAAT
Statistics
Matches: 527, Mismatches: 43, Indels: 68
0.83 0.07 0.11
Matches are distributed among these distances:
25 4 0.01
26 11 0.02
27 27 0.05
28 60 0.11
29 224 0.43
30 48 0.09
31 13 0.02
32 9 0.02
33 11 0.02
34 87 0.17
35 33 0.06
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:34876879 original size:63 final size:63
Alignment explanation
Indices: 34876765--34877375 Score: 705
Period size: 63 Copynumber: 10.1 Consensus size: 63
34876755 TAGGGTTTTT
* * *
34876765 AATTAAAATATGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTA
1 AATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* * * *
34876829 AATTAAATTAGGTTAGGGTTAGGGTTTTCAATTAAAATAAGTTAGGGTTAGAGTTTTTAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* *
34876892 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTAAATTA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* *
34876955 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAAATA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
34877018 AATT-AA--A--TTA-GGTTA-GGTTTTTAATTAAAATAGGTTAGGGTTAGGG--TTT--TT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* *
34877069 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTACGGTTTTTAATT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
34877131 -A--AAA-TAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGCTAAGGGTTAGGGTTTTTA
1 AATTAAATTAGGTTAGGGTTAGGG--TTT--TT-AATTAAATTAGG-TTAGGGTTAGGGTTTTTA
34877192 ATTA
60 ATTA
* *
34877196 AATTAAATTAGGCTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* **
34877259 AATT-AA--A--TT-GGGTTAGGATTTTTAATTAAATTAAATTA-GGTTAGGG--TTT--TT-
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
*
34877310 AATTAAATTAGGTTAGGGTTTAGGG-TTTT--TT--ATTACGGTTAGGGGTTAGGGTTTTTAAAT
1 AATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTA-GGTTA-GGGTTAGGGTTTTTAATT
34877370 A
63 A
34877371 AATTA
1 AATTA
34877376 GGTTAGGGTA
Statistics
Matches: 474, Mismatches: 36, Indels: 77
0.81 0.06 0.13
Matches are distributed among these distances:
51 8 0.02
52 6 0.01
53 4 0.01
54 11 0.02
55 2 0.00
56 50 0.11
57 43 0.09
58 56 0.12
59 3 0.01
60 9 0.02
61 6 0.01
62 8 0.02
63 198 0.42
64 46 0.10
65 2 0.00
66 1 0.00
67 3 0.01
68 3 0.01
69 15 0.03
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (63 bp):
AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
Found at i:34877242 original size:23 final size:26
Alignment explanation
Indices: 34877209--34877384 Score: 112
Period size: 28 Copynumber: 6.5 Consensus size: 26
34877199 TAAATTAGGC
34877209 TAGGGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATTAAA--A-GT
* *
34877238 TAGGGTTAGGGTTTTTAAATAAATTAAAT
1 TAGGGTTAGGGTTTTT-AATTAA--AAGT
* *
34877267 T-GGGTTAGGATTTTTAATTAAATTAAAT
1 TAGGGTTAGGGTTTTTAATT-AA--AAGT
34877295 TA-GGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATTAAA--A-GT
* **
34877323 TAGGGTTTAGGGTTTTTTATT-ACGGT
1 TAGGG-TTAGGGTTTTTAATTAAAAGT
*
34877349 TAGGGGTTAGGGTTTTTAAAT-AAA-T
1 TA-GGGTTAGGGTTTTTAATTAAAAGT
34877374 TA-GGTTAGGGT
1 TAGGGTTAGGGT
34877385 ATCAAATAAT
Statistics
Matches: 123, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
23 9 0.07
25 4 0.03
26 18 0.15
27 9 0.07
28 41 0.33
29 21 0.17
30 20 0.16
32 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (26 bp):
TAGGGTTAGGGTTTTTAATTAAAAGT
Found at i:34877351 original size:26 final size:25
Alignment explanation
Indices: 34877316--34877365 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
34877306 TTTTAATTAA
*
34877316 ATTAGGTTAGGGTTTAGGGTTTTTT
1 ATTAGGTTAGGGGTTAGGGTTTTTT
34877341 ATTACGGTTAGGGGTTAGGGTTTTT
1 ATTA-GGTTAGGGGTTAGGGTTTTT
34877366 AAATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (25 bp):
ATTAGGTTAGGGGTTAGGGTTTTTT
Found at i:34879548 original size:14 final size:15
Alignment explanation
Indices: 34879531--34879563 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34879521 TAATAATTAT
34879531 ATAAAAATA-CATAA
1 ATAAAAATATCATAA
*
34879545 ATAAAAATATCTTAA
1 ATAAAAATATCATAA
34879560 ATAA
1 ATAA
34879564 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAATATCATAA
Found at i:34879682 original size:10 final size:10
Alignment explanation
Indices: 34879669--34879718 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
34879659 ATATTAAAAA
34879669 ATTTAAAATT
1 ATTTAAAATT
**
34879679 ATTTTAAAAAA
1 A-TTTAAAATT
*
34879690 ATATAAAATT
1 ATTTAAAATT
34879700 ATTTAAAATT
1 ATTTAAAATT
34879710 ATCTTAAAA
1 AT-TTAAAA
34879719 AATGAAATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 18 0.56
11 14 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:34879691 original size:31 final size:31
Alignment explanation
Indices: 34879656--34879720 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
34879646 GCCATTGTTG
*
34879656 AAAATATTAAAA-AATTTAAAATTATTTTAAA
1 AAAATA-TAAAATAATTTAAAATTATCTTAAA
*
34879687 AAAATATAAAATTATTTAAAATTATCTTAAA
1 AAAATATAAAATAATTTAAAATTATCTTAAA
34879718 AAA
1 AAA
34879721 TGAAATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATATAAAATAATTTAAAATTATCTTAAA
Found at i:34879718 original size:21 final size:21
Alignment explanation
Indices: 34879664--34879707 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
34879654 TGAAAATATT
34879664 AAAAAATTTAAAATTATTTTA
1 AAAAAATTTAAAATTATTTTA
*
34879685 AAAAAATATAAAATTA-TTTA
1 AAAAAATTTAAAATTATTTTA
34879705 AAA
1 AAA
34879708 TTATCTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATTTAAAATTATTTTA
Found at i:34879742 original size:17 final size:18
Alignment explanation
Indices: 34879716--34879749 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34879706 AATTATCTTA
34879716 AAAAATGAAATTGAATAG
1 AAAAATGAAATTGAATAG
*
34879734 AAAAA-GAAATTTAATA
1 AAAAATGAAATTGAATA
34879750 TGGATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAATGAAATTGAATAG
Found at i:34883717 original size:26 final size:25
Alignment explanation
Indices: 34883688--34883786 Score: 65
Period size: 26 Copynumber: 3.6 Consensus size: 25
34883678 ATCTTTTTGA
*
34883688 TTTTTTATTTGTTTGTCCTTTTTCC
1 TTTTTTATTTGTTTGTCCTTTTTCT
* *
34883713 TTTTTTATTT-TTTTTCTTTATTTCATTTTTTT
1 TTTTTTATTTGTTTGTC-------C-TTTTTCT
34883745 CTTTTTTTATTTGTTTGTCCTTTTTCT
1 -TTTT-TTATTTGTTTGTCCTTTTTCT
34883772 TATTTTTATTTGTTT
1 T-TTTTTATTTGTTT
34883787 TTCTTTATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 23
0.67 0.06 0.27
Matches are distributed among these distances:
24 5 0.09
25 10 0.18
26 11 0.19
27 9 0.16
28 1 0.02
31 1 0.02
32 5 0.09
33 4 0.07
34 6 0.11
35 5 0.09
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (25 bp):
TTTTTTATTTGTTTGTCCTTTTTCT
Found at i:34883726 original size:17 final size:17
Alignment explanation
Indices: 34883706--34883769 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
34883696 TTGTTTGTCC
34883706 TTTTTCCTTTTTTATTT
1 TTTTTCCTTTTTTATTT
34883723 TTTTT-CTTTATTTCA-TT
1 TTTTTCCTTT-TTT-ATTT
*
34883740 TTTTTCTTTTTTTATTT
1 TTTTTCCTTTTTTATTT
*
34883757 GTTTGTCCTTTTT
1 -TTTTTCCTTTTT
34883770 CTTATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 5 0.13
17 20 0.51
18 14 0.36
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTCCTTTTTTATTT
Found at i:34883736 original size:25 final size:23
Alignment explanation
Indices: 34883679--34883848 Score: 71
Period size: 25 Copynumber: 7.0 Consensus size: 23
34883669 CCTATTGTCA
**
34883679 TCTTTTTGATTTTTTATTTGTTTGT
1 TCTTTTTTCTTTTTTATTT-TTT-T
* *
34883704 CCTTTTTCCTTTTTTATTTTTTT
1 TCTTTTTTCTTTTTTATTTTTTT
34883727 TCTTTATTTCATTTTTT-TCTTTTTT
1 TCTTT-TTTC-TTTTTTAT-TTTTTT
* * * *
34883752 TATTTGTTTGTCCTTTTTCTTATTTT
1 T-CTT-TTT-TCTTTTTTATTTTTTT
* *
34883778 TATTTGTTT-TTCTTTATTTCATTTT
1 TCTTT-TTTCTTTTTTATTT--TTTT
*
34883803 TC--TCTT-TTTTTTATTTGTTTT
1 TCTTTTTTCTTTTTTATTT-TTTT
34883824 TCTTTATTTCATTTTTCTATTTTTT
1 TCTTT-TTTC-TTTTT-TATTTTTT
34883849 ATTTGTTTAT
Statistics
Matches: 111, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
21 6 0.05
22 11 0.10
23 13 0.12
24 11 0.10
25 38 0.34
26 23 0.21
27 9 0.08
ACGTcount: A:0.08, C:0.11, G:0.04, T:0.77
Consensus pattern (23 bp):
TCTTTTTTCTTTTTTATTTTTTT
Found at i:34883744 original size:34 final size:35
Alignment explanation
Indices: 34883706--34883856 Score: 157
Period size: 34 Copynumber: 4.6 Consensus size: 35
34883696 TTGTTTGTCC
*
34883706 TTTTTCCTTTTTTATTT-TTTTTCTTTATTTCATT
1 TTTTTCTTTTTTTATTTGTTTTTCTTTATTTCATT
*
34883740 TTTTTCTTTTTTTATTTGTTTGTC-------C---
1 TTTTTCTTTTTTTATTTGTTTTTCTTTATTTCATT
34883765 TTTTTCTTATTTTTATTTGTTTTTCTTTATTTCATT
1 TTTTTCTT-TTTTTATTTGTTTTTCTTTATTTCATT
*
34883801 TTTCTCTTTTTTTTATTTGTTTTTCTTTATTTCA--
1 TTTTTC-TTTTTTTATTTGTTTTTCTTTATTTCATT
34883835 TTTTTCTATTTTTTATTTGTTT
1 TTTTTCT-TTTTTTATTTGTTT
34883857 ATTATTTTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.08
26 15 0.15
28 1 0.01
33 2 0.02
34 35 0.36
35 5 0.05
36 30 0.31
37 2 0.02
ACGTcount: A:0.09, C:0.10, G:0.03, T:0.78
Consensus pattern (35 bp):
TTTTTCTTTTTTTATTTGTTTTTCTTTATTTCATT
Found at i:34883788 original size:36 final size:34
Alignment explanation
Indices: 34883765--34883863 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 34
34883755 TTGTTTGTCC
*
34883765 TTTTTCTTATTTTTATTTGTTTTTCTTTATTTCA
1 TTTTTCTTATTTTTATTTGTTTTTATTTATTTCA
* *
34883799 TTTTTCTCTTTTTTTTATTTGTTTTTCTTTATTTCA
1 -TTTT-TCTTATTTTTATTTGTTTTTATTTATTTCA
34883835 TTTTTC-TATTTTTTATTTGTTTATTATTT
1 TTTTTCTTA-TTTTTATTTGTTT-TTATTT
34883864 TTTATAATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
33 1 0.02
34 15 0.26
35 13 0.22
36 29 0.50
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (34 bp):
TTTTTCTTATTTTTATTTGTTTTTATTTATTTCA
Found at i:34883803 original size:26 final size:25
Alignment explanation
Indices: 34883739--34883847 Score: 87
Period size: 26 Copynumber: 4.2 Consensus size: 25
34883729 TTTATTTCAT
*
34883739 TTTTTTCTTTTTTTATTTGTTTGTC
1 TTTTTTCTTTTTTTATTTGTTTTTC
*
34883764 CTTTTTCTTATTTTTATTTGTTTTTC
1 TTTTTTCTT-TTTTTATTTGTTTTTC
* * *
34883790 TTTATTTCATTTTTCTCTTT-TTTTTA
1 TTT-TTTC-TTTTTTTATTTGTTTTTC
* * *
34883816 TTTGTT-TTTCTTTATTTCATTTTTC
1 TTTTTTCTTTTTTTATTT-GTTTTTC
34883841 TATTTTT
1 T-TTTTT
34883848 TATTTGTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
23 8 0.12
25 16 0.24
26 29 0.44
27 11 0.17
28 2 0.03
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTTTTCTTTTTTTATTTGTTTTTC
Found at i:34884084 original size:11 final size:10
Alignment explanation
Indices: 34884062--34884105 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
34884052 ATGGAGGACC
*
34884062 AAAAAATAAA
1 AAAAAATGAA
34884072 AAAAAACTGAA
1 AAAAAA-TGAA
34884083 AAAAAATGAGA
1 AAAAAATGA-A
34884094 AAAAAATTGAA
1 AAAAAA-TGAA
34884105 A
1 A
34884106 GTTGAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.30
11 18 0.60
12 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:34890264 original size:23 final size:21
Alignment explanation
Indices: 34890235--34890286 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
34890225 TTAAAAATAA
34890235 TTTTAAAAAATTATATTTAAAAT
1 TTTTAAAAAA--ATATTTAAAAT
*
34890258 TTTTAAAAAAGTATTTAAAAT
1 TTTTAAAAAAATATTTAAAAT
*
34890279 TCTTAAAA
1 TTTTAAAA
34890287 TATACATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAAAAAATATTTAAAAT
Found at i:34890298 original size:22 final size:22
Alignment explanation
Indices: 34890241--34890298 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
34890231 ATAATTTTAA
*
34890241 AAAAT-TATATTTAAAATTTTT
1 AAAATATATATTTAAAATTCTT
34890262 AAAA-A-AGTATTTAAAATTCTT
1 AAAATATA-TATTTAAAATTCTT
*
34890283 AAAATATACATTTAAA
1 AAAATATATATTTAAA
34890299 TGTTATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 21 0.68
22 8 0.26
23 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATATATATTTAAAATTCTT
Found at i:34890383 original size:23 final size:23
Alignment explanation
Indices: 34890356--34890421 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
34890346 ATATATTTTA
*
34890356 AATATTTTATAACATTAAAAAAT
1 AATATTTTAAAACATTAAAAAAT
* **
34890379 TATA-TTTAAAATTTTAAAAAAT
1 AATATTTTAAAACATTAAAAAAT
* *
34890401 AATATTATAAAACATTTAAAA
1 AATATTTTAAAACATTAAAAA
34890422 TATACATTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATTTTAAAACATTAAAAAAT
Found at i:34890395 original size:22 final size:22
Alignment explanation
Indices: 34890370--34890444 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
34890360 TTTTATAACA
34890370 TTAAAAAATTATATTTAAAATT
1 TTAAAAAATTATATTTAAAATT
* *
34890392 TTAAAAAATAATATTATAAAACAT
1 TTAAAAAATTATATT-TAAAA-TT
* *
34890416 TTAAAATA-TACATTTAAAATAT
1 TTAAAAAATTATATTTAAAAT-T
*
34890438 TTTAAAA
1 TTAAAAA
34890445 CAAATAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 25 0.60
23 9 0.21
24 8 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAAATTATATTTAAAATT
Found at i:34890415 original size:45 final size:46
Alignment explanation
Indices: 34890356--34890444 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
34890346 ATATATTTTA
* * *
34890356 AATATTTTATAACATTAAAAA-ATTATATTTAAAAT-TTTAAAAAAT
1 AATATTATAAAACATTAAAAATA-TACATTTAAAATATTTAAAAAAT
* *
34890401 AATATTATAAAACATTTAAAATATACATTTAAAATATTTTAAAA
1 AATATTATAAAACATTAAAAATATACATTTAAAATATTTAAAAA
34890445 CAAATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 29 0.78
46 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (46 bp):
AATATTATAAAACATTAAAAATATACATTTAAAATATTTAAAAAAT
Found at i:34890428 original size:13 final size:13
Alignment explanation
Indices: 34890412--34890437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34890402 ATATTATAAA
34890412 ACATTTAAAATAT
1 ACATTTAAAATAT
34890425 ACATTTAAAATAT
1 ACATTTAAAATAT
34890438 TTTAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:34890441 original size:23 final size:22
Alignment explanation
Indices: 34890374--34890444 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
34890364 ATAACATTAA
34890374 AAAAT-TATATTT-AAAATTTT
1 AAAATATATATTTAAAAATTTT
*
34890394 AAAAAATAATATTATAAAACA-TTT
1 AAAATAT-ATATT-TAAAA-ATTTT
*
34890418 AAAATATACATTTAAAATATTTT
1 AAAATATATATTTAAAA-ATTTT
34890441 AAAA
1 AAAA
34890445 CAAATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 11 0.27
23 12 0.29
24 12 0.29
25 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATATATTTAAAAATTTT
Found at i:34892349 original size:25 final size:24
Alignment explanation
Indices: 34892321--34892436 Score: 135
Period size: 25 Copynumber: 4.7 Consensus size: 24
34892311 TCCCAATAAA
* *
34892321 TGGCTCTCTTGAGCTTTCCGTTATT
1 TGGCTCTCATGAGCTTCCCGTTA-T
*
34892346 TGGCTCTCACGAGCTTCCCGTTAAT
1 TGGCTCTCATGAGCTTCCCGTT-AT
*
34892371 TGGCTCTCATGAGCTTCCCGATTAA
1 TGGCTCTCATGAGCTTCCCG-TTAT
*
34892396 TGGCTCTCCA-GAGCTTCCCGATAT
1 TGGCTCT-CATGAGCTTCCCGTTAT
*
34892420 TGGCTCGCATGAGCTTC
1 TGGCTCTCATGAGCTTC
34892437 TCGAATTTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
23 2 0.03
24 15 0.19
25 57 0.72
26 5 0.06
ACGTcount: A:0.15, C:0.29, G:0.22, T:0.34
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCCCGTTAT
Found at i:34894733 original size:26 final size:26
Alignment explanation
Indices: 34894704--34894757 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
34894694 TAAAAAGAAG
34894704 ATAGAGACATGAATATTGATTGTTAA
1 ATAGAGACATGAATATTGATTGTTAA
34894730 ATAGAGACATGAATATTGATTGTTAA
1 ATAGAGACATGAATATTGATTGTTAA
34894756 AT
1 AT
34894758 CAGAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (26 bp):
ATAGAGACATGAATATTGATTGTTAA
Found at i:34894948 original size:21 final size:22
Alignment explanation
Indices: 34894924--34894972 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
34894914 CCCATTGCTT
*
34894924 GTGGCTATACAA-TTGTTTCCA
1 GTGGCTATACAATTTATTTCCA
* *
34894945 GTGGCTATATAATTTATTTGCA
1 GTGGCTATACAATTTATTTCCA
34894967 GTGGCT
1 GTGGCT
34894973 CCATCTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (22 bp):
GTGGCTATACAATTTATTTCCA
Found at i:34900044 original size:26 final size:27
Alignment explanation
Indices: 34900004--34900085 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
34899994 TAAGAACATT
*
34900004 TTATGAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* *
34900031 TT-TTAAATTGTATTTAATCATATATT-
1 TTATTAAATTATATTTAATAATA-ATTA
* *
34900057 TTAATTAAAATATATTTAATATTAATTA
1 TT-ATTAAATTATATTTAATAATAATTA
34900085 T
1 T
34900086 AGTATCATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:34900167 original size:18 final size:17
Alignment explanation
Indices: 34900139--34900173 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34900129 ATTATTAAGA
*
34900139 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34900156 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34900174 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34900262 original size:120 final size:119
Alignment explanation
Indices: 34900088--34900310 Score: 401
Period size: 120 Copynumber: 1.9 Consensus size: 119
34900078 TTAATTATAG
34900088 TATCATATATTATGATTTGAATAAATTATATAAGAATATGAATTATTAAGAATTTTATTAAATTA
1 TATCATATATTATGATTTGAATAAATTATATAAGAATATGAATTATTAAGAATTTTATTAAATTA
* *
34900153 TATATTTTAATTAAAATATATTTAATAATATTTATGTTAATTTATATTTTACAA
66 TATATTTTAATTAAAATATATTTAATAAAAATTATGTTAATTTATATTTTACAA
* *
34900207 TATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 TATCATATATTATGATTTGAATAAATT-ATATAAGAATATGAATTATTAAGAATTTTATTAAATT
34900272 ATATATTTTAATTAAAATATATTTAATAAAAATTATGTT
65 ATATATTTTAATTAAAATATATTTAATAAAAATTATGTT
34900311 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 26 0.26
120 73 0.74
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (119 bp):
TATCATATATTATGATTTGAATAAATTATATAAGAATATGAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAAAAATTATGTTAATTTATATTTTACAA
Found at i:34900287 original size:18 final size:17
Alignment explanation
Indices: 34900259--34900293 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34900249 ATTATTAAGA
*
34900259 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34900276 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34900294 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34900293 original size:16 final size:16
Alignment explanation
Indices: 34900259--34900313 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
34900249 ATTATTAAGA
34900259 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
34900276 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
34900292 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
34900306 ATGTTTAA
1 AT-TTTAA
34900314 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:34900447 original size:156 final size:157
Alignment explanation
Indices: 34900247--34900562 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 157
34900237 ATAAGAATAT
34900247 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
* *
34900312 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
34900377 TAATCATTTACCAAAACAAATTTATGC
131 TAATCATTTACCAAAACAAATTTATAC
* *
34900404 TAATTA-TAAGAATTTTATTAAATTGTATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
34900468 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
34900533 TAATCATTTACCAAAACAATTTTATAC
131 TAATCATTTACCAAAACAAATTTATAC
34900560 TAA
1 TAA
34900563 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 147 0.96
157 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATCATTTACCAAAACAAATTTATAC
Found at i:34900679 original size:44 final size:45
Alignment explanation
Indices: 34900614--34900704 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
34900604 ACCTCTATTC
* * *
34900614 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
34900658 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
34900703 CA
1 CA
34900705 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:34900706 original size:16 final size:16
Alignment explanation
Indices: 34900685--34900720 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
34900675 GATTAGCTAT
34900685 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34900701 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
34900717 TACA
1 TACA
34900721 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:34904149 original size:39 final size:39
Alignment explanation
Indices: 34904106--34904180 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
34904096 TCACTCTTCC
34904106 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
34904145 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
34904181 ACTTGTCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (39 bp):
CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
Found at i:34904205 original size:51 final size:51
Alignment explanation
Indices: 34904142--34904292 Score: 257
Period size: 51 Copynumber: 3.0 Consensus size: 51
34904132 ACCACTTATC
*
34904142 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
* *
34904193 TCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
* *
34904244 TCACTGATCAGATAAGTGCAGCTGAAGCTACTACTTATCACTTGTCACT
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACT
34904293 GATCAGAAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (51 bp):
TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
Found at i:34908313 original size:13 final size:13
Alignment explanation
Indices: 34908282--34908322 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
34908272 CGGCCCATAT
*
34908282 TAATTTTTTTAGA
1 TAATTTTTTTAAA
* *
34908295 TTATTTTATTAAA
1 TAATTTTTTTAAA
34908308 TAATTTTTTTAAA
1 TAATTTTTTTAAA
34908321 TA
1 TA
34908323 TAATAAATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TAATTTTTTTAAA
Found at i:34908487 original size:12 final size:12
Alignment explanation
Indices: 34908470--34908496 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34908460 AGTTAGAACT
34908470 AAATTAATAATA
1 AAATTAATAATA
34908482 AAATTAATAATA
1 AAATTAATAATA
34908494 AAA
1 AAA
34908497 CAAAAGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAATAATA
Found at i:34908586 original size:11 final size:11
Alignment explanation
Indices: 34908562--34908634 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
34908552 AATAACTGCG
34908562 AAACAACA-ATA
1 AAACAACACA-A
*
34908573 AAACACCACAA
1 AAACAACACAA
* *
34908584 AAAGCAGCACCA
1 AAA-CAACACAA
34908596 AAACAACATC-A
1 AAACAACA-CAA
*
34908607 AAACAACATAAA
1 AAACAACA-CAA
*
34908619 AAACAGCACAA
1 AAACAACACAA
34908630 AAACA
1 AAACA
34908635 GTATCACCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 32 0.63
12 19 0.37
ACGTcount: A:0.66, C:0.26, G:0.04, T:0.04
Consensus pattern (11 bp):
AAACAACACAA
Found at i:34908600 original size:34 final size:34
Alignment explanation
Indices: 34908562--34908634 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
34908552 AATAACTGCG
* * *
34908562 AAACAACAAT-AAAACACCACAAAAAGCAGCACCA
1 AAACAAC-ATCAAAACAACACAAAAAACAGCACAA
*
34908596 AAACAACATCAAAACAACATAAAAAACAGCACAA
1 AAACAACATCAAAACAACACAAAAAACAGCACAA
34908630 AAACA
1 AAACA
34908635 GTATCACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.66, C:0.26, G:0.04, T:0.04
Consensus pattern (34 bp):
AAACAACATCAAAACAACACAAAAAACAGCACAA
Found at i:34914104 original size:16 final size:17
Alignment explanation
Indices: 34914085--34914119 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34914075 CAATTAAATA
34914085 AATTG-GAAATAAATTC
1 AATTGAGAAATAAATTC
34914101 AATTGAGAAATAAATTC
1 AATTGAGAAATAAATTC
34914118 AA
1 AA
34914120 ATTTTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
AATTGAGAAATAAATTC
Found at i:34916065 original size:22 final size:22
Alignment explanation
Indices: 34916017--34916065 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
34916007 GCAAAAATCG
* *
34916017 ATCAATCATGTATACTTACTAT
1 ATCAATCATGCATACTTACCAT
34916039 ATCAATCATGCATACTTACCAT
1 ATCAATCATGCATACTTACCAT
*
34916061 TTCAA
1 ATCAA
34916066 CCCCCCACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (22 bp):
ATCAATCATGCATACTTACCAT
Found at i:34934343 original size:17 final size:17
Alignment explanation
Indices: 34934323--34934357 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34934313 AATGGCATAG
34934323 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
34934340 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
34934357 A
1 A
34934358 TACATAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:34934789 original size:22 final size:22
Alignment explanation
Indices: 34934720--34934792 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
34934710 TATTTGTTTT
* *
34934720 TAAAATATATATATGTATAGAT-
1 TAAAA-ATAAATATGTATATATA
** *
34934742 TAAAAAT-AATAAATACAT-TA
1 TAAAAATAAATATGTATATATA
34934762 TCAAAAATAAATATGTATATATA
1 T-AAAAATAAATATGTATATATA
34934785 TAAAAATA
1 TAAAAATA
34934793 TTAGTTTGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 7 0.18
21 8 0.21
22 20 0.51
23 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (22 bp):
TAAAAATAAATATGTATATATA
Found at i:34937398 original size:7 final size:7
Alignment explanation
Indices: 34937386--34937410 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34937376 TAGTCGATTG
34937386 GTATTTA
1 GTATTTA
34937393 GTATTTA
1 GTATTTA
34937400 GTATTTA
1 GTATTTA
34937407 GTAT
1 GTAT
34937411 CATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:34938089 original size:18 final size:18
Alignment explanation
Indices: 34938062--34938101 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
34938052 CAGGTGCGTT
*
34938062 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
34938080 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
34938098 TCCT
1 TCCT
34938102 TTTTCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:34938558 original size:25 final size:25
Alignment explanation
Indices: 34938530--34938647 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
34938520 TATTTTGATA
34938530 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
34938555 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* * ** *
34938580 TT-TTT--T-TAGTTATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
34938599 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
34938625 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
34938648 TATTTTGAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 9 0.12
22 1 0.01
23 1 0.01
24 9 0.12
25 50 0.67
26 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:34938603 original size:70 final size:71
Alignment explanation
Indices: 34938520--34938653 Score: 261
Period size: 70 Copynumber: 1.9 Consensus size: 71
34938510 ATATTTTGAA
34938520 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAA-ATTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTTT
34938584 TTTAGT
66 TTTAGT
34938590 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTT
34938654 GAATATTTTG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
70 58 0.92
71 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.48
Consensus pattern (71 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTTT
TTTAGT
Done.