Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 177 of 187
Found at i:52948392 original size:24 final size:22
Alignment explanation
Indices: 52948330--52948394 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 22
52948320 ATTTTGTTTT
*
52948330 AAATAGAAAATTTAATTATTTATA
1 AAATA-AAAATTTTA-TATTTATA
* *
52948354 TAATAAATAACTTTATATTTCATA
1 AAATAAA-AATTTTATATTT-ATA
52948378 AAATATAAAATTTTATA
1 AAATA-AAAATTTTATA
52948395 AACATAGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 7 0.21
24 24 0.73
25 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATAAAAATTTTATATTTATA
Found at i:52948696 original size:20 final size:21
Alignment explanation
Indices: 52948668--52948715 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
52948658 ATATTGTACA
*
52948668 TTAAATATG-GTAAAAAAATT
1 TTAATTATGAGTAAAAAAATT
* *
52948688 TTAATTATGATTTAAAAAATT
1 TTAATTATGAGTAAAAAAATT
52948709 TT-ATTAT
1 TTAATTAT
52948716 TGTGATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (21 bp):
TTAATTATGAGTAAAAAAATT
Found at i:52951475 original size:104 final size:105
Alignment explanation
Indices: 52951264--52951490 Score: 244
Period size: 104 Copynumber: 2.2 Consensus size: 105
52951254 ACAGAGAGTT
* * *
52951264 ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGTGGTTCTAAATCATAAATTGTGAGTTAC
1 ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTAC
* * * *** *
52951329 AAGGCCTGGGCACACGCCCATATCCTTGCCCGTGTGGCTC
66 AAGGCCTGGACACAAGCCCATACCCTTGCAAATATGGCTC
* * * *
52951369 ACACGGCCTGGACACACGCTCATGT--TCTTGCCCGTGCGGTTCTAAAGCTTAAATAGTGAGTTA
1 ACACGGCCTGGGCACACGCCCATGTCGTC-TGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTA
* * * *
52951432 CACGGCTTGGACACAAGCTCATACCCTTAG-AAATATGGTTC
65 CAAGGCCTGGACACAAGCCCATACCCTT-GCAAATATGGCTC
*
52951473 ACATGGCCTGGGCACACG
1 ACACGGCCTGGGCACACG
52951491 TCTATGTCCT
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
103 2 0.02
104 74 0.74
105 24 0.24
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (105 bp):
ACACGGCCTGGGCACACGCCCATGTCGTCTGCCCATGCGGTTCTAAAGCATAAATAGTGAGTTAC
AAGGCCTGGACACAAGCCCATACCCTTGCAAATATGGCTC
Found at i:52953420 original size:15 final size:17
Alignment explanation
Indices: 52953388--52953421 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
52953378 TTTTTGCTAG
52953388 AATAATATTAACTTAAA
1 AATAATATTAACTTAAA
52953405 AATAATA-TAA-TTAAA
1 AATAATATTAACTTAAA
52953420 AA
1 AA
52953422 AATTAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATATTAACTTAAA
Found at i:52962608 original size:41 final size:41
Alignment explanation
Indices: 52962563--52962707 Score: 227
Period size: 41 Copynumber: 3.5 Consensus size: 41
52962553 GACTTTAAGT
52962563 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
52962604 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* * * * *
52962645 CTAGCAAGCTATGTGTCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* *
52962686 CTAGCAGGCTAAGTGCGGGTGA
1 CTAGCAGGCTATGTGCCGGTGA
52962708 ATACGCTAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
Found at i:52965649 original size:20 final size:20
Alignment explanation
Indices: 52965592--52965667 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
52965582 AATAAAGAGG
*
52965592 AAAGAAA-AAGAATCGAAAAAT
1 AAAGAAAGAAGAA--GAAAAAA
52965613 AAAGAAAAGAA-AAGAAAAAA
1 AAAG-AAAGAAGAAGAAAAAA
*
52965633 AAAGAAAGAAGAGGAAAAAA
1 AAAGAAAGAAGAAGAAAAAA
*
52965653 ATAG-AAGAAGAAGAA
1 AAAGAAAGAAGAAGAA
52965668 CTAATGTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 16 0.33
20 21 0.44
21 4 0.08
22 5 0.10
23 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAGAAAGAAGAAGAAAAAA
Found at i:52974131 original size:43 final size:43
Alignment explanation
Indices: 52974099--52974296 Score: 220
Period size: 42 Copynumber: 4.7 Consensus size: 43
52974089 GTTACTATAA
* * *
52974099 AACATGACCTTTAGCGGCGCTTTTCCCAAAAACACAACTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
* * *
52974142 AACATGACCTTTAGCGGCGC-TTTCCCACAAATGCCGCTATAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
** ** * *
52974184 AACATGATGTTTAGATGCGCTTTCCCCACAAA-GCCATTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
* * *
52974226 AACATGACCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
** *
52974269 AACATGACCTTTAATGGCGCTTTCCCCA
1 AACATGACCTTTAGCGGCGCTTTTCCCA
52974297 GAAGCACCGC
Statistics
Matches: 126, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 65 0.52
43 61 0.48
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAG
Found at i:52974253 original size:85 final size:84
Alignment explanation
Indices: 52974099--52974296 Score: 247
Period size: 85 Copynumber: 2.3 Consensus size: 84
52974089 GTTACTATAA
** * * * *
52974099 AACATGACCTTTAGCGGCGCTTTTCCCA-AAAACACAACTAAAGAACATGACCTTTAGCGGCGCT
1 AACATGACCTTTAATGGCGCTTTCCCCACAAAGC-C-ATTAAAGAACATGACCTTTAGCGACGCT
** *
52974163 TTCCCACAAATGCCGCTATAG
64 TTCCCACAAACACCGCTAAAG
**
52974184 AACATGATGTTTAGAT-GCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGCTT
1 AACATGACCTTTA-ATGGCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGC-T
52974248 TTCCCACAAACACCGCTAAAG
64 TTCCCACAAACACCGCTAAAG
52974269 AACATGACCTTTAATGGCGCTTTCCCCA
1 AACATGACCTTTAATGGCGCTTTCCCCA
52974297 GAAGCACCGC
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
84 27 0.28
85 65 0.68
86 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (84 bp):
AACATGACCTTTAATGGCGCTTTCCCCACAAAGCCATTAAAGAACATGACCTTTAGCGACGCTTT
CCCACAAACACCGCTAAAG
Found at i:52974305 original size:43 final size:43
Alignment explanation
Indices: 52974099--52974310 Score: 230
Period size: 43 Copynumber: 5.0 Consensus size: 43
52974089 GTTACTATAA
* * **
52974099 AACATGACCTTTAGCGGCGCTTTTCCCAAAAACACAACTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** *
52974142 AACATGACCTTTAGCGGCGCTTT-CCCACAAATGCCGCTATAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** ** * **
52974184 AACATGATGTTTAGATGCGCTTTCCCCACAAA-GCCATTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
* *
52974226 AACATGACCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAG
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
** * *
52974269 AACATGACCTTTAATGGCGCTTTCCCCAGAAGCACCGCTAAA
1 AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAA
52974311 AGTCATGTTC
Statistics
Matches: 139, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
42 65 0.47
43 74 0.53
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAG
Found at i:52980352 original size:13 final size:13
Alignment explanation
Indices: 52980334--52980360 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52980324 TGATTATCAT
52980334 CTTTAAATTTTAA
1 CTTTAAATTTTAA
52980347 CTTTAAATTTTAA
1 CTTTAAATTTTAA
52980360 C
1 C
52980361 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:52982703 original size:22 final size:22
Alignment explanation
Indices: 52982660--52982703 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52982650 AACATATAAT
*
52982660 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
52982682 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
52982704 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:52990693 original size:2 final size:2
Alignment explanation
Indices: 52990686--52990712 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52990676 TTGTTTTGGT
52990686 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52990713 TGGTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52998212 original size:26 final size:27
Alignment explanation
Indices: 52998148--52998219 Score: 103
Period size: 26 Copynumber: 2.7 Consensus size: 27
52998138 TTTTCTCGGG
*
52998148 ATTTTACTAGGGGTAAAATCATCAAAA
1 ATTTTACTAAGGGTAAAATCATCAAAA
*
52998175 ATTTTA-TCAAGGGTAAAATCGTC-AAA
1 ATTTTACT-AAGGGTAAAATCATCAAAA
52998201 ATTTTACTAAGGGTAAAAT
1 ATTTTACTAAGGGTAAAAT
52998220 AGTGATGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (27 bp):
ATTTTACTAAGGGTAAAATCATCAAAA
Found at i:53012369 original size:43 final size:43
Alignment explanation
Indices: 53012306--53012443 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
53012296 GCGCCGTAAA
* * *
53012306 AAACGCCGCTATAGAGCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
53012349 AAACGCCGCTAAAGAACATGACCTTTAACGGCTCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
53012392 AAACGCTGCTAAAGAACATGACCTTTAGCGGTGC---TCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
53012432 AAACGCCACTAA
1 AAACGCCGCTAA
53012444 TTTTAGTAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 15 0.18
43 67 0.82
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:53013929 original size:33 final size:35
Alignment explanation
Indices: 53013892--53013957 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
53013882 CAGTAAAATA
*
53013892 TTTTCCGTAAAATGATTT-CT-GAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
53013925 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
53013958 CTGATGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.59
34 2 0.07
35 10 0.34
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53013931 original size:19 final size:20
Alignment explanation
Indices: 53013907--53013945 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53013897 CGTAAAATGA
*
53013907 TTTCTG-AAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
53013926 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
53013946 GGAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:53014069 original size:20 final size:20
Alignment explanation
Indices: 53014044--53014082 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53014034 GTTTTTACAT
53014044 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
53014064 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
53014083 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:53017315 original size:11 final size:11
Alignment explanation
Indices: 53017299--53017324 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53017289 AACCATCTGT
53017299 ATATAACCAAA
1 ATATAACCAAA
53017310 ATATAACCAAA
1 ATATAACCAAA
53017321 ATAT
1 ATAT
53017325 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:53017595 original size:25 final size:25
Alignment explanation
Indices: 53017567--53017616 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53017557 AGAAGAGAAG
*
53017567 ATGAAGATCAGAAGAAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
* *
53017592 ATGAAGAACGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
53017617 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.32, T:0.06
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:53023894 original size:77 final size:76
Alignment explanation
Indices: 53023734--53024137 Score: 450
Period size: 77 Copynumber: 5.2 Consensus size: 76
53023724 GAAATTAGCA
* * * ** *
53023734 AACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAACGAACCGTAAAAATTATAGAAGCGAAAT
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCGATAT
*
53023799 TAAATCAAGTG
66 TAAATCAAGCG
* * * *
53023810 AACTGTTAAAATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGTAAAAATGACAGCTGCGATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAGCCGCGATA
**
53023875 TTAAATCAATTG
65 TTAAATCAAGCG
* * * ** * *
53023887 AATTGTTAAAATATTGAAGGTCGCGATCTTAAATCGAGTGAACCGTAAAAATGACAGCCACAATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAGCCGCGATA
* *
53023952 TTAAATCGAGCA
65 TTAAATCAAGCG
* * * * * * * *
53023964 AACTATTAGAATATCAAAGGTCGCAATCTTAAATTAAGTGGACCGTAAAAATGACAGTCGCAATA
1 AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAA-CGAACCGTAAAAATGACAGCCGCGATA
53024029 TTAAATCAAGCG
65 TTAAATCAAGCG
* *
53024041 AACTGTTAGAATATCGAAGGTCGCGATCTTAAAATCAAGCGAACTGTAAAAATGACAACCGCTG-
1 AACTGTTAGAATATCGAAGGTCGCGATCTT-AAATCAA-CGAACCGTAAAAATGACAGCCGC-GA
*
53024105 TATTAAATCAAGAG
63 TATTAAATCAAGCG
53024119 AACTGTTAGAATATCGAAG
1 AACTGTTAGAATATCGAAG
53024138 ATCATGATAG
Statistics
Matches: 279, Mismatches: 45, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
76 34 0.12
77 188 0.67
78 57 0.20
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (76 bp):
AACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAGCCGCGATAT
TAAATCAAGCG
Found at i:53023938 original size:40 final size:39
Alignment explanation
Indices: 53023743--53023938 Score: 127
Period size: 40 Copynumber: 5.1 Consensus size: 39
53023733 AAACTGTTAG
*
53023743 AATATCGAAGGTTGCGATCTTAAATC-AACGAACCGTAAA
1 AATATCGAAGG-TGCGATCTTAAATCAAATGAACCGTAAA
* ** * * *
53023782 AATTATAGAA---GCGAAATTAAATCAAGTGAACTGTTAA
1 AA-TATCGAAGGTGCGATCTTAAATCAAATGAACCGTAAA
* * *
53023819 AATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGT-AA
1 AATATCGAAGG-TGCGATCTTAAATCAAATGAACCGTAAA
* * * ** *
53023858 AA-AT-GACAGCTGCGATATTAAATCAATTGAATTGTTAA
1 AATATCGA-AGGTGCGATCTTAAATCAAATGAACCGTAAA
* * *
53023896 AATATTGAAGGTCGCGATCTTAAATCGAGTGAACCGTAAA
1 AATATCGAAGGT-GCGATCTTAAATCAAATGAACCGTAAA
53023936 AAT
1 AAT
53023939 GACAGCCACA
Statistics
Matches: 116, Mismatches: 30, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
36 17 0.15
37 31 0.27
38 8 0.07
39 11 0.09
40 49 0.42
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (39 bp):
AATATCGAAGGTGCGATCTTAAATCAAATGAACCGTAAA
Found at i:53032301 original size:2 final size:2
Alignment explanation
Indices: 53032294--53032331 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
53032284 TCACATTGTT
* *
53032294 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53032332 ATGTTGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:53032868 original size:21 final size:22
Alignment explanation
Indices: 53032832--53032883 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
53032822 TTAAATATAA
53032832 ATTATAAAATTCATAAAAACTT
1 ATTATAAAATTCATAAAAACTT
* *
53032854 ATTAT-AAATTTATAAAAAGTT
1 ATTATAAAATTCATAAAAACTT
53032875 A-TA-AAAATT
1 ATTATAAAATT
53032884 ATTAGAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.26
21 15 0.56
22 5 0.19
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTATAAAATTCATAAAAACTT
Found at i:53032869 original size:30 final size:28
Alignment explanation
Indices: 53032827--53032899 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 28
53032817 ATTTTTTAAA
53032827 TATAAATTATAAAA-TTCATAAAAACTTAT
1 TATAAATTATAAAAGTT-ATAAAAA-TTAT
53032856 TATAAATTTATAAAAAGTTATAAAAATTAT
1 TATAAA-TTAT-AAAAGTTATAAAAATTAT
*
53032886 TAGAAATTATAAAA
1 TATAAATTATAAAA
53032900 AATAAATGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 4 0.10
29 10 0.25
30 13 0.32
31 11 0.28
32 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (28 bp):
TATAAATTATAAAAGTTATAAAAATTAT
Found at i:53032878 original size:10 final size:9
Alignment explanation
Indices: 53032830--53032900 Score: 63
Period size: 10 Copynumber: 7.3 Consensus size: 9
53032820 TTTTAAATAT
53032830 AAATTAT-A
1 AAATTATAA
53032838 AAATTCATAA
1 AAATT-ATAA
53032848 AAACTTATTATA
1 AAA-TTA-TA-A
*
53032860 AATTTATAA
1 AAATTATAA
53032869 AAAGTTATAA
1 AAA-TTATAA
*
53032879 AAATTATTAG
1 AAATTA-TAA
53032889 AAATTATAA
1 AAATTATAA
53032898 AAA
1 AAA
53032901 ATAAATGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 5 0.10
9 13 0.25
10 24 0.46
11 7 0.13
12 3 0.06
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
AAATTATAA
Found at i:53032901 original size:30 final size:31
Alignment explanation
Indices: 53032844--53032900 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 31
53032834 TATAAAATTC
*
53032844 ATAAAAACTTATTATAAATTTATAAAAAGTT
1 ATAAAAACTTATTAGAAATTTATAAAAAGTT
53032875 ATAAAAA-TTATTAGAAA-TTATAAAAA
1 ATAAAAACTTATTAGAAATTTATAAAAA
53032901 ATAAATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 9 0.36
30 9 0.36
31 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (31 bp):
ATAAAAACTTATTAGAAATTTATAAAAAGTT
Found at i:53032938 original size:23 final size:22
Alignment explanation
Indices: 53032903--53032959 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
53032893 TATAAAAAAT
* * *
53032903 AAATGTTATAAAAGTGTTTATAA
1 AAATATTAGAAAA-TGTTTAGAA
*
53032926 AAATATTAGAAAATTTTTAGAA
1 AAATATTAGAAAATGTTTAGAA
53032948 AAATTATT-GAAA
1 AAA-TATTAGAAA
53032960 CATCATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATATTAGAAAATGTTTAGAA
Found at i:53033020 original size:10 final size:10
Alignment explanation
Indices: 53032832--53033021 Score: 55
Period size: 10 Copynumber: 19.1 Consensus size: 10
53032822 TTAAATATAA
53032832 ATTATAAAATT
1 ATTA-AAAATT
53032843 CA-TAAAAACTT
1 -ATTAAAAA-TT
*
53032854 ATTATAAATT
1 ATTAAAAATT
53032864 -TATAAAAAGTT
1 AT-TAAAAA-TT
53032875 A-TAAAAATT
1 ATTAAAAATT
*
53032884 ATTAGAAATT
1 ATTAAAAATT
53032894 A-TAAAAA--
1 ATTAAAAATT
**
53032901 A-TAAATGTT
1 ATTAAAAATT
*
53032910 A-TAAAAGTGT
1 ATTAAAAAT-T
*
53032920 -TTATAAAAAT
1 ATTA-AAAATT
53032930 ATTAGAAAATT
1 ATTA-AAAATT
*
53032941 TTTAGAAAAATT
1 ATT--AAAAATT
* *
53032953 ATTGAAACATC
1 ATT-AAAAATT
*
53032964 ATTAAATATT
1 ATTAAAAATT
*
53032974 A-T-AAAATA
1 ATTAAAAATT
53032982 ATATAAAAA-T
1 AT-TAAAAATT
* *
53032992 AGTATAAATT
1 ATTAAAAATT
*
53033002 -TTTAAAATT
1 ATTAAAAATT
53033011 ATTAAAAATT
1 ATTAAAAATT
53033021 A
1 A
53033022 CAAATAAGTT
Statistics
Matches: 133, Mismatches: 26, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
7 5 0.04
8 5 0.04
9 28 0.21
10 48 0.36
11 37 0.28
12 9 0.07
13 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:53033062 original size:31 final size:30
Alignment explanation
Indices: 53033004--53033070 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
53032994 TATAAATTTT
*
53033004 TAAAATTATTAAAAATTACAAATAAGTTAGA
1 TAAAATTATTAAAAATTACAAAGAAGTT-GA
* *
53033035 TAAAATTATTAAAAAATTA-ATAGAAGTTTA
1 TAAAATTATT-AAAAATTACAAAGAAGTTGA
53033065 TAAAAT
1 TAAAAT
53033071 AAAAATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 17 0.53
32 8 0.25
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.34
Consensus pattern (30 bp):
TAAAATTATTAAAAATTACAAAGAAGTTGA
Found at i:53033543 original size:16 final size:16
Alignment explanation
Indices: 53033522--53033554 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53033512 CGTTTGGTTC
53033522 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
*
53033538 GCTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
53033554 G
1 G
53033555 GCATAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.30, T:0.24
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:53033903 original size:12 final size:12
Alignment explanation
Indices: 53033886--53033932 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
53033876 TATAATACTA
53033886 TAAAATATAATT
1 TAAAATATAATT
*
53033898 TAAAATAATTATT
1 TAAAAT-ATAATT
*
53033911 ATTAAATATAATT
1 -TAAAATATAATT
53033924 TAAAATATA
1 TAAAATATA
53033933 TAATTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 14 0.48
13 10 0.34
14 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:53033918 original size:26 final size:26
Alignment explanation
Indices: 53033872--53033943 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
53033862 CTAAAATCAT
53033872 AATATATAATACTATAAAATATAATTTAA
1 AATATATAAT--TAT-AAATATAATTTAA
*
53033901 AATA-ATTATTATTAAATATAATTTAA
1 AATATATAATTA-TAAATATAATTTAA
53033927 AATATATAATTATAAAT
1 AATATATAATTATAAAT
53033944 TCTTAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 24 0.62
27 7 0.18
28 4 0.10
29 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATATAATTATAAATATAATTTAA
Found at i:53036644 original size:49 final size:49
Alignment explanation
Indices: 53036572--53036675 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
53036562 GAAAAAAAAC
* * *
53036572 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
53036621 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
53036670 AAATTA
1 AAATTA
53036676 TAACACGTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:53039400 original size:2 final size:2
Alignment explanation
Indices: 53039381--53039438 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
53039371 ATAAAGAAAA
* *
53039381 AT AT AT AA AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53039423 AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
53039439 ACATATGTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53040218 original size:22 final size:21
Alignment explanation
Indices: 53040183--53040240 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
53040173 AAAAGGTATC
* *
53040183 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
53040204 TACAAAATCATATCTTCTAATAT
1 TAC-AAATCATATC-TCTAAGAT
* *
53040227 TGCATATCATATCT
1 TACAAATCATATCT
53040241 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:53040844 original size:30 final size:29
Alignment explanation
Indices: 53040806--53040868 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
53040796 TAGGTATATG
*
53040806 TATAATTGAGCTAAAATTAAGATTT-CATT
1 TATAATTGAACTAAAATTAA-ATTTACATT
* *
53040835 TATATATTGAATTAAAATTAAATTTATATT
1 TATA-ATTGAACTAAAATTAAATTTACATT
53040865 TATA
1 TATA
53040869 CAATTGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
TATAATTGAACTAAAATTAAATTTACATT
Found at i:53041017 original size:16 final size:16
Alignment explanation
Indices: 53040998--53041031 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53040988 AATACATTGG
53040998 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
53041014 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
53041030 AA
1 AA
53041032 ATATAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:53042593 original size:20 final size:20
Alignment explanation
Indices: 53042568--53042611 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
53042558 CATAGAACAC
53042568 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
53042588 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
53042608 AAAA
1 AAAA
53042612 ATCATCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAAGAAGGGCCAAGTAGAA
Found at i:53042706 original size:12 final size:12
Alignment explanation
Indices: 53042686--53042715 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53042676 GCGATAAAGG
*
53042686 AAACGCTATATT
1 AAACTCTATATT
53042698 AAACTCTATATT
1 AAACTCTATATT
53042710 AAACTC
1 AAACTC
53042716 AGCAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (12 bp):
AAACTCTATATT
Found at i:53044480 original size:13 final size:13
Alignment explanation
Indices: 53044462--53044496 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
53044452 TGATTTTATG
53044462 AAAATTTCGTTAA
1 AAAATTTCGTTAA
*
53044475 AAAATTTCGTTCA
1 AAAATTTCGTTAA
53044488 AAAATTTCG
1 AAAATTTCG
53044497 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (13 bp):
AAAATTTCGTTAA
Found at i:53045228 original size:30 final size:29
Alignment explanation
Indices: 53045160--53045229 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
53045150 TGAAGTTAAA
53045160 TTTCC-AAGCTTTGGGGCAAAAGTATAATT
1 TTTCCAAAG-TTTGGGGCAAAAGTATAATT
* * *
53045189 ATGCAAAAGTTTAGGGGCAAAA-TCATAATT
1 TTTCCAAAGTTT-GGGGCAAAAGT-ATAATT
53045219 TTTCCAAAGTT
1 TTTCCAAAGTT
53045230 CGAGTCAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTCCAAAGTTTGGGGCAAAAGTATAATT
Found at i:53045679 original size:50 final size:50
Alignment explanation
Indices: 53045566--53045862 Score: 276
Period size: 50 Copynumber: 5.8 Consensus size: 50
53045556 ATTTGGGTAA
* * *
53045566 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGAATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
**
53045622 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
53045672 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTAGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * * *
53045722 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** ** * * **
53045772 AGAACTCCCATGTAAGACCACATCTGGGATATGGCATTGGCA--GTACAAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGACG
* ** *
53045821 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53045863 TGTTATTATC
Statistics
Matches: 208, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 122 0.59
51 2 0.01
52 1 0.00
53 4 0.02
55 2 0.01
56 37 0.18
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:53053494 original size:19 final size:19
Alignment explanation
Indices: 53053430--53053494 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
53053420 ACAAAAAATA
* *
53053430 ATTTTTTTATAAAATGACTT
1 ATTTTTTGA-AAAATAACTT
*
53053450 ATTATTTTGAAAAATAGAAATT
1 ATT-TTTTGAAAAAT--AACTT
*
53053472 ATTTTTTGAAAAATAACTC
1 ATTTTTTGAAAAATAACTT
53053491 ATTT
1 ATTT
53053495 ATAAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 16 0.43
22 6 0.16
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (19 bp):
ATTTTTTGAAAAATAACTT
Found at i:53054360 original size:18 final size:17
Alignment explanation
Indices: 53054337--53054384 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
53054327 CTGATACTAA
53054337 TTATTACAAAATATCATT
1 TTATTACAAAATATC-TT
*
53054355 TTATTATAAAATATCTT
1 TTATTACAAAATATCTT
53054372 TTGATTATCAAAA
1 TT-ATTA-CAAAA
53054385 GAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (17 bp):
TTATTACAAAATATCTT
Found at i:53055618 original size:2 final size:2
Alignment explanation
Indices: 53055611--53055663 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
53055601 ATAATCACAT
53055611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53055653 TA TA TA CTA TA
1 TA TA TA -TA TA
53055664 CTACTACTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53062028 original size:35 final size:35
Alignment explanation
Indices: 53061962--53062029 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
53061952 TAACAAATAA
* *
53061962 TTTAAAAATTATAAAAAAATTCAAATTTTAAAAAT
1 TTTAAAAAATATAAAAAAATTCAAATATTAAAAAT
*
53061997 TTTAAAAAATATATAAAATATTCAAA-ATTAAAA
1 TTTAAAAAATATA-AAAAAATTCAAATATTAAAA
53062030 TTAGCATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (35 bp):
TTTAAAAAATATAAAAAAATTCAAATATTAAAAAT
Found at i:53063194 original size:17 final size:17
Alignment explanation
Indices: 53063174--53063216 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
53063164 TTTTTCTTAG
53063174 ATTAATAT-TTATTTAAA
1 ATTAATATCTT-TTTAAA
*
53063191 ATTATTATCTTTTTAAA
1 ATTAATATCTTTTTAAA
53063208 ATTACATAT
1 ATTA-ATAT
53063217 ATAATACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAATATCTTTTTAAA
Found at i:53069368 original size:20 final size:21
Alignment explanation
Indices: 53069339--53069378 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53069329 CTCAACGTTT
*
53069339 ACTTTTTTTTCTT-AATTTGG
1 ACTTTATTTTCTTAAATTTGG
*
53069359 ACTTTATTTTGTTAAATTTG
1 ACTTTATTTTCTTAAATTTG
53069379 ACCACCAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.62
Consensus pattern (21 bp):
ACTTTATTTTCTTAAATTTGG
Found at i:53072663 original size:22 final size:24
Alignment explanation
Indices: 53072632--53072678 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
53072622 CAAGTAAGGC
53072632 TCCTTCT-C-CTTCCGTTCTTCAT
1 TCCTTCTCCGCTTCCGTTCTTCAT
*
53072654 TCCTTTTCCTGCTTCCGTTCTTCAT
1 TCCTTCTCC-GCTTCCGTTCTTCAT
53072679 CTTCTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
25 14 0.67
ACGTcount: A:0.04, C:0.38, G:0.06, T:0.51
Consensus pattern (24 bp):
TCCTTCTCCGCTTCCGTTCTTCAT
Found at i:53079331 original size:9 final size:9
Alignment explanation
Indices: 53079319--53079344 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53079309 AAGAAAAAGG
53079319 TTTAGGAAT
1 TTTAGGAAT
53079328 TTTAGGAAT
1 TTTAGGAAT
53079337 TTTAGGAA
1 TTTAGGAA
53079345 CTTTGGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (9 bp):
TTTAGGAAT
Found at i:53079370 original size:6 final size:6
Alignment explanation
Indices: 53079359--53079402 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
53079349 GGGTGTTTGT
*
53079359 TTTTTC TTTTTC TTTTCTT TTTTTC TTTTTC TTTCTCTC TTTTT
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTT-T-TC TTTTT
53079403 TCCTTGTGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 21 0.64
7 7 0.21
8 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:53079380 original size:19 final size:21
Alignment explanation
Indices: 53079358--53079404 Score: 80
Period size: 19 Copynumber: 2.3 Consensus size: 21
53079348 TGGGTGTTTG
53079358 TTTTTTCTTTTTCTTT-TCT-
1 TTTTTTCTTTTTCTTTCTCTC
53079377 TTTTTTCTTTTTCTTTCTCTC
1 TTTTTTCTTTTTCTTTCTCTC
53079398 TTTTTTC
1 TTTTTTC
53079405 CTTGTGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.62
20 3 0.12
21 7 0.27
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTCTTTCTCTC
Found at i:53079388 original size:14 final size:14
Alignment explanation
Indices: 53079365--53079402 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
53079355 TTGTTTTTTC
53079365 TTTTTC-TTTTCTT
1 TTTTTCTTTTTCTT
53079378 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
* *
53079392 TCTCTCTTTTT
1 TTTTTCTTTTT
53079403 TCCTTGTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:53095789 original size:17 final size:18
Alignment explanation
Indices: 53095757--53095791 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53095747 TAAAAAATTA
*
53095757 TAAAATTTATTTAAAAAG
1 TAAAAATTATTTAAAAAG
53095775 TAAAAATTA-TTAAAAAG
1 TAAAAATTATTTAAAAAG
53095792 GTATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAAAATTATTTAAAAAG
Found at i:53097701 original size:22 final size:21
Alignment explanation
Indices: 53097657--53097743 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 21
53097647 ATGAATGTTG
*
53097657 TTTAAATTTATCACATATTAT
1 TTTAAATTTATCATATATTAT
53097678 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
* * *
53097700 TTTAAGTTT-TCATGTATCAT
1 TTTAAATTTATCATATATTAT
* *
53097720 TCTTCAAATTTATTATGTATTAT
1 T-TT-AAATTTATCATATATTAT
53097743 T
1 T
53097744 CTATATATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 5 0.09
21 22 0.40
22 18 0.33
23 10 0.18
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:53111408 original size:89 final size:87
Alignment explanation
Indices: 53111262--53111469 Score: 201
Period size: 89 Copynumber: 2.4 Consensus size: 87
53111252 TCGCATCTAG
* * * * *
53111262 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAG-AAGCAAGTCCTATCCTCCTGAAGTTACA
*
53111327 GT-GAGGCAGACTGAAAATGGCAAA
65 GTAGA-GCAGA-TGAAAATCGCAAA
53111351 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAA-AACCGACAA-TCCTAT-CTCCCTGAAGTT
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAGAA--G-CAAGTCCTATCCT-CCTGAAGTT
* * * *
53111413 ACAGTAGAGCGGATTAAAATCTCAGA
62 ACAGTAGAGCAGATGAAAATCGCAAA
** *
53111439 TCTTATCTTTCTAAAGTTGCAG-AGAGCAGAT
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
53111470 CGCATCTAGT
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
87 10 0.10
88 31 0.31
89 55 0.54
90 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (87 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAGAAGCAAGTCCTATCCTCCTGAAGTTACAG
TAGAGCAGATGAAAATCGCAAA
Found at i:53111536 original size:217 final size:217
Alignment explanation
Indices: 53111177--53111629 Score: 789
Period size: 217 Copynumber: 2.1 Consensus size: 217
53111167 AGTGGCCGGG
* * *
53111177 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTAAAGTTGC
53111242 AAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGT
66 AAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGT
*
53111307 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAAATGGCAAATCTTACCTCCCTAAAGTTGCA
53111372 GTGGAGCAGATTAAAACCGACA
196 GTGGAGCAGATTAAAACCGACA
*
53111394 ATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTATCTTTCTAAAGTTGC
1 ATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTAAAGTTGC
* * *
53111459 AGAGAGCAGATCGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
66 AAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGT
* *
53111524 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTACCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAAATGGCAAATCTTACCTCCCTAAAGTTGCA
* *
53111589 GTGGAGCAGATTAAAGCCGTCA
196 GTGGAGCAGATTAAAACCGACA
*
53111611 ATCCTATCTCCTTGAAGTT
1 ATCCTATCTCCCTGAAGTT
53111630 GTAGTGGGCA
Statistics
Matches: 223, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 223 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (217 bp):
ATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTAAAGTTGC
AAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGT
CTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAAATGGCAAATCTTACCTCCCTAAAGTTGCA
GTGGAGCAGATTAAAACCGACA
Found at i:53111730 original size:305 final size:306
Alignment explanation
Indices: 53111262--53111834 Score: 920
Period size: 305 Copynumber: 1.9 Consensus size: 306
53111252 TCGCATCTAG
* *
53111262 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTACCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCCTATCCTCCTGAAGTTGCA
53111327 GTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCGA
66 GTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCGA
* *
53111392 CAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTATCTTTCTAAAGTT
131 CAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTAACTCTCTAAAGTT
*
53111457 GCAGAGAGCAGATCGCATCTAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
196 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
53111522 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAA
261 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAA
* * **
53111568 TCTTACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCGTCAA-TCCTAT-CTCCTTGAAGTT
1 TCTTACCTCCCTGAAGTTGCAGTGGAGCAAACT-AAGTAAG-CAAGTCCTATCCTCC-TGAAGTT
* * * *
53111630 GTAGTG-GGCAGACTGAAGATGGCAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGC
63 GCAGTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAAC
* * *
53111694 CGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCAGATCTTAACTCTCTGAA
128 CGACAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTAACTCTCTAAA
*
53111759 GTTGCAGAGAGCAGATCGTATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
193 GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
* *
53111824 TAGGTCTTATC
258 CAAGTCTTATC
53111835 TCCCTAAGAA
Statistics
Matches: 245, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
305 191 0.78
306 48 0.20
307 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (306 bp):
TCTTACCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCCTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCGA
CAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCAGATCTTAACTCTCTAAAGTT
GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAA
Found at i:53111799 original size:40 final size:44
Alignment explanation
Indices: 53111176--53111814 Score: 417
Period size: 44 Copynumber: 14.8 Consensus size: 44
53111166 TAGTGGCCGG
* *
53111176 GATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* ** ***
53111220 GATCTTATCTCTCTGAAGTTGCA-AAGAGCAGA-TCGCATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
53111261 G-TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* **
53111305 G-TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAAATGGCA
1 GATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCTCA
* * * *
53111349 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCGACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TCA
* * * *
53111394 -ATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
** * * ***
53111437 GATCTTATCTTTCTAAAGTTGCAG-AGAGCAGA-TCGCATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * *
53111478 G-TTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTCA
* * **
53111522 G-TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 GATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCTCA
* * **
53111566 AATCTTACCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TCA
* * * * * **
53111611 -ATCCTATCTCCTTGAAGTTGTAGTGG-GCAGACTGAAGATGGCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATCTCA
* * * ** *
53111654 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCCGACA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TCA
* *
53111699 -ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
* * * ***
53111742 GATCTTAACTCTCTGAAGTTGCAG-AGAGCAGA-TCGTATCT-A
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
53111783 G-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
53111815 CTAAGTAAGT
Statistics
Matches: 457, Mismatches: 105, Indels: 69
0.72 0.17 0.11
Matches are distributed among these distances:
40 58 0.13
41 26 0.06
42 17 0.04
43 39 0.09
44 246 0.54
45 65 0.14
46 6 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTCA
Found at i:53112005 original size:44 final size:45
Alignment explanation
Indices: 53111957--53112085 Score: 124
Period size: 45 Copynumber: 2.9 Consensus size: 45
53111947 TGAAGATTGA
53111957 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AATGA-AAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAA-GATAAC
* **
53112001 AAGTCTGATC-CTCCTGGAA-TTGCAGT-GAGGTAGACTGAAGATGGC
1 AAGTCTTATCTC-CCT-GAAGTTGCAGTGGA-GTAGACTGAAGATAAC
* * * *
53112046 AAATCTTATCTCACTGAAGATGCAGTGGAGTAGATTGAAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG
53112086 CACTAGTTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
43 3 0.04
44 31 0.45
45 32 0.46
46 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAAC
Found at i:53114706 original size:30 final size:30
Alignment explanation
Indices: 53114664--53114721 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
53114654 TATTTTTAAC
* *
53114664 TCCATTTTTTTATCT-ATTTTAAATTTTCT
1 TCCATTTATTTATCTAATTTAAAATTTTCT
*
53114693 TCCATATTATTTATTTAATTTAAAATTTT
1 TCCAT-TTATTTATCTAATTTAAAATTTT
53114722 TATACCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 8 0.33
31 11 0.46
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (30 bp):
TCCATTTATTTATCTAATTTAAAATTTTCT
Found at i:53116756 original size:25 final size:26
Alignment explanation
Indices: 53116707--53116758 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
53116697 CTACACGCTC
* **
53116707 ATGTGGAAGAGGCACACGCTTGTGTG
1 ATGTGGAAGAAGCACACGCCCGTGTG
53116733 ATGT-GAAGAAGCACACGCCCGTGTG
1 ATGTGGAAGAAGCACACGCCCGTGTG
53116758 A
1 A
53116759 AAGGAGGCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (26 bp):
ATGTGGAAGAAGCACACGCCCGTGTG
Found at i:53117038 original size:17 final size:17
Alignment explanation
Indices: 53117016--53117049 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53117006 GTATGAACCC
53117016 CCCGTGTGCGGCACACG
1 CCCGTGTGCGGCACACG
*
53117033 CCCGTGTGTGGCACACG
1 CCCGTGTGCGGCACACG
53117050 TGTGGTCACG
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:0.12, C:0.38, G:0.35, T:0.15
Consensus pattern (17 bp):
CCCGTGTGCGGCACACG
Found at i:53118041 original size:2 final size:2
Alignment explanation
Indices: 53118034--53118062 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53118024 ATTAAAAGTA
53118034 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53118063 CTAAAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53118120 original size:20 final size:18
Alignment explanation
Indices: 53118097--53118133 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
53118087 ATATAAAATT
53118097 TTAGAAATTAGTAAAAAAAA
1 TTAGAAA-TA-TAAAAAAAA
53118117 TTAGAAATATAAAAAAA
1 TTAGAAATATAAAAAAA
53118134 TATAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
TTAGAAATATAAAAAAAA
Found at i:53126045 original size:16 final size:16
Alignment explanation
Indices: 53126025--53126057 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53126015 ACTGAAATTT
*
53126025 TAAAATTTAAAA-ATA
1 TAAAAATTAAAATATA
53126040 TAAAAATTAAAATATA
1 TAAAAATTAAAATATA
53126056 TA
1 TA
53126058 GACAAAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATTAAAATATA
Found at i:53128276 original size:19 final size:19
Alignment explanation
Indices: 53128252--53128289 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53128242 GGCGAGAGTG
53128252 GATGTTATTAAATCCATCA
1 GATGTTATTAAATCCATCA
*
53128271 GATGTTATTGAATCCATCA
1 GATGTTATTAAATCCATCA
53128290 CCACTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
GATGTTATTAAATCCATCA
Found at i:53132388 original size:17 final size:18
Alignment explanation
Indices: 53132368--53132401 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53132358 TAATTAATTT
53132368 TTTA-TATTTTTTAAATC
1 TTTATTATTTTTTAAATC
53132385 TTTATTATTTTTTAAAT
1 TTTATTATTTTTTAAAT
53132402 AATTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTTTTTAAATC
Found at i:53133041 original size:5 final size:5
Alignment explanation
Indices: 53133031--53133063 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
53133021 ACAAGATTAC
53133031 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATC
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA ATC
53133064 TTTACAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCAA
Found at i:53137945 original size:17 final size:17
Alignment explanation
Indices: 53137923--53137962 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
53137913 ATTATGAAAT
53137923 GTAATTAAATTTGAGCC
1 GTAATTAAATTTGAGCC
53137940 GTAATTAAATTTGAGCC
1 GTAATTAAATTTGAGCC
*
53137957 TTAATT
1 GTAATT
53137963 GAGCGTACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (17 bp):
GTAATTAAATTTGAGCC
Found at i:53142054 original size:15 final size:16
Alignment explanation
Indices: 53142026--53142055 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53142016 GTTGGACTAA
53142026 ATTGAATATGAGTTAT
1 ATTGAATATGAGTTAT
53142042 ATTGAAT-TGAGTTA
1 ATTGAATATGAGTTA
53142056 AATTCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAATATGAGTTAT
Found at i:53142405 original size:25 final size:24
Alignment explanation
Indices: 53142371--53142453 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
53142361 CACAACTTAT
53142371 ATGAGCTTCCCGTTATACAGCTCGC
1 ATGAGCTTCCCGTTAT-CAGCTCGC
* * *
53142396 ATGAGCTTCCTGTTACTCAGGTCGT
1 ATGAGCTTCCCGTTA-TCAGCTCGC
*
53142421 ATGAGCTTCCCGTTATTCAGCTCGG
1 ATGAGCTTCCCGTTA-TCAGCTCGC
*
53142446 AAGAGCTT
1 ATGAGCTT
53142454 ATTGTTTACA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGAGCTTCCCGTTATCAGCTCGC
Found at i:53142922 original size:20 final size:20
Alignment explanation
Indices: 53142897--53142938 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
53142887 AATTCCAGTT
53142897 ATAATGACATGTATAGGTTA
1 ATAATGACATGTATAGGTTA
53142917 ATAATGACATGTATAGGTTA
1 ATAATGACATGTATAGGTTA
53142937 AT
1 AT
53142939 TGTTTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (20 bp):
ATAATGACATGTATAGGTTA
Found at i:53145049 original size:20 final size:20
Alignment explanation
Indices: 53145006--53145049 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
53144996 TGTAATATTT
*
53145006 TAATAAATAAAAAACTAAAT
1 TAATAAATAAAAAACTAAAA
** *
53145026 TAATAAATATTAAATTAAAA
1 TAATAAATAAAAAACTAAAA
53145046 TAAT
1 TAAT
53145050 GTAAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAAATAAAAAACTAAAA
Found at i:53147872 original size:24 final size:26
Alignment explanation
Indices: 53147834--53147899 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
53147824 TACTATTATC
*
53147834 ATTATTTATT-TTTATGTTATTCAT-A
1 ATTATTTATTACTTATGTTATT-ATAA
53147859 A-TATTT-TTACTTATG-TATTATAA
1 ATTATTTATTACTTATGTTATTATAA
53147882 ATTATTTATTAC-TATGTT
1 ATTATTTATTACTTATGTT
53147900 TACCTCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.06
23 8 0.23
24 19 0.54
25 6 0.17
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTATTTATTACTTATGTTATTATAA
Found at i:53148130 original size:18 final size:19
Alignment explanation
Indices: 53148107--53148143 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
53148097 ATTATAGTAT
53148107 TTAATC-AATAAAAT-ATAA
1 TTAATCTAA-AAAATGATAA
53148125 TTAATCTAAAAAATGATAA
1 TTAATCTAAAAAATGATAA
53148144 GATATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
TTAATCTAAAAAATGATAA
Found at i:53152309 original size:14 final size:13
Alignment explanation
Indices: 53152269--53152319 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
53152259 TGAAGTATAT
*
53152269 TATTATTTTATTA
1 TATTATTATATTA
* *
53152282 TATT-GTAAATTA
1 TATTATTATATTA
53152294 TATTAATTATATTA
1 TATT-ATTATATTA
53152308 TATTATTATATT
1 TATTATTATATT
53152320 TCAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:53152995 original size:17 final size:17
Alignment explanation
Indices: 53152965--53153007 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
53152955 GAAAGTATGA
53152965 GAAA-GTGA-TTGAATT
1 GAAATGTGATTTGAATT
53152980 GAAATGTGATTTGAATT
1 GAAATGTGATTTGAATT
53152997 GAAATGTGATT
1 GAAATGTGATT
53153008 CGGAAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (17 bp):
GAAATGTGATTTGAATT
Found at i:53155808 original size:85 final size:86
Alignment explanation
Indices: 53155681--53155841 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 86
53155671 TGGTTGCCCA
* *
53155681 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCGAATATGTTGTGCACTCACAACAAGTGACAA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
53155746 TAACTGCAAATATGTGGTTCG
66 TAACTGCAAATATGTGGTTCG
* *
53155767 TCCAC-AAACCCAGTGGCAGTTTGTTTAATCTG-AAACCATGTTGTGCACTCACAACAAGTGGCA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAA-CATGTTGTGCACTCACAACAAGTGACA
*
53155830 GTAACTGCAAAT
65 ATAACTGCAAAT
53155842 GTTTTTATCT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
84 2 0.03
85 62 0.90
86 5 0.07
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (86 bp):
TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
TAACTGCAAATATGTGGTTCG
Found at i:53157814 original size:29 final size:30
Alignment explanation
Indices: 53157748--53157819 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
53157738 TATTTTAGGA
*
53157748 GCTCAATTGATTGCCAACTTTCAATTAATG
1 GCTCAATTGATTGCCAACTTTCAATTAAGG
53157778 GCTCAATTGATTG-CAA-TTTACAATTAAGG
1 GCTCAATTGATTGCCAACTTT-CAATTAAGG
*
53157807 GCTTAATTGATTG
1 GCTCAATTGATTG
53157820 TATTCTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 3 0.08
29 23 0.59
30 13 0.33
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (30 bp):
GCTCAATTGATTGCCAACTTTCAATTAAGG
Found at i:53164715 original size:20 final size:20
Alignment explanation
Indices: 53164686--53164734 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
53164676 TACTTTTTTT
* *
53164686 TTTAACTTTTAAAATTTATA
1 TTTAATTTTTAAAACTTATA
*
53164706 TTTAATTTTTATAACTTATA
1 TTTAATTTTTAAAACTTATA
*
53164726 ATT-ATTTTT
1 TTTAATTTTT
53164735 TTCTCATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATTTTTAAAACTTATA
Found at i:53167127 original size:20 final size:20
Alignment explanation
Indices: 53167102--53167143 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53167092 TGCTTTCCGT
53167102 TTATCTC-TCATGAGCTTCAG
1 TTATCTCAT-ATGAGCTTCAG
*
53167122 TTATCTCATATGAGTTTCAG
1 TTATCTCATATGAGCTTCAG
53167142 TT
1 TT
53167144 TAACCCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (20 bp):
TTATCTCATATGAGCTTCAG
Found at i:53167190 original size:42 final size:42
Alignment explanation
Indices: 53167130--53167236 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 42
53167120 AGTTATCTCA
* *
53167130 TATGAGTTTCAGTTTAACCCTTCTGGG-TTTCAGTTCAGCTATT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTC-GTTCAGCT-TT
*
53167173 T-TGAGCTTCAATTTAACCCTTATGGGTTTTCGTTCAGCTTT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTTT
*
53167214 TATGAGCTTCCGTTTAACCCTTA
1 TATGAGCTTCAGTTTAACCCTTA
53167237 CAGGTTTCCA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 49 0.86
43 5 0.09
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTTT
Found at i:53171815 original size:101 final size:101
Alignment explanation
Indices: 53171703--53171981 Score: 479
Period size: 101 Copynumber: 2.8 Consensus size: 101
53171693 TGGTCATGTT
*
53171703 TGTAGTACTATGTGTAGGCTACTACATGTACCAGAATGATAGGTCGCATGTGTAGTACTATGTGC
1 TGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGTGC
*
53171768 AGGCTACTATGCGTATCGGATAGCTTCGATCACGTG
66 AGGCTACTATGCGTACCGGATAGCTTCGATCACGTG
53171804 TGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGTGC
1 TGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGTGC
53171869 AGGCTACTATGCGTACCGGATAGCTTCGATCACGTG
66 AGGCTACTATGCGTACCGGATAGCTTCGATCACGTG
* * *
53171905 TGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTGAT-GGTCACATGTGTAGTACTATGT
1 TGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGTACTATGT
*
53171969 GCATGCTACTATG
64 GCAGGCTACTATG
53171982 TGAATCTGCA
Statistics
Matches: 170, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
101 132 0.78
102 34 0.20
103 4 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (101 bp):
TGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTATGTGC
AGGCTACTATGCGTACCGGATAGCTTCGATCACGTG
Found at i:53171816 original size:51 final size:50
Alignment explanation
Indices: 53171749--53171981 Score: 272
Period size: 51 Copynumber: 4.6 Consensus size: 50
53171739 TGATAGGTCG
*
53171749 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TTCGATCA
* * * * * * * * *
53171800 CGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGGTCG
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA-GTTCGATCA
53171850 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TTCGATCA
* * * *
53171901 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTGAT-GGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT--TCGATCA
*
53171952 CATGTGTAGTACTATGTGCATGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
53171982 TGAATCTGCA
Statistics
Matches: 151, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
50 41 0.27
51 109 0.72
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTCGATCA
Found at i:53171983 original size:26 final size:26
Alignment explanation
Indices: 53171903--53171983 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
53171893 TTCGATCACG
*
53171903 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
53171929 CGTGTACCGGA-TA-GTG-ATGGTCAC-A
1 TGTGTA--GTACTATGTGCATGCT-ACTA
53171954 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
53171980 TGTG
1 TGTG
53171984 AATCTGCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 14 0.34
26 19 0.46
27 2 0.05
28 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:53172107 original size:42 final size:43
Alignment explanation
Indices: 53171994--53172202 Score: 241
Period size: 43 Copynumber: 4.9 Consensus size: 43
53171984 AATCTGCATA
*
53171994 ATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 ATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * *
53172037 CTT-AACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-CCGCATC
1 ATTGAA-TAT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
53172079 ATTGAATATAACGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 ATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * *
53172122 CTTGACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-CCGTATC
1 ATTGAATAT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
53172164 ATTG-ATTTTAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
53172203 GTAACAATTA
Statistics
Matches: 138, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
40 4 0.03
41 25 0.18
42 44 0.32
43 56 0.41
44 9 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (43 bp):
ATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC
Found at i:53172137 original size:85 final size:84
Alignment explanation
Indices: 53171989--53172202 Score: 356
Period size: 85 Copynumber: 2.5 Consensus size: 84
53171979 ATGTGAATCT
* *
53171989 GCATAATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCATATCCTTAACTGTGAAAGGGG
1 GCATCATTGAATAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGGGG
53172054 TTGCTATGTGCTGATTCCCC
65 TTGCTATGTGCTGATTCCCC
*
53172074 GCATCATTGAATATAACGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGACTGTGAAAGGGG
1 GCATCATTGAATATAA-GGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGGGG
53172139 TTGCTATGTGCTGATTCCCC
65 TTGCTATGTGCTGATTCCCC
* * *
53172159 GTATCATTGATTTTAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 GCATCATTGAATATAAGGTGGTTGCTAAGTGCTGATTCCACCGT
53172203 GTAACAATTA
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
84 30 0.25
85 92 0.75
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
GCATCATTGAATATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAACTGTGAAAGGGGT
TGCTATGTGCTGATTCCCC
Found at i:53175190 original size:15 final size:16
Alignment explanation
Indices: 53175170--53175202 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53175160 TTAATCTTTA
53175170 TTTATACTAA-TATAT
1 TTTATACTAAGTATAT
*
53175185 TTTATATTAAGTATAT
1 TTTATACTAAGTATAT
53175201 TT
1 TT
53175203 GTTATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTATACTAAGTATAT
Found at i:53175244 original size:21 final size:20
Alignment explanation
Indices: 53175210--53175250 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
53175200 TTTGTTATTG
*
53175210 AAATTTATTTCAAATATATA
1 AAATTTATTCCAAATATATA
*
53175230 AAATTATATTCCAAATTTATA
1 AAATT-TATTCCAAATATATA
53175251 TTTCATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTATTCCAAATATATA
Found at i:53175464 original size:26 final size:26
Alignment explanation
Indices: 53175435--53175485 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
53175425 AACACTTAAA
53175435 TTTTAAATCAAGCT-TTT-CAAAAGTAC
1 TTTT-AAT-AAGCTCTTTCCAAAAGTAC
*
53175461 TTTTGATAAGCTCTTTCCAAAAGTA
1 TTTTAATAAGCTCTTTCCAAAAGTA
53175486 ACGAGAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 5 0.23
25 5 0.23
26 12 0.55
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (26 bp):
TTTTAATAAGCTCTTTCCAAAAGTAC
Found at i:53177674 original size:25 final size:25
Alignment explanation
Indices: 53177646--53177695 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53177636 AGATAGAAAA
53177646 ACAAAAGAAAATGGAAGAATCTAAG
1 ACAAAAGAAAATGGAAGAATCTAAG
53177671 ACAAAAGAAAATGGAAGAATCTAAG
1 ACAAAAGAAAATGGAAGAATCTAAG
53177696 TAAAGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.20, T:0.12
Consensus pattern (25 bp):
ACAAAAGAAAATGGAAGAATCTAAG
Found at i:53178107 original size:20 final size:20
Alignment explanation
Indices: 53178065--53178107 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
53178055 CTATTTCCAA
* *
53178065 AAATATCTTAAATAAAATTC
1 AAATATCTTAAAAAAAATAC
53178085 AAATAT-TTAAAAAAAACTAC
1 AAATATCTTAAAAAAAA-TAC
53178105 AAA
1 AAA
53178108 CAACAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATATCTTAAAAAAAATAC
Found at i:53184065 original size:90 final size:89
Alignment explanation
Indices: 53183963--53184207 Score: 348
Period size: 90 Copynumber: 2.7 Consensus size: 89
53183953 ATCCATGTGA
* * * *
53183963 TGCCATAATATCTTTGAACTATGGTCTTATTCGTATCAGATTTAATGCCATAGTATCTTTCAACT
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCAT-TCAGATTTAGTGCCATAGTATCTTTCAACT
53184028 ACGGTCTTACACATTTCCAGTTTAG
65 ACGGTCTTACACATTTCCAGTTTAG
* * **
53184053 TGCCATAGTATCTTTCAACCACGGTCTTACACATTTCCAG-TTTAGTGCCATAGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCA-TT-CAGATTTAGTGCCATAGTATCTTTCAAC
53184117 TACGGTCTTACACATTTCCAGTTTAG
64 TACGGTCTTACACATTTCCAGTTTAG
* * **
53184143 TGCCATAGTATCTTTCAACTATAGTCTTATTCATTCCGATTTAGTATCATAGTATCTTTCAACTA
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCATTCAGATTTAGTGCCATAGTATCTTTCAACTA
53184208 TAGTCTTTCT
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
88 2 0.01
89 26 0.19
90 104 0.76
91 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (89 bp):
TGCCATAGTATCTTTCAACTATGGTCTTATTCATTCAGATTTAGTGCCATAGTATCTTTCAACTA
CGGTCTTACACATTTCCAGTTTAG
Found at i:53184221 original size:44 final size:45
Alignment explanation
Indices: 53183963--53184207 Score: 316
Period size: 45 Copynumber: 5.5 Consensus size: 45
53183953 ATCCATGTGA
* * * ** * * *
53183963 TGCCATAATATCTTTGAACTATGGTCTTATTCGTAT-CAGATTTAA
1 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAG-TTTAG
53184008 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
1 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
*
53184053 TGCCATAGTATCTTTCAACCACGGTCTTACACATTTCCAGTTTAG
1 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
53184098 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
1 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
** **
53184143 TGCCATAGTATCTTTCAACTATAGTCTTATTCA-TTCC-GATTTAG
1 TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAG-TTTAG
**
53184187 TATCATAGTATCTTTCAACTA
1 TGCCATAGTATCTTTCAACTA
53184208 TAGTCTTTCT
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
43 1 0.01
44 28 0.15
45 150 0.82
46 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (45 bp):
TGCCATAGTATCTTTCAACTACGGTCTTACACATTTCCAGTTTAG
Found at i:53187777 original size:67 final size:67
Alignment explanation
Indices: 53187697--53187824 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
53187687 GGACAAATTC
53187697 TTTGTTTAAATATATAAATCCTGTCATTGAATCCTTTTTTATTTCCAGTAAATGAAGGTTTCTAT
1 TTTGTTTAAATATATAAATCCTGTCATTGAATCCTTTTTTATTTCCAGTAAATGAAGGTTTCTAT
53187762 TT
66 TT
* * * *
53187764 TTTGTTTAAATATATAAATCTTGTCATTGAATCCTTTTTTATTTCTAGTTAATGGAGGTTT
1 TTTGTTTAAATATATAAATCCTGTCATTGAATCCTTTTTTATTTCCAGTAAATGAAGGTTT
53187825 TTAACTTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (67 bp):
TTTGTTTAAATATATAAATCCTGTCATTGAATCCTTTTTTATTTCCAGTAAATGAAGGTTTCTAT
TT
Found at i:53190482 original size:12 final size:12
Alignment explanation
Indices: 53190439--53190482 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
53190429 GTAGTTTCTT
53190439 TAAAAAAAACTT-
1 TAAAAAAAA-TTC
*
53190451 TTAAAAAAATTC
1 TAAAAAAAATTC
53190463 -AAAAAAAATTC
1 TAAAAAAAATTC
53190474 TAAAAAAAA
1 TAAAAAAAA
53190483 AACTAGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAAAAAAATTC
Found at i:53190542 original size:14 final size:14
Alignment explanation
Indices: 53190519--53190576 Score: 107
Period size: 14 Copynumber: 4.1 Consensus size: 14
53190509 ATTGGATATC
53190519 AAATTGTGAAAAAA
1 AAATTGTGAAAAAA
*
53190533 AAATTTTGAAAAAA
1 AAATTGTGAAAAAA
53190547 AAATTGTGAAAAAA
1 AAATTGTGAAAAAA
53190561 AAATTGTGAAAAAA
1 AAATTGTGAAAAAA
53190575 AA
1 AA
53190577 GAGAGAGCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (14 bp):
AAATTGTGAAAAAA
Found at i:53201120 original size:16 final size:16
Alignment explanation
Indices: 53201105--53201142 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53201095 TTATTAAATT
53201105 TTAT-TTAATA-ATAA
1 TTATATTAATATATAA
53201119 TTATATTAATATATAA
1 TTATATTAATATATAA
*
53201135 TTAAATTA
1 TTATATTA
53201143 TTTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 6 0.29
16 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATTAATATATAA
Found at i:53202007 original size:7 final size:7
Alignment explanation
Indices: 53201973--53202004 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53201963 TAAGTTGGGG
53201973 GTTGAGA
1 GTTGAGA
53201980 GTTGAGA
1 GTTGAGA
53201987 GTTGAGA
1 GTTGAGA
*
53201994 GTTGGGA
1 GTTGAGA
53202001 GTTG
1 GTTG
53202005 GGACCTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (7 bp):
GTTGAGA
Found at i:53203919 original size:3 final size:3
Alignment explanation
Indices: 53203911--53203940 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53203901 TGTTGAAATC
53203911 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
53203941 AGTTGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:53208550 original size:77 final size:77
Alignment explanation
Indices: 53208448--53208603 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 77
53208438 ATATAATTTA
* * *
53208448 ATTTTATCAATGATGCCTTGGTTGTGTTTACAAGGTTAAGGCCCTC-AAACTTCCATAGTCTATG
1 ATTTTATCAATGATGCATTAGTTGTGTTTACAAGGTTAAGGCCC-CGAAACTTCCATAGTCTATA
53208512 TTTGAGGCTCGCC
65 TTTGAGGCTCGCC
* *
53208525 ATTTTATCAATGATGCATTAGTTGTGTTTACAAGGTTAAGGCCCCGTAACTTTCATAGTCTATAT
1 ATTTTATCAATGATGCATTAGTTGTGTTTACAAGGTTAAGGCCCCGAAACTTCCATAGTCTATAT
* *
53208590 TTGAGTCTTGCC
66 TTGAGGCTCGCC
53208602 AT
1 AT
53208604 GCACAAATGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
76 1 0.01
77 70 0.99
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (77 bp):
ATTTTATCAATGATGCATTAGTTGTGTTTACAAGGTTAAGGCCCCGAAACTTCCATAGTCTATAT
TTGAGGCTCGCC
Found at i:53223374 original size:28 final size:28
Alignment explanation
Indices: 53223335--53223390 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53223325 GCTGCTTGTA
53223335 AAATTGACTGCCCAACCTTCCTTTCTTT
1 AAATTGACTGCCCAACCTTCCTTTCTTT
53223363 AAATTGACTGCCCAACCTTCCTTTCTTT
1 AAATTGACTGCCCAACCTTCCTTTCTTT
53223391 CTCATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.07, T:0.39
Consensus pattern (28 bp):
AAATTGACTGCCCAACCTTCCTTTCTTT
Found at i:53223512 original size:26 final size:25
Alignment explanation
Indices: 53223466--53223515 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
53223456 AGAGATACTA
53223466 CAAACTTCATTTTGGGAAAGGATGG
1 CAAACTTCATTTTGGGAAAGGATGG
*
53223491 CAAACTTTGATTTATGGG-AAGGATG
1 CAAAC-TTCATTT-TGGGAAAGGATG
53223516 TATGTTCCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 13 0.59
27 4 0.18
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (25 bp):
CAAACTTCATTTTGGGAAAGGATGG
Found at i:53230436 original size:6 final size:6
Alignment explanation
Indices: 53230417--53230456 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
53230407 GGTTTCCAAA
* * *
53230417 AATGGA AATAGG AATGGG AATGGG AATGGG AATGGA AATG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG AATG
53230457 ATCCATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:53234229 original size:2 final size:2
Alignment explanation
Indices: 53234222--53234259 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
53234212 AGCTTTCAAG
*
53234222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53234260 CACAACCACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53241848 original size:28 final size:28
Alignment explanation
Indices: 53241790--53241860 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
53241780 TAATGAGATT
*
53241790 AGCACTAAGTGTGCGAGTATAAGGGTAA
1 AGCACTAAGTGTGCGAGTATAAGGATAA
* * ** *
53241818 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTATAAGGATAA
53241846 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53241861 TACTTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATAAGGATAA
Found at i:53242996 original size:22 final size:23
Alignment explanation
Indices: 53242933--53243248 Score: 185
Period size: 22 Copynumber: 13.4 Consensus size: 23
53242923 CCAAATTTGA
53242933 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
* *
53242958 TGTCC-ATTTTAATGTGTA-ATGT
1 TGTCCAATTTTGA-GTGTATATGC
53242980 TGTCCAATTTTGAGTGTACTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
*
53243005 TGTCC-ATTTT-AATGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
53243027 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
* *
53243052 TGTCC-ATTTT-AATATATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* * *
53243074 TGTCCAATTGTGAGTATATTTAAGC
1 TGTCCAATTTTGAGTGTA--TATGC
*
53243099 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* * *
53243121 TGTCCAATTGTGAGTATATTTAAGC
1 TGTCCAATTTTGAGTGTA--TATGC
*
53243146 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* *
53243168 TGTCCAATTTTCG-GTATATTTAAGC
1 TGTCCAATTTT-GAGTGTA--TATGC
*
53243193 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
53243215 TGTCC-ATTTTGAGCATGT-TATTGC
1 TGTCCAATTTTGAG--TGTATA-TGC
53243239 TGTCCAATTT
1 TGTCCAATTT
53243249 GTTGAGTAAT
Statistics
Matches: 227, Mismatches: 33, Indels: 62
0.70 0.10 0.19
Matches are distributed among these distances:
21 4 0.02
22 63 0.28
23 42 0.19
24 53 0.23
25 62 0.27
26 3 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTCCAATTTTGAGTGTATATGC
Found at i:53243003 original size:47 final size:47
Alignment explanation
Indices: 53242933--53243227 Score: 351
Period size: 47 Copynumber: 6.3 Consensus size: 47
53242923 CCAAATTTGA
* *
53242933 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGT
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
*
53242980 TGTCCAATTTTGAGTGTACTGATGCTGTCCATTTTAATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
*
53243027 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * * *
53243074 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * * *
53243121 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * *
53243168 TGTCCAATTTTCG-GTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTT-GAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
53243215 TGTCC-ATTTTGAG
1 TGTCCAATTTTGAG
53243228 CATGTTATTG
Statistics
Matches: 232, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
45 1 0.00
46 6 0.03
47 224 0.97
48 1 0.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (47 bp):
TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
Found at i:53243101 original size:94 final size:94
Alignment explanation
Indices: 53242933--53243227 Score: 405
Period size: 94 Copynumber: 3.1 Consensus size: 94
53242923 CCAAATTTGA
* * *
53242933 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGTTGTCCAATTTTGAGTGTA
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
* * * * * *
53242998 CTGATGCTGTCCATTTTAATGTATAATGC
66 TTTAAGCTGTCTAATTTGATGTATAATGC
* *
53243027 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAGTATA
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
53243092 TTTAAGCTGTCTAATTTGATGTATAATGC
66 TTTAAGCTGTCTAATTTGATGTATAATGC
* * * * * * *
53243121 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTCG-GTAT
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTT-GAGTAT
53243185 ATTTAAGCTGTCTAATTTGATGTATAATGC
65 ATTTAAGCTGTCTAATTTGATGTATAATGC
53243215 TGTCC-ATTTTGAG
1 TGTCCAATTTTGAG
53243228 CATGTTATTG
Statistics
Matches: 179, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
93 7 0.04
94 171 0.96
95 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (94 bp):
TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
TTTAAGCTGTCTAATTTGATGTATAATGC
Found at i:53243263 original size:94 final size:93
Alignment explanation
Indices: 53242933--53243268 Score: 326
Period size: 94 Copynumber: 3.6 Consensus size: 93
53242923 CCAAATTTGA
* * * * * *
53242933 TGTCCAATTTTGAGTGTATTGA-TGCTGTCCATTTTAATGTG-TAATGTTGTCCAATTTTGAGTG
1 TGTCCAATTTTGAGTATATT-ATTGCTGTCCAATTT-GT-TGATAATGCTGTCCAATTGTGAGTA
* * * * * *
53242996 TACTGATGCTGTCCATTTTAATGTATAATGC
63 TATTTAAGCTGTCTAATTTGATGTATAATGC
* * *
53243027 TGTCCAATTTTGAGTGTATTGA-TGCTGTCCATTTTAATAT-ATAATGCTGTCCAATTGTGAGTA
1 TGTCCAATTTTGAGTATATT-ATTGCTGTCCAATTT-GT-TGATAATGCTGTCCAATTGTGAGTA
53243090 TATTTAAGCTGTCTAATTTGATGTATAATGC
63 TATTTAAGCTGTCTAATTTGATGTATAATGC
* * * * *
53243121 TGTCCAATTGTGAGTATATT-TAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTCG-GTA
1 TGTCCAATTTTGAGTATATTAT-TGCTGTCCAATTTGTTG-ATAATGCTGTCCAATTGT-GAGTA
53243184 TATTTAAGCTGTCTAATTTGATGTATAATGC
63 TATTTAAGCTGTCTAATTTGATGTATAATGC
* *
53243215 TGTCC-ATTTTGAGCATGTTATTGCTGTCCAATTTGTTGAGTAATTGCTGTCCAA
1 TGTCCAATTTTGAGTATATTATTGCTGTCCAATTTGTTGA-TAA-TGCTGTCCAA
53243269 AATAGAGTTG
Statistics
Matches: 209, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
92 2 0.01
93 28 0.13
94 178 0.85
95 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (93 bp):
TGTCCAATTTTGAGTATATTATTGCTGTCCAATTTGTTGATAATGCTGTCCAATTGTGAGTATAT
TTAAGCTGTCTAATTTGATGTATAATGC
Found at i:53243263 original size:141 final size:141
Alignment explanation
Indices: 53242933--53243268 Score: 338
Period size: 141 Copynumber: 2.4 Consensus size: 141
53242923 CCAAATTTGA
* ** * * * * * * * *
53242933 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGTTGTCCAATTTTGAGTGTA
1 TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
* * * * *
53242998 CTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTA
66 CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTA
53243063 ATATATAATGC
131 ATATATAATGC
* *
53243074 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
1 TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
* * * * * *
53243139 TTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTCG-GTATATTTAAGCTGTCTAATTT
66 CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTT-GAGTATATTGAAGCTGTCCAATTT
* *
53243203 GATGTATAATGC
130 AATATATAATGC
* * * *
53243215 TGTCC-ATTTTGAGCAT-GTTATTGCTGTCCAATTTGTTG-AGTAATTGCTGTCCAA
1 TGTCCAATTGTGAGCATATTTA-AGCTGTCCAATTTGATGTA-TAA-TGCTGTCCAA
53243269 AATAGAGTTG
Statistics
Matches: 161, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
139 4 0.02
140 26 0.16
141 130 0.81
142 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (141 bp):
TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTA
ATATATAATGC
Found at i:53243342 original size:27 final size:27
Alignment explanation
Indices: 53243304--53243359 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53243294 AGTATGTTAC
53243304 ATAGTTAATCATTTATTAATGAAATAA
1 ATAGTTAATCATTTATTAATGAAATAA
53243331 ATAGTTAATCATTTATTAATGAAATAA
1 ATAGTTAATCATTTATTAATGAAATAA
53243358 AT
1 AT
53243360 GTATGCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
ATAGTTAATCATTTATTAATGAAATAA
Found at i:53249764 original size:28 final size:28
Alignment explanation
Indices: 53249706--53249776 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
53249696 TAATGAGATT
*
53249706 AGCACTAAGTGTGCGAGTATAAGGGTAA
1 AGCACTAAGTGTGCGAGTATAAGGATAA
* * ** *
53249734 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTATAAGGATAA
53249762 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53249777 TACTTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATAAGGATAA
Found at i:53250826 original size:22 final size:23
Alignment explanation
Indices: 53250763--53251078 Score: 183
Period size: 22 Copynumber: 13.4 Consensus size: 23
53250753 CCAAATTTGA
53250763 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
* *
53250788 TGTCC-ATTTTAATGTGTA-ATGT
1 TGTCCAATTTTGA-GTGTATATGC
53250810 TGTCCAATTTTGAGTGTACTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
*
53250835 TGTCC-ATTTT-AATGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
53250857 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCCAATTTTGAGTGTA-T-ATGC
* *
53250882 TGTCC-ATTTT-AATATATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* * *
53250904 TGTCCAATTGTGAGTATATTTAAGC
1 TGTCCAATTTTGAGTGTA--TATGC
*
53250929 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* * *
53250951 TGTCCAATTGTGAGTATATTTAAGC
1 TGTCCAATTTTGAGTGTA--TATGC
*
53250976 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
* * * *
53250998 TGTCCAATTTTGGGTATATTTAAGT
1 TGTCCAATTTTGAGTGTA--TATGC
*
53251023 TGTCTAA-TTTGA-TGTATAATGC
1 TGTCCAATTTTGAGTGTAT-ATGC
53251045 TGTCC-ATTTTGAGCATGT-TATTGC
1 TGTCCAATTTTGAG--TGTATA-TGC
53251069 TGTCCAATTT
1 TGTCCAATTT
53251079 GTTGAGTAAT
Statistics
Matches: 225, Mismatches: 37, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
21 4 0.02
22 62 0.28
23 42 0.19
24 53 0.24
25 61 0.27
26 3 0.01
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (23 bp):
TGTCCAATTTTGAGTGTATATGC
Found at i:53250833 original size:47 final size:47
Alignment explanation
Indices: 53250763--53251057 Score: 349
Period size: 47 Copynumber: 6.3 Consensus size: 47
53250753 CCAAATTTGA
* *
53250763 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGT
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
*
53250810 TGTCCAATTTTGAGTGTACTGATGCTGTCCATTTTAATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
*
53250857 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * * *
53250904 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * * *
53250951 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
* * * * * * * *
53250998 TGTCCAATTTTGGGTATATTTAAGTTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
53251045 TGTCC-ATTTTGAG
1 TGTCCAATTTTGAG
53251058 CATGTTATTG
Statistics
Matches: 231, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
46 7 0.03
47 224 0.97
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (47 bp):
TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
Found at i:53250931 original size:94 final size:94
Alignment explanation
Indices: 53250763--53251057 Score: 403
Period size: 94 Copynumber: 3.1 Consensus size: 94
53250753 CCAAATTTGA
* * *
53250763 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGTTGTCCAATTTTGAGTGTA
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
* * * * * *
53250828 CTGATGCTGTCCATTTTAATGTATAATGC
66 TTTAAGCTGTCTAATTTGATGTATAATGC
* *
53250857 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAGTATA
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
53250922 TTTAAGCTGTCTAATTTGATGTATAATGC
66 TTTAAGCTGTCTAATTTGATGTATAATGC
* * * * * * * *
53250951 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTGGGTATA
1 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
*
53251016 TTTAAGTTGTCTAATTTGATGTATAATGC
66 TTTAAGCTGTCTAATTTGATGTATAATGC
53251045 TGTCC-ATTTTGAG
1 TGTCCAATTTTGAG
53251058 CATGTTATTG
Statistics
Matches: 178, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
93 7 0.04
94 171 0.96
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (94 bp):
TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
TTTAAGCTGTCTAATTTGATGTATAATGC
Found at i:53251093 original size:94 final size:93
Alignment explanation
Indices: 53250763--53251098 Score: 324
Period size: 94 Copynumber: 3.6 Consensus size: 93
53250753 CCAAATTTGA
* * * * * *
53250763 TGTCCAATTTTGAGTGTATTGA-TGCTGTCCATTTTAATGTG-TAATGTTGTCCAATTTTGAGTG
1 TGTCCAATTTTGAGTATATT-ATTGCTGTCCAATTT-GT-TGATAATGCTGTCCAATTGTGAGTA
* * * * * *
53250826 TACTGATGCTGTCCATTTTAATGTATAATGC
63 TATTTAAGCTGTCTAATTTGATGTATAATGC
* * *
53250857 TGTCCAATTTTGAGTGTATTGA-TGCTGTCCATTTTAATAT-ATAATGCTGTCCAATTGTGAGTA
1 TGTCCAATTTTGAGTATATT-ATTGCTGTCCAATTT-GT-TGATAATGCTGTCCAATTGTGAGTA
53250920 TATTTAAGCTGTCTAATTTGATGTATAATGC
63 TATTTAAGCTGTCTAATTTGATGTATAATGC
* * * * * *
53250951 TGTCCAATTGTGAGTATATT-TAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTGGGTAT
1 TGTCCAATTTTGAGTATATTAT-TGCTGTCCAATTTGTTG-ATAATGCTGTCCAATTGTGAGTAT
*
53251015 ATTTAAGTTGTCTAATTTGATGTATAATGC
64 ATTTAAGCTGTCTAATTTGATGTATAATGC
* *
53251045 TGTCC-ATTTTGAGCATGTTATTGCTGTCCAATTTGTTGAGTAATTGCTGTCCAA
1 TGTCCAATTTTGAGTATATTATTGCTGTCCAATTTGTTGA-TAA-TGCTGTCCAA
53251099 AATAGAGTTG
Statistics
Matches: 208, Mismatches: 26, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
92 2 0.01
93 28 0.13
94 178 0.86
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.44
Consensus pattern (93 bp):
TGTCCAATTTTGAGTATATTATTGCTGTCCAATTTGTTGATAATGCTGTCCAATTGTGAGTATAT
TTAAGCTGTCTAATTTGATGTATAATGC
Found at i:53251093 original size:141 final size:141
Alignment explanation
Indices: 53250763--53251098 Score: 336
Period size: 141 Copynumber: 2.4 Consensus size: 141
53250753 CCAAATTTGA
* ** * * * * * * * *
53250763 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGTTGTCCAATTTTGAGTGTA
1 TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
* * * * *
53250828 CTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTA
66 CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTA
53250893 ATATATAATGC
131 ATATATAATGC
* *
53250904 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
1 TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
* * * * * * * * *
53250969 TTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTGGGTATATTTAAGTTGTCTAATTTG
66 CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTA
*
53251034 ATGTATAATGC
131 ATATATAATGC
* * * *
53251045 TGTCC-ATTTTGAGCAT-GTTATTGCTGTCCAATTTGTTG-AGTAATTGCTGTCCAA
1 TGTCCAATTGTGAGCATATTTA-AGCTGTCCAATTTGATGTA-TAA-TGCTGTCCAA
53251099 AATAGAGTTG
Statistics
Matches: 160, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
139 4 0.03
140 26 0.16
141 130 0.81
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.44
Consensus pattern (141 bp):
TGTCCAATTGTGAGCATATTTAAGCTGTCCAATTTGATGTATAATGCTGTCCAATTGTGAGTATA
CTGAAGCTGTCCAATTTAATGTATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTA
ATATATAATGC
Found at i:53252489 original size:52 final size:52
Alignment explanation
Indices: 53252410--53252607 Score: 195
Period size: 52 Copynumber: 3.7 Consensus size: 52
53252400 CATAAATTCA
* *
53252410 AAAAAAAGTTTTTGGGGTTCGGAGGAAGTAAAAGTTTTGAGAGAAAGCAAAAGG
1 AAAAAAA--TTTTGGGGTTTGGGGGAAGTAAAAGTTTTGAGAGAAAGCAAAAGG
* * *
53252464 AAAAAAAATTTGGGAGTTT-GGGGAAGTAAAAGTTTTAGGGAGAAAGTAAAAGG
1 AAAAAAATTTTGGG-GTTTGGGGGAAGTAAAAGTTTT-GAGAGAAAGCAAAAGG
** * * *
53252517 -AAAATTTTTTAGGGGTTTGGGGGAAGTAAAACTTTTGCAG-GAAATCAAAAAG
1 AAAAAAATTTT-GGGGTTTGGGGGAAGTAAAAGTTTTG-AGAGAAAGCAAAAGG
*
53252569 AAAAAAAGTTTTTGGGGATTTGGGGGAAGTAAAATTTTT
1 AAAAAAA--TTTTGGGG-TTTGGGGGAAGTAAAAGTTTT
53252608 AGGGGAAAAG
Statistics
Matches: 119, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
52 43 0.36
53 41 0.34
54 11 0.09
55 24 0.20
ACGTcount: A:0.41, C:0.03, G:0.30, T:0.27
Consensus pattern (52 bp):
AAAAAAATTTTGGGGTTTGGGGGAAGTAAAAGTTTTGAGAGAAAGCAAAAGG
Done.