Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 14 of 193
Found at i:5014424 original size:64 final size:62
Alignment explanation
Indices: 5014242--5014403 Score: 270
Period size: 64 Copynumber: 2.6 Consensus size: 62
5014232 ATTAGCACTG
* * *
5014242 TGTGTGCTCTCTGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
*
5014304 TGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
1 TGTGTACTCTCTG-T-TTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
5014368 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
5014404 TTGCCCAGCA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
62 33 0.35
63 1 0.01
64 59 0.63
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (62 bp):
TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
Found at i:5018720 original size:16 final size:16
Alignment explanation
Indices: 5018699--5018732 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5018689 AGATACTAGC
* *
5018699 TTGAGAAGTGAAAGAA
1 TTGAGAAATAAAAGAA
5018715 TTGAGAAATAAAAGAA
1 TTGAGAAATAAAAGAA
5018731 TT
1 TT
5018733 CCTCTAGTAA
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:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (16 bp):
TTGAGAAATAAAAGAA
Found at i:5020697 original size:23 final size:23
Alignment explanation
Indices: 5020671--5020855 Score: 190
Period size: 23 Copynumber: 8.2 Consensus size: 23
5020661 ACACTAGCGC
5020671 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
5020694 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
5020717 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
5020742 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
5020765 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
5020788 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
5020804 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
5020829 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
5020852 GCTC
1 GCTC
5020856 AGTACTTTGT
Statistics
Matches: 137, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
16 11 0.08
18 3 0.02
21 3 0.02
22 4 0.03
23 78 0.57
24 1 0.01
25 34 0.25
26 3 0.02
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:5020740 original size:48 final size:45
Alignment explanation
Indices: 5020671--5020850 Score: 194
Period size: 48 Copynumber: 4.0 Consensus size: 45
5020661 ACACTAGCGC
* *
5020671 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCT-GT
5020717 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTC-TGT
* * * *
5020765 GCTCTCTGATTAGCACTTTGTGTG--CTC--AGTA-C-TTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
*
5020804 ACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTT-TGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
5020850 G
1 G
5020851 TGCTCAGTAC
Statistics
Matches: 112, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
39 10 0.09
40 2 0.02
41 16 0.14
42 3 0.03
43 3 0.03
44 3 0.03
45 3 0.03
46 27 0.24
47 2 0.02
48 42 0.38
49 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.42
Consensus pattern (45 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
Found at i:5020821 original size:41 final size:39
Alignment explanation
Indices: 5020756--5020832 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
5020746 TCTGATTAGC
* *
5020756 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
*
5020795 ACTTTGTGTACTCTCTGTTATTAGCACTGTGTGTGCTC
1 ACTTCGTGTACTCTCTG--ATTAGCACTGTGTGTGCTC
5020833 TCTGATTAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.45
41 18 0.55
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
Found at i:5020886 original size:87 final size:84
Alignment explanation
Indices: 5020689--5020900 Score: 232
Period size: 87 Copynumber: 2.4 Consensus size: 84
5020679 ATTAGCACTG
* *
5020689 TGTGTGCTCTCTGTTTAGCACGTCTCGTG-CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT
1 TGTGTACTCTCTGTTTAGCAC-T-TTGTGTCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT
5020753 AGCACTTCGTGTGCTCTCTGAT
64 AGCACTTCGTGTGCTCTCT-AT
* * * * * *
5020775 T-AGCACTTTGTGTGCTCAGTACTTTGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT
1 TGTGTACTCTCTGT--TTAGCACTTTGTGT-CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT
*
5020839 TAGCACTTTGTGTGCTCAGTACT-T
63 TAGCACTTCGTGTGCTC--T-CTAT
5020863 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
1 TGTGTACTCTCTGTTTAGCACTTTGTGT-CTCTCTGTT
5020901 GCCCAGCACT
Statistics
Matches: 102, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
85 11 0.11
86 2 0.02
87 76 0.75
88 2 0.02
89 9 0.09
90 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (84 bp):
TGTGTACTCTCTGTTTAGCACTTTGTGTCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAG
CACTTCGTGTGCTCTCTAT
Found at i:5020889 original size:23 final size:23
Alignment explanation
Indices: 5020854--5020947 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
5020844 CTTTGTGTGC
*
5020854 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
5020877 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
5020900 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
5020925 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
5020947 T
1 T
5020948 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:5020919 original size:64 final size:62
Alignment explanation
Indices: 5020737--5020898 Score: 270
Period size: 64 Copynumber: 2.6 Consensus size: 62
5020727 ATTAGCACTG
* * *
5020737 TGTGTGCTCTCTGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
*
5020799 TGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
1 TGTGTACTCTCTG-T-TTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
5020863 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG
5020899 TTGCCCAGCA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
62 33 0.35
63 1 0.01
64 59 0.63
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (62 bp):
TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
Found at i:5025144 original size:21 final size:21
Alignment explanation
Indices: 5025120--5025163 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5025110 ACATTAAACG
5025120 CAACTTAAGTAAATGTCACTT
1 CAACTTAAGTAAATGTCACTT
* * *
5025141 CAACTTAGGTGAATTTCACTT
1 CAACTTAAGTAAATGTCACTT
5025162 CA
1 CA
5025164 TGTAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (21 bp):
CAACTTAAGTAAATGTCACTT
Found at i:5030060 original size:30 final size:28
Alignment explanation
Indices: 5029995--5030138 Score: 112
Period size: 30 Copynumber: 4.8 Consensus size: 28
5029985 TAAAATGGGG
* *
5029995 TTTTAGGTTCCTAAAAAGTTGGAAAAAAAATA
1 TTTTAGGTCCCTTAAAAGTT---AAAAAAA-A
*
5030027 TTTTAGGTCCCTTAAAAATTAATAAAAAAA
1 TTTTAGGTCCCTTAAAAGTT-A-AAAAAAA
*
5030057 TTTTATGGGCCCTTAAAAGTTAAAAAAAA
1 TTTTA-GGTCCCTTAAAAGTTAAAAAAAA
* *
5030086 TATTTGGGTCCCCTTAAAAGTTGGCAAAAAAA
1 T-TTTAGGT-CCCTTAAAAGTT--AAAAAAAA
*
5030118 TTTTA-G-CCTTTAAAAGTTAAA
1 TTTTAGGTCCCTTAAAAGTTAAA
5030139 TTTTTTTTGA
Statistics
Matches: 95, Mismatches: 11, Indels: 18
0.77 0.09 0.15
Matches are distributed among these distances:
26 2 0.02
28 11 0.12
29 10 0.11
30 25 0.26
31 22 0.23
32 25 0.26
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (28 bp):
TTTTAGGTCCCTTAAAAGTTAAAAAAAA
Found at i:5030070 original size:31 final size:30
Alignment explanation
Indices: 5030017--5030090 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 30
5030007 AAAAAGTTGG
*
5030017 AAAAAAAATATTTTAGGTCCCTTAAAAATT
1 AAAAAAAATATTTTAGGGCCCTTAAAAATT
*
5030047 AATAAAAAA-ATTTTATGGGCCCTTAAAAGTT
1 AA-AAAAAATATTTTA-GGGCCCTTAAAAATT
5030078 AAAAAAAATATTT
1 AAAAAAAATATTT
5030091 GGGTCCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (30 bp):
AAAAAAAATATTTTAGGGCCCTTAAAAATT
Found at i:5033307 original size:17 final size:17
Alignment explanation
Indices: 5033285--5033318 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5033275 TCTAAATAGG
*
5033285 CTAAATATAAATAATAA
1 CTAAATAGAAATAATAA
5033302 CTAAATAGAAATAATAA
1 CTAAATAGAAATAATAA
5033319 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
CTAAATAGAAATAATAA
Found at i:5033314 original size:32 final size:31
Alignment explanation
Indices: 5033255--5033314 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
5033245 CTATTTAACT
**
5033255 TAAATTAAATAATAATAAATTCTAAATAGGC
1 TAAATTAAATAATAATAAATTAGAAATAGGC
5033286 TAAATATAAATAATAACTAAA-TAGAAATA
1 TAAAT-TAAATAATAA-TAAATTAGAAATA
5033315 ATAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 16 0.64
33 4 0.16
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (31 bp):
TAAATTAAATAATAATAAATTAGAAATAGGC
Found at i:5033346 original size:28 final size:31
Alignment explanation
Indices: 5033289--5033394 Score: 94
Period size: 34 Copynumber: 3.4 Consensus size: 31
5033279 AATAGGCTAA
**
5033289 ATATAAATAATAACTAAATAGAAATAATAAT
1 ATATAAATAATATTTAAATAGAAATAATAAT
*
5033320 -T-TAAATAATATTTAATTA-AAATAATAAT
1 ATATAAATAATATTTAAATAGAAATAATAAT
*
5033348 ATATATAATAATATTATAAGAATA-ATATAATAAT
1 ATATA-AATAATATT-T-A-AATAGAAATAATAAT
*
5033382 AGATAGAATAATA
1 ATATA-AATAATA
5033395 AAATAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 10 0.16
29 15 0.24
30 3 0.05
31 9 0.15
32 1 0.02
33 1 0.02
34 23 0.37
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (31 bp):
ATATAAATAATATTTAAATAGAAATAATAAT
Found at i:5033371 original size:11 final size:11
Alignment explanation
Indices: 5033312--5033382 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
5033302 CTAAATAGAA
5033312 ATAATAAT-TT
1 ATAATAATATT
5033322 A-AATAATATT
1 ATAATAATATT
5033332 -TAATTAA-A--
1 ATAA-TAATATT
5033340 ATAATAATATAT
1 ATAATAATAT-T
5033352 ATAATAATATT
1 ATAATAATATT
* *
5033363 ATAAGAATAAT
1 ATAATAATATT
5033374 ATAATAATA
1 ATAATAATA
5033383 GATAGAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 6 0.12
11 21 0.42
12 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
ATAATAATATT
Found at i:5033394 original size:15 final size:14
Alignment explanation
Indices: 5033338--5033410 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 14
5033328 TATTTAATTA
*
5033338 AAATAATAATATAT
1 AAATAATAATAGAT
5033352 ATAATAATATTATAAGAAT
1 A-AATAATA--AT-AG-AT
5033371 AATATAATAATAGAT
1 AA-ATAATAATAGAT
5033386 AGAATAATAA-A-AT
1 A-AATAATAATAGAT
5033399 AAATAAT-ATAGA
1 AAATAATAATAGA
5033411 AATATAGATT
Statistics
Matches: 49, Mismatches: 1, Indels: 19
0.71 0.01 0.28
Matches are distributed among these distances:
11 1 0.02
12 7 0.14
13 4 0.08
14 2 0.04
15 17 0.35
16 3 0.06
17 4 0.08
18 2 0.04
19 9 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (14 bp):
AAATAATAATAGAT
Found at i:5033472 original size:29 final size:29
Alignment explanation
Indices: 5033430--5033563 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 29
5033420 TTCTAAATCG
5033430 AAATATATTAATATAAATATAAAAATATAT
1 AAAT-TATTAATATAAATATAAAAATATAT
*
5033460 TAATTATTAATATAAATATAATATTAATATA-
1 AAATTATTAATATAAATATAA-A--AATATAT
* *
5033491 AATATTATTAATTACTTAATATAAAGAT-TAT
1 AA-ATTATTAA-TA-TAAATATAAAAATATAT
* * *
5033522 TAATTACTTAATATTAATA-ACAAATAATAT
1 AAATTA-TTAATATAAATATAAAAAT-ATAT
*
5033552 AAATTAATAATA
1 AAATTATTAATA
5033564 ATTGATAATA
Statistics
Matches: 85, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
28 4 0.05
29 28 0.33
30 20 0.24
31 8 0.09
32 14 0.16
33 3 0.04
34 8 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (29 bp):
AAATTATTAATATAAATATAAAAATATAT
Found at i:5033475 original size:23 final size:23
Alignment explanation
Indices: 5033430--5033535 Score: 95
Period size: 23 Copynumber: 4.9 Consensus size: 23
5033420 TTCTAAATCG
*
5033430 AAATATATTAA-TATAAATATAA
1 AAATATATTAATTATTAATATAA
5033452 AAATATATTAATTATTAATAT--
1 AAATATATTAATTATTAATATAA
5033473 -AA-ATA-TAA-TATTAATATAA
1 AAATATATTAATTATTAATATAA
* *
5033492 ATATT-ATTAATTACTTAATATAA
1 AAATATATTAATTA-TTAATATAA
*
5033515 AGAT-TATTAATTACTTAATAT
1 AAATATATTAATTA-TTAATAT
5033536 TAATAACAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
17 9 0.13
18 3 0.04
19 3 0.04
20 4 0.06
21 3 0.04
22 13 0.18
23 36 0.51
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (23 bp):
AAATATATTAATTATTAATATAA
Found at i:5033486 original size:17 final size:17
Alignment explanation
Indices: 5033434--5033495 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
5033424 AAATCGAAAT
5033434 ATATTAATATAAATATA
1 ATATTAATATAAATATA
5033451 A-A--AATAT--AT-TA
1 ATATTAATATAAATATA
5033462 ATTATTAATATAAATATA
1 A-TATTAATATAAATATA
5033480 ATATTAATATAAATAT
1 ATATTAATATAAATAT
5033496 TATTAATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 3 0.08
12 2 0.05
13 1 0.03
14 5 0.13
15 5 0.13
16 1 0.03
17 18 0.47
18 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAATATAAATATA
Found at i:5033540 original size:6 final size:6
Alignment explanation
Indices: 5033434--5033497 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
5033424 AAATCGAAAT
* * * *
5033434 ATATTA ATATAA ATA-TA AAAAT- ATATTA ATTATTA ATATAA ATA-TA
1 ATATTA ATATTA ATATTA ATATTA ATATTA A-TATTA ATATTA ATATTA
*
5033480 ATATTA ATATAA ATATTA
1 ATATTA ATATTA ATATTA
5033498 TTAATTACTT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
5 10 0.22
6 29 0.64
7 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATTA
Found at i:5033649 original size:20 final size:20
Alignment explanation
Indices: 5033626--5033665 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5033616 AATATATAAT
5033626 TTCGATTGTTAATTGGTTTA
1 TTCGATTGTTAATTGGTTTA
5033646 TTCGATTGTTAATTGGTTTA
1 TTCGATTGTTAATTGGTTTA
5033666 GTAGTGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (20 bp):
TTCGATTGTTAATTGGTTTA
Found at i:5039643 original size:29 final size:28
Alignment explanation
Indices: 5039607--5039836 Score: 118
Period size: 30 Copynumber: 7.8 Consensus size: 28
5039597 GAAACATCCG
* *
5039607 GGGGTAAAATTGTAATTTTGGAAGTGTC
1 GGGGTAAAAATGTAATTTTGGAAGTGTA
* * * *
5039635 GAGGTTAAAAATGGAATTTTTGGAATTTTA
1 G-GGGTAAAAATGTAA-TTTTGGAAGTGTA
* *
5039665 GGGGTAAAAATGTAATTTTGGGAGGTCTAGTTT
1 GGGGTAAAAATGTAATTTT-GGAAG--T-G-TA
* * *
5039698 GAGGGCAAAAATGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGTAA-TTTTGGAAGTGTA
* *
5039728 GGGGTCAAAAATGAAATTTTTGGAAGTTTA
1 GGGGT-AAAAATGTAA-TTTTGGAAGTGTA
* * * *
5039758 AGGGTAAAAGTGTAATTTTTGGATGTTTTA
1 GGGGTAAAAATGTAA-TTTTGGAAG-TGTA
* * * * * *
5039788 AGGGCAAAAGTGTAATTTTAGAAGTTTT
1 GGGGTAAAAATGTAATTTTGGAAGTGTA
* *
5039816 GAGGTTAAAATGTAATTTTGG
1 GGGGTAAAAATGTAATTTTGG
5039837 GGAAGTTCGG
Statistics
Matches: 159, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
28 23 0.14
29 53 0.33
30 58 0.36
31 1 0.01
32 1 0.01
33 2 0.01
34 17 0.11
35 4 0.03
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTGGAAGTGTA
Found at i:5039656 original size:30 final size:30
Alignment explanation
Indices: 5039608--5039834 Score: 171
Period size: 29 Copynumber: 7.6 Consensus size: 30
5039598 AAACATCCGG
* *
5039608 GGGTAAAATTGTAA-TTTTGGAAGTGTCGA
1 GGGTAAAAATGTAATTTTTGGAAGTGTTGA
* * *
5039637 GGTTAAAAATGGAATTTTTGGAA-T-TTTA
1 GGGTAAAAATGTAATTTTTGGAAGTGTTGA
* *
5039665 GGGGTAAAAATGTAATTTTGGGAGGTCTAGTTTGA
1 -GGGTAAAAATGTAATTTTTGGAAG--T-G-TTGA
* *
5039700 GGGCAAAAATGTAATTTTTGGAAGTTTTG-
1 GGGTAAAAATGTAATTTTTGGAAGTGTTGA
* *
5039729 GGGTCAAAAATGAAATTTTTGGAAGT-TTAA
1 GGGT-AAAAATGTAATTTTTGGAAGTGTTGA
* * * *
5039759 GGGTAAAAGTGTAATTTTTGGATGTTTTAA
1 GGGTAAAAATGTAATTTTTGGAAGTGTTGA
* * * *
5039789 GGGCAAAAGTGTAA-TTTTAGAAGTTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTGTTGA
*
5039818 -GGTTAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
5039835 GGGGAAGTTC
Statistics
Matches: 159, Mismatches: 27, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
28 12 0.08
29 69 0.43
30 52 0.33
32 2 0.01
34 21 0.13
35 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGGAAGTGTTGA
Found at i:5039778 original size:59 final size:60
Alignment explanation
Indices: 5039607--5039843 Score: 211
Period size: 59 Copynumber: 4.0 Consensus size: 60
5039597 GAAACATCCG
* * * *
5039607 GGGGT-AAAATTGTAA-TTTTGGAAGTGTCGAGGTTAAAAATGGAATTTTTGGAA-TTTTA
1 GGGGTCAAAAATGTAATTTTTGGAAGT-TTGAGGGTAAAAATGTAATTTTTGGAAGTTTTA
* *
5039665 GGGGT-AAAAATGTAATTTTGGGAGGTCTAGTTTGAGGGCAAAAATGTAATTTTTGGAAGTTTT-
1 GGGGTCAAAAATGTAATTTTTGGA-----AGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTA
* * * *
5039728 GGGGTCAAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAGTGTAATTTTTGGATGTTTTA
1 GGGGTCAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTA
* * * * *
5039788 AGGG-CAAAAGTGTAA-TTTTAGAAGTTTTGA-GGTTAAAATGTAATTTTGGGGAAGTT
1 GGGGTCAAAAATGTAATTTTTGGAAG-TTTGAGGGTAAAAATGTAATTTT-TGGAAGTT
5039844 CGGGGGTCAA
Statistics
Matches: 147, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
58 37 0.25
59 56 0.38
60 3 0.02
63 28 0.19
64 23 0.16
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.37
Consensus pattern (60 bp):
GGGGTCAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTA
Found at i:5040878 original size:3 final size:3
Alignment explanation
Indices: 5040872--5040910 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
5040862 TATTTAATAA
* *
5040872 TAT TAT TAA TAT TAT TAT TAT AAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
5040911 AAAGTTTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5040882 original size:12 final size:12
Alignment explanation
Indices: 5040865--5040903 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5040855 GGTTTTTTAT
5040865 TTAATAATATTA
1 TTAATAATATTA
*
5040877 TTAATATTATTA
1 TTAATAATATTA
5040889 TT-ATAATTATTA
1 TTAATAA-TATTA
5040901 TTA
1 TTA
5040904 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:5044979 original size:22 final size:24
Alignment explanation
Indices: 5044951--5044998 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5044941 TTACAGAATT
*
5044951 AAATACAT-AAT-ATATTTTATTA
1 AAATACATCAATAATATTTTACTA
*
5044973 AAATACATCCATAATATTTTACTA
1 AAATACATCAATAATATTTTACTA
5044997 AA
1 AA
5044999 TTTGGCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATACATCAATAATATTTTACTA
Found at i:5050250 original size:2 final size:2
Alignment explanation
Indices: 5050243--5050300 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5050233 TTCATCAATT
5050243 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5050285 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
5050301 TATATATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5050305 original size:2 final size:2
Alignment explanation
Indices: 5050300--5050325 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5050290 ACACACACAC
5050300 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
5050326 TCATATGTCA
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:5051718 original size:17 final size:17
Alignment explanation
Indices: 5051696--5051730 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5051686 ATGAGGTATC
* *
5051696 AAAATTCTAAAAACATA
1 AAAATTATAAAAAAATA
5051713 AAAATTATAAAAAAATA
1 AAAATTATAAAAAAATA
5051730 A
1 A
5051731 GATTTGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATTATAAAAAAATA
Found at i:5053271 original size:12 final size:12
Alignment explanation
Indices: 5053254--5053278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5053244 ATTAACATTA
5053254 ATTTAATTTAAT
1 ATTTAATTTAAT
5053266 ATTTAATTTAAT
1 ATTTAATTTAAT
5053278 A
1 A
5053279 ATCTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAATTTAAT
Found at i:5057125 original size:23 final size:23
Alignment explanation
Indices: 5057052--5057191 Score: 133
Period size: 23 Copynumber: 6.1 Consensus size: 23
5057042 TATACGGAAC
* *
5057052 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
5057074 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5057095 GGACAACAGAGAGCACACACAGTGCT
1 --A-AACAGAGAGCACACAAAGTGCT
* * *
5057121 AAACAGAGAGTACACAAAATACT
1 AAACAGAGAGCACACAAAGTGCT
*
5057144 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
5057167 AATCAGAGAGCACACACAGCGCT
1 AAACAGAGAGCACACAAAGTGCT
5057190 AA
1 AA
5057192 TAATAGAGAG
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
21 17 0.18
23 60 0.62
24 1 0.01
25 13 0.13
26 6 0.06
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:5057174 original size:69 final size:68
Alignment explanation
Indices: 5057052--5057191 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 68
5057042 TATACGGAAC
* *
5057052 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGACAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAATACTAACAGAGAGCACAAAAGTGCT-GACAACAGAGAGCACACACAG
*
5057117 TGCT
65 CGCT
*
5057121 AAACAGAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCT-A-ATCAGAGAGCACACAC
1 AAACAGAGAGTAC-CAAAATACTAA-CAGAGAGCACA-AAAGTGCTGACAACAGAGAGCACACAC
5057184 AGCGCT
63 AGCGCT
5057190 AA
1 AA
5057192 TAATAGAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
69 35 0.55
70 11 0.17
71 11 0.17
72 7 0.11
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAATACTAACAGAGAGCACAAAAGTGCTGACAACAGAGAGCACACACAGC
GCT
Found at i:5057199 original size:23 final size:23
Alignment explanation
Indices: 5057102--5057204 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 23
5057092 GCTGGACAAC
* *
5057102 AGAGAGCACACACAGTGCTAA-A
1 AGAGAGCACACAAAGCGCTAATA
* *** *
5057124 CAGAGAGTACACAAAATACTAATC
1 -AGAGAGCACACAAAGCGCTAATA
* *
5057148 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGCGCTAATA
*
5057171 AGAGAGCACACACAGCGCTAATAA
1 AGAGAGCACACAAAGCGCTAAT-A
5057195 TAGAGAGCAC
1 -AGAGAGCAC
5057205 GAGACATGCT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 57 0.86
25 9 0.14
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGCGCTAATA
Found at i:5065254 original size:25 final size:25
Alignment explanation
Indices: 5065187--5065257 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 25
5065177 TAAATAAATG
5065187 AGTTTTTTTATTTAATATGGTACTTT
1 AGTTTTTTT-TTTAATATGGTACTTT
*
5065213 AGTTTGATTTTTTTAATATGGT-TTTT
1 AGTTT--TTTTTTTAATATGGTACTTT
5065239 ATGTTTTTTTTTTAATATG
1 A-GTTTTTTTTTTAATATG
5065258 ATATTTGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 13 0.32
26 9 0.22
27 15 0.37
28 4 0.10
ACGTcount: A:0.21, C:0.01, G:0.13, T:0.65
Consensus pattern (25 bp):
AGTTTTTTTTTTAATATGGTACTTT
Found at i:5079204 original size:10 final size:10
Alignment explanation
Indices: 5079189--5079218 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
5079179 GAAATTCATA
5079189 GGAAACAGCC
1 GGAAACAGCC
5079199 GGAAACAGCC
1 GGAAACAGCC
5079209 GGAAACAGCC
1 GGAAACAGCC
5079219 ACTAAGGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.30, T:0.00
Consensus pattern (10 bp):
GGAAACAGCC
Found at i:5090394 original size:37 final size:37
Alignment explanation
Indices: 5090347--5090426 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
5090337 AACTAGGGCC
*
5090347 AGCAACTTTCAGGCACAAAATGCATCCATACATAGTT
1 AGCAATTTTCAGGCACAAAATGCATCCATACATAGTT
5090384 AGCAATTTTCAGGCACAAAATGCATCCATACATAGTT
1 AGCAATTTTCAGGCACAAAATGCATCCATACATAGTT
5090421 AGCAAT
1 AGCAAT
5090427 AGGGCAATCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (37 bp):
AGCAATTTTCAGGCACAAAATGCATCCATACATAGTT
Found at i:5095101 original size:2 final size:2
Alignment explanation
Indices: 5095094--5095126 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5095084 TAATTAAAAA
5095094 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5095127 TTATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5095330 original size:16 final size:17
Alignment explanation
Indices: 5095301--5095347 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
5095291 AAAATTATAG
*
5095301 AAAATTATAAAATATTT
1 AAAATTATAAAATATGT
5095318 AAAATTA-AAAATATGT
1 AAAATTATAAAATATGT
5095334 AAAAATATATAAAA
1 -AAAAT-TATAAAA
5095348 GTGCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 12 0.46
18 2 0.08
19 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAATATGT
Found at i:5095536 original size:21 final size:21
Alignment explanation
Indices: 5095512--5095552 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5095502 AAATATCAAA
*
5095512 ATTAAATAAAATTTAAAAATT
1 ATTAAATAAAATATAAAAATT
* *
5095533 ATTATATAAACTATAAAAAT
1 ATTAAATAAAATATAAAAAT
5095553 AGTCACTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTAAATAAAATATAAAAATT
Found at i:5096044 original size:19 final size:19
Alignment explanation
Indices: 5096022--5096060 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5096012 AATTTTTATG
5096022 TTTTTATAAA-ATTTATTAA
1 TTTTTATAAATATTT-TTAA
*
5096041 TTTTTCTAAATATTTTTAA
1 TTTTTATAAATATTTTTAA
5096060 T
1 T
5096061 AACTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATAAATATTTTTAA
Found at i:5096708 original size:27 final size:29
Alignment explanation
Indices: 5096670--5096726 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 29
5096660 ACTAATTAAT
* *
5096670 AAATATACTTTAGATCCA-TAC-AATAAA
1 AAATATACTTTACATACATTACAAATAAA
5096697 AAATAT-CATTTACATACATTACAAATAAA
1 AAATATAC-TTTACATACATTACAAATAAA
5096726 A
1 A
5096727 TTATATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.04
27 14 0.56
28 3 0.12
29 7 0.28
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (29 bp):
AAATATACTTTACATACATTACAAATAAA
Found at i:5099810 original size:24 final size:24
Alignment explanation
Indices: 5099762--5099806 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5099752 GTGATAATGC
*
5099762 TTAAATATGATATATTTTTTGATA
1 TTAAATATGATATATTTTTAGATA
5099786 TTAAATAT-ATATATTTTTAGA
1 TTAAATATGATATATTTTTAGA
5099807 ATATGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TTAAATATGATATATTTTTAGATA
Found at i:5100044 original size:19 final size:19
Alignment explanation
Indices: 5100022--5100066 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5100012 TTATATTAGG
5100022 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
5100041 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
5100060 ATTTAAT
1 ATTTAAT
5100067 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:5104441 original size:8 final size:8
Alignment explanation
Indices: 5104428--5104484 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
5104418 AACCCAATTA
5104428 TTTTTATT
1 TTTTTATT
5104436 TTTTTATTT
1 TTTTTA-TT
5104445 TTTTTATT
1 TTTTTATT
*
5104453 TTTCTATCT
1 TTTTTAT-T
5104462 TATTTTATT
1 T-TTTTATT
*
5104471 TATTTATT
1 TTTTTATT
5104479 TATTTT
1 T-TTTT
5104485 TGTCCAGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 21 0.51
9 15 0.37
10 5 0.12
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:5104450 original size:17 final size:17
Alignment explanation
Indices: 5104428--5104485 Score: 71
Period size: 18 Copynumber: 3.3 Consensus size: 17
5104418 AACCCAATTA
5104428 TTTTTATTTTTTTATTT
1 TTTTTATTTTTTTATTT
*
5104445 TTTTTATTTTTCTATCTT
1 TTTTTATTTTTTTAT-TT
* *
5104463 ATTTTATTTATTTATTT
1 TTTTTATTTTTTTATTT
5104480 ATTTTT
1 -TTTTT
5104486 GTCCAGGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 16 0.47
18 18 0.53
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTATTTTTTTATTT
Found at i:5105280 original size:102 final size:102
Alignment explanation
Indices: 5105171--5105360 Score: 285
Period size: 102 Copynumber: 1.9 Consensus size: 102
5105161 ATGTGTTAGA
* * *
5105171 CTGAGTAACCGGGGTGGAGTGCTTGGTTGTCATTTCACTTCGCGTCAAAAGGGCTAATGCATTC-
1 CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTCT
5105235 TAAA-AAAAAAGAGAAGAAAAAATTGAGAGCATGTTGGG
66 TAAAGAAAAAA-A-AAGAAAAAATTGAGAGCATGTTGGG
* * *
5105273 CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGTATTCT
1 CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTCT
*
5105338 TAAAGAAAAAAAAGGAAAAAATT
66 TAAAGAAAAAAAAAGAAAAAATT
5105361 CACAAAATAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 68 0.86
103 5 0.06
104 6 0.08
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (102 bp):
CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTCT
TAAAGAAAAAAAAAGAAAAAATTGAGAGCATGTTGGG
Found at i:5105926 original size:19 final size:19
Alignment explanation
Indices: 5105904--5105948 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5105894 TTATATTAGG
5105904 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
5105923 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
5105942 ATTTAAT
1 ATTTAAT
5105949 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:5114368 original size:2 final size:2
Alignment explanation
Indices: 5114361--5114400 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5114351 ATTTAATATG
5114361 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5114401 TATGCATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5123420 original size:6 final size:6
Alignment explanation
Indices: 5123382--5123418 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
5123372 GCGGGAAGGT
*
5123382 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GAAGAG G
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG G
5123419 AAAGAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:5124052 original size:3 final size:3
Alignment explanation
Indices: 5124044--5124074 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5124034 TGAAAGTCTA
5124044 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5124075 ACTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5124518 original size:22 final size:21
Alignment explanation
Indices: 5124485--5124542 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
5124475 ACAATTGAAC
5124485 AAAAAATTTAAATTTTA-AAAGT
1 AAAAAA-TTAAATTTTAGAAA-T
5124507 AAAGAAATTAAATTTTTAGAAAT
1 AAA-AAATTAAA-TTTTAGAAAT
5124530 AAAAAA-TAAATTT
1 AAAAAATTAAATTT
5124543 AAATTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 11 0.33
23 12 0.36
24 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAAATTAAATTTTAGAAAT
Found at i:5131742 original size:13 final size:14
Alignment explanation
Indices: 5131724--5131752 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5131714 GAATAAATAC
5131724 TTATTTTTTAT-TT
1 TTATTTTTTATATT
5131737 TTATTTTTTATATT
1 TTATTTTTTATATT
5131751 TT
1 TT
5131753 GAAATCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTTATATT
Found at i:5135478 original size:20 final size:20
Alignment explanation
Indices: 5135453--5135491 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5135443 ATGAAAATGA
5135453 TTTGAA-AATTAATTTAATTT
1 TTTGAATAATT-ATTTAATTT
*
5135473 TTTGAATTATTATTTAATT
1 TTTGAATAATTATTTAATT
5135492 AAATAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTGAATAATTATTTAATTT
Found at i:5137174 original size:23 final size:24
Alignment explanation
Indices: 5137112--5137183 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
5137102 ATTCATTAAC
*
5137112 ATTGTTCGTGAACATGTTCAATT-
1 ATTGTTCGTGAACATGTTCGATTA
* *
5137135 ATATGTTCATGAACATGTTCGTTTA
1 AT-TGTTCGTGAACATGTTCGATTA
5137160 ATTGTT-GTGAACATGTTCGATTA
1 ATTGTTCGTGAACATGTTCGATTA
5137183 A
1 A
5137184 GTTAAATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 18 0.43
24 22 0.52
25 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTGTTCGTGAACATGTTCGATTA
Found at i:5137193 original size:23 final size:22
Alignment explanation
Indices: 5137120--5137201 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 22
5137110 ACATTGTTCG
*
5137120 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTT-A
* *
5137144 TGAACATGTTCGTTTAATTGTTG
1 TGAACATGTTCGATTAA-TGTTA
5137167 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT--A
5137190 TGAACATGTTCG
1 TGAACATGTTCG
5137202 TGAACATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.06
23 29 0.58
24 18 0.36
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (22 bp):
TGAACATGTTCGATTAATGTTA
Found at i:5137211 original size:23 final size:23
Alignment explanation
Indices: 5137167--5137212 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5137157 TTAATTGTTG
* *
5137167 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
5137190 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
5137213 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:5138424 original size:20 final size:20
Alignment explanation
Indices: 5138401--5138438 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5138391 AATTTTTACA
*
5138401 TATAAAATTATTATTTTATT
1 TATAAAATTATAATTTTATT
5138421 TATAAAATTATAATTTTA
1 TATAAAATTATAATTTTA
5138439 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAAAATTATAATTTTATT
Found at i:5138948 original size:22 final size:21
Alignment explanation
Indices: 5138919--5138959 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5138909 GAAAATTACA
* *
5138919 AAATAAAAATATTTAGAAACC
1 AAATAAAAAAATTGAGAAACC
5138940 AAATAAAAAAAATTGAGAAA
1 AAAT-AAAAAAATTGAGAAA
5138960 TTCAGAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (21 bp):
AAATAAAAAAATTGAGAAACC
Found at i:5147032 original size:20 final size:20
Alignment explanation
Indices: 5147004--5147042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5146994 CCATGACTTT
*
5147004 CATTATTAAGTTTAATTAAC
1 CATTATTAACTTTAATTAAC
*
5147024 CATTTTTAACTTTAATTAA
1 CATTATTAACTTTAATTAA
5147043 ACCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAACTTTAATTAAC
Found at i:5147051 original size:20 final size:20
Alignment explanation
Indices: 5147009--5147052 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5146999 ACTTTCATTA
* *
5147009 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
5147029 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
5147049 TTAA
1 TTAA
5147053 AAGTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:5150259 original size:21 final size:21
Alignment explanation
Indices: 5150235--5150286 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5150225 GATTTGTATG
*
5150235 TTTTGTTAAGAAATTATTTTC
1 TTTTGGTAAGAAATTATTTTC
5150256 TTTTGGTAAGAAATTATTTTC
1 TTTTGGTAAGAAATTATTTTC
5150277 TTTTGGTAAG
1 TTTTGGTAAG
5150287 GTGTTTGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (21 bp):
TTTTGGTAAGAAATTATTTTC
Found at i:5155018 original size:60 final size:59
Alignment explanation
Indices: 5154940--5155287 Score: 219
Period size: 61 Copynumber: 6.0 Consensus size: 59
5154930 TTTTGGGTGT
* *
5154940 CCTGTTTCAGAAAAAAAAATTC-AATTTTTTTTGTGTTGGCCATCAAATGGCCGACACCAA
1 CCTGTTTCAGAAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACA-C-A
* * * *
5155000 CCT-TTTCTCGAGAAAAAAATTTCAAAATTTTTTCATGTTGGCCATCAAATGACCGACACA
1 CCTGTTTC-AGA-AAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACACA
* * **
5155060 CCTGTTTCAGAAAAAAAAATTCTAATTTTTTTGGGTGTTGG--------TGA--TTC-C-
1 CCTGTTTCAGAAAAAAAAATTCAAATTTTTTT-CGTGTTGGCCATCAAATGACCGACACA
* * * * * *
5155108 CTTTTCTCGAG-AAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCC
1 CCTGTTTC-AGAAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACA-CA
* * * * * * *
5155168 CCTATTCTC-GAGAAAAAAGATTTAAATTTTTTTGGTGTTAGCCATCAAATGACAGACACCC
1 CCTGTT-TCAGA-AAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACA-CA
* * *
5155229 CCT-TTTCTCGAATAAAAAAATTTC-AATTTTTTTTGTGTTGGCCATCAAATGGCCGACAC
1 CCTGTTTC-AGAA-AAAAAAA-TTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACAC
5155288 CAATTTCTCC
Statistics
Matches: 227, Mismatches: 35, Indels: 52
0.72 0.11 0.17
Matches are distributed among these distances:
47 8 0.04
48 25 0.11
49 3 0.01
50 1 0.00
52 3 0.01
55 2 0.01
57 1 0.00
59 26 0.11
60 24 0.11
61 102 0.45
62 32 0.14
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (59 bp):
CCTGTTTCAGAAAAAAAAATTCAAATTTTTTTCGTGTTGGCCATCAAATGACCGACACA
Found at i:5155131 original size:168 final size:169
Alignment explanation
Indices: 5154951--5155269 Score: 452
Period size: 168 Copynumber: 1.9 Consensus size: 169
5154941 CTGTTTCAGA
* *
5154951 AAAAAAAATTC-AATTTTTTTTGTGTTGGCCATCAAATGGCCGACACCAACCTTTTCTCGAGAAA
1 AAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC-ACCTATTCTCGAGAAA
* *
5155015 AAA-ATTTCAAAATTTTTTCATGTTGGCCATCAAATGACCGACA-CACCTGTTTC-AGAA-AAAA
65 AAAGATTT-AAAATTTTTTCATGTTAGCCATCAAATGACAGACACCACCT-TTTCTAGAATAAAA
5155076 AAA-TTCTAATTTTTTTGGGTGTTGGTGATTCCCTTTTCTCGAG
128 AAATTTC-AATTTTTTT-GGTGTTGGTGATTCCCTTTTCTCGAG
*
5155119 AAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTCTCGAGAAAA
1 AAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCACCTATTCTCGAGAAAA
* ** * *
5155184 AAGATTTAAATTTTTTTGGTGTTAGCCATCAAATGACAGACACCCCCTTTTCTCGAATAAAAAAA
66 AAGATTTAAAATTTTTTCATGTTAGCCATCAAATGACAGACACCACCTTTTCTAGAATAAAAAAA
*
5155249 TTTCAATTTTTTTTGTGTTGG
131 TTTCAATTTTTTTGGTGTTGG
5155270 CCATCAAATG
Statistics
Matches: 134, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
168 62 0.46
169 53 0.40
170 16 0.12
171 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (169 bp):
AAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCACCTATTCTCGAGAAAA
AAGATTTAAAATTTTTTCATGTTAGCCATCAAATGACAGACACCACCTTTTCTAGAATAAAAAAA
TTTCAATTTTTTTGGTGTTGGTGATTCCCTTTTCTCGAG
Found at i:5155206 original size:61 final size:61
Alignment explanation
Indices: 5155106--5155288 Score: 278
Period size: 61 Copynumber: 3.0 Consensus size: 61
5155096 GTTGGTGATT
*
5155106 CCCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
1 CCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
* * * * *
5155167 CCCTATTCTCGAGAAAAAAGATTTAAATTTTTTTGGTGTTAGCCATCAAATGACAGACACC
1 CCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
* *
5155228 CCCTTTTCTCGA-ATAAAAAAATTTCAATTTTTTTTGTGTTGGCCATCAAATGGCCGACACC
1 CCCTTTTCTCGAGA-AAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
5155289 AATTTCTCCT
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
60 1 0.01
61 107 0.99
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (61 bp):
CCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
Found at i:5158446 original size:20 final size:20
Alignment explanation
Indices: 5158417--5158466 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
5158407 TGGATGAAAC
5158417 TCGATCAACGGCGGACAAAG
1 TCGATCAACGGCGGACAAAG
*
5158437 TCGGTCAACGGCGGACAAAG
1 TCGATCAACGGCGGACAAAG
5158457 TCGATCAACG
1 TCGATCAACG
5158467 ACGATCAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.30, T:0.12
Consensus pattern (20 bp):
TCGATCAACGGCGGACAAAG
Found at i:5158484 original size:10 final size:10
Alignment explanation
Indices: 5158421--5158492 Score: 54
Period size: 10 Copynumber: 7.2 Consensus size: 10
5158411 TGAAACTCGA
5158421 TCAACGGCGG
1 TCAACGGCGG
* * *
5158431 ACAAAGTCGG
1 TCAACGGCGG
5158441 TCAACGGCGG
1 TCAACGGCGG
* * * *
5158451 ACAAAGTCGA
1 TCAACGGCGG
* *
5158461 TCAACGACGA
1 TCAACGGCGG
*
5158471 TCAACGGTGG
1 TCAACGGCGG
5158481 TCAACGGCGG
1 TCAACGGCGG
5158491 TC
1 TC
5158493 TCGGGACGTT
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
10 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.12
Consensus pattern (10 bp):
TCAACGGCGG
Found at i:5158790 original size:83 final size:83
Alignment explanation
Indices: 5158651--5159338 Score: 1134
Period size: 83 Copynumber: 8.3 Consensus size: 83
5158641 ATAATTTAAA
* *
5158651 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5158716 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
*
5158734 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5158799 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
* *
5158817 ATATGATAAAAATTATAATATAAT-AAAATTTTTATTTAAAGATATAAAATTAATAAATAATATA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5158881 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
5158899 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5158964 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
*
5158982 ATATGATAAAAATTATAATATAAT-AAAATTTTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5159046 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
5159064 ATATGATAAAAATTATAATATAAT-AAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
5159128 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
*** *
5159146 ATATGATAAAAATTATAATATAATAAATTTTTTTATTTAAAGATATAAAATTAATAAATAATATA
1 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
*
5159211 TTGTCAAATCAATACATT
66 TTGTCAAATCAACACATT
* *
5159229 ATATGATAAAAATTATAATATAATAAAAATTTTTACTTT-AA-ATATGAAAATTTGATAAATAAT
1 ATATGATAAAAATTATAATATAATAAAAAATTTTA-TTTAAAGATAT-AAAA-TTAATAAATAAT
* * * *
5159292 ATATTGTCAAATTAATACAAT
63 GTATTGTCAAATCAACACATT
* * *
5159313 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTATAATATAATAA
5159339 CTATCTTTTT
Statistics
Matches: 579, Mismatches: 21, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
82 246 0.42
83 277 0.48
84 56 0.10
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (83 bp):
ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
TTGTCAAATCAACACATT
Found at i:5158924 original size:165 final size:165
Alignment explanation
Indices: 5158651--5159338 Score: 1157
Period size: 165 Copynumber: 4.2 Consensus size: 165
5158641 ATAATTTAAA
* ** *
5158651 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATGATAAAAATTATAATATAAT-AAAATTTTTATTTAAAGATATAAAATTAATAAATAATATA
*
5158716 TTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATA
65 TTGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATA
5158781 AAATTAATAAATAATGTATTGTCAAATCAACACATT
130 AAATTAATAAATAATGTATTGTCAAATCAACACATT
5158817 ATATGATAAAAATTATAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATAATATAT
1 ATATGATAAAAATTATAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATAATATAT
5158882 TGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAA
66 TGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAA
5158947 AATTAATAAATAATGTATTGTCAAATCAACACATT
131 AATTAATAAATAATGTATTGTCAAATCAACACATT
*
5158982 ATATGATAAAAATTATAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATAATGTAT
1 ATATGATAAAAATTATAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATAATATAT
5159047 TGTCAAATCAACACATTATATGATAAAAATTATAATATAAT-AAAAATTTTATTTAAAGATATAA
66 TGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAA
5159111 AATTAATAAATAATGTATTGTCAAATCAACACATT
131 AATTAATAAATAATGTATTGTCAAATCAACACATT
*
5159146 ATATGATAAAAATTATAATATAATAAATTTTTTTATTTAAAGATATAAAATTAATAAATAATATA
1 ATATGATAAAAATTATAATATAATAAA-ATTTTTATTTAAAGATATAAAATTAATAAATAATATA
* *
5159211 TTGTCAAATCAATACATTATATGATAAAAATTATAATATAATAAAAATTTTTACTTT-AA-ATAT
65 TTGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTA-TTTAAAGATAT
* * * * *
5159274 GAAAATTTGATAAATAATATATTGTCAAATTAATACAAT
129 -AAAA-TTAATAAATAATGTATTGTCAAATCAACACATT
* * *
5159313 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTATAATATAATAA
5159339 CTATCTTTTT
Statistics
Matches: 499, Mismatches: 18, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
164 85 0.17
165 322 0.65
166 38 0.08
167 54 0.11
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (165 bp):
ATATGATAAAAATTATAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATAATATAT
TGTCAAATCAACACATTATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAA
AATTAATAAATAATGTATTGTCAAATCAACACATT
Found at i:5163370 original size:61 final size:61
Alignment explanation
Indices: 5163240--5163501 Score: 328
Period size: 61 Copynumber: 4.3 Consensus size: 61
5163230 AGGAGAAGTT
* * *
5163240 GGTGTCGGCCATTTGATGGCAAACACAAAAAAAAAAATTGAAATTTTTTTATTCGAGAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACAC--AAAAAAAAATTAAAATTTTTTT-CTCGAGAAAAGGG
* * * *
5163304 AGTGTCGGCCATTTGGTGGCCAACACAAAAAAAAATTAGAATTTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTAAAATTTTTTTCTCGAGAAAAGGG
* * * * * *
5163365 GGTGTCGACCATTTGATGACTAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTAAAATTTTTTTCTCGAGAAAAGGG
* * * *
5163426 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTAAAATTATTTT-TCGAGAAAAGAG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTAAAATTTTTTTCTCGAGAAAAGGG
*
5163486 GGTGTCGACCATTTGA
1 GGTGTCGGCCATTTGA
5163502 AAATTTTTTT
Statistics
Matches: 176, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
60 25 0.14
61 108 0.61
62 20 0.11
64 23 0.13
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (61 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAATTAAAATTTTTTTCTCGAGAAAAGGG
Found at i:5164863 original size:22 final size:23
Alignment explanation
Indices: 5164833--5164875 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5164823 AAAAGAATAT
*
5164833 AAAAGAAAAAATTA-AATTGTTC
1 AAAAGAAAAAAATATAATTGTTC
*
5164855 AAAATAAAAAAATATAATTGT
1 AAAAGAAAAAAATATAATTGT
5164876 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (23 bp):
AAAAGAAAAAAATATAATTGTTC
Found at i:5183529 original size:12 final size:12
Alignment explanation
Indices: 5183514--5183538 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5183504 TTTCTATATT
5183514 ATAGATTATAGG
1 ATAGATTATAGG
5183526 ATAGATTATAGG
1 ATAGATTATAGG
5183538 A
1 A
5183539 AAACGGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAGATTATAGG
Found at i:5188349 original size:79 final size:79
Alignment explanation
Indices: 5188218--5188378 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 79
5188208 AAGGCAGGGA
*
5188218 CAACCAAATTCCGGTCTCCTATATGCTGGATACAAGTTATTACTTTTATTTGGTTTTATAATACA
1 CAACCAAATTCCGGTCTCCTATAAGCTGGATACAAGTTATTACTTTTATTTGGTTTTATAATACA
5188283 GGAACAGATTTGAC
66 GGAACAGATTTGAC
* *
5188297 CAACCAAATTCTGGTTTCCTATAAGCTGGATACAAGTTATTACTTTTATTTGGTTTTATAATACA
1 CAACCAAATTCCGGTCTCCTATAAGCTGGATACAAGTTATTACTTTTATTTGGTTTTATAATACA
5188362 GGAACAGATTTGAC
66 GGAACAGATTTGAC
5188376 CAA
1 CAA
5188379 TACTGCAAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (79 bp):
CAACCAAATTCCGGTCTCCTATAAGCTGGATACAAGTTATTACTTTTATTTGGTTTTATAATACA
GGAACAGATTTGAC
Found at i:5189229 original size:17 final size:16
Alignment explanation
Indices: 5189194--5189225 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5189184 GTTTTGCATA
5189194 ACATATTGAAAAAATT
1 ACATATTGAAAAAATT
5189210 ACATATTGAAAAAATT
1 ACATATTGAAAAAATT
5189226 TACAAACTAA
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:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
ACATATTGAAAAAATT
Found at i:5193691 original size:30 final size:30
Alignment explanation
Indices: 5193624--5193693 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
5193614 AATATTAATA
*
5193624 AGTGATTGATTTATTATTTTTTGATAATATT
1 AGTGATTGATTTATTATTTTTT-ATAAAATT
* *
5193655 AATGATTGTTTTATTATTTTTT-TAAAACTT
1 AGTGATTGATTTATTATTTTTTATAAAA-TT
5193685 AGTGATTGA
1 AGTGATTGA
5193694 AATAAAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 9 0.27
31 20 0.61
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (30 bp):
AGTGATTGATTTATTATTTTTTATAAAATT
Found at i:5199213 original size:31 final size:29
Alignment explanation
Indices: 5199175--5199257 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
5199165 ATTGGGAAAT
*
5199175 GTTAGTGACTGTTTTGTC-ACTTTTCGGTAAA
1 GTTAGTGACTGTTTTGTCAAATTTTC---AAA
*
5199206 GTTAGTGATTGTTTTGTCAAATTTTCAAA
1 GTTAGTGACTGTTTTGTCAAATTTTCAAA
* *
5199235 GTTGAGTGACTGTTGTGTTAAAT
1 GTT-AGTGACTGTTTTGTCAAAT
5199258 GTAACCGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.13
30 16 0.36
31 17 0.38
32 6 0.13
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (29 bp):
GTTAGTGACTGTTTTGTCAAATTTTCAAA
Found at i:5213990 original size:14 final size:15
Alignment explanation
Indices: 5213960--5213993 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5213950 AAATATATAA
*
5213960 TAATAAACATGAATT
1 TAATAAACATCAATT
5213975 TAATAAA-ATCAATT
1 TAATAAACATCAATT
5213989 TAATA
1 TAATA
5213994 TTAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (15 bp):
TAATAAACATCAATT
Found at i:5215801 original size:14 final size:14
Alignment explanation
Indices: 5215782--5215828 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
5215772 AATCTAATGA
5215782 TTTAAATAAATTTT
1 TTTAAATAAATTTT
5215796 TTTAAAT-AATTTCAT
1 TTTAAATAAATTT--T
5215811 AATTTAAATAAATTTT
1 --TTTAAATAAATTTT
5215827 TT
1 TT
5215829 ACATAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 1 0.04
16 1 0.04
17 7 0.25
18 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAATAAATTTT
Found at i:5227129 original size:18 final size:18
Alignment explanation
Indices: 5227093--5227130 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5227083 ATAATTTATT
*
5227093 TAATTAAATTGAATGAAC
1 TAATTAAATTGAATAAAC
5227111 TAATTAAA-TGAATCAAAC
1 TAATTAAATTGAAT-AAAC
5227129 TA
1 TA
5227131 GAAATAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
TAATTAAATTGAATAAAC
Found at i:5228611 original size:15 final size:15
Alignment explanation
Indices: 5228591--5228621 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5228581 ATAAGATTCG
5228591 TTAACTCGACTCGAT
1 TTAACTCGACTCGAT
*
5228606 TTAACTCGATTCGAT
1 TTAACTCGACTCGAT
5228621 T
1 T
5228622 CGATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (15 bp):
TTAACTCGACTCGAT
Found at i:5231069 original size:18 final size:17
Alignment explanation
Indices: 5231036--5231069 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5231026 AAGATACTAT
*
5231036 ATAAAAATTTTCAATAA
1 ATAAAAATTTTAAATAA
5231053 ATAAAAATTATTAAATA
1 ATAAAAATT-TTAAATA
5231070 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAAATTTTAAATAA
Found at i:5233396 original size:27 final size:23
Alignment explanation
Indices: 5233347--5233402 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
5233337 TATTATTATT
5233347 ATTATT-ATTATTTAAAACATCGA
1 ATTATTGA-TATTTAAAACATCGA
5233370 ATATATTGATATTTGAAAACCATTCGA
1 AT-TATTGATATTT-AAAA-CA-TCGA
5233397 ATTATT
1 ATTATT
5233403 TCGACTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.07
24 9 0.32
25 5 0.18
26 6 0.21
27 6 0.21
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTATTGATATTTAAAACATCGA
Found at i:5236334 original size:10 final size:10
Alignment explanation
Indices: 5236321--5236345 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5236311 TTTAAAATTA
5236321 TAAAAATATT
1 TAAAAATATT
5236331 TAAAAATATT
1 TAAAAATATT
5236341 TAAAA
1 TAAAA
5236346 TTTTAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATATT
Found at i:5245638 original size:32 final size:32
Alignment explanation
Indices: 5245597--5245660 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
5245587 TAATCCGATT
5245597 ATACACAATATCTTTCTCTTCTCATAAATTAA
1 ATACACAATATCTTTCTCTTCTCATAAATTAA
5245629 ATACACAATATCTTTCTCTTCTCATAAATTAA
1 ATACACAATATCTTTCTCTTCTCATAAATTAA
5245661 GGTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (32 bp):
ATACACAATATCTTTCTCTTCTCATAAATTAA
Found at i:5247610 original size:69 final size:69
Alignment explanation
Indices: 5247499--5247638 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
5247489 AGAGTTTTAT
*
5247499 TTTATCACTTTAATAAGAGTTTAATGAAATTATATATATTCATTATCAATGTATTTACAACCATT
1 TTTATCACTTTAATAAAAGTTTAATGAAATTATATATATTCATTATCAATGTATTTACAACCATT
5247564 AAAA
66 AAAA
*
5247568 TTTATCACTTTAATAAAAGTTTAATGAAATTATATATATTCATTATTAATGTATTTACAACCATT
1 TTTATCACTTTAATAAAAGTTTAATGAAATTATATATATTCATTATCAATGTATTTACAACCATT
5247633 AAAA
66 AAAA
5247637 TT
1 TT
5247639 AGGTCGTATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (69 bp):
TTTATCACTTTAATAAAAGTTTAATGAAATTATATATATTCATTATCAATGTATTTACAACCATT
AAAA
Found at i:5249941 original size:117 final size:117
Alignment explanation
Indices: 5249735--5249964 Score: 291
Period size: 117 Copynumber: 2.0 Consensus size: 117
5249725 TATTAGTCTA
**** * *
5249735 GTAGTGTTTACAGTGTCACTATTGCTTCAGTATAGCATTGCGGTGTTTACAGTGTCACCGCCAAT
1 GTAGTGTTTACAGTGTCACTACCAATTCAGTATAACATTGCAGTGTTTACAGTGTCACCGCCAAT
* * *
5249800 TCAGTATAGCATTGCAGTGCTTACAGTGTCGCAT-CCAGTTCAGTATATCATT
66 TCAATATAACATTGCAGTGCTTACAGTGTCAC-TGCCAGTTCAGTATATCATT
* * * ***
5249852 GTAGTGTTTACAGTGTCACTACCAATTCAGTATAACGTTGTAGTGTTTACAGTGTCACTGCTGGT
1 GTAGTGTTTACAGTGTCACTACCAATTCAGTATAACATTGCAGTGTTTACAGTGTCACCGCCAAT
* *
5249917 TCAATATAACATTGCAGTGTTTACAGTGTCACTGCCGGTTCAGTATAT
66 TCAATATAACATTGCAGTGCTTACAGTGTCACTGCCAGTTCAGTATAT
5249965 TTTCGACGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
116 1 0.01
117 94 0.99
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (117 bp):
GTAGTGTTTACAGTGTCACTACCAATTCAGTATAACATTGCAGTGTTTACAGTGTCACCGCCAAT
TCAATATAACATTGCAGTGCTTACAGTGTCACTGCCAGTTCAGTATATCATT
Found at i:5249950 original size:39 final size:39
Alignment explanation
Indices: 5249737--5249963 Score: 242
Period size: 39 Copynumber: 5.8 Consensus size: 39
5249727 TTAGTCTAGT
*** *
5249737 AGTGTTTACAGTGTCACT-ATTGCTTCAGTATAGCATTGC
1 AGTGTTTACAGTGTCACTGCCAG-TTCAGTATAACATTGC
* * * *
5249776 GGTGTTTACAGTGTCACCGCCAATTCAGTATAGCATTGC
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATTGC
* * * *
5249815 AGTGCTTACAGTGTCGCAT-CCAGTTCAGTATATCATTGT
1 AGTGTTTACAGTGTCAC-TGCCAGTTCAGTATAACATTGC
* * * *
5249854 AGTGTTTACAGTGTCACTACCAATTCAGTATAACGTTGT
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATTGC
** *
5249893 AGTGTTTACAGTGTCACTGCTGGTTCAATATAACATTGC
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATTGC
*
5249932 AGTGTTTACAGTGTCACTGCCGGTTCAGTATA
1 AGTGTTTACAGTGTCACTGCCAGTTCAGTATA
5249964 TTTTCGACGT
Statistics
Matches: 158, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
38 1 0.01
39 157 0.99
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGTTCAGTATAACATTGC
Found at i:5251744 original size:11 final size:11
Alignment explanation
Indices: 5251713--5251754 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5251703 CCCAACTTGG
5251713 ATTTTAAATTA
1 ATTTTAAATTA
* *
5251724 AGTTTGAATTA
1 ATTTTAAATTA
*
5251735 ATTTTAAATTT
1 ATTTTAAATTA
5251746 A-TTTAAATT
1 ATTTTAAATT
5251755 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:5251754 original size:17 final size:17
Alignment explanation
Indices: 5251715--5251776 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
5251705 CAACTTGGAT
*
5251715 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
5251731 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
5251747 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
5251764 TTTAAATTTAAAT
1 TTTAAATTTAAAT
5251777 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:5251757 original size:22 final size:22
Alignment explanation
Indices: 5251713--5251754 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5251703 CCCAACTTGG
*
5251713 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
5251735 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
5251755 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:5251760 original size:27 final size:27
Alignment explanation
Indices: 5251719--5251810 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
5251709 TTGGATTTTA
* *
5251719 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
5251746 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * * * *
5251773 AAATACATTTAAAATAATTTGAAACTTAA
1 AATTAAATTTAAATTAATTTTAAA-TT-T
5251802 AATTAAATT
1 AATTAAATT
5251811 AATAATGTCC
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
27 39 0.81
28 2 0.04
29 7 0.15
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:5251785 original size:16 final size:16
Alignment explanation
Indices: 5251732--5251785 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5251722 TAAGTTTGAA
* *
5251732 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
5251748 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
5251765 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
5251781 TTAAA
1 TTAAA
5251786 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:5253675 original size:29 final size:30
Alignment explanation
Indices: 5253637--5253781 Score: 103
Period size: 29 Copynumber: 4.9 Consensus size: 30
5253627 AGTCCCCAAG
5253637 CTTTCC-AAAATTCCATTTTTGACCCCAAAA
1 CTTTCCAAAAATTCCATTTTT-ACCCCAAAA
* *
5253667 C-TTCTAAAAATTACCA-TTTTACCCCTAAA
1 CTTTCCAAAAATT-CCATTTTTACCCCAAAA
* *
5253696 CTTTCC-AAAATCCCATTTTTAACCCC--GA
1 CTTTCCAAAAATTCCATTTTT-ACCCCAAAA
*
5253724 -TTTCACCAAAAATTACCA-TTTTACCCTAAAA
1 CTTT--CCAAAAATT-CCATTTTTACCCCAAAA
*
5253755 -TTTCC-AAAATCCCATTTTTAACCCCAA
1 CTTTCCAAAAATTCCATTTTT-ACCCCAA
5253782 TTTCACCAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
27 6 0.07
28 13 0.14
29 35 0.38
30 28 0.30
31 10 0.11
ACGTcount: A:0.35, C:0.30, G:0.01, T:0.33
Consensus pattern (30 bp):
CTTTCCAAAAATTCCATTTTTACCCCAAAA
Found at i:5253735 original size:59 final size:59
Alignment explanation
Indices: 5253672--5254048 Score: 535
Period size: 59 Copynumber: 6.4 Consensus size: 59
5253662 CAAAACTTCT
5253672 AAAAATTACCATTTTACCC-CTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTC-AAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* *
5253731 AAAAATTACCATTTTACCCT-AAAATTTCCAAAATCCCATTTTTAACCCCAATTTCACC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * * *
5253789 AAAAATTACTATTTTACTCTCGAACCTTCCAAAATCCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
5253848 AAAAATTACCATTTTACCCTCGAATTTTCCAAAATCCCATTTTTAGCCCCGATTTCACC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * * * *
5253907 AAAAATTACCATTTTACCCTCGAACTTTCTAAAATCCCATTTTTAACCTCGGTTTCACT
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * * * *
5253966 AAAAATTATCGTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACC
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
*
5254025 AAAAATTA-CATTTTTACCCCCAAA
1 AAAAATTACCA-TTTTACCCTCAAA
5254049 AGTCAAAAAT
Statistics
Matches: 285, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 55 0.19
59 230 0.81
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:5253950 original size:29 final size:28
Alignment explanation
Indices: 5253697--5253957 Score: 96
Period size: 29 Copynumber: 8.9 Consensus size: 28
5253687 ACCCCTAAAC
*
5253697 TTTCCAAAATCCCATTTTTAACCC-CG-A
1 TTTCAAAAATCCCATTTTT-ACCCTCGAA
* **
5253724 TTTCACCAAAAATTACCA-TTTTACCCTAAAA
1 TTT---CAAAAA-TCCCATTTTTACCCTCGAA
*
5253755 TTTCCAAAATCCCATTTTTAACCC-C-AA
1 TTTCAAAAATCCCATTTTT-ACCCTCGAA
** *
5253782 TTTCACCAAAAATTAC-TATTTTACTCTCGAA
1 TTT---CAAAAATCCCAT-TTTTACCCTCGAA
* *
5253813 CCTTCCAAAATCCCATTTTTAACCC-CG-A
1 -TTTCAAAAATCCCATTTTT-ACCCTCGAA
*
5253841 TTTCACCAAAAATTACCA-TTTTACCCTCGAA
1 TTT---CAAAAA-TCCCATTTTTACCCTCGAA
*
5253872 TTTTCCAAAATCCCATTTTTAGCCC-CG-A
1 -TTTCAAAAATCCCATTTTTA-CCCTCGAA
*
5253900 TTTCACCAAAAATTACCA-TTTTACCCTCGAA
1 TTT---CAAAAA-TCCCATTTTTACCCTCGAA
* *
5253931 CTTTCTAAAATCCCATTTTTAACCTCG
1 -TTTCAAAAATCCCATTTTTACCCTCG
5253958 GTTTCACTAA
Statistics
Matches: 174, Mismatches: 26, Indels: 66
0.65 0.10 0.25
Matches are distributed among these distances:
27 17 0.10
28 19 0.11
29 59 0.34
30 51 0.29
31 20 0.11
32 8 0.05
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTCAAAAATCCCATTTTTACCCTCGAA
Found at i:5253967 original size:29 final size:29
Alignment explanation
Indices: 5253702--5253971 Score: 125
Period size: 30 Copynumber: 9.2 Consensus size: 29
5253692 TAAACTTTCC
*
5253702 AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAATCCCATTTTTAACCTCGATTTCA-CA
* * **
5253732 AAAATTACCA-TTTTACCCTAAAATTTC-C-
1 AAAA-TCCCATTTTTAACCT-CGATTTCACA
* *
5253760 AAAATCCCATTTTTAACCCCAATTTCACCA
1 AAAATCCCATTTTTAACCTCGATTTCA-CA
** *
5253790 AAAATTAC-TATTTT-ACTCTCGAACCTTC-C-
1 AAAATCCCAT-TTTTAAC-CTCG-A-TTTCACA
*
5253819 AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAATCCCATTTTTAACCTCGATTTCA-CA
* *
5253849 AAAATTACCA-TTTTACCCTCGAATTTTC-C-
1 AAAA-TCCCATTTTTAACCTCG-A-TTTCACA
* *
5253878 AAAATCCCATTTTTAGCCCCGATTTCACCA
1 AAAATCCCATTTTTAACCTCGATTTCA-CA
* * *
5253908 AAAATTACCA-TTTTACCCTCGAACTTT--CT
1 AAAA-TCCCATTTTTAACCTCG-A-TTTCACA
*
5253937 AAAATCCCATTTTTAACCTCGGTTTCACTA
1 AAAATCCCATTTTTAACCTCGATTTCAC-A
5253967 AAAAT
1 AAAAT
5253972 TATCGTTTTA
Statistics
Matches: 179, Mismatches: 32, Indels: 58
0.67 0.12 0.22
Matches are distributed among these distances:
27 20 0.11
28 21 0.12
29 49 0.27
30 59 0.33
31 20 0.11
32 10 0.06
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATCCCATTTTTAACCTCGATTTCACA
Found at i:5257519 original size:23 final size:23
Alignment explanation
Indices: 5257493--5257628 Score: 132
Period size: 23 Copynumber: 6.0 Consensus size: 23
5257483 TTACCGTTCA
* *
5257493 GCACTGTGTGTGCTTACTGTTTT
1 GCACTATGTGTGCCTACTGTTTT
* * * *
5257516 GCACTTTGTGTGCTTATTGTTTC
1 GCACTATGTGTGCCTACTGTTTT
* **
5257539 GCACTTTGTGTGCCTACTGTTCC
1 GCACTATGTGTGCCTACTGTTTT
*
5257562 GCACT-TCGTGTGCCTACTGATTT
1 GCACTAT-GTGTGCCTACTGTTTT
* *
5257585 GCACTATGTGCGCCTACTG-ATT
1 GCACTATGTGTGCCTACTGTTTT
*
5257607 GCACTATGTGTGCTTACTGTTT
1 GCACTATGTGTGCCTACTGTTT
5257629 CCCCAGCACT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
22 20 0.21
23 75 0.78
24 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GCACTATGTGTGCCTACTGTTTT
Found at i:5257549 original size:46 final size:46
Alignment explanation
Indices: 5257493--5257629 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
5257483 TTACCGTTCA
* * *
5257493 GCACTGTGTGTGCTTACTGTTTTGCACTTTGTGTGCTTATTGTTTC
1 GCACTTTGTGTGCCTACTGTTTTGCACTTTGTGTGCTTACTGTTTC
** * *
5257539 GCACTTTGTGTGCCTACTGTTCCGCACTTCGTGTGCCTACTGATTT-
1 GCACTTTGTGTGCCTACTGTTTTGCACTTTGTGTGCTTACTG-TTTC
* * * *
5257585 GCACTATGTGCGCCTACTG-ATTGCACTATGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTTGCACTTTGTGTGCTTACTGTTTC
5257630 CCCAGCACTT
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
44 3 0.04
45 16 0.22
46 52 0.70
47 3 0.04
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (46 bp):
GCACTTTGTGTGCCTACTGTTTTGCACTTTGTGTGCTTACTGTTTC
Found at i:5261035 original size:18 final size:18
Alignment explanation
Indices: 5261002--5261036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5260992 TCACAGTTTG
*
5261002 GATAAAATTGAATTAATC
1 GATAAAATCGAATTAATC
*
5261020 GATAAAATCGATTTAAT
1 GATAAAATCGAATTAAT
5261037 TTAGTTAATG
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:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (18 bp):
GATAAAATCGAATTAATC
Found at i:5271337 original size:6 final size:6
Alignment explanation
Indices: 5271328--5271366 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5271318 AACGCTAAAA
5271328 CACCGC CACCGC CACCGC CACCGC CACCGC CACCGC CAC
1 CACCGC CACCGC CACCGC CACCGC CACCGC CACCGC CAC
5271367 TCACTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.67, G:0.15, T:0.00
Consensus pattern (6 bp):
CACCGC
Found at i:5276611 original size:486 final size:485
Alignment explanation
Indices: 5275802--5276844 Score: 1737
Period size: 486 Copynumber: 2.1 Consensus size: 485
5275792 AGCCTCTGCA
* *
5275802 GTCCTCAGCTTTTCAGCAAGATCATTCTTCTCTTGAGCCACTTCCTGCATCATTTAAGTTTTGAC
1 GTCCTCAGCTTTTCAGCAAGATCATACTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTT-AC
* *
5275867 CTCAGTTAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCGATAGAGGCTTT
65 CTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTT
* * *
5275932 TGTCCTTCTGCGAAGATAATCTAGCAAGGACAACCGGGTCGGATGCAAAACAAAATTGAGCTGAA
130 TGTCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAA
*
5275997 TGTGAAGTTTTAGATTCATGGTAGCAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAA
195 TGTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAA
* * * *
5276062 GAAACAAACCTGCAAACTATTCAACTTTACTTCCAGCTCATAATTATAGTTTTTGCAGCGTCCAA
260 GAAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCAA
*
5276127 TTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCTTCAACATCTGGACT
325 TTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGACT
5276192 TCATTTGAAAGTGACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATTC
390 TCATTTGAAAGTGACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATTC
5276257 TTCAACAAATCTATTCTTATCAGCTTCAGTG
455 TTCAACAAATCTATTCTTATCAGCTTCAGTG
* *
5276288 GTCCGCAGCTTTTCAGCTAGATCATACTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTCAC
1 GTCCTCAGCTTTTCAGCAAGATCATACTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTT-AC
5276353 CTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTT
65 CTCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTT
*
5276418 TGTCCTTCTGCGAGGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAA
130 TGTCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAA
* * *
5276483 TGTGAAGTTTTAGATTCTTGGTAGAAAGAGCCATTATCTTAACTAGGACCCAGAGAAAGTAAGAA
195 TGTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAA
* * *
5276548 GAAACAAACCTGCAAACTATTCAGCTTCACTTTCAGCTCATCATTATAGATCTTACAGCGTCCAA
260 GAAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCAA
* * * * *
5276613 TTTCCTGTTCCTTCTCCTGTTTCTCTCTTTTGATCTGCTTGAGTTCTTGCCTCAACCTCTGGACT
325 TTTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGACT
*
5276678 TCATTTGAAAGTGACTGTTGTTCTGCTTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATTC
390 TCATTTGAAAGTGACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATTC
** * *
5276743 TTCAATGAATCTGTTCTTATCAGCTTCGGTG
455 TTCAACAAATCTATTCTTATCAGCTTCAGTG
* * *
5276774 GTCCTCAGCTTTTTAGCAAGACCA-ATCTTCTCTTGAACTACTTCCTGCATCATTTAAGTTTTAC
1 GTCCTCAGCTTTTCAGCAAGATCATA-CTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTAC
5276838 CTCAGTA
65 CTCAGTA
5276845 CGATAAACAA
Statistics
Matches: 518, Mismatches: 38, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
485 10 0.02
486 508 0.98
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (485 bp):
GTCCTCAGCTTTTCAGCAAGATCATACTTCTCTTGAGCTACTTCCTGCATCATTTAAGTTTTACC
TCAGTAAGATGACTCCTCAAAGGCAAAGGGCAGTTGGAAACATTTTACAGCCAATAGAGGCTTTT
GTCCTTCTGCGAAGATAATCTAGCAAGGACAACCAGGTCAGATGCAAAACAAAATTGAACTGAAT
GTGAAGTTTTAGATTCATGGTAGAAAGAACCATTATCATAACTAGGACCCAGAGAAAGTAAGAAG
AAACAAACCTGCAAACTATTCAACTTCACTTCCAGCTCATAATTATAGATCTTACAGCGTCCAAT
TTCCTCTTCCTTCTCCTGTTTCTCTCTTTCGATCTGCCTAAGTTCTTGCCTCAACATCTGGACTT
CATTTGAAAGTGACTGTTGTTCTGCCTTTTGAGCTTCAACTTCTGAAGTGCATCTTCTCAATTCT
TCAACAAATCTATTCTTATCAGCTTCAGTG
Found at i:5281967 original size:15 final size:16
Alignment explanation
Indices: 5281946--5281990 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
5281936 GTTATATACT
*
5281946 TTTATCATTTTAGTCA
1 TTTATCATTTTAGTAA
5281962 -TTATCATTTTA-TAA
1 TTTATCATTTTAGTAA
5281976 TTTTATCATTTTAGT
1 -TTTATCATTTTAGT
5281991 TACCCATCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 11 0.44
17 1 0.04
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTATCATTTTAGTAA
Found at i:5281973 original size:8 final size:8
Alignment explanation
Indices: 5281945--5281988 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
5281935 TGTTATATAC
5281945 TTTTATCA
1 TTTTATCA
5281953 TTTTAGTCA
1 TTTTA-TCA
5281962 --TTATCA
1 TTTTATCA
*
5281968 TTTTATAA
1 TTTTATCA
5281976 TTTTATCA
1 TTTTATCA
5281984 TTTTA
1 TTTTA
5281989 GTTACCCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 22 0.71
9 3 0.10
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.61
Consensus pattern (8 bp):
TTTTATCA
Found at i:5283646 original size:31 final size:31
Alignment explanation
Indices: 5283605--5283665 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
5283595 ATGACAAATT
* *
5283605 AACGATGATGACTAAAATGATAAAATTATAA
1 AACGACGATGACTAAAATGATAAAAGTATAA
5283636 AACGACGATGACTAAAATGATAAAAGTATA
1 AACGACGATGACTAAAATGATAAAAGTATA
5283666 TAACAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (31 bp):
AACGACGATGACTAAAATGATAAAAGTATAA
Found at i:5289506 original size:43 final size:43
Alignment explanation
Indices: 5289452--5289538 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5289442 AGGCAGAACA
5289452 ACAGTCACTTTCAAATTAAGTCCAGATGTTGAAGCAAGAACTT
1 ACAGTCACTTTCAAATTAAGTCCAGATGTTGAAGCAAGAACTT
5289495 ACAGTCACTTTCAAATTAAGTCCAGATGTTGAAGCAAGAACTT
1 ACAGTCACTTTCAAATTAAGTCCAGATGTTGAAGCAAGAACTT
5289538 A
1 A
5289539 GGCAGATCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (43 bp):
ACAGTCACTTTCAAATTAAGTCCAGATGTTGAAGCAAGAACTT
Found at i:5292084 original size:248 final size:248
Alignment explanation
Indices: 5291646--5293041 Score: 2296
Period size: 248 Copynumber: 5.6 Consensus size: 248
5291636 GAGAGGAAAA
* * * *
5291646 TCATACTTTCTTATAATCTTAAAAGATTGCCAAAGGGTACAAGAAAGAGGAAAGAGTGGGGTCTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
* **
5291711 CTCAACTCTCACCTGGTATTGATCTTTACATGTGTCCTTACAGTGATGCCATAATCACCATACTT
66 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
* *
5291776 GCAGAACGTGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
131 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
* * * * *
5291841 TGGTCATATAGTGCCTCGGATGCATCTAGAGGATTTCTGATGCAAATATCAAC
196 TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
* *
5291894 TCATACTTTATTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAATGGGAAAGAGTGGGGTTTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
* *
5291959 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGCTGCCATAATCACCATCCTT
66 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
*
5292024 GCAAAACATGGTTTCTTCAAGGGTTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
131 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
* * *
5292089 TGGTCATATAATGACTGGGATGCATCTTGAGGATTTTTTATGTAAATATCAAT
196 TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
5292142 TCATA----CTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
* * *
5292203 CTCAACTCTCACCTCGTATTGATCTTTACATATGTCCTCGCAGTGCTGCCATAATCAACATACTT
66 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
* * *
5292268 GCCAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGCAGGTTGGTTGAGAAGGAACATGAAGA
131 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
* *
5292333 TGGTCATATAGTGGCTGGGATGCATCTTGAGGATTTCTGATGTAAATACCAAT
196 TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
*
5292386 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGCGTGGGGTTTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
* * *
5292451 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGTCATAATAACCATAATT
66 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
*
5292516 GCAAGACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
131 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
*
5292581 TTGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
196 TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
* * *
5292634 TCATACTTTTTTGTAAACTTAACAGATTGCCGAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
*
5292699 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACAATACTT
66 CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
* * *
5292764 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGACGTATGTTGGTTAAAAAGGAACATGAAGA
131 GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
* *
5292829 TGGTCATATAGTGGCTGGGATGCATCTTGAGGATTTCTGATGTAAATATTAAT
196 TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
*
5292882 TCGTACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
1 TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
5292947 CTCAACTCTCACCTGGTAATGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACC
66 CTCAACTCTCACC------TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACC
5293012 ATACTTGCAAAACATGGTTTCTTCAAGGGC
125 ATACTTGCAAAACATGGTTTCTTCAAGGGC
5293042 ATGGCTGCTG
Statistics
Matches: 1068, Mismatches: 70, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
244 230 0.22
248 763 0.71
254 75 0.07
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (248 bp):
TCATACTTTCTTGTAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTG
CTCAACTCTCACCTGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTT
GCAAAACATGGTTTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGA
TGGTCATATAGTGACTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAAT
Found at i:5292589 original size:492 final size:493
Alignment explanation
Indices: 5291659--5293041 Score: 2286
Period size: 492 Copynumber: 2.8 Consensus size: 493
5291649 TACTTTCTTA
* * *
5291659 TAATCTTAAAAGATTGCCAAAGGGTACAAGAAAGAGGAAAGAGTGGGGTCTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* ** * *
5291724 TGGTATTGATCTTTACATGTGTCCTTACAGTGATGCCATAATCACCATACTTG-CAGAACGTGGT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTGCCA-AACATGGT
5291788 TTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGT
130 TTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGT
* * * * * *
5291853 GCCTCGGATGCATCTAGAGGATTTCTGATGCAAATATCAACTCATACTTTATTGTAATCTTAACA
195 GGCTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTCTTGTAATCTTAACA
*
5291918 GATTGCCAAAGGGTACAAGAAATGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTATTGATC
260 GATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTATTGATC
* * *
5291983 TTTACATATGTCCTCGCAGTGCTGCCATAATCACCATCCTTGCAAAACATGGTTTCTTCAAGGGT
325 TTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTTTCTTCAAGGGC
5292048 TGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAATGACTGGGATGCA
390 TGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAATGACTGGGATGCA
* *
5292113 TCTTGAGGATTTTTTATGTAAATATCAATTCATAC-TTG
455 TCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTG
5292151 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
* *
5292216 TCGTATTGATCTTTACATATGTCCTCGCAGTGCTGCCATAATCAACATACTTGCCAAACATGGTT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTGCCAAACATGGTT
* *
5292281 TCTTCAAGGGCTGGGATGAATGAGGCAGGTTGGTTGAGAAGGAACATGAAGATGGTCATATAGTG
131 TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
*
5292346 GCTGGGATGCATCTTGAGGATTTCTGATGTAAATACCAATTCATACTTTCTTGTAATCTTAACAG
196 GCTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTCTTGTAATCTTAACAG
*
5292411 ATTGCCAAAGGGTACAAGAAAGGGGAAAGCGTGGGGTTTGCTCAACTCTCACCTGGTATTGATCT
261 ATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTATTGATCT
* * * *
5292476 TTACATATGTCCTCGCAGTGATGTCATAATAACCATAATTGCAAGACATGGTTTCTTCAAGGGCT
326 TTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTTTCTTCAAGGGCT
* *
5292541 GGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATTGTCATATAGTGACTGGGATGCAT
391 GGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAATGACTGGGATGCAT
5292606 CTTGAGGATTTCTGATGTAAATATCAATTCATACTTTTTTG
456 CTTGAGGATTTCTGATGTAAATATCAATTCATAC---TTTG
* *
5292647 TAAACTTAACAGATTGCCGAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
1 TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
*
5292712 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATC-ACAATACTTGCAAAACATGGT
66 TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAAC-ATACTTGCCAAACATGGT
* * *
5292776 TTCTTCAAGGGCTGGGATGAATGACGTATGTTGGTTAAAAAGGAACATGAAGATGGTCATATAGT
130 TTCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGT
* *
5292841 GGCTGGGATGCATCTTGAGGATTTCTGATGTAAATATTAATTCGTACTTTCTTGTAATCTTAACA
195 GGCTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTCTTGTAATCTTAACA
5292906 GATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTAATGGTA
260 GATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC------TGGTA
5292971 TTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTTTCTTC
319 TTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTTTCTTC
5293036 AAGGGC
384 AAGGGC
5293042 ATGGCTGCTG
Statistics
Matches: 829, Mismatches: 50, Indels: 14
0.93 0.06 0.02
Matches are distributed among these distances:
492 454 0.55
493 2 0.00
495 2 0.00
496 299 0.36
502 72 0.09
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (493 bp):
TAATCTTAACAGATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACC
TGGTATTGATCTTTACATATGTCCTCGCAGTGATGCCATAATCAACATACTTGCCAAACATGGTT
TCTTCAAGGGCTGGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAGTG
GCTGGGATGCATCTTGAGGATTTCTGATGTAAATATCAATTCATACTTTCTTGTAATCTTAACAG
ATTGCCAAAGGGTACAAGAAAGGGGAAAGAGTGGGGTTTGCTCAACTCTCACCTGGTATTGATCT
TTACATATGTCCTCGCAGTGATGCCATAATCACCATACTTGCAAAACATGGTTTCTTCAAGGGCT
GGGATGAATGAGGTAGGTTGGTTGAAAAGGAACATGAAGATGGTCATATAATGACTGGGATGCAT
CTTGAGGATTTCTGATGTAAATATCAATTCATACTTTG
Found at i:5305693 original size:58 final size:59
Alignment explanation
Indices: 5305630--5305766 Score: 206
Period size: 59 Copynumber: 2.4 Consensus size: 59
5305620 TTTGGATACC
* * *
5305630 CGGGGGCAAAATGGTAATTTTAGTTGGAATTG-GGTTAAAAATGGGATTTTTAGAAGTT
1 CGGGGGCAAAATGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGGATTTTTAGAAGTT
* *
5305688 TGGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTTAGAAGTT
1 CGGGGGCAAAATGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGGATTTTTAGAAGTT
*
5305747 CGGGGGTAAAAT-GTAATTTT
1 CGGGGGCAAAATGGTAATTTT
5305767 TGAAAAGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
58 35 0.49
59 36 0.51
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
CGGGGGCAAAATGGTAATTTTAGGTGAAATCGAGGTTAAAAATGGGATTTTTAGAAGTT
Found at i:5305740 original size:59 final size:58
Alignment explanation
Indices: 5305630--5305768 Score: 208
Period size: 58 Copynumber: 2.4 Consensus size: 58
5305620 TTTGGATACC
* * * *
5305630 CGGGGGCAAAATGGTAATTTTAGTTGGAATTGGGTTAAAAATGGGATTTTTAGAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGGATTTTTAGAAGTT
*
5305688 TGGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTTAGAAGTT
1 CGGGGGCAAAATGGTAATTTTTGGTGAAATCG-GGTTAAAAATGGGATTTTTAGAAGTT
*
5305747 CGGGGGTAAAAT-GTAATTTTTG
1 CGGGGGCAAAATGGTAATTTTTG
5305769 AAAAGTTTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 37 0.51
59 36 0.49
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (58 bp):
CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGGATTTTTAGAAGTT
Found at i:5305826 original size:30 final size:29
Alignment explanation
Indices: 5305734--5305956 Score: 238
Period size: 30 Copynumber: 7.5 Consensus size: 29
5305724 TAAAAATGGG
*
5305734 ATTTTTAG-AAGTTCGGGGGT-AAAATGTA
1 ATTTTTAGAAAGTT-TGGGGTCAAAATGTA
5305762 ATTTTT-GAAAAGTTTAGAGGGATCAAAATGTA
1 ATTTTTAG-AAAGTTT-G-GGG-TCAAAATGTA
* *
5305794 ATTTTTAGAAAGTATTGGGGTTAAAATATA
1 ATTTTTAGAAAGT-TTGGGGTCAAAATGTA
* * *
5305824 ATTTTTAGGAAGTTTTAGGGCCAAAATGTA
1 ATTTTTAGAAAG-TTTGGGGTCAAAATGTA
*
5305854 ATTTTTAGAAAGTTTTGGGGTTAAAATGTA
1 ATTTTTAGAAAG-TTTGGGGTCAAAATGTA
**
5305884 ATTTTTAGAAAGTTTTAGGTCAAAATGTA
1 ATTTTTAGAAAGTTTGGGGTCAAAATGTA
*
5305913 ATTTTTAGAAAGTTTGAGGGTCAAAATATA
1 ATTTTTAGAAAGTTTG-GGGTCAAAATGTA
5305943 ATTTTT-GAACAGTT
1 ATTTTTAGAA-AGTT
5305957 CAGGGACCTA
Statistics
Matches: 166, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
27 1 0.01
28 6 0.04
29 38 0.23
30 93 0.56
31 5 0.03
32 20 0.12
33 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (29 bp):
ATTTTTAGAAAGTTTGGGGTCAAAATGTA
Found at i:5305849 original size:60 final size:59
Alignment explanation
Indices: 5305734--5305956 Score: 283
Period size: 60 Copynumber: 3.7 Consensus size: 59
5305724 TAAAAATGGG
* * * *
5305734 ATTTTTAG-AAGTTCGGGGGTAAAATGTAATTTTT-GAAAAGTTTAGAGGGATCAAAATGTA
1 ATTTTTAGAAAGTTTGGGGTTAAAATATAATTTTTAG-AAAGTTT-TAGGG-TCAAAATGTA
* *
5305794 ATTTTTAGAAAGTATTGGGGTTAAAATATAATTTTTAGGAAGTTTTAGGGCCAAAATGTA
1 ATTTTTAGAAAGT-TTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATGTA
*
5305854 ATTTTTAGAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTTTTA-GGTCAAAATGTA
1 ATTTTTAGAAAG-TTTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATGTA
*
5305913 ATTTTTAGAAAGTTTGAGGGTCAAAATATAATTTTT-GAACAGTT
1 ATTTTTAGAAAGTTTG-GGGTTAAAATATAATTTTTAGAA-AGTT
5305957 CAGGGACCTA
Statistics
Matches: 146, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
58 7 0.05
59 44 0.30
60 60 0.41
61 9 0.06
62 25 0.17
63 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (59 bp):
ATTTTTAGAAAGTTTGGGGTTAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATGTA
Found at i:5306651 original size:14 final size:14
Alignment explanation
Indices: 5306634--5306664 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5306624 TTCTCTTTTC
5306634 CTTTTTCTTTTGTT
1 CTTTTTCTTTTGTT
*
5306648 CTTTTTGTTTTGTT
1 CTTTTTCTTTTGTT
5306662 CTT
1 CTT
5306665 AAACTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTTGTT
Found at i:5307573 original size:19 final size:18
Alignment explanation
Indices: 5307529--5307579 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
5307519 AATTCAAATT
**
5307529 AAATTTAAACTT-AATTA
1 AAATTTAAACTTAAAAGA
5307546 AAATTTAAACTTAAAAGA
1 AAATTTAAACTTAAAAGA
5307564 AAAGTTTAAACTTAAA
1 AAA-TTTAAACTTAAA
5307580 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.40
18 6 0.20
19 12 0.40
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATTTAAACTTAAAAGA
Found at i:5308058 original size:92 final size:92
Alignment explanation
Indices: 5307901--5308735 Score: 1442
Period size: 92 Copynumber: 9.2 Consensus size: 92
5307891 AGGTTTTATT
5307901 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
* *
5307966 GAAAACTCATCTTGCTTTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
* * * *
5307993 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAGCTTTAAGAGGATAAGAATTAAGATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308058 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
*
5308085 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTAACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
*
5308150 GAAAATTCATCTTACTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
* * *
5308177 TTCAGACAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTCACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308242 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
*
5308269 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGTCATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308334 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
5308361 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGA-G----G-ATTGACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308420 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
*
5308447 TTCAGAGAAATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGA-G----G-ATTGACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
*
5308506 GAAAATTCATCTTACTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
*
5308533 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTAGAACTTCAAGAGGATAAGAATTGACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308598 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
*
5308625 TTCAGAGAGATAAAAATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
1 TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
5308690 GAAAATTCATCTTGCTCTTACTATAAC
66 GAAAATTCATCTTGCTCTTACTATAAC
5308717 TTCAGAGAGATAAAGATTC
1 TTCAGAGAGATAAAGATTC
5308736 ATCGCCGTGG
Statistics
Matches: 710, Mismatches: 27, Indels: 12
0.95 0.04 0.02
Matches are distributed among these distances:
86 165 0.23
87 2 0.00
91 2 0.00
92 541 0.76
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (92 bp):
TTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATTT
GAAAATTCATCTTGCTCTTACTATAAC
Found at i:5320533 original size:30 final size:30
Alignment explanation
Indices: 5320441--5320604 Score: 165
Period size: 30 Copynumber: 5.5 Consensus size: 30
5320431 TAAAAATAGG
** *
5320441 ATTTTTAG-AAGTTCAGGGG-CAAAATGTA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
* *
5320469 ATTTTT-GAAAAGTTTGAGGGGATCAAAATGTA
1 ATTTTTAG-AAAGTTT-TGGGG-TCAAAATATA
*
5320501 ATTTTTAGAAAGTTTTGGGGTTAAAATATA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
5320531 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
* ** * *
5320561 ATTTTTAGGAAGTTTTAAGATTAAAATATA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
5320591 ATTTTT-GAATAGTT
1 ATTTTTAGAA-AGTT
5320605 CAGGGACCTA
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
27 1 0.01
28 6 0.05
29 7 0.06
30 77 0.65
31 4 0.03
32 22 0.19
33 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.40
Consensus pattern (30 bp):
ATTTTTAGAAAGTTTTGGGGTCAAAATATA
Found at i:5320575 original size:60 final size:61
Alignment explanation
Indices: 5320461--5320604 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 61
5320451 GTTCAGGGGC
* * ** *
5320461 AAAATGTAATTTTTGAAAAGTTTGAGGGGATCAAAATGTAATTTTTAGAAAGTTTTGGGGTT
1 AAAATATAATTTTTG-AAAGTTTGAGGGGATCAAAATATAATTTTTAGAAAGTTTTAAGATT
* *
5320523 AAAATATAATTTTTAGAAAGTTT-TGGGG-TCAAAATATAATTTTTAGGAAGTTTTAAGATT
1 AAAATATAATTTTT-GAAAGTTTGAGGGGATCAAAATATAATTTTTAGAAAGTTTTAAGATT
5320583 AAAATATAATTTTTGAATAGTT
1 AAAATATAATTTTTGAA-AGTT
5320605 CAGGGACCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
59 3 0.04
60 45 0.62
61 4 0.05
62 20 0.27
63 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.19, T:0.41
Consensus pattern (61 bp):
AAAATATAATTTTTGAAAGTTTGAGGGGATCAAAATATAATTTTTAGAAAGTTTTAAGATT
Found at i:5321300 original size:14 final size:14
Alignment explanation
Indices: 5321283--5321313 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5321273 TTCTCTTTTC
5321283 CTTTTTCTTTTGTT
1 CTTTTTCTTTTGTT
*
5321297 CTTTTTGTTTTGTT
1 CTTTTTCTTTTGTT
5321311 CTT
1 CTT
5321314 AAACTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTTGTT
Found at i:5322167 original size:17 final size:17
Alignment explanation
Indices: 5322149--5322204 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5322139 GACTTTTTAA
5322149 TTAATTTTAAATTTAAA-
1 TTAA-TTTAAATTTAAAC
* *
5322166 TTCAAATTGAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
5322184 TTAATTAAAATTTAAAC
1 TTAATTTAAATTTAAAC
5322201 TTAA
1 TTAA
5322205 AAGAAAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 28 0.88
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Found at i:5322218 original size:19 final size:18
Alignment explanation
Indices: 5322175--5322224 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
5322165 ATTCAAATTG
**
5322175 AATTTAAACTT-AATTAA
1 AATTTAAACTTAAAAGAA
5322192 AATTTAAACTTAAAAGAA
1 AATTTAAACTTAAAAGAA
5322210 AAGTTTAAACTTAAA
1 AA-TTTAAACTTAAA
5322225 CTAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.38
18 6 0.21
19 12 0.41
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (18 bp):
AATTTAAACTTAAAAGAA
Found at i:5332570 original size:26 final size:24
Alignment explanation
Indices: 5332531--5332596 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 24
5332521 ATTTTTTATA
*
5332531 AAAAAAAT-TAAATTTTTAAATAT
1 AAAAAATTATAAATTTTTAAATAT
*
5332554 ATATAAATTATATAATTTTTTTAAATAT
1 A-AAAAATTATA-AA--TTTTTAAATAT
5332582 AAAAAATTATAAATT
1 AAAAAATTATAAATT
5332597 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
23 1 0.03
24 7 0.20
25 2 0.06
26 4 0.11
27 9 0.26
28 12 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAAAATTATAAATTTTTAAATAT
Done.