Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 11 of 16
Found at i:1523253 original size:23 final size:23
Alignment explanation
Indices: 1523222--1523305 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 23
1523212 TAAATAAATT
*
1523222 ATAAAATAATATTTTATTAATAA
1 ATAATATAATATTTTATTAATAA
* *
1523245 ATAATATAAAAATTTTA-AAATAA
1 ATAATAT-AATATTTTATTAATAA
1523268 ATATATATAATTATTTT-TTAAAATAA
1 ATA-ATATAA-TATTTTATT--AATAA
*
1523294 ATAATATCATAT
1 ATAATATAATAT
1523306 GATTTTTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
23 16 0.33
24 20 0.41
25 5 0.10
26 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATATAATATTTTATTAATAA
Found at i:1523311 original size:26 final size:26
Alignment explanation
Indices: 1523257--1523313 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1523247 AATATAAAAA
*
1523257 TTTTAAAATAAATATATATAATTATT
1 TTTTAAAATAAATATATATAATGATT
1523283 TTTTAAAATAAATA-ATATCATATGATT
1 TTTTAAAATAAATATATAT-A-ATGATT
1523310 TTTT
1 TTTT
1523314 TGTCCATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 15 0.54
27 9 0.32
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTAAAATAAATATATATAATGATT
Found at i:1523387 original size:2 final size:2
Alignment explanation
Indices: 1523369--1523403 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1523359 TTTCTCTAGC
* *
1523369 TA TA TG TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1523404 CACGAGTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1525722 original size:39 final size:40
Alignment explanation
Indices: 1525679--1525756 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
1525669 ATTTGAGGGA
* * *
1525679 TCAATTTATATATTAAATCATAAATAAACTTTA-TTGGGG
1 TCAATTCATATATTAAACCATAAACAAACTTTACTTGGGG
* *
1525718 TCAATTCATATATTAACCCATAAGCAAACTTTACTTGGG
1 TCAATTCATATATTAAACCATAAACAAACTTTACTTGGG
1525757 ATTTTATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (40 bp):
TCAATTCATATATTAAACCATAAACAAACTTTACTTGGGG
Found at i:1526748 original size:8 final size:7
Alignment explanation
Indices: 1526737--1526779 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
1526727 ACTTTTAAAT
1526737 ATATATA
1 ATATATA
1526744 TATATATA
1 -ATATATA
*
1526752 ATATAAA
1 ATATATA
1526759 GATATATAA
1 -ATATAT-A
1526768 ATATATA
1 ATATATA
1526775 ATATA
1 ATATA
1526780 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 12 0.39
8 18 0.58
9 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:1526763 original size:23 final size:23
Alignment explanation
Indices: 1526732--1526780 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1526722 TCAAAACTTT
* *
1526732 TAAATATATATATATATATAATA
1 TAAAGATATATAAATATATAATA
1526755 TAAAGATATATAAATATATAATA
1 TAAAGATATATAAATATATAATA
1526778 TAA
1 TAA
1526781 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAGATATATAAATATATAATA
Found at i:1526842 original size:22 final size:21
Alignment explanation
Indices: 1526793--1526842 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
1526783 AATTTTTTAA
* *
1526793 AAATTTATATAAATATAATAT
1 AAATTTTTATAAATAAAATAT
1526814 --ATTTTTATAAATAAAATATT
1 AAATTTTTATAAATAAAATA-T
1526834 AAATTTTTA
1 AAATTTTTA
1526843 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 16 0.67
20 1 0.04
22 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTTTATAAATAAAATAT
Found at i:1527178 original size:27 final size:26
Alignment explanation
Indices: 1527130--1527180 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1527120 TTAATGGATT
*
1527130 TAAAAAAAATTAATTTTAAATAAACA
1 TAAAAAAAATTAATATTAAATAAACA
1527156 TAAAATAAAATTAATAATT-AATAAA
1 TAAAA-AAAATTAAT-ATTAAATAAA
1527181 ATATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 15 0.68
28 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAAAAATTAATATTAAATAAACA
Found at i:1527665 original size:23 final size:26
Alignment explanation
Indices: 1527635--1527698 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
1527625 TCAAATTATT
*
1527635 TTTATTATA-T-AATGATA-AATTTA
1 TTTATTATATTAAATAATACAATTTA
1527658 TTTATTATATTAAATAATACAATTTA
1 TTTATTATATTAAATAATACAATTTA
*
1527684 TTTATTAGATTAAAT
1 TTTATTATATTAAAT
1527699 TACCTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 9 0.25
24 1 0.03
25 6 0.17
26 20 0.56
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TTTATTATATTAAATAATACAATTTA
Found at i:1527782 original size:18 final size:19
Alignment explanation
Indices: 1527749--1527785 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1527739 GATAACATAT
1527749 TTATATATTATTTAAAATA
1 TTATATATTATTTAAAATA
1527768 TTATATATT-TTTAAAATA
1 TTATATATTATTTAAAATA
1527786 AAATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATTATTTAAAATA
Found at i:1527806 original size:7 final size:6
Alignment explanation
Indices: 1527780--1527818 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1527770 ATATATTTTT
*
1527780 AAAAT- AAAATA AAATTA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1527819 CCTCCTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:1528659 original size:39 final size:41
Alignment explanation
Indices: 1528615--1528703 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 41
1528605 CAGTATTGGC
1528615 GGTGTTGGCGGCTTCACAA-T-AGGACTTGGAGAGACAGGA
1 GGTGTTGGCGGCTTCACAATTGAGGACTTGGAGAGACAGGA
*
1528654 GGTGTTGGTGGCTTCACAATTGGAGGACTTGGAGAGACAGGA
1 GGTGTTGGCGGCTTCACAATT-GAGGACTTGGAGAGACAGGA
1528696 GGTGTTGG
1 GGTGTTGG
1528704 AGGCAGAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 18 0.39
40 1 0.02
42 27 0.59
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (41 bp):
GGTGTTGGCGGCTTCACAATTGAGGACTTGGAGAGACAGGA
Found at i:1528690 original size:102 final size:100
Alignment explanation
Indices: 1528561--1528762 Score: 316
Period size: 102 Copynumber: 2.0 Consensus size: 100
1528551 CTCAACTGGG
* *
1528561 GGTGGCTTCACAATAGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGTATTGGCGGTGTTGGCGG
1 GGTGGCTTCACAATAGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGAACTGGCGGTGTTGGCGG
1528626 CTTCACAAT-AGGACTTGGAGAGACAGGAGGTGTT
66 CTTCACAATGAGGACTTGGAGAGACAGGAGGTGTT
1528660 GGTGGCTTCACAATTGGAGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGAACTGGCGGTGTTGG
1 GGTGGCTTCACAA-T--AGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGAACTGGCGGTGTTGG
* *
1528725 TGGCTTCACAATAGGAGGACTTGGATAGACAGGAGGTG
63 CGGCTTCACAAT--GAGGACTTGGAGAGACAGGAGGTG
1528763 CTGGAGGCAG
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
99 13 0.14
100 1 0.01
102 57 0.61
105 22 0.24
ACGTcount: A:0.24, C:0.13, G:0.41, T:0.22
Consensus pattern (100 bp):
GGTGGCTTCACAATAGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGAACTGGCGGTGTTGGCGG
CTTCACAATGAGGACTTGGAGAGACAGGAGGTGTT
Found at i:1528726 original size:63 final size:63
Alignment explanation
Indices: 1528654--1528972 Score: 462
Period size: 63 Copynumber: 5.1 Consensus size: 63
1528644 AGAGACAGGA
* * *
1528654 GGTGTTGGTGGCTTCACAATTGGAGGACTTGGAGAGACAGGAGGTGTTGGAGGCAGAACTGGC
1 GGTGTTGGTGGCTTCACAATTGGAGGACTAGGATAGACAGGAGGTGTTGGAGGCAGAATTGGC
* * *
1528717 GGTGTTGGTGGCTTCACAATAGGAGGACTTGGATAGACAGGAGGTGCTGGAGGCAGAATTGGC
1 GGTGTTGGTGGCTTCACAATTGGAGGACTAGGATAGACAGGAGGTGTTGGAGGCAGAATTGGC
* *
1528780 GGTGTTGGTGGCTTCACAATAGGAGGACTAGGATAAACAGGAGGTGTTGGAGGCAGAATTGGC
1 GGTGTTGGTGGCTTCACAATTGGAGGACTAGGATAGACAGGAGGTGTTGGAGGCAGAATTGGC
* * * *
1528843 GATGTTGGTGGCTTCACAATTGGAGGACTAGGATAAACAGGAGGTGCTGGAGGCAGAATTGGT
1 GGTGTTGGTGGCTTCACAATTGGAGGACTAGGATAGACAGGAGGTGTTGGAGGCAGAATTGGC
* * * *
1528906 GGCGTTGGTGGCTTCACAATTGGAGGAC-ACGGAGAGACAGGAGGCT-TTGGAGGCAGAACTGGT
1 GGTGTTGGTGGCTTCACAATTGGAGGACTA-GGATAGACAGGAGG-TGTTGGAGGCAGAATTGGC
1528969 GGTG
1 GGTG
1528973 ATATGACCGG
Statistics
Matches: 236, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
62 1 0.00
63 234 0.99
64 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.41, T:0.22
Consensus pattern (63 bp):
GGTGTTGGTGGCTTCACAATTGGAGGACTAGGATAGACAGGAGGTGTTGGAGGCAGAATTGGC
Found at i:1529130 original size:36 final size:36
Alignment explanation
Indices: 1529083--1529208 Score: 89
Period size: 36 Copynumber: 3.3 Consensus size: 36
1529073 CGGCACGTAG
*
1529083 GGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGACA
1 GGAGGTTTGGGTGTAAAAGGTGGAGGCTTTACGACA
* *
1529119 GGAGGTTT-GG-GTACATA-G-GGTGGCTTTGGCACTGGCACGTA
1 GGAGGTTTGGGTGTA-AAAGGTGGAGGCTTT---AC--G-AC--A
* *
1529160 GGGAGGTTTTGGTGTATAAGGTGGAGGCTTTACGACA
1 -GGAGGTTTGGGTGTAAAAGGTGGAGGCTTTACGACA
1529197 GGAGGTTTGGGT
1 GGAGGTTTGGGT
1529209 ACATAGGGAG
Statistics
Matches: 69, Mismatches: 7, Indels: 28
0.66 0.07 0.27
Matches are distributed among these distances:
33 8 0.12
34 4 0.06
35 4 0.06
36 20 0.29
37 1 0.01
38 1 0.01
39 4 0.06
40 1 0.01
41 1 0.01
42 10 0.14
43 3 0.04
44 4 0.06
45 8 0.12
ACGTcount: A:0.20, C:0.10, G:0.43, T:0.27
Consensus pattern (36 bp):
GGAGGTTTGGGTGTAAAAGGTGGAGGCTTTACGACA
Found at i:1529157 original size:78 final size:78
Alignment explanation
Indices: 1529053--1529225 Score: 283
Period size: 78 Copynumber: 2.2 Consensus size: 78
1529043 GGGCTTAGGA
* *
1529053 ACATAAGGTGGCTTGGGCACCGGCACGTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGAC
1 ACATAGGGTGGCTTTGGCACCGGCACGTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGAC
1529118 AGGAGGTTTGGGT
66 AGGAGGTTTGGGT
* * * *
1529131 ACATAGGGTGGCTTTGGCACTGGCACGTAGGGAGGTTTTGGTGTATAAGGTGGAGGCTTTACGAC
1 ACATAGGGTGGCTTTGGCACCGGCACGTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGAC
1529196 AGGAGGTTTGGGT
66 AGGAGGTTTGGGT
*
1529209 ACATAGGGAGGCTTTGG
1 ACATAGGGTGGCTTTGG
1529226 AGTATAAGGT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 88 1.00
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.25
Consensus pattern (78 bp):
ACATAGGGTGGCTTTGGCACCGGCACGTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGAC
AGGAGGTTTGGGT
Found at i:1529239 original size:174 final size:177
Alignment explanation
Indices: 1529014--1529357 Score: 487
Period size: 174 Copynumber: 2.0 Consensus size: 177
1529004 TGGGGGTTTG
* *
1529014 ACGACAGGAGGTTTGGGTACGTAAGGTGGGGGCTTAGGAACATAAGGTGGCTTGGGCACCGGCAC
1 ACGACAGGAGGTTTGGGTACATAAGGTGGAGGCTTAGGAACATAAGGTGGCTTGGGCACCGGCAC
* *
1529079 GTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGACAGGAGGTTTGGGTACATAGGGTGGCT
66 GTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGACAGGAGGTTTGGGTACATAAGGTGGCC
* * * *
1529144 TTGGCACTGGCACGTAGGGAGGTTTTGGTGTATAAGGTGGAGGCTTT
131 TGGGCACGGGCACGTAGGGAGGCTTTGGAGTATAAGGTGGAGGCTTT
* ** *
1529191 ACGACAGGAGGTTTGGGTACAT-A-G-GGAGGCTTTGGAGTATAAGGTGGCTTGGGCACTGGCAC
1 ACGACAGGAGGTTTGGGTACATAAGGTGGAGGCTTAGGAACATAAGGTGGCTTGGGCACCGGCAC
* * * * * **
1529253 GTAGGGAGGTTTTGGTGTATAAGGTGGTGGTTTTACGACAGGAGGTTTGGGTGTATAAGGTGGCC
66 GTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGACAGGAGGTTTGGGTACATAAGGTGGCC
*
1529318 TGGGTACGGGCACGTAGGGAGGCTTTGGAGTATAAGGTGG
131 TGGGCACGGGCACGTAGGGAGGCTTTGGAGTATAAGGTGG
1529358 CTTGGGTACC
Statistics
Matches: 147, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
174 124 0.84
175 1 0.01
176 1 0.01
177 21 0.14
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (177 bp):
ACGACAGGAGGTTTGGGTACATAAGGTGGAGGCTTAGGAACATAAGGTGGCTTGGGCACCGGCAC
GTAGGGAGGCTTGGGTGTAAAAGGTGGAGGCTTTACGACAGGAGGTTTGGGTACATAAGGTGGCC
TGGGCACGGGCACGTAGGGAGGCTTTGGAGTATAAGGTGGAGGCTTT
Found at i:1529259 original size:42 final size:41
Alignment explanation
Indices: 1529212--1529399 Score: 194
Period size: 42 Copynumber: 4.6 Consensus size: 41
1529202 TTTGGGTACA
* *
1529212 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGCACTGGCACG
1 TAGGGAGGCTTTGGTGTATAAGGTGGCTTGGGTAC-GGCACG
* *
1529254 TAGGGAGGTTTTGGTGTATAAGGTGG--TGGTTTTAC-G-AC-
1 TAGGGAGGCTTTGGTGTATAAGGTGGCTTGG--GTACGGCACG
*
1529292 -A-GGAGG-TTTGGGTGTATAAGGTGGCCTGGGTACGGGCACG
1 TAGGGAGGCTTT-GGTGTATAAGGTGGCTTGGGTAC-GGCACG
*
1529332 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGTACCGGCACG
1 TAGGGAGGCTTTGGTGTATAAGGTGGCTTGGGTA-CGGCACG
* *
1529374 TAGGGAGGCTTGGGTGTGTAAGGTGG
1 TAGGGAGGCTTTGGTGTATAAGGTGG
1529400 AGGCTTTACA
Statistics
Matches: 123, Mismatches: 10, Indels: 26
0.77 0.06 0.16
Matches are distributed among these distances:
35 3 0.02
36 22 0.18
37 1 0.01
38 4 0.03
39 4 0.03
40 4 0.03
41 1 0.01
42 80 0.65
43 4 0.03
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.27
Consensus pattern (41 bp):
TAGGGAGGCTTTGGTGTATAAGGTGGCTTGGGTACGGCACG
Found at i:1529352 original size:120 final size:120
Alignment explanation
Indices: 1529212--1529429 Score: 337
Period size: 120 Copynumber: 1.8 Consensus size: 120
1529202 TTTGGGTACA
* * *
1529212 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGCACTGGCACGTAGGGAGGTTTTGGTGTATAAGG
1 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGCACCGGCACGTAGGGAGGCTTGGGTGTATAAGG
* * * * *
1529277 TGGTGGTTTTACGACAGGAGGTTTGGGTGTATAAGGTGGCCTGGGTACGGGCACG
66 TGGAGGCTTTACAACAGGAGGCTTGGGTATATAAGGTGGCCTGGGTACGGGCACG
* *
1529332 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGTACCGGCACGTAGGGAGGCTTGGGTGTGTAAGG
1 TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGCACCGGCACGTAGGGAGGCTTGGGTGTATAAGG
*
1529397 TGGAGGCTTTACAACAGGTGGCTTGGGTATATA
66 TGGAGGCTTTACAACAGGAGGCTTGGGTATATA
1529430 GGGAGGCTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 87 1.00
ACGTcount: A:0.19, C:0.11, G:0.43, T:0.27
Consensus pattern (120 bp):
TAGGGAGGCTTTGGAGTATAAGGTGGCTTGGGCACCGGCACGTAGGGAGGCTTGGGTGTATAAGG
TGGAGGCTTTACAACAGGAGGCTTGGGTATATAAGGTGGCCTGGGTACGGGCACG
Found at i:1529439 original size:33 final size:33
Alignment explanation
Indices: 1529398--1529560 Score: 155
Period size: 33 Copynumber: 4.7 Consensus size: 33
1529388 TGTGTAAGGT
* *
1529398 GGAGGCTTTACAACAGGTGGCTTGGGTATATAG
1 GGAGGCTTTACAACAGGAGGCTTGGGTACATAG
*
1529431 GGAGGCTTTACAACAGGAGGTTTGGGTACATAG
1 GGAGGCTTTACAACAGGAGGCTTGGGTACATAG
* * *
1529464 GGAGGCTTTACCACCGGAGGCTTAGGTGGCTTGGGTATATGG
1 GGAGGCTTTA-CA----A--C--AGGAGGCTTGGGTACATAG
* *
1529506 GGAGGCTTTACAACAGGAGGTTTGGGTACATGG
1 GGAGGCTTTACAACAGGAGGCTTGGGTACATAG
* *
1529539 GGAGGCTTTACCACCGGAGGCT
1 GGAGGCTTTACAACAGGAGGCT
1529561 GAGGTGGCTT
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
33 75 0.69
34 2 0.02
35 1 0.01
37 1 0.01
38 1 0.01
40 1 0.01
41 2 0.02
42 25 0.23
ACGTcount: A:0.22, C:0.15, G:0.38, T:0.25
Consensus pattern (33 bp):
GGAGGCTTTACAACAGGAGGCTTGGGTACATAG
Found at i:1529511 original size:42 final size:41
Alignment explanation
Indices: 1529452--1529573 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 41
1529442 AACAGGAGGT
*
1529452 TTGGGTACATAGGGAGGCTTTACCACCGGAGGCTTAGGTGGC
1 TTGGGTACATGGGGAGGCTTTACCACCGGAGGC-TAGGTGGC
* *
1529494 TTGGGTATATGGGGAGGCTTTA-CAAC--AGG--AGGT---
1 TTGGGTACATGGGGAGGCTTTACCACCGGAGGCTAGGTGGC
1529527 TTGGGTACATGGGGAGGCTTTACCACCGGAGGCTGAGGTGGC
1 TTGGGTACATGGGGAGGCTTTACCACCGGAGGCT-AGGTGGC
1529569 TTGGG
1 TTGGG
1529574 AGGATGGGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
33 21 0.32
34 3 0.05
36 7 0.11
39 7 0.11
41 3 0.05
42 25 0.38
ACGTcount: A:0.19, C:0.16, G:0.41, T:0.25
Consensus pattern (41 bp):
TTGGGTACATGGGGAGGCTTTACCACCGGAGGCTAGGTGGC
Found at i:1529582 original size:75 final size:75
Alignment explanation
Indices: 1529412--1529573 Score: 297
Period size: 75 Copynumber: 2.2 Consensus size: 75
1529402 GCTTTACAAC
*
1529412 AGGTGGCTTGGGTATATAGGGAGGCTTTACAACAGGAGGTTTGGGTACATAGGGAGGCTTTACCA
1 AGGTGGCTTGGGTATATGGGGAGGCTTTACAACAGGAGGTTTGGGTACATAGGGAGGCTTTACCA
*
1529477 CCGGAGGCTT
66 CCGGAGGCTG
*
1529487 AGGTGGCTTGGGTATATGGGGAGGCTTTACAACAGGAGGTTTGGGTACATGGGGAGGCTTTACCA
1 AGGTGGCTTGGGTATATGGGGAGGCTTTACAACAGGAGGTTTGGGTACATAGGGAGGCTTTACCA
1529552 CCGGAGGCTG
66 CCGGAGGCTG
1529562 AGGTGGCTTGGG
1 AGGTGGCTTGGG
1529574 AGGATGGGGT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.20, C:0.14, G:0.41, T:0.25
Consensus pattern (75 bp):
AGGTGGCTTGGGTATATGGGGAGGCTTTACAACAGGAGGTTTGGGTACATAGGGAGGCTTTACCA
CCGGAGGCTG
Found at i:1529638 original size:63 final size:63
Alignment explanation
Indices: 1529566--1529741 Score: 226
Period size: 63 Copynumber: 2.8 Consensus size: 63
1529556 AGGCTGAGGT
* ** * *
1529566 GGCTTGGGAGGATGGGGTGGACGTTTTGGTGGTTTCTGGTGATATGGAGGATTTGCTACAGGA
1 GGCTTGGGAGGATGGGGTGGACGTTTGGGTGGTTTAGGGTGAAATGGAGGATTTACTACAGGA
* * *
1529629 GGCTTGGGAGGATGGGGTAGATGTTTGGGTGGTTTAGGGTGAAATGGAGGCTTTACTACAGGA
1 GGCTTGGGAGGATGGGGTGGACGTTTGGGTGGTTTAGGGTGAAATGGAGGATTTACTACAGGA
* * * * * *
1529692 GGCTTGGGATGATGGGGTGGATGTCTGGGCGGTTTAGGATAAAATGGAGG
1 GGCTTGGGAGGATGGGGTGGACGTTTGGGTGGTTTAGGGTGAAATGGAGG
1529742 CTTCACAACG
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 99 1.00
ACGTcount: A:0.19, C:0.07, G:0.45, T:0.29
Consensus pattern (63 bp):
GGCTTGGGAGGATGGGGTGGACGTTTGGGTGGTTTAGGGTGAAATGGAGGATTTACTACAGGA
Found at i:1529756 original size:63 final size:63
Alignment explanation
Indices: 1529623--1529756 Score: 187
Period size: 63 Copynumber: 2.1 Consensus size: 63
1529613 AGGATTTGCT
* * * * * *
1529623 ACAGGAGGCTTGGGAGGATGGGGTAGATGTTTGGGTGGTTTAGGGTGAAATGGAGGCTTTACT
1 ACAGGAGGCTTGGGAGGATGGGGTAGATGTCTGGGCGGTTTAGGATAAAATGGAGGCTTCACA
* *
1529686 ACAGGAGGCTTGGGATGATGGGGTGGATGTCTGGGCGGTTTAGGATAAAATGGAGGCTTCACA
1 ACAGGAGGCTTGGGAGGATGGGGTAGATGTCTGGGCGGTTTAGGATAAAATGGAGGCTTCACA
*
1529749 ACGGGAGG
1 ACAGGAGG
1529757 ATGTTTGGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.25
Consensus pattern (63 bp):
ACAGGAGGCTTGGGAGGATGGGGTAGATGTCTGGGCGGTTTAGGATAAAATGGAGGCTTCACA
Found at i:1530542 original size:18 final size:18
Alignment explanation
Indices: 1530516--1530552 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1530506 ATAATTTTAA
1530516 AATAAATATATTATATTT
1 AATAAATATATTATATTT
* *
1530534 AATATATATCTTATATTT
1 AATAAATATATTATATTT
1530552 A
1 A
1530553 TTTTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAAATATATTATATTT
Found at i:1531020 original size:18 final size:18
Alignment explanation
Indices: 1530977--1531020 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1530967 ACAAATTTTT
1530977 TAATA-TAAAAAATATTA
1 TAATATTAAAAAATATTA
*
1530994 TAATTTTAAAAAA-ATTA
1 TAATATTAAAAAATATTA
1531011 TAAATATTAA
1 T-AATATTAA
1531021 TATTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATATTAAAAAATATTA
Found at i:1531057 original size:15 final size:15
Alignment explanation
Indices: 1531011--1531060 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1531001 AAAAAAATTA
*
1531011 TAAATATTAA-TATT
1 TAAATATTAATTAAT
* *
1531025 TAAATTTTAAATTTAT
1 TAAATATT-AATTAAT
1531041 TAAATATTAATTAAT
1 TAAATATTAATTAAT
1531056 TAAAT
1 TAAAT
1531061 TGAGATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 7 0.24
15 13 0.45
16 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATTAATTAAT
Found at i:1531355 original size:26 final size:24
Alignment explanation
Indices: 1531309--1531357 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1531299 TAAAATTATT
*
1531309 TATATTTAAATATAATTAATAAAA
1 TATATTTAAATATAATGAATAAAA
1531333 TATATTTAAATATATAATGAATAAA
1 TATATTT-AA-ATATAATGAATAAA
1531358 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 2 0.09
26 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TATATTTAAATATAATGAATAAAA
Found at i:1531373 original size:26 final size:25
Alignment explanation
Indices: 1531316--1531373 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
1531306 ATTTATATTT
* * * *
1531316 AAATATAATTAATAAAATATATTTA
1 AAATATAATGAATAAAAAAAATATA
1531341 AATATATAATGAATAAATAAAAATATA
1 AA-ATATAATGAATAAA-AAAAATATA
1531368 AAATAT
1 AAATAT
1531374 GATACATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.07
26 17 0.63
27 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATATAATGAATAAAAAAAATATA
Found at i:1531495 original size:26 final size:26
Alignment explanation
Indices: 1531466--1531588 Score: 79
Period size: 24 Copynumber: 5.0 Consensus size: 26
1531456 TTATAATTTT
1531466 TTATATTAATAATTAATATATTTATA
1 TTATATTAATAATTAATATATTTATA
* * *
1531492 TTATATT--TATTTATTTTATTCTATAA
1 TTATATTAATAATTAATATATT-TAT-A
1531518 TTATATT--TAA--AATAT-TTTATA
1 TTATATTAATAATTAATATATTTATA
*
1531539 TT-TATATAA-ATTTAATATA-TTATA
1 TTATAT-TAATAATTAATATATTTATA
* * *
1531563 TTTTA-AAATAATTTATATATTTATA
1 TTATATTAATAATTAATATATTTATA
1531588 T
1 T
1531589 ATTTTTAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
20 3 0.04
21 4 0.05
22 4 0.05
23 4 0.05
24 33 0.43
25 11 0.14
26 17 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATTAATAATTAATATATTTATA
Found at i:1531572 original size:17 final size:18
Alignment explanation
Indices: 1531519--1531585 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 18
1531509 ATTCTATAAT
*
1531519 TATATTTAAAATATTTTA
1 TATATTTAAAATAATTTA
*
1531537 TAT-TTATATAAATTTAATATA
1 TATATT-TA-AAA--TAATTTA
1531558 TTATATTTTAAAATAATTTA
1 -TATA-TTTAAAATAATTTA
1531578 TATATTTA
1 TATATTTA
1531586 TATATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
17 2 0.05
18 9 0.23
19 7 0.18
20 6 0.15
21 5 0.13
22 6 0.15
23 2 0.05
24 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTTAAAATAATTTA
Found at i:1531596 original size:43 final size:41
Alignment explanation
Indices: 1531492--1531597 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 41
1531482 TATATTTATA
* **
1531492 TTATATTTATTTATTTTATTCTATAATTATATTTAAAATATT
1 TTATATTTATATATTTT-TAATATAATTATATTTAAAATATT
**
1531534 TTATATTTATATAAATTTAATAT-ATTATATTTTAAAATAATT
1 TTATATTTATATATTTTTAATATAATTATA-TTTAAAAT-ATT
1531576 TATATATTTATATATTTTTAAT
1 T-TATATTTATATATTTTTAAT
1531598 TAGATCGTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
40 6 0.11
41 12 0.22
42 18 0.33
43 18 0.33
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (41 bp):
TTATATTTATATATTTTTAATATAATTATATTTAAAATATT
Found at i:1534361 original size:8 final size:8
Alignment explanation
Indices: 1534350--1534384 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1534340 GATATTATAA
*
1534350 TTATTATT
1 TTATAATT
1534358 TTATAATT
1 TTATAATT
*
1534366 TTATTATT
1 TTATAATT
1534374 TTATAATT
1 TTATAATT
1534382 TTA
1 TTA
1534385 ATTTTTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATAATT
Found at i:1534371 original size:16 final size:16
Alignment explanation
Indices: 1534350--1534384 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1534340 GATATTATAA
1534350 TTATTATTTTATAATT
1 TTATTATTTTATAATT
1534366 TTATTATTTTATAATT
1 TTATTATTTTATAATT
1534382 TTA
1 TTA
1534385 ATTTTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTTTATAATT
Found at i:1536464 original size:312 final size:312
Alignment explanation
Indices: 1535899--1536521 Score: 1237
Period size: 312 Copynumber: 2.0 Consensus size: 312
1535889 TCGAGGGTAA
1535899 AATAATGCTCTAATCCTGTTTCAATTCTGTTTATCAATCAATCTGGATGAAGCACCAAAATAAAT
1 AATAATGCTCTAATCCTGTTTCAATTCTGTTTATCAATCAATCTGGATGAAGCACCAAAATAAAT
1535964 CCAAATGTTATTTGGCAGTGAAACCAAAAAACAACTAAGTATTACCAACTTTATCAAAAACAATA
66 CCAAATGTTATTTGGCAGTGAAACCAAAAAACAACTAAGTATTACCAACTTTATCAAAAACAATA
1536029 TTTAAACAACTTAGCAAAACCTTCATAACGCCAATACCACAGGGGAATTGCAAGAAACTTCTCAA
131 TTTAAACAACTTAGCAAAACCTTCATAACGCCAATACCACAGGGGAATTGCAAGAAACTTCTCAA
1536094 AATTTAACAAAATGGTCAAGAGAGGATTACCTAAGTAATACCAATGTTTTTCTAATGCTGTCTTC
196 AATTTAACAAAATGGTCAAGAGAGGATTACCTAAGTAATACCAATGTTTTTCTAATGCTGTCTTC
1536159 GACTCAACTGACAATATGAAATCAAAAAACTAAAAGTTTTTAACTAGTCGAC
261 GACTCAACTGACAATATGAAATCAAAAAACTAAAAGTTTTTAACTAGTCGAC
1536211 AATAATGCTCTAATCCTGTTTCAATTCTGTTTATCAATCAATCTGGATGAAGCACCAAAATAAAT
1 AATAATGCTCTAATCCTGTTTCAATTCTGTTTATCAATCAATCTGGATGAAGCACCAAAATAAAT
1536276 CCAAATGTTATTTGGCAGTGAAACCAAAAAACAACTAAGTATTACCAACTTTATCAAAAACAATA
66 CCAAATGTTATTTGGCAGTGAAACCAAAAAACAACTAAGTATTACCAACTTTATCAAAAACAATA
1536341 TTTAAACAACTTAGCAAAACCTTCATAACGCCAATACCACAGGGGAATTGCAAGAAACTTCTCAA
131 TTTAAACAACTTAGCAAAACCTTCATAACGCCAATACCACAGGGGAATTGCAAGAAACTTCTCAA
*
1536406 AATTTAACAAAATGGTCAAGAGAGGATTACCTAAGTAATACCAATGTTTTTCTAATGCTGTTTTC
196 AATTTAACAAAATGGTCAAGAGAGGATTACCTAAGTAATACCAATGTTTTTCTAATGCTGTCTTC
1536471 GACTCAACTGACAATATGAAATCAAAAAACTAAAAGTTTTTAACTAGTCGA
261 GACTCAACTGACAATATGAAATCAAAAAACTAAAAGTTTTTAACTAGTCGA
1536522 ATAACAAAAC
Statistics
Matches: 310, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
312 310 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (312 bp):
AATAATGCTCTAATCCTGTTTCAATTCTGTTTATCAATCAATCTGGATGAAGCACCAAAATAAAT
CCAAATGTTATTTGGCAGTGAAACCAAAAAACAACTAAGTATTACCAACTTTATCAAAAACAATA
TTTAAACAACTTAGCAAAACCTTCATAACGCCAATACCACAGGGGAATTGCAAGAAACTTCTCAA
AATTTAACAAAATGGTCAAGAGAGGATTACCTAAGTAATACCAATGTTTTTCTAATGCTGTCTTC
GACTCAACTGACAATATGAAATCAAAAAACTAAAAGTTTTTAACTAGTCGAC
Found at i:1539053 original size:23 final size:26
Alignment explanation
Indices: 1539009--1539056 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 26
1538999 AATACAATAC
1539009 ATTTAAAATATGTGTAATATATTTAT
1 ATTTAAAATATGTGTAATATATTTAT
1539035 ATTTAAAAT-T-T-TAATATATTTA
1 ATTTAAAATATGTGTAATATATTTA
1539057 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 1 0.05
26 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTAAAATATGTGTAATATATTTAT
Found at i:1542195 original size:10 final size:10
Alignment explanation
Indices: 1542180--1542209 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1542170 AATAAGATAA
1542180 ATATTTAAAT
1 ATATTTAAAT
1542190 ATATTTAAAT
1 ATATTTAAAT
1542200 AT-TTTAAAT
1 ATATTTAAAT
1542209 A
1 A
1542210 ATTAATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATTTAAAT
Found at i:1544057 original size:14 final size:14
Alignment explanation
Indices: 1544038--1544064 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1544028 TTTTAATTGT
1544038 TCATTAAGAGATGC
1 TCATTAAGAGATGC
1544052 TCATTAAGAGATG
1 TCATTAAGAGATG
1544065 GGAGTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (14 bp):
TCATTAAGAGATGC
Found at i:1550652 original size:17 final size:18
Alignment explanation
Indices: 1550630--1550669 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1550620 CATAATCGTG
1550630 TTTAAAAAATTTT-ATAT
1 TTTAAAAAATTTTGATAT
1550647 TTTAAAAAATTTTGATAT
1 TTTAAAAAATTTTGATAT
*
1550665 ATTAA
1 TTTAA
1550670 TATGTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAAAAAATTTTGATAT
Found at i:1553156 original size:12 final size:12
Alignment explanation
Indices: 1553139--1553169 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1553129 TAATCACATG
1553139 ATAATAATGATA
1 ATAATAATGATA
1553151 ATAATAATGATA
1 ATAATAATGATA
1553163 ATAATAA
1 ATAATAA
1553170 CAACAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
ATAATAATGATA
Found at i:1555307 original size:4 final size:4
Alignment explanation
Indices: 1555298--1555324 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1555288 TTGGAAGAAA
1555298 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1555325 ATCAAGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1556218 original size:16 final size:16
Alignment explanation
Indices: 1556188--1556217 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1556178 TTTCTTTTCA
1556188 AATTTATAATTTTTTG
1 AATTTATAATTTTTTG
1556204 AATTTA-AATTTTTT
1 AATTTATAATTTTTT
1556218 TAGTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
AATTTATAATTTTTTG
Found at i:1556225 original size:16 final size:16
Alignment explanation
Indices: 1556206--1556252 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
1556196 ATTTTTTGAA
*
1556206 TTTAAATTTTTTTAGT
1 TTTAAATTATTTTAGT
1556222 TTTAAATTATTTTAGT
1 TTTAAATTATTTTAGT
1556238 TTTAAATTATTTTAG
1 TTTAAATTATTTTAG
1556253 ATTCAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTAAATTATTTTAGT
Found at i:1556674 original size:16 final size:17
Alignment explanation
Indices: 1556632--1556678 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1556622 TGATACATTC
*
1556632 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
1556649 ATATTATATTTTA-ATT
1 ATATTATATTTTATATT
* *
1556665 ATTTTTTATTTTAT
1 ATATTATATTTTAT
1556679 TTTAATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1556919 original size:3 final size:3
Alignment explanation
Indices: 1556913--1556958 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1556903 TAATTTAGCC
1556913 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1556959 AGTTTAGGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1557128 original size:22 final size:21
Alignment explanation
Indices: 1557056--1557132 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
1557046 ATTAATATCT
*
1557056 ATTTTTAT-TATATTTATATTA
1 ATTTTAATATATATTTATA-TA
* * *
1557077 TTTTTAAATTTTATAATTATATA
1 ATTTT-AA-TATATATTTATATA
*
1557100 A-TGTAATATATATTTATATAA
1 ATTTTAATATATATTTATAT-A
1557121 ATTTTAATATAT
1 ATTTTAATATAT
1557133 TATAATATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 11 0.26
21 8 0.19
22 12 0.28
23 3 0.07
24 9 0.21
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
ATTTTAATATATATTTATATA
Found at i:1557163 original size:30 final size:30
Alignment explanation
Indices: 1557103--1557171 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
1557093 TTATATAATG
* *
1557103 TAATATATATTTATATAAATTTTAATATATT
1 TAATAT-TATTTATATAAAATTTAACATATT
*
1557134 ATAATATTA-TTATATAAAATTTGACATATT
1 -TAATATTATTTATATAAAATTTAACATATT
1557164 TATATATT
1 TA-ATATT
1557172 CATATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.06
30 23 0.70
31 2 0.06
32 6 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (30 bp):
TAATATTATTTATATAAAATTTAACATATT
Found at i:1557482 original size:94 final size:93
Alignment explanation
Indices: 1557362--1557596 Score: 303
Period size: 94 Copynumber: 2.5 Consensus size: 93
1557352 TTCTAATAAC
1557362 AATTAAATTAAATTTATCAAATTAAATTACAAAATATTAATAAAATCATAAATAATTTT-ATATA
1 AATTAAATTAAATTTATCAAATTAAATTACAAAATATTAATAAAATCATAAAT-ATTTTCATATA
* * *
1557426 AATTATTAAAATACATGATCTTTCAACCAAA
65 AATTAAT-AAATACATAATATTTCAA-CAAA
* * * *
1557457 AA-TAAATTTAATTTACCAAAATAAATTACAAAATATTAATAAAATCATAAATATTTTCATTTAA
1 AATTAAATTAAATTTATCAAATTAAATTACAAAATATTAATAAAATCATAAATATTTTCATATAA
* * *
1557521 ATTAATCATTACCTAATATTTCAACAAA
66 ATTAATAAATACATAATATTTCAACAAA
** **
1557549 AATTAAATTAAATTTATCAAATTAAATTACCTAATATTCCTAAAATCA
1 AATTAAATTAAATTTATCAAATTAAATTACAAAATATTAATAAAATCA
1557597 AACTAAACTA
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
92 6 0.05
93 56 0.46
94 57 0.47
95 2 0.02
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (93 bp):
AATTAAATTAAATTTATCAAATTAAATTACAAAATATTAATAAAATCATAAATATTTTCATATAA
ATTAATAAATACATAATATTTCAACAAA
Found at i:1557585 original size:93 final size:92
Alignment explanation
Indices: 1557333--1557596 Score: 318
Period size: 93 Copynumber: 2.8 Consensus size: 92
1557323 TAGCTGATTA
* *
1557333 AAATTAATCATTACCTA-ATTTCTAATAACAATTAAATTAAATTTATCAAATTAAATTACAAAAT
1 AAATTAATCATTACCTATATTTC-AACAAAAATTAAATTAAATTTATCAAATTAAATTACAAAAT
1557397 ATTAATAAAATCATAAATAATTTTATAT
65 ATTAATAAAATCATAAATAATTTTATAT
* * * * * * * *
1557425 AAATTATTAAAATACATGATCTTTCAACCAAAAA-TAAATTTAATTTACCAAAATAAATTACAAA
1 AAATTAAT-CATTACCT-ATATTTCAA-CAAAAATTAAATTAAATTTATCAAATTAAATTACAAA
*
1557489 ATATTAATAAAATCATAAAT-ATTTTCATTT
63 ATATTAATAAAATCATAAATAATTTT-ATAT
**
1557519 AAATTAATCATTACCTAATATTTCAACAAAAATTAAATTAAATTTATCAAATTAAATTACCTAAT
1 AAATTAATCATTACCT-ATATTTCAACAAAAATTAAATTAAATTTATCAAATTAAATTACAAAAT
**
1557584 ATTCCTAAAATCA
65 ATTAATAAAATCA
1557597 AACTAAACTA
Statistics
Matches: 142, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
92 13 0.09
93 61 0.43
94 60 0.42
95 8 0.06
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (92 bp):
AAATTAATCATTACCTATATTTCAACAAAAATTAAATTAAATTTATCAAATTAAATTACAAAATA
TTAATAAAATCATAAATAATTTTATAT
Found at i:1560965 original size:22 final size:22
Alignment explanation
Indices: 1560939--1560982 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1560929 TTTATTAATT
* *
1560939 TTATATATTTTAAAATAAATAA
1 TTATAAATTTAAAAATAAATAA
*
1560961 TTATAAATTTAAAAATAGATAA
1 TTATAAATTTAAAAATAAATAA
1560983 AATAACGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATAAATTTAAAAATAAATAA
Found at i:1561941 original size:20 final size:20
Alignment explanation
Indices: 1561916--1561981 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 20
1561906 TAAAATAATT
1561916 AAAATTATTATTATAATATA
1 AAAATTATTATTATAATATA
1561936 AAAATTATTAAAATTATAATATA
1 AAAATTATT---ATTATAATATA
**
1561959 ATTATTATAATATTATAATATA
1 AAAATTAT--TATTATAATATA
1561981 A
1 A
1561982 TTGTTATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 9 0.23
22 12 0.31
23 17 0.44
25 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTATTATTATAATATA
Found at i:1561975 original size:17 final size:17
Alignment explanation
Indices: 1561922--1561977 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1561912 AATTAAAATT
* *
1561922 ATTATTATAATATAAAA
1 ATTATTATAATATTATA
*
1561939 ATTATTAAAATTATAATATA
1 ATTATTATAA-TAT--TATA
1561959 ATTATTATAATATTATA
1 ATTATTATAATATTATA
1561976 AT
1 AT
1561978 ATAATTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 15 0.47
18 3 0.09
19 3 0.09
20 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATTATAATATTATA
Found at i:1562075 original size:2 final size:2
Alignment explanation
Indices: 1562070--1562100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1562060 CCCCACACAC
1562070 AT AT 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 AT AT A
1562101 AAAGAGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1563611 original size:15 final size:17
Alignment explanation
Indices: 1563579--1563649 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
1563569 TAAAAAATAT
1563579 AATATTATATTAATAAA
1 AATATTATATTAATAAA
* *
1563596 AATATTATTTTAAAAAA
1 AATATTATATTAATAAA
* * ** *
1563613 TAAAATAATAAAAATAAT
1 -AATATTATATTAATAAA
1563631 AATATTATATTAATAAA
1 AATATTATATTAATAAA
1563648 AA
1 AA
1563650 ATTTATGATA
Statistics
Matches: 39, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
17 29 0.74
18 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATTATATTAATAAA
Found at i:1563617 original size:20 final size:20
Alignment explanation
Indices: 1563566--1563619 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 20
1563556 AAAGGATTTC
*
1563566 TTTTAAAAAATATAATATTA
1 TTTTAAAAAATAAAATATTA
* *
1563586 TATT--AATA-AAAATATTA
1 TTTTAAAAAATAAAATATTA
1563603 TTTTAAAAAATAAAATA
1 TTTTAAAAAATAAAATA
1563620 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
19 3 0.12
20 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTAAAAAATAAAATATTA
Found at i:1563636 original size:35 final size:37
Alignment explanation
Indices: 1563566--1563648 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 37
1563556 AAAGGATTTC
* **
1563566 TTTTAAAAAATATAATATTATATTAATAAAAATATTA
1 TTTTAAAAAATATAATATAATAAAAATAAAAATATTA
*
1563603 TTTTAAAAAATA-AA-ATAATAAAAATAATAATATTA
1 TTTTAAAAAATATAATATAATAAAAATAAAAATATTA
*
1563638 TATTAATAAAA
1 TTTTAA-AAAA
1563649 AATTTATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 22 0.55
36 6 0.15
37 12 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
TTTTAAAAAATATAATATAATAAAAATAAAAATATTA
Found at i:1564083 original size:25 final size:24
Alignment explanation
Indices: 1564029--1564085 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1564019 ATTAAATTTT
*
1564029 TGAAATAAAATTCATATAATATAA
1 TGAAATAAAATCCATATAATATAA
* *
1564053 TAAAATATAAATCCA-ATAATTATCA
1 TGAAATA-AAATCCATATAA-TATAA
1564078 TGAAATAA
1 TGAAATAA
1564086 CTATTAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (24 bp):
TGAAATAAAATCCATATAATATAA
Found at i:1564865 original size:20 final size:19
Alignment explanation
Indices: 1564831--1564873 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1564821 AAAAATATAA
*
1564831 ATAAAAAAATTTAATAAAT
1 ATAAAAAAATATAATAAAT
*
1564850 ATAAAAATAATATAATTAAT
1 ATAAAAA-AATATAATAAAT
1564870 ATAA
1 ATAA
1564874 TACAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAAAATATAATAAAT
Found at i:1564866 original size:25 final size:25
Alignment explanation
Indices: 1564812--1564875 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
1564802 ATAATTTTAG
*
1564812 ATATAATATAA-AAATATAAATAAA
1 ATATAATTTAATAAATATAAATAAA
1564836 A-A-AATTTAATAAATATAAA-AATA
1 ATATAATTTAATAAATATAAATAA-A
1564859 ATATAA-TTAATATAATA
1 ATATAATTTAATA-AATA
1564876 CAATATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 8 0.24
23 12 0.35
24 8 0.24
25 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAATTTAATAAATATAAATAAA
Found at i:1565878 original size:18 final size:18
Alignment explanation
Indices: 1565864--1565897 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1565854 TATTTAAATT
1565864 TAAAA-ATT-AATTTAAA
1 TAAAATATTAAATTTAAA
1565880 TAAAATATTAAATTTAAA
1 TAAAATATTAAATTTAAA
1565898 AATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATATTAAATTTAAA
Found at i:1566016 original size:23 final size:22
Alignment explanation
Indices: 1565990--1566048 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1565980 TCTAACTTAT
1565990 TTTTTAATTATATAATATATTAA
1 TTTTTAATTATATAATATA-TAA
*
1566013 -TTTTAATTTATATATTATATAA
1 TTTTTAA-TTATATAATATATAA
*
1566035 TTTTT-ACTATATAA
1 TTTTTAATTATATAA
1566049 AGAATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.19
22 10 0.32
23 15 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAATTATATAATATATAA
Found at i:1567059 original size:4 final size:4
Alignment explanation
Indices: 1567052--1567077 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1567042 TTCTTTCTTC
1567052 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
1567078 GGGAGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1567658 original size:2 final size:2
Alignment explanation
Indices: 1567631--1567676 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1567621 AAATTGATTT
1567631 TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1567669 TA TG TA TA
1 TA TA TA TA
1567677 CACACACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1568507 original size:33 final size:33
Alignment explanation
Indices: 1568458--1568530 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
1568448 TAGTTTTTAA
* * *
1568458 TTATTATTTGACATAAATATGATTTTAATTTAT
1 TTATTATTTAACATAAATATAATTTTAAATTAT
* *
1568491 TTTTTATTTAATATAAATATAATTTTAAATTAT
1 TTATTATTTAACATAAATATAATTTTAAATTAT
1568524 TTATTAT
1 TTATTAT
1568531 ACATATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (33 bp):
TTATTATTTAACATAAATATAATTTTAAATTAT
Found at i:1571866 original size:17 final size:17
Alignment explanation
Indices: 1571844--1571879 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1571834 AAATACTTAT
*
1571844 TTATAAAAAGTTTTCAA
1 TTATAAAAAATTTTCAA
1571861 TTATAAAAAATTTTCAA
1 TTATAAAAAATTTTCAA
1571878 TT
1 TT
1571880 TCACATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TTATAAAAAATTTTCAA
Found at i:1573660 original size:18 final size:18
Alignment explanation
Indices: 1573639--1573673 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1573629 AAAAGTAACA
1573639 TAATATATAATATAAAAT
1 TAATATATAATATAAAAT
*
1573657 TAATATATATTATAAAA
1 TAATATATAATATAAAA
1573674 CTATGCTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATATAATATAAAAT
Found at i:1573670 original size:23 final size:23
Alignment explanation
Indices: 1573613--1573671 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1573603 ATTTACATAT
*
1573613 ATATATATTTTAAGATAAAAGTA
1 ATATATATTATAAGATAAAAGTA
* * *
1573636 ACATA-ATATATAATATAAAATTA
1 ATATATAT-TATAAGATAAAAGTA
1573659 ATATATATTATAA
1 ATATATATTATAA
1573672 AACTATGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
ATATATATTATAAGATAAAAGTA
Found at i:1573754 original size:17 final size:18
Alignment explanation
Indices: 1573711--1573756 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1573701 TAATATTTTA
1573711 TTATTTTTTAATTAAATC
1 TTATTTTTTAATTAAATC
* *
1573729 TAATTTTTTATTTAAAT-
1 TTATTTTTTAATTAAATC
*
1573746 TTATATTTTAA
1 TTATTTTTTAA
1573757 ATTTAATAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTTTTTAATTAAATC
Found at i:1573755 original size:13 final size:13
Alignment explanation
Indices: 1573739--1573777 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1573729 TAATTTTTTA
1573739 TTTAAATTTATAT
1 TTTAAATTTATAT
*
1573752 TTTAAATTTAATAG
1 TTTAAATTT-ATAT
1573766 TTT-AATTTATAT
1 TTTAAATTTATAT
1573778 CTTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTAAATTTATAT
Found at i:1574205 original size:18 final size:18
Alignment explanation
Indices: 1574182--1574216 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1574172 ATTTATTAAG
1574182 TTAAATGTTTAA-AATTTA
1 TTAAAT-TTTAATAATTTA
1574200 TTAAATTTTAATAATTT
1 TTAAATTTTAATAATTT
1574217 TATATATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATTTTAATAATTTA
Found at i:1574311 original size:9 final size:10
Alignment explanation
Indices: 1574267--1574315 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
1574257 ATATAAAAAT
1574267 AATATAA-TA
1 AATATAATTA
*
1574276 AATATAATTT
1 AATATAATTA
* *
1574286 GATATATTTA
1 AATATAATTA
1574296 AATATAATTA
1 AATATAATTA
1574306 AA-ATAATTA
1 AATATAATTA
1574315 A
1 A
1574316 TTCATCACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (10 bp):
AATATAATTA
Found at i:1574364 original size:15 final size:15
Alignment explanation
Indices: 1574330--1574390 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
1574320 TCACTTTTAA
*
1574330 TATATTTATTATATT
1 TATATTTATAATATT
*
1574345 TATATTTATAATTTT
1 TATATTTATAATATT
1574360 AATATATTTAATAATACGTGT
1 --TATATTT-ATAATA--T-T
1574381 TATATTTATA
1 TATATTTATA
1574391 CTTATACAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 13 0.35
17 7 0.19
18 8 0.22
19 7 0.19
20 1 0.03
21 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (15 bp):
TATATTTATAATATT
Found at i:1574697 original size:15 final size:17
Alignment explanation
Indices: 1574677--1574709 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1574667 AATTTAAATT
1574677 TTTAATT-AAAT-CAAA
1 TTTAATTCAAATACAAA
1574692 TTTAATTCAAATACAAA
1 TTTAATTCAAATACAAA
1574709 T
1 T
1574710 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAATTCAAATACAAA
Found at i:1576707 original size:14 final size:14
Alignment explanation
Indices: 1576688--1576731 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1576678 ATTAACATAA
1576688 TTAATATTTAAAAT
1 TTAATATTTAAAAT
1576702 TTAATATTATAAAAT
1 TTAATATT-TAAAAT
*
1576717 TT-ATTTTTAAAAT
1 TTAATATTTAAAAT
1576730 TT
1 TT
1576732 TAAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 8 0.29
14 12 0.43
15 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATATTTAAAAT
Found at i:1576717 original size:28 final size:28
Alignment explanation
Indices: 1576686--1576744 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1576676 TTATTAACAT
*
1576686 AATTAATATTTAAAA-TTTAATATTATAA
1 AATTAATATTTAAAATTTTAA-AATATAA
* *
1576714 AATTTATTTTTAAAATTTTAAAATATAA
1 AATTAATATTTAAAATTTTAAAATATAA
1576742 AAT
1 AAT
1576745 AGGATACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTAATATTTAAAATTTTAAAATATAA
Found at i:1576729 original size:13 final size:15
Alignment explanation
Indices: 1576688--1576731 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
1576678 ATTAACATAA
1576688 TTAATA-TTTAAAAT
1 TTAATATTTTAAAAT
*
1576702 TTAATATTATAAAAT
1 TTAATATTTTAAAAT
1576717 TT-AT-TTTTAAAAT
1 TTAATATTTTAAAAT
1576730 TT
1 TT
1576732 TAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 10 0.37
14 8 0.30
15 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATATTTTAAAAT
Found at i:1577939 original size:16 final size:16
Alignment explanation
Indices: 1577898--1577940 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1577888 TTATTAAAAA
*
1577898 TTAAAAATAAATTTAT
1 TTAATAATAAATTTAT
*
1577914 TTGATAATAAATTTAT
1 TTAATAATAAATTTAT
*
1577930 TTAATTATAAA
1 TTAATAATAAA
1577941 ATAAATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTAATAATAAATTTAT
Found at i:1578217 original size:20 final size:18
Alignment explanation
Indices: 1578174--1578218 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
1578164 GGATGTTTCG
1578174 ATTTAAAATAATATTTTT
1 ATTTAAAATAATATTTTT
*
1578192 AATTAAAATAATATATTTTT
1 ATTTAAAAT-A-ATATTTTT
1578212 ATTTAAA
1 ATTTAAA
1578219 TTTAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAAATAATATTTTT
Found at i:1578219 original size:19 final size:18
Alignment explanation
Indices: 1578174--1578219 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1578164 GGATGTTTCG
1578174 ATTTAAAATAATATTTTTA
1 ATTT-AAATAATATTTTTA
* *
1578193 ATTAAAATAATATATTTTT
1 ATTTAAATAATAT-TTTTA
1578212 ATTTAAAT
1 ATTTAAAT
1578220 TTAATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAATAATATTTTTA
Found at i:1578275 original size:19 final size:19
Alignment explanation
Indices: 1578235--1578300 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
1578225 TATAAATTTT
*
1578235 ATAAATATTAATATAA-AA
1 ATAAATTTTAATATAATAA
*
1578253 ATAAATTTTTATATAATAA
1 ATAAATTTTAATATAATAA
*
1578272 ATAATAATTTAAATATAAATAA
1 AT-A-AATTTTAATAT-AATAA
1578294 ATAAATT
1 ATAAATT
1578301 AAATTATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.35
19 4 0.10
20 5 0.12
21 10 0.25
22 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAATTTTAATATAATAA
Found at i:1578302 original size:19 final size:18
Alignment explanation
Indices: 1578268--1578304 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1578258 TTTTTATATA
*
1578268 ATAAATAATAATTTAAAT
1 ATAAATAATAAATTAAAT
1578286 ATAAATAAATAAATTAAAT
1 ATAAAT-AATAAATTAAAT
1578305 TATGAGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAATAATAAATTAAAT
Found at i:1578704 original size:23 final size:23
Alignment explanation
Indices: 1578678--1578723 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1578668 TCACAAAATT
1578678 TATAATTTTATAAT-ATAATTATA
1 TATAATTTT-TAATAATAATTATA
*
1578701 TATACTTTTTAATAATAATTATA
1 TATAATTTTTAATAATAATTATA
1578724 ATTGTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAATTTTTAATAATAATTATA
Found at i:1579020 original size:16 final size:16
Alignment explanation
Indices: 1578999--1579041 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1578989 TTGTTATTAT
1578999 ATTTTAATTTTGTTAA
1 ATTTTAATTTTGTTAA
*
1579015 ATTTT-ATTATTTTTAA
1 ATTTTAATT-TTGTTAA
*
1579031 TTTTTAATTTT
1 ATTTTAATTTT
1579042 TATTGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTTTAATTTTGTTAA
Found at i:1581608 original size:2 final size:2
Alignment explanation
Indices: 1581597--1581630 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1581587 TATGATATCA
1581597 AT AT -T AT 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 AT AT AT AT A
1581631 CACTCTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1582708 original size:28 final size:28
Alignment explanation
Indices: 1582674--1582732 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1582664 AATATAATTT
*
1582674 TTTTATATA-T-ATTTAATAATTAAAAA
1 TTTTATATATTAATTAAATAATTAAAAA
* *
1582700 TTTTATATATTAATTAAATAGTTAAAAT
1 TTTTATATATTAATTAAATAATTAAAAA
1582728 TTTTA
1 TTTTA
1582733 ATTTATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 9 0.32
27 1 0.04
28 18 0.64
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTTATATATTAATTAAATAATTAAAAA
Found at i:1582891 original size:2 final size:2
Alignment explanation
Indices: 1582884--1582911 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1582874 AGAATATTAC
1582884 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
1582912 TGCTAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1583630 original size:20 final size:22
Alignment explanation
Indices: 1583589--1583630 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1583579 ATATTTAAGC
1583589 TTATTTATTTTATATTTAAATTT
1 TTATTTATTTTATA-TTAAATTT
1583612 TTATTTA-TTTATA-TAAATT
1 TTATTTATTTTATATTAAATT
1583631 AAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTTATTTTATATTAAATTT
Found at i:1584388 original size:70 final size:69
Alignment explanation
Indices: 1584275--1584409 Score: 191
Period size: 70 Copynumber: 1.9 Consensus size: 69
1584265 GGATTACTAG
* * * *
1584275 GGAGCTGTTCGATCAAACGCTTAAAGGAAAAATATTTTATAGAATTTTATATTTTTTTGGGTACA
1 GGAGCTGTTCGATAAAACGCTCAAAGGAAAAATATTTTATAGAATTTGATA-TCTTTTGGGTACA
1584340 ATACT
65 ATACT
* *
1584345 GGAGCTGTTTGATAAAATGCTCCAAAGG-AAAATATTTTATAGAATTTGATATCTTTTGGGTACA
1 GGAGCTGTTCGATAAAACGCT-CAAAGGAAAAATATTTTATAGAATTTGATATCTTTTGGGTACA
1584409 A
65 A
1584410 CACATAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
69 13 0.22
70 40 0.69
71 5 0.09
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (69 bp):
GGAGCTGTTCGATAAAACGCTCAAAGGAAAAATATTTTATAGAATTTGATATCTTTTGGGTACAA
TACT
Found at i:1589837 original size:2 final size:2
Alignment explanation
Indices: 1589830--1589861 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1589820 ATAGGATGTC
1589830 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
1589862 CAGAGACAAT
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:1596792 original size:4 final size:4
Alignment explanation
Indices: 1596783--1596809 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1596773 TGAAGATTTT
1596783 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1596810 TAGTTAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:1598800 original size:12 final size:12
Alignment explanation
Indices: 1598783--1598809 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1598773 ATCTTTTCAT
1598783 AAAAAAATAATA
1 AAAAAAATAATA
1598795 AAAAAAATAATA
1 AAAAAAATAATA
1598807 AAA
1 AAA
1598810 TAATATAATT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:1598836 original size:17 final size:17
Alignment explanation
Indices: 1598793--1598844 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1598783 AAAAAAATAA
* * *
1598793 TAAAAAAAATAATAAAA
1 TAAAAAAATTAATTAAT
* *
1598810 TAATATAATTAATTAAT
1 TAAAAAAATTAATTAAT
1598827 TAAAAAAATTAATTAAT
1 TAAAAAAATTAATTAAT
1598844 T
1 T
1598845 TTGCATTTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAAATTAATTAAT
Found at i:1598888 original size:14 final size:15
Alignment explanation
Indices: 1598857--1598891 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1598847 GCATTTGCAC
*
1598857 GTGCTATGTGTCCAA
1 GTGCTAAGTGTCCAA
1598872 GTGCTAAGTGT-CAA
1 GTGCTAAGTGTCCAA
1598886 GTGCTA
1 GTGCTA
1598892 TATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (15 bp):
GTGCTAAGTGTCCAA
Found at i:1601384 original size:32 final size:34
Alignment explanation
Indices: 1601348--1601415 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 34
1601338 TTCTAAATGA
1601348 ATATTAAATATGAATATATG-ATT-AATACAAAT
1 ATATTAAATATGAATATATGTATTAAATACAAAT
* * * *
1601380 ATATTTATTTTGAATGTATGTATTAAATACAAAT
1 ATATTAAATATGAATATATGTATTAAATACAAAT
1601414 AT
1 AT
1601416 CGAATACTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 16 0.53
33 3 0.10
34 11 0.37
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (34 bp):
ATATTAAATATGAATATATGTATTAAATACAAAT
Found at i:1615713 original size:15 final size:15
Alignment explanation
Indices: 1615693--1615722 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1615683 TAGTTAAACA
1615693 TTTATTAATTTTAGT
1 TTTATTAATTTTAGT
1615708 TTTATTAATTTTAGT
1 TTTATTAATTTTAGT
1615723 AAATTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTATTAATTTTAGT
Found at i:1616437 original size:2 final size:2
Alignment explanation
Indices: 1616430--1616455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1616420 ATGAAAATAG
1616430 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
1616456 TTGATGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1617596 original size:15 final size:16
Alignment explanation
Indices: 1617560--1617601 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1617550 AAATTCACAT
1617560 ATAAATTATAA-A-ATA
1 ATAAATTA-AATATATA
1617575 ATAAATTAAATATATA
1 ATAAATTAAATATATA
1617591 AT-AATTAAATA
1 ATAAATTAAATA
1617602 CATCTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATTAAATATATA
Found at i:1617706 original size:15 final size:16
Alignment explanation
Indices: 1617686--1617717 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1617676 ATTTATAAAA
1617686 AAATTAATAAAT-TAT
1 AAATTAATAAATATAT
1617701 AAATTAATAAATATAT
1 AAATTAATAAATATAT
1617717 A
1 A
1617718 TTTTATACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATAAATATAT
Found at i:1619472 original size:16 final size:15
Alignment explanation
Indices: 1619451--1619480 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1619441 TATAATACTT
1619451 TGATCAATTGTGCTTA
1 TGATCAATT-TGCTTA
1619467 TGATCAATTTGCTT
1 TGATCAATTTGCTT
1619481 GGAATAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (15 bp):
TGATCAATTTGCTTA
Found at i:1619652 original size:3 final size:3
Alignment explanation
Indices: 1619644--1619677 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1619634 AGACAAAGGC
1619644 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1619678 TAGGGTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1619809 original size:15 final size:15
Alignment explanation
Indices: 1619791--1619820 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1619781 GTATTTTATT
1619791 TATTTATTTATAAAA
1 TATTTATTTATAAAA
*
1619806 TATTTATTTTTAAAA
1 TATTTATTTATAAAA
1619821 ATTCATGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATTTATAAAA
Found at i:1621123 original size:18 final size:19
Alignment explanation
Indices: 1621093--1621128 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1621083 TAATTAAAAA
1621093 ATTTAATATTTAAATTTAG
1 ATTTAATATTTAAATTTAG
*
1621112 ATTTAA-ATTTAATTTTA
1 ATTTAATATTTAAATTTA
1621129 TCTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAATTTAG
Found at i:1621128 original size:12 final size:12
Alignment explanation
Indices: 1621091--1621128 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1621081 TATAATTAAA
1621091 AAATTTAATATTT
1 AAATTTAAT-TTT
1621104 AAATTTAGA-TTT
1 AAATTTA-ATTTT
1621116 AAATTTAATTTT
1 AAATTTAATTTT
1621128 A
1 A
1621129 TCTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 14 0.61
13 7 0.30
14 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
AAATTTAATTTT
Found at i:1624433 original size:25 final size:25
Alignment explanation
Indices: 1624364--1624433 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
1624354 TAATTATAAT
1624364 TTAATTATAA-AAT-ATATAAAAAAA
1 TTAA-TATAATAATAATATAAAAAAA
* *
1624388 TTAATATAATATTAATGTAAAAAAA
1 TTAATATAATAATAATATAAAAAAA
**
1624413 TTAA-ATTTTACATAATATAAA
1 TTAATATAATA-ATAATATAAA
1624434 TTATTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
23 5 0.14
24 10 0.27
25 22 0.59
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (25 bp):
TTAATATAATAATAATATAAAAAAA
Found at i:1624468 original size:27 final size:28
Alignment explanation
Indices: 1624427--1624481 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1624417 ATTTTACATA
1624427 ATATAAATTATTAAT-TTATTAAA-ATTT
1 ATATAAATTATTAATATTA-TAAATATTT
1624454 ATATAAA-TATATAATATTATAAATATTT
1 ATATAAATTAT-TAATATTATAAATATTT
1624482 TTATCCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 3 0.12
27 15 0.60
28 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATAAATTATTAATATTATAAATATTT
Found at i:1640265 original size:16 final size:16
Alignment explanation
Indices: 1640219--1640273 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
1640209 TATACACAAT
1640219 ATATAAA-ATTTTATA
1 ATATAAATATTTTATA
1640234 A-ATAAATAAGTTTTTTATA
1 ATATAAAT-A---TTTTATA
1640253 ATATAAATATTTTATA
1 ATATAAATATTTTATA
*
1640269 TTATA
1 ATATA
1640274 TAGTAATACG
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
16 12 0.36
19 9 0.27
20 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATAAATATTTTATA
Found at i:1640274 original size:18 final size:18
Alignment explanation
Indices: 1640218--1640275 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1640208 TTATACACAA
1640218 TATATAAA-ATTTTATA-
1 TATATAAATATTTTATAT
*
1640234 -A-ATAAATAAGTTTTTTAT
1 TATATAAAT-A-TTTTATAT
*
1640252 AATATAAATATTTTATAT
1 TATATAAATATTTTATAT
1640270 TATATA
1 TATATA
1640276 GTAATACGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
16 1 0.03
17 6 0.18
18 12 0.36
19 2 0.06
20 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATATAAATATTTTATAT
Found at i:1641184 original size:2 final size:2
Alignment explanation
Indices: 1641177--1641201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1641167 TTTAGTAATC
1641177 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 A
1641202 GTTTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1642450 original size:23 final size:25
Alignment explanation
Indices: 1642419--1642466 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1642409 TTTTAATATG
1642419 TTAACAAAT-TATATTATAT-AAATT
1 TTAACAAATATAT-TTATATCAAATT
1642443 TTAA-AAATATATTTATATCAAATT
1 TTAACAAATATATTTATATCAAATT
1642467 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAACAAATATATTTATATCAAATT
Found at i:1642465 original size:24 final size:24
Alignment explanation
Indices: 1642419--1642466 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1642409 TTTTAATATG
1642419 TTAACAAATTATATTATATAAATT
1 TTAACAAATTATATTATATAAATT
1642443 TTAA-AAA-TATATTTATATCAAATT
1 TTAACAAATTATA-TTATAT-AAATT
1642467 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAACAAATTATATTATATAAATT
Found at i:1643000 original size:12 final size:11
Alignment explanation
Indices: 1642983--1643040 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
1642973 TATATCTGAA
1642983 TTATATTCATTT
1 TTATATT-ATTT
1642995 TTATATTATGTT
1 TTATATTAT-TT
*
1643007 TTAT-TTAATT
1 TTATATTATTT
*
1643017 TTATATTATAT
1 TTATATTATTT
*
1643028 TTGTATTATTT
1 TTATATTATTT
1643039 TT
1 TT
1643041 TGTATATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 6 0.15
11 20 0.51
12 13 0.33
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (11 bp):
TTATATTATTT
Found at i:1644811 original size:21 final size:20
Alignment explanation
Indices: 1644787--1644832 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1644777 TCTCAATTAA
1644787 TATTTATATTGTATTT-TAATT
1 TATTTATATT-T-TTTATAATT
1644808 TATTTTATATTTTTTATAATT
1 TA-TTTATATTTTTTATAATT
1644829 TATT
1 TATT
1644833 ATAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTTATATTTTTTATAATT
Found at i:1644813 original size:10 final size:10
Alignment explanation
Indices: 1644798--1644853 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 10
1644788 ATTTATATTG
1644798 TATTTTAATT
1 TATTTTAATT
1644808 TATTTTATATT
1 TATTTTA-ATT
1644819 T-TTTATAATT
1 TATTT-TAATT
1644829 TATTATAATAATT
1 TATT-T--TAATT
1644842 TAATTTTAATT
1 T-ATTTTAATT
1644853 T
1 T
1644854 TAAATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 14 0.35
11 14 0.35
12 1 0.03
13 8 0.20
14 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TATTTTAATT
Found at i:1645165 original size:16 final size:16
Alignment explanation
Indices: 1645146--1645198 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1645136 TTTAAATATC
1645146 TATTAATATTTTAATA
1 TATTAATATTTTAATA
* * *
1645162 TATTAATGTATTAAAA
1 TATTAATATTTTAATA
1645178 TAATTATATATTTTTAATA
1 T-ATTA-ATA-TTTTAATA
1645197 TA
1 TA
1645199 AAAGTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 3 0.11
19 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TATTAATATTTTAATA
Found at i:1645467 original size:18 final size:19
Alignment explanation
Indices: 1645438--1645476 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1645428 ATTATAAGTC
1645438 TTTTTTATATAAATT-TTTA
1 TTTTTTATAT-AATTATTTA
1645457 TTTTTTA-ATAATTATTTA
1 TTTTTTATATAATTATTTA
1645475 TT
1 TT
1645477 ATAATAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTATATAATTATTTA
Found at i:1645516 original size:43 final size:43
Alignment explanation
Indices: 1645455--1645545 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
1645445 TATAAATTTT
* * * * *
1645455 TATTTTTTAATAATTATTTATTATAATAAT-GATATATAATAAA
1 TATTTTTTAACAAATATTTATTATAACAATAG-TAAATAAAAAA
*
1645498 TATTTTTTAGCAAATATTTATTATAACAATAGTAAATAAAAAA
1 TATTTTTTAACAAATATTTATTATAACAATAGTAAATAAAAAA
1645541 TATTT
1 TATTT
1645546 CTTGTTCGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (43 bp):
TATTTTTTAACAAATATTTATTATAACAATAGTAAATAAAAAA
Found at i:1645731 original size:11 final size:11
Alignment explanation
Indices: 1645715--1645752 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1645705 ATATAATTTT
1645715 ATATTTATATC
1 ATATTTATATC
*
1645726 ATATTTATATT
1 ATATTTATATC
*
1645737 ATTTTTATATC
1 ATATTTATATC
1645748 ATATT
1 ATATT
1645753 GTATTTGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTTATATC
Found at i:1645751 original size:27 final size:27
Alignment explanation
Indices: 1645711--1645777 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1645701 ATTAATATAA
*
1645711 TTTTATATTTATATCATATTTATATTAT
1 TTTTATA-TCATATCATATTTATATTAT
** * *
1645739 TTTTATATCATATTGTATTTGTGTTAT
1 TTTTATATCATATCATATTTATATTAT
1645766 TTTT-TATCATAT
1 TTTTATATCATAT
1645778 TTATTTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 8 0.24
27 19 0.56
28 7 0.21
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTTATATCATATCATATTTATATTAT
Found at i:1645783 original size:16 final size:16
Alignment explanation
Indices: 1645762--1645795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1645752 TGTATTTGTG
* *
1645762 TTATTTTTTATCATAT
1 TTATTTTATATAATAT
1645778 TTATTTTATATAATAT
1 TTATTTTATATAATAT
1645794 TT
1 TT
1645796 TAATTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTATATAATAT
Found at i:1646071 original size:22 final size:24
Alignment explanation
Indices: 1646044--1646092 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1646034 TAATTCGTAC
1646044 TATATAAATATTA-ATATA-ATTA
1 TATATAAATATTATATATATATTA
* *
1646066 TATATACATATTATATTTATATTA
1 TATATAAATATTATATATATATTA
1646090 TAT
1 TAT
1646093 TATATCTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 4 0.17
24 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATAAATATTATATATATATTA
Done.