Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 287 of 325
Found at i:88534995 original size:18 final size:16
Alignment explanation
Indices: 88534962--88535001 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
88534952 AAAATTTCTT
88534962 TTAAAAATATAAAACA
1 TTAAAAATATAAAACA
88534978 TTAAAAATACTAAAAACA
1 TTAAAAATA-T-AAAACA
88534996 TTAAAA
1 TTAAAA
88535002 TAAATATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 12 0.55
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (16 bp):
TTAAAAATATAAAACA
Found at i:88535216 original size:13 final size:12
Alignment explanation
Indices: 88535198--88535226 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
88535188 AAAGAACAAT
88535198 AAAAAAAATAGC
1 AAAAAAAATAGC
88535210 AAAAAAAATAGC
1 AAAAAAAATAGC
88535222 AAAAA
1 AAAAA
88535227 GAAAACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAATAGC
Found at i:88536642 original size:52 final size:53
Alignment explanation
Indices: 88536580--88536694 Score: 169
Period size: 54 Copynumber: 2.2 Consensus size: 53
88536570 AAATGGTAAC
* * *
88536580 AATTTATTTTAAATTTTGAATATTATTT-AGTTTTTTCCATTTATGTATTTTT
1 AATTAATTTTAAATTTTGAATATTATTTAAATTTTTTCCATTTATGTAATTTT
* *
88536632 AATTAATTTTAATTTTTGAATATTATTTAAAATTTTTTTCATTTATGTAATTTT
1 AATTAATTTTAAATTTTGAATATTATTT-AAATTTTTTCCATTTATGTAATTTT
88536686 AATTAATTT
1 AATTAATTT
88536695 GTATTTTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 26 0.46
54 30 0.54
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (53 bp):
AATTAATTTTAAATTTTGAATATTATTTAAATTTTTTCCATTTATGTAATTTT
Found at i:88536661 original size:18 final size:17
Alignment explanation
Indices: 88536580--88536661 Score: 51
Period size: 18 Copynumber: 4.6 Consensus size: 17
88536570 AAATGGTAAC
*
88536580 AATTTATTTTAAATTTTG
1 AATTTA-TTTAATTTTTG
* *
88536598 AATATTATTTAGTTTTTTC
1 AAT-TTATTTA-ATTTTTG
* *
88536617 CATTTATGT-ATTTTT-
1 AATTTATTTAATTTTTG
*
88536632 AATTAATTTTAATTTTTG
1 AATTTA-TTTAATTTTTG
88536650 AATATTATTTAA
1 AAT-TTATTTAA
88536662 AATTTTTTTC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
15 4 0.08
16 7 0.15
17 6 0.12
18 20 0.42
19 11 0.23
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATTTTTG
Found at i:88538076 original size:31 final size:31
Alignment explanation
Indices: 88538012--88538077 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
88538002 CATCCAAGAG
* *
88538012 TTAGCGTGCACCCCGGATTACATACAATGGT
1 TTAGCGTGCACCCCGAATTACATACAATAGT
* * * *
88538043 TTAGCGTGCACCCTGAATTATATGCCATAGT
1 TTAGCGTGCACCCCGAATTACATACAATAGT
88538074 TTAG
1 TTAG
88538078 GATCTATAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (31 bp):
TTAGCGTGCACCCCGAATTACATACAATAGT
Found at i:88538299 original size:18 final size:18
Alignment explanation
Indices: 88538276--88538312 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
88538266 TGCCAGGTGC
*
88538276 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
88538294 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
88538312 T
1 T
88538313 TTCTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:88541609 original size:126 final size:126
Alignment explanation
Indices: 88541376--88541879 Score: 683
Period size: 126 Copynumber: 4.0 Consensus size: 126
88541366 GGCCAATCAT
* * * * *
88541376 GAACTATTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTACTAACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTGCATC
* *
88541441 CTGCTTGAAGCATTTTTGACACTATTTGTTCA-AAAATATCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACT-TCTTCTCAAAATTATTTTTTCAG
* *
88541502 GAACTATTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTACATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTGCATC
* * *
88541567 CTGCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACTTCTTCTCAAAATTATTTTTCCAT
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACTTCTTCTCAAAATTATTTTTTCAG
* * * *
88541628 GAACTACTGTAGAAAAAGAGCGTCCACATGGTAGCTTTTTTCCGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTGCATC
*
88541693 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTA--TTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACTTCTTCTCAAAATTATTTTTTCAG
* * * * * * * *
88541752 AAACTACTGTAGATAAAAAGAGCATCCACGTGAGAGCTTTTTTCTGTATTTTTGCTGACAGTGTA
1 GAACTACTGTAG--AAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTGCA
* * * * *
88541817 TCCTGTTTGAAGCGATTTTGACACTAGTTGTTCAGAAACATCTTCTCAAAA-TAATTTTTCAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACTTCTTCTCAAAATTATTTTTTCAG
88541879 G
1 G
88541880 GTAAAAGTAG
Statistics
Matches: 340, Mismatches: 33, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
124 16 0.05
125 2 0.01
126 311 0.91
127 11 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTACTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACTTCTTCTCAAAATTATTTTTTCAG
Found at i:88542008 original size:30 final size:30
Alignment explanation
Indices: 88541969--88542062 Score: 109
Period size: 30 Copynumber: 3.0 Consensus size: 30
88541959 ATTTAACCCT
*
88541969 AAACTCTAATTTAATTTATTTAAAACCTTA
1 AAACCCTAATTTAATTTATTTAAAACCTTA
*
88541999 AAACCCTAATTTATTTAATTTATTTAAAAACCAT-
1 AAACCCT-A---ATTTAATTTATTT-AAAACCTTA
*
88542033 AAACCCCAATTTAATTTATTTAAAACCTTA
1 AAACCCTAATTTAATTTATTTAAAACCTTA
88542063 TTTAATTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
29 7 0.13
30 19 0.35
31 1 0.02
33 1 0.02
34 19 0.35
35 7 0.13
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (30 bp):
AAACCCTAATTTAATTTATTTAAAACCTTA
Found at i:88542015 original size:34 final size:30
Alignment explanation
Indices: 88541976--88542062 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 30
88541966 CCTAAACTCT
88541976 AATTTAATTTATTTAAAACCTTAAAACCCTA
1 AATTTAATTTATTTAAAACCTTAAAACCC-A
* *
88542007 ATTTATTTAATTTATTTAAAAACCAT-AAACCCC
1 A---ATTTAATTTATTT-AAAACCTTAAAACCCA
88542040 AATTTAATTTATTTAAAACCTTA
1 AATTTAATTTATTTAAAACCTTA
88542063 TTTAATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
29 7 0.15
30 13 0.27
31 1 0.02
33 1 0.02
34 19 0.40
35 7 0.15
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTTAATTTATTTAAAACCTTAAAACCCA
Found at i:88542047 original size:64 final size:63
Alignment explanation
Indices: 88541934--88542062 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 63
88541924 TAAAAAAACT
* * *
88541934 AAACCCTAATTTAATTTAATTTAACATTTAACCCTAAACTCTAATTTAATTTATTTAAAACCTTA
1 AAACCCTAATTTAATTTAATTT-A-ATTTAACCATAAACCCCAATTTAATTTATTTAAAACCTTA
88541999 AAACCCTAATTT-ATTTAATTT-ATTTAAAAACCATAAACCCCAATTTAATTTATTTAAAACCTT
1 AAACCCTAATTTAATTTAATTTAATTT---AACCATAAACCCCAATTTAATTTATTTAAAACCTT
88542062 A
63 A
88542063 TTTAATTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
61 4 0.07
64 42 0.72
65 12 0.21
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (63 bp):
AAACCCTAATTTAATTTAATTTAATTTAACCATAAACCCCAATTTAATTTATTTAAAACCTTA
Found at i:88542056 original size:21 final size:21
Alignment explanation
Indices: 88542032--88542081 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
88542022 TTAAAAACCA
*
88542032 TAAACCCCAATTTAATTTATT
1 TAAAACCCAATTTAATTTATT
**
88542053 TAAAACCTTATTTAATTTATT
1 TAAAACCCAATTTAATTTATT
88542074 TAAAACCC
1 TAAAACCC
88542082 TAAACCCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAACCCAATTTAATTTATT
Found at i:88542079 original size:85 final size:88
Alignment explanation
Indices: 88541969--88542210 Score: 334
Period size: 85 Copynumber: 2.8 Consensus size: 88
88541959 ATTTAACCCT
*
88541969 AAACTCTAATTTAATTTATTTAAAACCTTAAAACCCTAATTTAT-TTAATTTATTTAAAAACCAT
1 AAACCCTAATTTAATTTATTTAAAACCTTAAAACCCTAATTT-TCTTAATTTATTTAAAAACCAT
* *
88542033 AAAC-CCCAA-TTTAATTTATTTA
65 AAACTCCAAACTCTAATTTATTTA
* *
88542055 AAA-CCTTATTTAATTTATTTAAAACCCT-AAACCCTAATTTTCTTAATTTATTTAAAAACCAT-
1 AAACCCTAATTTAATTTATTTAAAACCTTAAAACCCTAATTTTCTTAATTTATTTAAAAACCATA
*
88542117 AACTCTAAACTCTAATTTATTTA
66 AACTCCAAACTCTAATTTATTTA
* * * *
88542140 AAACCCTAACTTAATTTCTTTAAAACCCTAAAAACTCTAATTTTCTTAATTTATTTAAAAACCAT
1 AAACCCTAATTTAATTTATTTAAAA-CCTTAAAACCCTAATTTTCTTAATTTATTTAAAAACCAT
88542205 AAACTC
65 AAACTC
88542211 TAATTTGAAT
Statistics
Matches: 137, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
83 4 0.03
84 35 0.26
85 37 0.27
86 21 0.15
87 2 0.01
88 33 0.24
89 5 0.04
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (88 bp):
AAACCCTAATTTAATTTATTTAAAACCTTAAAACCCTAATTTTCTTAATTTATTTAAAAACCATA
AACTCCAAACTCTAATTTATTTA
Found at i:88542106 original size:33 final size:32
Alignment explanation
Indices: 88542064--88542148 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 32
88542054 AAAACCTTAT
**
88542064 TTAATTTATTTAAAACCCTAAACCCTAATTTTC
1 TTAATTTATTTAAAACCCTAAACCCTAA-ACTC
* *
88542097 TTAATTTATTTAAAAACC-ATAACTCTAAACTC
1 TTAATTTATTTAAAACCCTA-AACCCTAAACTC
88542129 -TAATTTATTTAAAACCCTAA
1 TTAATTTATTTAAAACCCTAA
88542149 CTTAATTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 17 0.38
32 4 0.09
33 24 0.53
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.40
Consensus pattern (32 bp):
TTAATTTATTTAAAACCCTAAACCCTAAACTC
Found at i:88542154 original size:22 final size:23
Alignment explanation
Indices: 88542124--88542170 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
88542114 CATAACTCTA
88542124 AACTCTAATTTATTTAAAACCCT
1 AACTCTAATTTATTTAAAACCCT
*
88542147 AACT-TAATTTCTTTAAAACCCT
1 AACTCTAATTTATTTAAAACCCT
88542169 AA
1 AA
88542171 AAACTCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (23 bp):
AACTCTAATTTATTTAAAACCCT
Found at i:88542214 original size:34 final size:35
Alignment explanation
Indices: 88542149--88542216 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
88542139 AAAACCCTAA
* *
88542149 CTTAATTTCTTTAAAACCCTAAAAACTCTAATTTT
1 CTTAATTTATTTAAAAACCTAAAAACTCTAATTTT
*
88542184 CTTAATTTATTTAAAAACC-ATAAACTCTAATTT
1 CTTAATTTATTTAAAAACCTAAAAACTCTAATTT
88542217 GAATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.43
Consensus pattern (35 bp):
CTTAATTTATTTAAAAACCTAAAAACTCTAATTTT
Found at i:88542224 original size:34 final size:34
Alignment explanation
Indices: 88542151--88542233 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
88542141 AACCCTAACT
* ***
88542151 TAATTTCTTTAAAACCCTAAAAACTCTAATTTTCT
1 TAATTT-TTTAAAAACCTAAAAACTCTAATTTGAA
*
88542186 TAATTTATTTAAAAACC-ATAAACTCTAATTTGAA
1 TAATTT-TTTAAAAACCTAAAAACTCTAATTTGAA
88542220 TAATTTTTATAAAA
1 TAATTTTT-TAAAA
88542234 TAAAACTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.05
34 24 0.59
35 15 0.37
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.42
Consensus pattern (34 bp):
TAATTTTTTAAAAACCTAAAAACTCTAATTTGAA
Found at i:88542812 original size:16 final size:15
Alignment explanation
Indices: 88542784--88542822 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
88542774 GTATATTTTG
88542784 AATTTGTATTTTTAAT
1 AATTT-TATTTTTAAT
*
88542800 AATTTTATATTTTTAT
1 AATTTTAT-TTTTAAT
88542816 AATTTTA
1 AATTTTA
88542823 AAAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
AATTTTATTTTTAAT
Found at i:88542879 original size:13 final size:13
Alignment explanation
Indices: 88542861--88542887 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88542851 AAAATTTAGG
88542861 ATAGCATTATTTA
1 ATAGCATTATTTA
88542874 ATAGCATTATTTA
1 ATAGCATTATTTA
88542887 A
1 A
88542888 AAATAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATAGCATTATTTA
Found at i:88543899 original size:16 final size:16
Alignment explanation
Indices: 88543831--88543902 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
88543821 TAAAGAATGC
88543831 TTTATTTTTTTATGTAA
1 TTTA-TTTTTTATGTAA
* *
88543848 TTTATTTGTTATGT-G
1 TTTATTTTTTATGTAA
*
88543863 TGTT-TTAAGTTTAT-TAGA
1 T-TTATT--TTTTATGTA-A
88543881 TTTATTTTTTATGTAA
1 TTTATTTTTTATGTAA
88543897 TTTATT
1 TTTATT
88543903 AGGCATGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 15
0.67 0.10 0.24
Matches are distributed among these distances:
15 3 0.07
16 24 0.57
17 12 0.29
18 3 0.07
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (16 bp):
TTTATTTTTTATGTAA
Found at i:88546226 original size:6 final size:6
Alignment explanation
Indices: 88546191--88546225 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
88546181 GCCCAAGTTC
* *
88546191 GAGCCA GAGCCA GAGCCA AAGCCA GAGCCC GAGCC
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCC
88546226 CTAGCCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.37, G:0.31, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:88546816 original size:48 final size:48
Alignment explanation
Indices: 88546716--88546808 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
88546706 ATTAATTGCA
88546716 ACATTACAACATTAAAACTTAGAACAAACTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTAGAACAAACTTTGTAATATAAATTAAAT
* * * *
88546764 ACATTATAACATTAAAACTTGGAACGAACTTTTTAATATAAATTA
1 ACATTACAACATTAAAACTTAGAACAAACTTTGTAATATAAATTA
88546809 GGTACATTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (48 bp):
ACATTACAACATTAAAACTTAGAACAAACTTTGTAATATAAATTAAAT
Found at i:88550515 original size:11 final size:11
Alignment explanation
Indices: 88550501--88550526 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
88550491 TTTCTTTCTT
88550501 TCTTCTTCCTC
1 TCTTCTTCCTC
88550512 TCTTCTTCCTC
1 TCTTCTTCCTC
88550523 TCTT
1 TCTT
88550527 TTTTCTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (11 bp):
TCTTCTTCCTC
Found at i:88550631 original size:27 final size:27
Alignment explanation
Indices: 88550601--88550674 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
88550591 AAATGGTACT
*
88550601 AGTGTCGCCTATCAGATATGGGTCACC
1 AGTGTCGCCTATCAGATAGGGGTCACC
* *
88550628 AGTGCCGCCTATCAGATAGGGGTCACT
1 AGTGTCGCCTATCAGATAGGGGTCACC
* *
88550655 GGTGTCGCCTATCAAATAGG
1 AGTGTCGCCTATCAGATAGG
88550675 CACCATACCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (27 bp):
AGTGTCGCCTATCAGATAGGGGTCACC
Found at i:88555974 original size:91 final size:91
Alignment explanation
Indices: 88555819--88556001 Score: 321
Period size: 91 Copynumber: 2.0 Consensus size: 91
88555809 TTTGCTCCAT
* * *
88555819 AATTTTATTCGAACTTATATGAGTCTTTCTCCTATTGAAGCGGAGTTGGGATAAGGATTACCTAG
1 AATTTTATTCGAACTTATATGAGTCTTTCTCCTATTAAAGAGGAGTTGGGAGAAGGATTACCTAG
*
88555884 TACTGTGATAGATGACGATGAACCGA
66 TAATGTGATAGATGACGATGAACCGA
88555910 AATTTTATTCGAACTTATATGAGTCTTTCTCCTATTAAAGAGGAGTTGGGAGAAGGATTACCTAG
1 AATTTTATTCGAACTTATATGAGTCTTTCTCCTATTAAAGAGGAGTTGGGAGAAGGATTACCTAG
*
88555975 TAATGTGATAGATGACGATGAATCGA
66 TAATGTGATAGATGACGATGAACCGA
88556001 A
1 A
88556002 TATCGTAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (91 bp):
AATTTTATTCGAACTTATATGAGTCTTTCTCCTATTAAAGAGGAGTTGGGAGAAGGATTACCTAG
TAATGTGATAGATGACGATGAACCGA
Found at i:88557778 original size:17 final size:17
Alignment explanation
Indices: 88557758--88557790 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
88557748 ATTAAGAATG
88557758 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
88557775 TTATTAAATTATATTT
1 TTATTAAATTATATTT
88557791 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:88557867 original size:26 final size:25
Alignment explanation
Indices: 88557832--88557883 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
88557822 ATTTATTATT
*
88557832 TTTTAATAAAATATATTTAACAATAA
1 TTTTAATAAAATATA-ATAACAATAA
* *
88557858 TTTTATTAAAATTTAATAACAATAA
1 TTTTAATAAAATATAATAACAATAA
88557883 T
1 T
88557884 AATAATCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTAATAAAATATAATAACAATAA
Found at i:88558379 original size:48 final size:48
Alignment explanation
Indices: 88558314--88558406 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
88558304 CCAATGTACC
88558314 TAATTTATATTAAAAAGTTCGTTCCAAGTTTTAATGTTATAATGTATT
1 TAATTTATATTAAAAAGTTCGTTCCAAGTTTTAATGTTATAATGTATT
* * * *
88558362 TAATTTATATTACAAAGTTTGTTCTAAGTTTTAATGTTGTAATGT
1 TAATTTATATTAAAAAGTTCGTTCCAAGTTTTAATGTTATAATGT
88558407 TGCAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (48 bp):
TAATTTATATTAAAAAGTTCGTTCCAAGTTTTAATGTTATAATGTATT
Found at i:88561243 original size:16 final size:16
Alignment explanation
Indices: 88561224--88561295 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
88561214 TAACATGCCT
88561224 AATAAATTACATAAAA
1 AATAAATTACATAAAA
88561240 AATAAATCTA-ATAAACCTA
1 AATAAAT-TACATAAA---A
* * *
88561259 AA-ACA-CACATAACA
1 AATAAATTACATAAAA
88561273 AATAAATTACATAAAAA
1 AATAAATTACAT-AAAA
88561290 AATAAA
1 AATAAA
88561296 GCATTCTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 15
0.67 0.10 0.24
Matches are distributed among these distances:
14 3 0.07
15 2 0.05
16 17 0.40
17 15 0.36
18 2 0.05
19 3 0.07
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAATTACATAAAA
Found at i:88561711 original size:20 final size:21
Alignment explanation
Indices: 88561671--88561711 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
88561661 TTCCCGCTCT
**
88561671 TTTCTTCTTCTCTTCTTCAAA
1 TTTCTTCTTCTCTTCGACAAA
88561692 TTTCTTC-TCTCTTCGACAAA
1 TTTCTTCTTCTCTTCGACAAA
88561712 AAATGAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.17, C:0.29, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTCTTCTTCTCTTCGACAAA
Found at i:88562257 original size:13 final size:13
Alignment explanation
Indices: 88562239--88562265 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88562229 GTTTTTATTT
88562239 TTAAATAATGCTA
1 TTAAATAATGCTA
88562252 TTAAATAATGCTA
1 TTAAATAATGCTA
88562265 T
1 T
88562266 CCTAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTAAATAATGCTA
Found at i:88562342 original size:16 final size:16
Alignment explanation
Indices: 88562304--88562334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88562294 TATTATTTTT
88562304 TAAAATTATAAAAATA
1 TAAAATTATAAAAATA
*
88562320 TAAAATTATTAAAAT
1 TAAAATTATAAAAAT
88562335 TACAAATTCA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTATAAAAATA
Found at i:88562975 original size:35 final size:34
Alignment explanation
Indices: 88562911--88562978 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
88562901 AAAATTATTC
* *
88562911 AAATTAGAGTTTATGGTTTTTAAATAAATTAAGA
1 AAATTAGAGTTTATGGGTTTTAAAGAAATTAAGA
*
88562945 AAATTAGAGTTTTTAGGGTTTTAAAGAAATTAAG
1 AAATTAGAGTTTAT-GGGTTTTAAAGAAATTAAG
88562979 TTAGGGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.40
Consensus pattern (34 bp):
AAATTAGAGTTTATGGGTTTTAAAGAAATTAAGA
Found at i:88562983 original size:22 final size:23
Alignment explanation
Indices: 88562957--88563003 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
88562947 ATTAGAGTTT
88562957 TTAGGGTTTTAAAGAAATTA-AG
1 TTAGGGTTTTAAAGAAATTAGAG
*
88562979 TTAGGGTTTTAAATAAATTAGAG
1 TTAGGGTTTTAAAGAAATTAGAG
88563002 TT
1 TT
88563004 TAGAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (23 bp):
TTAGGGTTTTAAAGAAATTAGAG
Found at i:88563059 original size:33 final size:32
Alignment explanation
Indices: 88562968--88563064 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
88562958 TAGGGTTTTA
88562968 AAGAAATTA-AG-TTAGGGTTTTAAATAAATT
1 AAGAAATTAGAGTTTAGGGTTTTAAATAAATT
** *
88562998 -AGAGTTTAGAGTTTATGGTTTTTAAATAAATT
1 AAGAAATTAGAGTTTA-GGGTTTTAAATAAATT
*
88563030 AAGAAAATTAGGGTTTAGGGTTTTAAATAAATT
1 AAG-AAATTAGAGTTTAGGGTTTTAAATAAATT
88563063 AA
1 AA
88563065 ATAAGGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.11
30 2 0.04
31 3 0.05
32 15 0.27
33 19 0.35
34 10 0.18
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (32 bp):
AAGAAATTAGAGTTTAGGGTTTTAAATAAATT
Found at i:88563074 original size:21 final size:21
Alignment explanation
Indices: 88563048--88563087 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
88563038 TAGGGTTTAG
88563048 GGTTTTAAATAAATTAAATAA
1 GGTTTTAAATAAATTAAATAA
88563069 GGTTTTAAATAAATTAAAT
1 GGTTTTAAATAAATTAAAT
88563088 TGGGGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (21 bp):
GGTTTTAAATAAATTAAATAA
Found at i:88563096 original size:21 final size:21
Alignment explanation
Indices: 88563046--88563096 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
88563036 ATTAGGGTTT
88563046 AGGGTTTTAAATAAATTAAATA
1 AGGG-TTTAAATAAATTAAATA
* *
88563068 AGGTTTTAAATAAATTAAATT
1 AGGGTTTAAATAAATTAAATA
*
88563089 GGGGTTTA
1 AGGGTTTA
88563097 TGGTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (21 bp):
AGGGTTTAAATAAATTAAATA
Found at i:88563105 original size:30 final size:29
Alignment explanation
Indices: 88562979--88563209 Score: 147
Period size: 34 Copynumber: 7.6 Consensus size: 29
88562969 AGAAATTAAG
* * *
88562979 TTAGGGTTTTAAATAAATTAGAGTTTAGAGT
1 TTAGGTTTTTAAATAAATTA-A-ATTAGGGT
88563010 TTATGGTTTTTAAATAAATTAAGAAAATTAGGGT
1 TTA-GGTTTTTAAATAAATT----AAATTAGGGT
*
88563044 TTAGGGTTTTAAATAAATTAAA-TA----
1 TTAGGTTTTTAAATAAATTAAATTAGGGT
*
88563068 --AGG-TTTTAAATAAATTAAATTGGGGT
1 TTAGGTTTTTAAATAAATTAAATTAGGGT
88563094 TTATGGTTTTTAAATAAATTAAATAAATTAGGGTT
1 TTA-GGTTTTTAAATAAA-T---TAAATTAGGG-T
*
88563129 TTAAGG-TTTTAAATAAATTAAATTAGAGT
1 TT-AGGTTTTTAAATAAATTAAATTAGGGT
88563158 TTAGGGTTAAATGTTAAATTAAATTAAATTAGGGT
1 TTA-GGTT---T-TTAAA-TAAATTAAATTAGGGT
*
88563193 TTAGTTTTTTTAAATAA
1 TTAG-GTTTTTAAATAA
88563210 CATTGTGTTT
Statistics
Matches: 163, Mismatches: 9, Indels: 57
0.71 0.04 0.25
Matches are distributed among these distances:
21 16 0.10
22 4 0.02
28 4 0.02
29 10 0.06
30 24 0.15
31 9 0.06
32 16 0.10
33 17 0.10
34 35 0.21
35 26 0.16
36 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (29 bp):
TTAGGTTTTTAAATAAATTAAATTAGGGT
Found at i:88563136 original size:64 final size:63
Alignment explanation
Indices: 88563066--88563194 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 63
88563056 ATAAATTAAA
* * *
88563066 TAAGGTTTTAAATAAATTAAATTGGGGTTTATGGTTTTTAAA-TAAATTAAA-TAAATTAGGGTT
1 TAAGGTTTTAAATAAATTAAATTAGAGTTTA-GG--GTTAAATTAAATTAAATTAAATTAGGGTT
88563129 T
63 T
88563130 TAAGGTTTTAAATAAATTAAATTAGAGTTTAGGGTTAAATGTTAAATTAAATTAAATTAGGGTTT
1 TAAGGTTTTAAATAAATTAAATTAGAGTTTAGGGTTAAA--TTAAATTAAATTAAATTAGGGTTT
88563195 AGTTTTTTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
61 5 0.09
63 2 0.03
64 38 0.66
65 13 0.22
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (63 bp):
TAAGGTTTTAAATAAATTAAATTAGAGTTTAGGGTTAAATTAAATTAAATTAAATTAGGGTTT
Found at i:88563717 original size:251 final size:251
Alignment explanation
Indices: 88563252--88563756 Score: 744
Period size: 251 Copynumber: 2.0 Consensus size: 251
88563242 ACTTTTACCC
* * * *
88563252 TGAAAAATTATTTTGAGAAGATGTTTCTGAACAACTAGTGTCAAAAACGCTTCAAACAGGATACA
1 TGAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAACAGGATACA
* * *
88563317 CTGTCAGCAAAAATACAGAAAAAAGCTCTCACGTGGATGCTCTTTTTATCTACAGTAGTTTCTGA
66 CTGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTATCTACAGTAGTTCCTGA
*
88563382 AAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGT
131 AAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGT
* *
88563447 CAGCAAAATTACGGAAAAAAGCTACCATGTGGACGCTCTTTTTCTACAGTAGTTCA
196 CAGCAAAATTACGGAAAAAAGCTACCACGTGGACGCTCTTTTTCTACAATAGTTCA
* **
88563503 TGAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGTA
1 TGAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAACAGGATACA
* * * *
88563568 CTGTTAGTAAAATTACAGAAAAAAGCTCCCATGTGGACGCTC-TTTT-TCTACAGTAGTTCCTGA
66 CTGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTATCTACAGTAGTTCCTG-
* * *
88563631 AAAAATAATTTTGAGAAGATGTTTTTGAACAAATAGTGTCAAAAATGCTTCAAGCAGGATGCAAT
130 -AAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAAT
* * * * * *
88563696 GTTAGTAAAATTTCTGAAAAAATCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCA
194 GTCAGCAAAATTACGGAAAAAAGCTACCACGTGGACGCTCTTTTTCTACAATAGTTCA
88563754 TGA
1 TGA
88563757 TTGGCCTTAG
Statistics
Matches: 226, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
249 15 0.07
250 4 0.02
251 207 0.92
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (251 bp):
TGAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAACAGGATACA
CTGTCAGCAAAAATACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTATCTACAGTAGTTCCTGA
AAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCAATGT
CAGCAAAATTACGGAAAAAAGCTACCACGTGGACGCTCTTTTTCTACAATAGTTCA
Found at i:88563752 original size:126 final size:125
Alignment explanation
Indices: 88563250--88563752 Score: 720
Period size: 126 Copynumber: 4.0 Consensus size: 125
88563240 CTACTTTTAC
* * * *
88563250 CCTGAAAAATTATTTTGAGAAGATGTTTCTGAACAACTAGTGTCAAAAACGCTTCAAACAGGATA
1 CCTGAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
* * *
88563315 CACTGTCAGCAAAAATACAGAAAAAAGCTCTCACGTGGATGCTCTTTTTATCTACAGTAGTT
66 CACTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTC-TTTT-TCTACAGTAGTT
* *
88563377 TCTG-AAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
1 CCTGAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
* * *
88563441 CACTGTCAGCAAAATTACGGAAAAAAGCTACCATGTGGACGCTCTTTTTCTACAGTAGTT
66 CACTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
* * *
88563501 CATGAAAAATAATTTTGAGAAGAAGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
1 CCTGAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
* * * *
88563566 TACTGTTAGTAAAATTACAGAAAAAAGCTCCCATGTGGACGCTCTTTTTCTACAGTAGTT
66 CACTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
* *
88563626 CCTGAAAAAATAATTTTGAGAAGATGTTTTTGAACAAATAGTGTCAAAAATGCTTCAAGCAGGAT
1 CCTG-AAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
* * * * * * *
88563691 GCAATGTTAGTAAAATTTCTGAAAAAATCTCCCACGTGGACGCTCTTTTTCTACAATAGTT
65 GCACTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
88563752 C
1 C
88563753 ATGATTGGCC
Statistics
Matches: 341, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
124 14 0.04
125 120 0.35
126 204 0.60
127 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (125 bp):
CCTGAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATG
CACTGTCAGCAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTT
Found at i:88567401 original size:34 final size:34
Alignment explanation
Indices: 88567356--88567420 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
88567346 TTCAGTACAT
*
88567356 AATGGGCTGTACAAGCTTAACCTAATTAACTGTC
1 AATGGGCTGTACAAGCTTAACCTAACTAACTGTC
*
88567390 AATGGGTTGTACAAGCTTAACCTAACTAACT
1 AATGGGCTGTACAAGCTTAACCTAACTAACT
88567421 CGTCCTACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (34 bp):
AATGGGCTGTACAAGCTTAACCTAACTAACTGTC
Found at i:88574859 original size:2 final size:2
Alignment explanation
Indices: 88574852--88574878 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88574842 GGATCACTGA
88574852 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
88574879 GTCTATACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88575389 original size:2 final size:2
Alignment explanation
Indices: 88575382--88575407 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88575372 TTTAGGGTAA
88575382 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
88575408 GACATCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:88578200 original size:22 final size:22
Alignment explanation
Indices: 88578172--88578217 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
88578162 TACTATTTAC
88578172 CAACATTCACTGCGCATTGCTT
1 CAACATTCACTGCGCATTGCTT
*
88578194 CAACATTCATTGCGCATTGCTT
1 CAACATTCACTGCGCATTGCTT
88578216 CA
1 CA
88578218 TATATGTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (22 bp):
CAACATTCACTGCGCATTGCTT
Found at i:88582459 original size:22 final size:20
Alignment explanation
Indices: 88582418--88582460 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
88582408 GATAATAGAT
*
88582418 ATAAAATTTTAAAGTAAATA
1 ATAAAATTTTAAAATAAATA
*
88582438 ATAAAATGATTTAAAATGAATA
1 ATAAAAT--TTTAAAATAAATA
88582460 A
1 A
88582461 CACATAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
ATAAAATTTTAAAATAAATA
Found at i:88585085 original size:204 final size:205
Alignment explanation
Indices: 88584673--88585155 Score: 704
Period size: 204 Copynumber: 2.4 Consensus size: 205
88584663 GGGAACATCC
* * * *
88584673 GAAAGTCAAATCTGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAGATCC-TCTTG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCA-AACCATCTTG
* * * * *
88584737 GATCTAGCTTCAATATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCTATTGAAATGG
65 GATC-AGCTTCAACATAAACATCCGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTCAAATGA
* * *
88584802 AGATGCCAGACTTCGATTTGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGTTTCA
129 AGATACCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
88584867 ACGTAAACACGT
194 ACGTAAACACGT
*
88584879 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
* * *
88584944 ATCCGCTTCAGCATAAACATCCGAAGG-CGAGATCTGCTATGTGTCTGCTCTCCA-TCAAAGTGA
66 ATCAGCTTCAACATAAACATCCGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATTCAAA-TGA
* *
88585007 AGATACCA-ACTTTGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
129 AGATACCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
* *
88585071 TCGTAAGCACGT
194 ACGTAAACACGT
*
88585083 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
*
88585148 ATCTGCTT
66 ATCAGCTT
88585156 TAACCAGATC
Statistics
Matches: 251, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
204 137 0.55
205 55 0.22
206 59 0.24
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (205 bp):
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
ATCAGCTTCAACATAAACATCCGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTCAAATGAAG
ATACCAGACTTCGATTCGTTCTCTGAAAATACAGAGACGACAAATCATCTTAGATTTGCTTCAAC
GTAAACACGT
Found at i:88585371 original size:44 final size:43
Alignment explanation
Indices: 88585311--88585515 Score: 173
Period size: 44 Copynumber: 4.7 Consensus size: 43
88585301 AAATTTGGCT
**
88585311 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATTTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTC-ATC
* * * * * * *
88585355 TGTTTCTCTACTGCTTAGGGTGAT-AAGATCTATGAACTTCAGC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTC-ATTAACTTCATC
* * **
88585398 TTGTTACCCTACTGCTTAGAGGGTTAAAGCTCGTTGCCTTCGATC
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTC-ATC
* * * * *
88585443 TGTTTCCCTATTGCTTAGGGGGTT-AAGATC-TGTAAATTCAGCC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TAACTTCA-TC
88585486 TGTTACCCTACTGCTTAGGGGGTTAAAGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCT
88585516 TGGTGAATTC
Statistics
Matches: 123, Mismatches: 31, Indels: 14
0.73 0.18 0.08
Matches are distributed among these distances:
42 2 0.02
43 39 0.32
44 75 0.61
45 7 0.06
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTAACTTCATC
Found at i:88585410 original size:88 final size:87
Alignment explanation
Indices: 88585267--88585515 Score: 300
Period size: 88 Copynumber: 2.9 Consensus size: 87
88585257 TACATTCAAC
* * *** * * **
88585267 CTGTTACCCTGCTGCTTAGGGATTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAAATTCAGCTTGTTACCCTACTGCTTAGGGG
**
88585332 GTTAAAGCTCATTATTTTCGAT
66 GTTAAAGCTCATTACCTTCGAT
* * * *
88585354 CTGTTTCTCTACTGCTTAGGGTGATAAGATCTATGAACTTCAGCTTGTTACCCTACTGCTTAGAG
1 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTAT-AAATTCAGCTTGTTACCCTACTGCTTAGGG
* *
88585419 GGTTAAAGCTCGTTGCCTTCGAT
65 GGTTAAAGCTCATTACCTTCGAT
* * * *
88585442 CTGTTTCCCTATTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAAATTCAGCTTGTTACCCTACTGCTTAGGGG
88585507 GTTAAAGCT
66 GTTAAAGCT
88585516 TGGTGAATTC
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
87 63 0.46
88 74 0.54
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (87 bp):
CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAAATTCAGCTTGTTACCCTACTGCTTAGGGG
GTTAAAGCTCATTACCTTCGAT
Found at i:88585501 original size:43 final size:43
Alignment explanation
Indices: 88585225--88585511 Score: 177
Period size: 43 Copynumber: 6.6 Consensus size: 43
88585215 GCATTTGATT
* * * ** * * *
88585225 TGTTTCCCTATTGCTTAAGGGGTTTTGATCCGTACATTCAACC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCC
* ** * ** *
88585268 TGTTACCCTGCTGCTTAGGGATTTAAGGTCTGTAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCC
* ** *
88585311 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TATTTTC-GATC
1 TGTTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAATTCAG-CC
* * * * * * *
88585355 TGTTTCTCTACTGCTTAGGGTGATAAGATCTATGAACTTCAGCT
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAGCC
* * *** *
88585399 TGTTACCCTACTGCTTAGAGGGTTAA-AGCTCGTTGCCTTC-GATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCT-G-TAAATTCAG-CC
* *
88585443 TGTTTCCCTATTGCTTAGGGGGTTAAGATCTGTAAATTCAGCC
1 TGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCC
88585486 TGTTACCCTACTGCTTAGGGGGTTAA
1 TGTTACCCTACTGCTTAGGGGGTTAA
88585512 AGCTTGGTGA
Statistics
Matches: 179, Mismatches: 54, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
42 1 0.01
43 89 0.50
44 83 0.46
45 6 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCC
Found at i:88587610 original size:27 final size:27
Alignment explanation
Indices: 88587572--88587626 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
88587562 ACTCACGATT
88587572 CTTCACATATCGCAAGATATCGTGGTA
1 CTTCACATATCGCAAGATATCGTGGTA
88587599 CTTCACATATCGCAAGATATCGTGGTA
1 CTTCACATATCGCAAGATATCGTGGTA
88587626 C
1 C
88587627 CAAGGGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (27 bp):
CTTCACATATCGCAAGATATCGTGGTA
Found at i:88597763 original size:22 final size:20
Alignment explanation
Indices: 88597722--88597764 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
88597712 GATAATAGAT
*
88597722 ATAAAATTTTAAAGTAAATA
1 ATAAAATTTTAAAATAAATA
*
88597742 ATAAAATGATTTAAAATGAATA
1 ATAAAAT--TTTAAAATAAATA
88597764 A
1 A
88597765 CACATAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
ATAAAATTTTAAAATAAATA
Found at i:88610485 original size:2 final size:2
Alignment explanation
Indices: 88610478--88610511 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
88610468 TACGTATTTA
88610478 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
88610512 TATTAGCCGA
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:88611818 original size:41 final size:41
Alignment explanation
Indices: 88611773--88611908 Score: 146
Period size: 41 Copynumber: 3.2 Consensus size: 41
88611763 TCCCAGAATG
* *
88611773 GGTCTTACATGAATCGAATTCGATGCTGATGTCTTAGACGT
1 GGTCTTACATGAATCGAATTCGATGCCGATGTCTCAGACGT
* * * * * *
88611814 GGTCTTACACGTAACCACATATATCGATGCCAACGTCCCAGACGT
1 GGTCTTACATG-AATC-GA-AT-TCGATGCCGATGTCTCAGACGT
* *
88611859 GGTCTTACATGAATCGAATACGATGCCGATGTCTCAGACAT
1 GGTCTTACATGAATCGAATTCGATGCCGATGTCTCAGACGT
88611900 GGTCTTACA
1 GGTCTTACA
88611909 CGTAACCACA
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
41 36 0.48
42 5 0.07
43 2 0.03
44 5 0.07
45 27 0.36
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (41 bp):
GGTCTTACATGAATCGAATTCGATGCCGATGTCTCAGACGT
Found at i:88611857 original size:45 final size:45
Alignment explanation
Indices: 88611808--88611969 Score: 197
Period size: 45 Copynumber: 3.7 Consensus size: 45
88611798 CTGATGTCTT
*
88611808 AGACGTGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
1 AGACATGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
* * * * * * *
88611853 AGACGTGGTCTTACATG-AATC-GA-ATA-CGATGCCGATGTCTC
1 AGACATGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
88611894 AGACATGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
1 AGACATGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
* * *
88611939 AGACATGGTCTTACATGAAATCACATATATC
1 AGACATGGTCTTACACGTAACCACATATATC
88611970 AAAATCCTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 27 0.28
42 6 0.06
43 2 0.02
44 6 0.06
45 56 0.58
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (45 bp):
AGACATGGTCTTACACGTAACCACATATATCGATGCCAACGTCCC
Found at i:88611867 original size:86 final size:86
Alignment explanation
Indices: 88611748--88611957 Score: 334
Period size: 86 Copynumber: 2.4 Consensus size: 86
88611738 ATGCTATCTC
* * * *
88611748 ATATCGATGTC-ACTGTCCCAGA-ATGGGTCTTACATGAATCGAATTCGATGCTGATGTCTTAGA
1 ATATCGATGCCAAC-GTCCCAGACAT-GGTCTTACATGAATCGAATACGATGCCGATGTCTCAGA
*
88611811 CGTGGTCTTACACGTAACCACAT
64 CATGGTCTTACACGTAACCACAT
*
88611834 ATATCGATGCCAACGTCCCAGACGTGGTCTTACATGAATCGAATACGATGCCGATGTCTCAGACA
1 ATATCGATGCCAACGTCCCAGACATGGTCTTACATGAATCGAATACGATGCCGATGTCTCAGACA
88611899 TGGTCTTACACGTAACCACAT
66 TGGTCTTACACGTAACCACAT
88611920 ATATCGATGCCAACGTCCCAGACATGGTCTTACATGAA
1 ATATCGATGCCAACGTCCCAGACATGGTCTTACATGAA
88611958 ATCACATATA
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
86 112 0.97
87 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (86 bp):
ATATCGATGCCAACGTCCCAGACATGGTCTTACATGAATCGAATACGATGCCGATGTCTCAGACA
TGGTCTTACACGTAACCACAT
Found at i:88613082 original size:14 final size:15
Alignment explanation
Indices: 88613065--88613093 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88613055 TCATGAAAAT
88613065 TTCACACAT-ATAAA
1 TTCACACATAATAAA
88613079 TTCACACATAATAAA
1 TTCACACATAATAAA
88613094 CACAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:88613922 original size:15 final size:16
Alignment explanation
Indices: 88613895--88613931 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
88613885 ATCAATTAGC
*
88613895 CACATACCAAACAACT
1 CACATACCAAACAAAT
88613911 CACATA-CAAACAAAT
1 CACATACCAAACAAAT
88613926 CACATA
1 CACATA
88613932 TAATAGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (16 bp):
CACATACCAAACAAAT
Found at i:88613963 original size:2 final size:2
Alignment explanation
Indices: 88613956--88613987 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88613946 TCATCGGTTC
88613956 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
88613988 CCAACCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88615456 original size:24 final size:24
Alignment explanation
Indices: 88615424--88615470 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
88615414 TGTTTTTTGC
88615424 CTAAAACTTTTACGACAACCCGCT
1 CTAAAACTTTTACGACAACCCGCT
88615448 CTAAAACTTTTACGACAACCCGC
1 CTAAAACTTTTACGACAACCCGC
88615471 ATCTTTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (24 bp):
CTAAAACTTTTACGACAACCCGCT
Found at i:88616559 original size:3 final size:3
Alignment explanation
Indices: 88616551--88616585 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
88616541 ATCTTTTTAT
*
88616551 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
88616586 GTGATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:88618621 original size:13 final size:13
Alignment explanation
Indices: 88618582--88618625 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
88618572 ATCCTAACAC
88618582 AATTTTAATTTTA
1 AATTTTAATTTTA
*
88618595 ATATTTTTATTTTA
1 A-ATTTTAATTTTA
*
88618609 AATTCTAATTTTA
1 AATTTTAATTTTA
88618622 AATT
1 AATT
88618626 GATAGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTTTAATTTTA
Found at i:88618695 original size:20 final size:21
Alignment explanation
Indices: 88618670--88618708 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
88618660 TTTATGGAAA
*
88618670 TTTAATTTA-AATAATATATT
1 TTTAATTTATAAAAATATATT
88618690 TTTAATTTATAAAAATATA
1 TTTAATTTATAAAAATATA
88618709 GTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATTTATAAAAATATATT
Found at i:88618713 original size:20 final size:20
Alignment explanation
Indices: 88618670--88618714 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
88618660 TTTATGGAAA
* *
88618670 TTTAATTTAAATAATATATT
1 TTTAATTTAAAAAATATATG
88618690 TTTAATTTATAAAAATATA-G
1 TTTAATTTA-AAAAATATATG
88618710 TTTAA
1 TTTAA
88618715 AATTCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATTTAAAAAATATATG
Found at i:88619188 original size:10 final size:10
Alignment explanation
Indices: 88619175--88619200 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
88619165 TTTTTAAAAT
88619175 ATTTTTTATA
1 ATTTTTTATA
88619185 ATTTTTTATA
1 ATTTTTTATA
88619195 ATTTTT
1 ATTTTT
88619201 AAATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:88625325 original size:9 final size:9
Alignment explanation
Indices: 88625235--88625398 Score: 57
Period size: 9 Copynumber: 17.2 Consensus size: 9
88625225 TTTGTTTTCC
88625235 TTATAAAAA
1 TTATAAAAA
*
88625244 TCATAAAAA
1 TTATAAAAA
88625253 TCT-TAAAAAA
1 T-TAT-AAAAA
*
88625263 TATATTTAAAA
1 T-TA-TAAAAA
* *
88625274 TTTTAAAATT
1 TTATAAAA-A
*
88625284 TTATATAAAC
1 TTATA-AAAA
**
88625294 TTATAAAGT
1 TTATAAAAA
88625303 TTATTAAAAA
1 TTA-TAAAAA
88625313 --ATAAAAA
1 TTATAAAAA
88625320 TTATAAAAA
1 TTATAAAAA
*
88625329 TGATTAAAAA
1 TTA-TAAAAA
88625339 -TATTAAAAA
1 TTA-TAAAAA
* *
88625348 TTTATATCAAC
1 -TTATA-AAAA
88625359 TTATAAAAA
1 TTATAAAAA
* **
88625368 TTTGTAAATT
1 -TTATAAAAA
*
88625378 TTATAGAAAC
1 TTATA-AAAA
88625388 TTATAAAAA
1 TTATAAAAA
88625397 TT
1 TT
88625399 TCATTAAAAA
Statistics
Matches: 114, Mismatches: 26, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
7 6 0.05
8 1 0.01
9 47 0.41
10 47 0.41
11 12 0.11
12 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:88625365 original size:29 final size:29
Alignment explanation
Indices: 88625333--88625399 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
88625323 TAAAAATGAT
**
88625333 TAAAAATATT-AAAAATTTATATCAACTTA
1 TAAAAAT-TTGAAAAATTTATAGAAACTTA
* *
88625362 TAAAAATTTGTAAATTTTATAGAAACTTA
1 TAAAAATTTGAAAAATTTATAGAAACTTA
88625391 TAAAAATTT
1 TAAAAATTT
88625400 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 2 0.06
29 31 0.94
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAAATTTGAAAAATTTATAGAAACTTA
Found at i:88625493 original size:10 final size:9
Alignment explanation
Indices: 88625471--88625562 Score: 80
Period size: 9 Copynumber: 10.0 Consensus size: 9
88625461 AATTTTATGC
88625471 AAAATTATA
1 AAAATTATA
88625480 AAAATTAATTA
1 AAAATT-A-TA
*
88625491 AAACTTATA
1 AAAATTATA
*
88625500 AATATTATA
1 AAAATTATA
*
88625509 AAATTTATA
1 AAAATTATA
* *
88625518 GTAAATTTTA
1 -AAAATTATA
88625528 ATAAATTATA
1 A-AAATTATA
88625538 AAAATTAT-
1 AAAATTATA
*
88625546 TAAA-TATA
1 AAAATTATA
88625554 AAAATTATA
1 AAAATTATA
88625563 TAAAGTCATT
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
7 3 0.05
8 6 0.09
9 33 0.51
10 16 0.25
11 7 0.11
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (9 bp):
AAAATTATA
Found at i:88625510 original size:29 final size:29
Alignment explanation
Indices: 88625472--88625562 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
88625462 ATTTTATGCA
88625472 AAATTATAAAAATTAATTAAAACTTATAA-
1 AAATTATAAAAATTAATTAAAA-TTATAAT
* * * *
88625501 ATATTATAAAATTTATAGT-AAATTTTAAT
1 AAATTATAAAAATTA-ATTAAAATTATAAT
88625530 AAATTATAAAAATT-ATT-AAA-TATAA-
1 AAATTATAAAAATTAATTAAAATTATAAT
88625555 AAATTATA
1 AAATTATA
88625563 TAAAGTCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.15
26 4 0.08
27 5 0.10
28 5 0.10
29 28 0.54
30 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
AAATTATAAAAATTAATTAAAATTATAAT
Found at i:88625555 original size:16 final size:18
Alignment explanation
Indices: 88625472--88625566 Score: 81
Period size: 20 Copynumber: 5.2 Consensus size: 18
88625462 ATTTTATGCA
88625472 AAATTATAAAAATTA-ATT
1 AAATTATAAAAATTATA-T
*
88625490 AAAACTTATAAATATTATA-
1 -AAA-TTATAAAAATTATAT
* *
88625509 AAATTTATAGTAAATTTTAAT
1 AAA-TTATA-AAAATTAT-AT
88625530 AAATTATAAAAATTAT-T
1 AAATTATAAAAATTATAT
88625547 AAA-TATAAAAATTATAT
1 AAATTATAAAAATTATAT
88625564 AAA
1 AAA
88625567 GTCATTTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
16 12 0.19
17 8 0.13
18 8 0.13
19 14 0.22
20 17 0.27
21 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
AAATTATAAAAATTATAT
Found at i:88633132 original size:16 final size:15
Alignment explanation
Indices: 88633106--88633154 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
88633096 AGTCATGCAG
88633106 TACTCAATTCATGAA
1 TACTCAATTCATGAA
*
88633121 TACATCATTTCAT-ACCA
1 TAC-TCAATTCATGA--A
88633138 TACTCAATTCATGAA
1 TACTCAATTCATGAA
88633153 TA
1 TA
88633155 TATAACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 7 0.25
16 16 0.57
17 5 0.18
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (15 bp):
TACTCAATTCATGAA
Found at i:88634360 original size:18 final size:18
Alignment explanation
Indices: 88634339--88634376 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
88634329 TCTGTTTTGT
88634339 TTCTATTCT-TTTCTTTTA
1 TTCT-TTCTGTTTCTTTTA
*
88634357 TTCTTTTTGTTTCTTTTA
1 TTCTTTCTGTTTCTTTTA
88634375 TT
1 TT
88634377 ATTTGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTCTGTTTCTTTTA
Found at i:88640532 original size:28 final size:28
Alignment explanation
Indices: 88640486--88640540 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
88640476 AGTTGCAAAG
* *
88640486 GACACACGGCCTTATCACATGCCCATAT
1 GACACACGGCCTTAACACACGCCCATAT
88640514 GACACACGG-CTTAGACACACGCCCATA
1 GACACACGGCCTTA-ACACACGCCCATA
88640541 GGCCCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.31, C:0.36, G:0.16, T:0.16
Consensus pattern (28 bp):
GACACACGGCCTTAACACACGCCCATAT
Found at i:88641210 original size:46 final size:47
Alignment explanation
Indices: 88641153--88641250 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 47
88641143 ACACACTGAA
* * *
88641153 GCCATAGCCCAGCTATGGTCTTACACG-GATCACATATCATACCAAT
1 GCCATAGCCCAGATATGGTCTTACACGAAAGCACATATCATACCAAT
* * * *
88641199 GCCATATCCCAGATATGGTCTTATACGAAAGCTCATATTATACCAAT
1 GCCATAGCCCAGATATGGTCTTACACGAAAGCACATATCATACCAAT
88641246 GCCAT
1 GCCAT
88641251 GGTCTTATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 24 0.55
47 20 0.45
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (47 bp):
GCCATAGCCCAGATATGGTCTTACACGAAAGCACATATCATACCAAT
Found at i:88649735 original size:136 final size:136
Alignment explanation
Indices: 88649492--88649776 Score: 518
Period size: 136 Copynumber: 2.1 Consensus size: 136
88649482 TATTGGGCCT
**
88649492 AAGCCCATTCAGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAATTACAATAAACTGGGCCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAATTACAATAAACTGGGCCTTA
88649557 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AAC
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
88649621 ATATGC
131 ATATGC
*
88649627 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCA-ATTACAATAAACTGGGCCTT
*
88649692 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
65 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
88649757 CATATGC
130 CATATGC
88649764 AAGCCCATTTGGG
1 AAGCCCATTTGGG
88649777 GAGACTACTC
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
135 41 0.28
136 81 0.56
137 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAATTACAATAAACTGGGCCTTA
GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
ATATGC
Found at i:88650061 original size:25 final size:27
Alignment explanation
Indices: 88650024--88650076 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
88650014 TCAAACATGC
88650024 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
88650050 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
88650076 A
1 A
88650077 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:88651593 original size:25 final size:25
Alignment explanation
Indices: 88651559--88651665 Score: 178
Period size: 25 Copynumber: 4.2 Consensus size: 25
88651549 CATGAAATTC
88651559 TTATCATGAAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
88651584 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
* *
88651610 TTATCATGGAATATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
*
88651635 TTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
88651660 TTATCA
1 TTATCA
88651666 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 55 0.71
26 23 0.29
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:88651635 original size:51 final size:50
Alignment explanation
Indices: 88651559--88651665 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 50
88651549 CATGAAATTC
88651559 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAA-CCA
* * *
88651610 TTATCATGGAATATTTACCTAACCATTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCA
88651660 TTATCA
1 TTATCA
88651666 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 9 0.17
51 44 0.83
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (50 bp):
TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCA
Found at i:88655665 original size:136 final size:137
Alignment explanation
Indices: 88655421--88655706 Score: 547
Period size: 136 Copynumber: 2.1 Consensus size: 137
88655411 TATTGGGCCT
**
88655421 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
88655486 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
88655550 CATATGC
131 CATATGC
88655557 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
88655622 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
88655687 CATATGC
131 CATATGC
88655694 AAGCCCATTTGGG
1 AAGCCCATTTGGG
88655707 GAGACTACTC
Statistics
Matches: 147, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 125 0.85
137 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:88655991 original size:25 final size:26
Alignment explanation
Indices: 88655954--88656005 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
88655944 TCAAACATGC
88655954 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
88655980 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
88656005 A
1 A
88656006 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:88657543 original size:26 final size:26
Alignment explanation
Indices: 88657485--88657593 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
88657475 CATGAAATTC
88657485 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
88657510 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
88657536 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
88657562 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
88657588 TTATCA
1 TTATCA
88657594 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 22 0.28
26 56 0.72
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:88658878 original size:36 final size:36
Alignment explanation
Indices: 88658838--88658910 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
88658828 CTTGGAAAAG
88658838 AAAAACAATAATACAGCTGATTATTGGACCCAAATT
1 AAAAACAATAATACAGCTGATTATTGGACCCAAATT
88658874 AAAAACAATAATACAGCTGATTATTGGACCCAAATT
1 AAAAACAATAATACAGCTGATTATTGGACCCAAATT
88658910 A
1 A
88658911 TCCTTAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (36 bp):
AAAAACAATAATACAGCTGATTATTGGACCCAAATT
Found at i:88659980 original size:13 final size:13
Alignment explanation
Indices: 88659962--88659987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88659952 ATTATTTCTT
88659962 ATTTTACATTAAA
1 ATTTTACATTAAA
88659975 ATTTTACATTAAA
1 ATTTTACATTAAA
88659988 TAATATATTA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTACATTAAA
Found at i:88668416 original size:18 final size:18
Alignment explanation
Indices: 88668389--88668423 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88668379 CAAAATTGAA
* *
88668389 TCAAATTAATTATTTAAG
1 TCAAAATAATTAATTAAG
88668407 TCAAAATAATTAATTAA
1 TCAAAATAATTAATTAA
88668424 ATTAATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
TCAAAATAATTAATTAAG
Found at i:88669903 original size:16 final size:16
Alignment explanation
Indices: 88669882--88669912 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
88669872 CATGCCATAA
88669882 TTATATTTAAAATTTC
1 TTATATTTAAAATTTC
88669898 TTATATTTAAAATTT
1 TTATATTTAAAATTT
88669913 TAATACATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTAAAATTTC
Found at i:88670431 original size:26 final size:26
Alignment explanation
Indices: 88670391--88670441 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
88670381 CATCTGACGG
* *
88670391 TTAACTTTAATAGTTGACCATTAAAC
1 TTAACTTTAACAGTTGACAATTAAAC
88670417 TTAACTTTAACAGTTGACAATTAAA
1 TTAACTTTAACAGTTGACAATTAAA
88670442 GCAGTTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (26 bp):
TTAACTTTAACAGTTGACAATTAAAC
Found at i:88670448 original size:16 final size:16
Alignment explanation
Indices: 88670427--88670458 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
88670417 TTAACTTTAA
88670427 CAGTTGACAATTAAAG
1 CAGTTGACAATTAAAG
88670443 CAGTTGACAATTAAAG
1 CAGTTGACAATTAAAG
88670459 TTAATTGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
CAGTTGACAATTAAAG
Found at i:88670598 original size:20 final size:20
Alignment explanation
Indices: 88670550--88670598 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
88670540 TAAAAATCAA
* *
88670550 TAAAAATT-ATAAAGATTAT
1 TAAAAATTAATAAAAAATAT
**
88670569 TAAATTTTAATAAAAAATAT
1 TAAAAATTAATAAAAAATAT
88670589 TAAAAATTAA
1 TAAAAATTAA
88670599 AATATATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAATTAATAAAAAATAT
Found at i:88670910 original size:20 final size:21
Alignment explanation
Indices: 88670856--88670910 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
88670846 TGGTACGATA
*
88670856 ATTTTTATAATTTT-TTTATG
1 ATTTTTATAATTTTCTTTATC
*
88670876 AATTTTAT-A-TTTCTTTA-C
1 ATTTTTATAATTTTCTTTATC
88670894 ATTTTTATAATTTTCTT
1 ATTTTTATAATTTTCTT
88670911 ACGACTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 10 0.34
19 6 0.21
20 13 0.45
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTATAATTTTCTTTATC
Found at i:88670936 original size:38 final size:37
Alignment explanation
Indices: 88670853--88670937 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 37
88670843 TTTTGGTACG
* * *
88670853 ATAATTTTTATAATTTTTTTATGAATTTTATATTTCT
1 ATAATTTTTATAATTTTCTTACGAATTTTAAATTTCT
* *
88670890 TTACATTTTTATAATTTTCTTACGACTTTATAAAATTT-T
1 ATA-ATTTTTATAATTTTCTTACGAATTT-T-AAATTTCT
88670929 ATAATTTTT
1 ATAATTTTT
88670938 TCTATATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.05
38 28 0.72
39 4 0.10
40 5 0.13
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (37 bp):
ATAATTTTTATAATTTTCTTACGAATTTTAAATTTCT
Found at i:88670956 original size:29 final size:27
Alignment explanation
Indices: 88670927--88671000 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
88670917 TTATAAAATT
*
88670927 TTATAATTTTTTCTATATTTCCATATATT
1 TTATAATTTTTTCTATATTTAC-TA-ATT
*
88670956 TTATAATTTTTTCTATTTTTACTAATT
1 TTATAATTTTTTCTATATTTACTAATT
*
88670983 TTA-AATATTTT-TATATTT
1 TTATAATTTTTTCTATATTT
88671001 TTTTATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.15
26 7 0.17
27 6 0.15
28 2 0.05
29 20 0.49
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATAATTTTTTCTATATTTACTAATT
Found at i:88671004 original size:29 final size:30
Alignment explanation
Indices: 88670953--88671027 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
88670943 ATTTCCATAT
* * *
88670953 ATTTTATAATTTTT-TCTATTTTTACT-AA
1 ATTTAATAATTTTTATATTTTTTTACTAAA
* *
88670981 TTTTAA-ATATTTTTATATTTTTTTATTAAA
1 ATTTAATA-ATTTTTATATTTTTTTACTAAA
88671011 ATTTAATAATTTTTATA
1 ATTTAATAATTTTTATA
88671028 GCTTTTATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.03
28 10 0.27
29 9 0.24
30 16 0.43
31 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTAATAATTTTTATATTTTTTTACTAAA
Found at i:88671367 original size:16 final size:16
Alignment explanation
Indices: 88671316--88671367 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
88671306 ATTCAAAAAG
88671316 AATAATTT-AAAATTA
1 AATAATTTCAAAATTA
* *
88671331 TAAAAATACTCAAATATTA
1 -AATAAT-TTCAAA-ATTA
88671350 AATAATTTCAAAATTA
1 AATAATTTCAAAATTA
88671366 AA
1 AA
88671368 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 11 0.38
17 6 0.21
18 8 0.28
19 4 0.14
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATTTCAAAATTA
Found at i:88671561 original size:25 final size:24
Alignment explanation
Indices: 88671523--88671583 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
88671513 ATAACTTTTT
88671523 TTAAAAAT-TGAAAG-CCAAATTTAA
1 TTAAAAATAT-AAAGACCAAA-TTAA
*
88671547 CTTAAAAATATAAAGATCAAATTAA
1 -TTAAAAATATAAAGACCAAATTAA
88671572 TTAAAAAATATA
1 TT-AAAAATATA
88671584 TAAAAATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.06
25 25 0.78
26 5 0.16
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (24 bp):
TTAAAAATATAAAGACCAAATTAA
Found at i:88675435 original size:2 final size:2
Alignment explanation
Indices: 88675428--88675466 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
88675418 TTCGTTTTGC
*
88675428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88675467 AAATTCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:88676461 original size:26 final size:26
Alignment explanation
Indices: 88676431--88676566 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
88676421 TGATACAAAT
88676431 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
88676457 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
88676483 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
88676509 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
88676535 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
88676561 TGATAA
1 TGATAA
88676567 GAATTTCATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:88678742 original size:137 final size:137
Alignment explanation
Indices: 88678354--88678776 Score: 749
Period size: 137 Copynumber: 3.1 Consensus size: 137
88678344 GAGTAGTCTC
88678354 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
88678419 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
88678484 ACTGTTA
131 ACTGTTA
* *
88678491 CCCAAATGGGCTTGCATATG-TTATTGATGTTACATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
88678555 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
88678620 ACTGTTA
131 ACTGTTA
88678627 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
88678692 TGTTATCTGAATAAGGGGCTAAGGTCCAGTTTATTGTAATCTAAAAAGGGCTCTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
*
88678757 ACTATTA
131 ACTGTTA
**
88678764 CCTGAATGGGCTT
1 CCCAAATGGGCTT
88678777 AGGCCCAATA
Statistics
Matches: 271, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
136 131 0.48
137 140 0.52
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
ACTGTTA
Found at i:88680089 original size:30 final size:29
Alignment explanation
Indices: 88680053--88680117 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
88680043 GGATAGATTG
* * * *
88680053 AAAGATTGAAGATTTGAAGCTTGGTTGGAT
1 AAAGATTAAAGATTTGAA-ATTAGCTGGAT
88680083 AAAGATTAAAGATTTGAAATTAGCTGGAT
1 AAAGATTAAAGATTTGAAATTAGCTGGAT
88680112 AAAGAT
1 AAAGAT
88680118 CTAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAGATTAAAGATTTGAAATTAGCTGGAT
Found at i:88683800 original size:26 final size:25
Alignment explanation
Indices: 88683771--88683819 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
88683761 AAATAATTTA
88683771 ATAAATAAAAATAAAAGTCTAAAACT
1 ATAAATAAAAAT-AAAGTCTAAAACT
* *
88683797 ATAACTAAAACTAAAGTCTAAAA
1 ATAAATAAAAATAAAGTCTAAAA
88683820 GTCTAAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.63, C:0.10, G:0.04, T:0.22
Consensus pattern (25 bp):
ATAAATAAAAATAAAGTCTAAAACT
Found at i:88684602 original size:58 final size:57
Alignment explanation
Indices: 88684511--88684662 Score: 171
Period size: 58 Copynumber: 2.6 Consensus size: 57
88684501 ATGTTGTTAT
* * * * *
88684511 AAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTAGGCATTTTCATACTGTCTTAA
1 AAATTGAATTAAAGCTGCTATTTTAGTGTTTCAAATTAAGCATTTTCATACTGTC--AA
* * *
88684570 AAATTGAA-TCAAGCTGCTATTTTAGTGTTTCAAATTAAGCATTTTCATCCTGTCAT
1 AAATTGAATTAAAGCTGCTATTTTAGTGTTTCAAATTAAGCATTTTCATACTGTCAA
* * * *
88684626 AAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATT
1 AAATTGAATTAAAGCTGCTATTTTAGTGTTTCAAATT
88684663 GATCATGCTG
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
56 9 0.11
57 23 0.29
58 39 0.49
59 8 0.10
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (57 bp):
AAATTGAATTAAAGCTGCTATTTTAGTGTTTCAAATTAAGCATTTTCATACTGTCAA
Found at i:88687354 original size:149 final size:149
Alignment explanation
Indices: 88687083--88687381 Score: 526
Period size: 149 Copynumber: 2.0 Consensus size: 149
88687073 TCATCATAAG
* * **
88687083 AAGACATCAAAAAGATTGAAGAACAAATCCAAGAGCTTGACAAGATTGAAAATGGTATATTTATT
1 AAGACATCAAAAAAATTGAAGAACAAATCCAAGAGCTTCACAAGATTGAAAATGACATATTTATT
* *
88687148 GTTTTATTTTAATAGTTTCAATTTTTTTACCGTATCACTCCTACTTATTTAATTGATTCAATGTT
66 GTTTTATTTTAATAGTTTCAATTTTTTTACCATATCACTCCTACTTATTTAACTGATTCAATGTT
88687213 TAGACTTTTCTTGGAATGC
131 TAGACTTTTCTTGGAATGC
*
88687232 AAGACATCAAAAAAATTGAAGAACAAATCCAAGAGCTTCACTAGATTGAAAATGACATATTTATT
1 AAGACATCAAAAAAATTGAAGAACAAATCCAAGAGCTTCACAAGATTGAAAATGACATATTTATT
*
88687297 GTTTTATTTTATTAGTTTCAATTTTTTTACCATATCACTCCTACTTATTTAACTGATTCAATGTT
66 GTTTTATTTTAATAGTTTCAATTTTTTTACCATATCACTCCTACTTATTTAACTGATTCAATGTT
88687362 TAGACTTTTCTTGGAATGC
131 TAGACTTTTCTTGGAATGC
88687381 A
1 A
88687382 TCAGAGCCTA
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 142 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (149 bp):
AAGACATCAAAAAAATTGAAGAACAAATCCAAGAGCTTCACAAGATTGAAAATGACATATTTATT
GTTTTATTTTAATAGTTTCAATTTTTTTACCATATCACTCCTACTTATTTAACTGATTCAATGTT
TAGACTTTTCTTGGAATGC
Found at i:88687664 original size:17 final size:17
Alignment explanation
Indices: 88687644--88687704 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
88687634 ATTTCAAGAC
88687644 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
88687661 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
88687680 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
88687698 TTATGTA
1 TTATGTA
88687705 GTGATTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 16 0.48
18 4 0.12
19 4 0.12
20 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:88687680 original size:37 final size:37
Alignment explanation
Indices: 88687639--88687713 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
88687629 TGTTAATTTC
88687639 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
88687676 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
88687713 A
1 A
88687714 TTTGGTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.45
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:88688050 original size:4 final size:4
Alignment explanation
Indices: 88688041--88688070 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
88688031 CTTTATACTG
*
88688041 TTTA TTTA TTTA TTCA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
88688071 ACTTCCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:88695213 original size:94 final size:91
Alignment explanation
Indices: 88694945--88695215 Score: 233
Period size: 94 Copynumber: 2.9 Consensus size: 91
88694935 GCTACAGGCT
* * * * * *
88694945 ACAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCACAAACCTTATCCCCCTAAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTAT-CCCCTGAAA
* *
88695010 TTGCAGTGGAGTAGGTT-AAAAAAATA
65 TTGCAGTGGAGCAGATTGAAAAAAATA
* * *** **
88695036 ACAAATTTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATTA-TAAATCCCATACCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT-AATCTTAT-CCCCTGAA
* * * * *
88695100 GTTGCAGTGG-GACGGATTGAAGTTATAATG
64 ATTGCAGTGGAG-CAGATTGAA--AAAAATA
* * * *
88695130 GCGAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGCCACTAATCTTATCTCCCTGAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATC-CCCTGAAA
*
88695195 TTGCAGTGGAGCAAATTGAAA
65 TTGCAGTGGAGCAGATTGAAA
88695216 TGATCAGTCC
Statistics
Matches: 136, Mismatches: 36, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
90 1 0.01
91 61 0.45
92 2 0.01
93 1 0.01
94 69 0.51
95 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (91 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCCCCTGAAAT
TGCAGTGGAGCAGATTGAAAAAAATA
Found at i:88695278 original size:138 final size:138
Alignment explanation
Indices: 88695043--88695298 Score: 300
Period size: 138 Copynumber: 1.9 Consensus size: 138
88695033 ATAACAAATT
* * * *
88695043 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATTATAAATCCCATACCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAATGATAAATCCCATACCCCTGAAGTTGCAGT
* * * * * * *
88695108 GGGACGGATTGAAGTTATAATGGCGAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGC
66 AGGACGGATTCAAATTACAATAGCGAACCTTATATCCCTAAAGTTGCAATGGAGCAGATTGAAGC
88695173 CACTAATC
131 CACTAATC
* * * *
88695181 TTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAATGATCAGTCCTATACCTCTGAAGTTGCAGT
1 TTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAATGATAAATCCCATACCCCTGAAGTTGCAGT
* * * * *
88695246 AGGTCGGA-TCAAATCTACCATAGC-AAGCCTTATATCCTTGAAGTTGCAGTGGA
66 AGGACGGATTCAAAT-TACAATAGCGAA-CCTTATATCCCTAAAGTTGCAATGGA
88695299 ATAGACTAAA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
137 6 0.06
138 90 0.94
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (138 bp):
TTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAATGATAAATCCCATACCCCTGAAGTTGCAGT
AGGACGGATTCAAATTACAATAGCGAACCTTATATCCCTAAAGTTGCAATGGAGCAGATTGAAGC
CACTAATC
Found at i:88696976 original size:20 final size:19
Alignment explanation
Indices: 88696953--88696995 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
88696943 CTTTATACTG
88696953 TTTATTTATT-CATTCATTT
1 TTTATTTATTAC-TTCATTT
88696972 ATTTATTTATTACTTCATTT
1 -TTTATTTATTACTTCATTT
88696992 TTTA
1 TTTA
88696996 CACTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTATTACTTCATTT
Found at i:88697189 original size:3 final size:3
Alignment explanation
Indices: 88697176--88697258 Score: 95
Period size: 3 Copynumber: 29.3 Consensus size: 3
88697166 TTTACCTTAT
* * * *
88697176 TTA TT- TTA TTA TTA TAA TCA -TA TT- TTA TTA TTA TAA TCA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
88697220 -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
88697259 CATAGTATTC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 8 0.12
3 61 0.88
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:88697199 original size:19 final size:19
Alignment explanation
Indices: 88697177--88697249 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
88697167 TTACCTTATT
88697177 TATTTTATTATTATAATCA
1 TATTTTATTATTATAATCA
88697196 TATTTTATTATTATAATCA
1 TATTTTATTATTATAATCA
* * *
88697215 TATTATATTATTATTATTA
1 TATTTTATTATTATAATCA
88697234 TTATTATTATTATTAT
1 -TATT-TTATTATTAT
88697250 TATTATTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 35 0.73
20 4 0.08
21 9 0.19
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATTATTATAATCA
Found at i:88700985 original size:29 final size:29
Alignment explanation
Indices: 88700950--88701013 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
88700940 GGGTAGATTG
*
88700950 AAAGATTAAAGATTT-AAAGTTGGCTTGAT
1 AAAGATTAAAGATTTGAAA-TTGGCTGGAT
88700979 AAAGATTAAAGATTTGAAATTGGCTGGAT
1 AAAGATTAAAGATTTGAAATTGGCTGGAT
88701008 AAAGAT
1 AAAGAT
88701014 CAAATTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (29 bp):
AAAGATTAAAGATTTGAAATTGGCTGGAT
Found at i:88702875 original size:12 final size:12
Alignment explanation
Indices: 88702860--88702937 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
88702850 AAGAAACATT
*
88702860 ATCAGAACTAGA
1 ATCAGAATTAGA
* *
88702872 ATCAAAATGAGA
1 ATCAGAATTAGA
*
88702884 ATCAGAATCAGA
1 ATCAGAATTAGA
*
88702896 ATCAG--GT-G-
1 ATCAGAATTAGA
88702904 A-CAGAATTAGA
1 ATCAGAATTAGA
88702915 ATCAGAATTAGA
1 ATCAGAATTAGA
88702927 ATCAGAATTAG
1 ATCAGAATTAG
88702938 GTGACAGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 3 0.06
8 1 0.02
9 2 0.04
10 1 0.02
11 1 0.02
12 45 0.85
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (12 bp):
ATCAGAATTAGA
Found at i:88702890 original size:6 final size:6
Alignment explanation
Indices: 88702860--88702984 Score: 69
Period size: 6 Copynumber: 20.3 Consensus size: 6
88702850 AAGAAACATT
* * *
88702860 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * * * * *
88702909 ATTAGA ATCAGA ATTAGA ATCAGA ATTAG- GTGACAGA ATCAAA ACCAGT
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
88702958 ATCAGGTA A-CAGA ATCAGA ATCAGA AT
1 ATCA-G-A ATCAGA ATCAGA ATCAGA AT
88702985 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
5 5 0.06
6 71 0.81
7 9 0.10
8 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:88702910 original size:37 final size:37
Alignment explanation
Indices: 88702869--88702975 Score: 126
Period size: 37 Copynumber: 2.9 Consensus size: 37
88702859 TATCAGAACT
*
88702869 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* * * *
88702906 AGAATTAGAATCAGAATTAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* *
88702943 AGAATCAAAACCAGTATCAGGTAA-CAGAATCAG
1 AGAATCAAAATCAGAATCA-G-AATCAGAATCAG
88702976 AATCAGAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
37 46 0.81
38 9 0.16
39 2 0.04
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.19
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:88702945 original size:25 final size:25
Alignment explanation
Indices: 88702917--88702984 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
88702907 GAATTAGAAT
* * *
88702917 CAGAATTAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
* * *
88702942 CAGAATCAAAACCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
88702967 CAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAAT
88702985 GTGAATGCAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:88703265 original size:22 final size:22
Alignment explanation
Indices: 88703240--88703301 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
88703230 CACAATAACA
*
88703240 GCACACAGCCATAATCAGGTTG
1 GCACAAAGCCATAATCAGGTTG
*
88703262 GCACAAAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTG
**
88703284 GTGCAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
88703302 AATAATTGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTG
Found at i:88703847 original size:27 final size:27
Alignment explanation
Indices: 88703817--88703930 Score: 124
Period size: 27 Copynumber: 4.2 Consensus size: 27
88703807 GGCAAAATGA
* *
88703817 TAATTTTACCCCACAAGGGTATCTCAG
1 TAATTTTACCCTACAAGGGTATTTCAG
* *
88703844 TAATTCTACCCTACAGGGGTATTTC-G
1 TAATTTTACCCTACAAGGGTATTTCAG
88703870 -ATATTTCTACCCTACAAGGGTATTTCAG
1 TA-ATTT-TACCCTACAAGGGTATTTCAG
* * * *
88703898 TAATTCTACCTTACAGGGGTATTTCAA
1 TAATTTTACCCTACAAGGGTATTTCAG
88703925 TAATTT
1 TAATTT
88703931 GTAAATCGAG
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 4 0.06
27 62 0.86
28 4 0.06
29 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (27 bp):
TAATTTTACCCTACAAGGGTATTTCAG
Found at i:88703862 original size:54 final size:54
Alignment explanation
Indices: 88703804--88703916 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 54
88703794 TTAACACCCT
88703804 AGGGGCAAAAT-GATAATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
1 AGGGG-AAAATCGAT-ATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
* ** * * *
88703858 AGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCTTAC
1 AGGGGAAAATCGATATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
88703912 AGGGG
1 AGGGG
88703917 TATTTCAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
53 6 0.12
54 45 0.88
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (54 bp):
AGGGGAAAATCGATATTTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTAC
Found at i:88703917 original size:54 final size:53
Alignment explanation
Indices: 88703819--88703922 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
88703809 CAAAATGATA
88703819 ATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGAT
1 ATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGAT
* * *
88703872 ATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCTTACAGGGGTATTTC
1 ATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTC
88703923 AATAATTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGAT
Found at i:88705964 original size:6 final size:6
Alignment explanation
Indices: 88705955--88706054 Score: 62
Period size: 6 Copynumber: 16.2 Consensus size: 6
88705945 AATCAAAAAG
* * *
88705955 AGAATC AGAATC AGAATC AG-GTGAC AGAATC AAAATC AGAATT AGAATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
* * * *
88706004 AAAATT AGGCGA-C AGAATC AGAATC AGTATC AGGTAA-C AGAATC AGAATC
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
88706054 A
1 A
88706055 AAATGTGAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
5 4 0.06
6 57 0.80
7 7 0.10
8 3 0.04
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:88705984 original size:19 final size:18
Alignment explanation
Indices: 88705960--88706030 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
88705950 AAAAGAGAAT
*
88705960 CAGAATCAGAATCAGGTGA
1 CAGAATCAAAATCAGG-GA
*
88705979 CAGAATCAAAATCA-GAA
1 CAGAATCAAAATCAGGGA
* *
88705996 TTAGAATCAAAATTAGGCGA
1 -CAGAATCAAAATCAGG-GA
*
88706016 CAGAATCAGAATCAG
1 CAGAATCAAAATCAG
88706031 TATCAGGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 1 0.02
18 13 0.32
19 26 0.63
20 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (18 bp):
CAGAATCAAAATCAGGGA
Found at i:88706019 original size:25 final size:25
Alignment explanation
Indices: 88705991--88706058 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
88705981 GAATCAAAAT
* * *
88705991 CAGAATTAGAATCAAAATTAGGCGA
1 CAGAATCAGAATCAAAATCAGGCAA
** *
88706016 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAAAATCAGGCAA
88706041 CAGAATCAGAATCAAAAT
1 CAGAATCAGAATCAAAAT
88706059 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAAAATCAGGCAA
Done.