Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 8 of 84
Found at i:1194465 original size:5 final size:5
Alignment explanation
Indices: 1194457--1194572 Score: 66
Period size: 5 Copynumber: 23.6 Consensus size: 5
1194447 TTATTTAAAG
* *
1194457 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAAT AAAA- ATAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* * *
1194505 AAAAT AAAAAT AAAGA- AAAGT AAAAC AAAA- AATA- AAAAT AAAAT AAAGAT
1 AAAAT -AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT
* * *
1194555 AAAAG AATAT TAAAT AAA
1 AAAAT AAAAT AAAAT AAA
1194573 CCTAATCTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
3 3 0.03
4 12 0.14
5 54 0.63
6 13 0.15
7 4 0.05
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1194491 original size:30 final size:30
Alignment explanation
Indices: 1194456--1194558 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
1194446 TTTATTTAAA
*
1194456 GAAAATAAAATAATAAA-ACAAAATAAAAGT
1 GAAAATAAAATAA-AAATAAAAAATAAAAGT
*
1194486 GAAAATAAAATAAAAATAAAAAATAAAAAT
1 GAAAATAAAATAAAAATAAAAAATAAAAGT
* * *
1194516 -AAAGA-AAAGT-AAAACAAAAAATAAAAAT
1 GAAA-ATAAAATAAAAATAAAAAATAAAAGT
1194544 -AAAATAAAGATAAAA
1 GAAAATAAA-ATAAAA
1194559 GAATATTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
27 1 0.02
28 23 0.37
29 11 0.17
30 28 0.44
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.15
Consensus pattern (30 bp):
GAAAATAAAATAAAAATAAAAAATAAAAGT
Found at i:1194492 original size:12 final size:11
Alignment explanation
Indices: 1194457--1194558 Score: 73
Period size: 11 Copynumber: 8.8 Consensus size: 11
1194447 TTATTTAAAG
1194457 AAAATAAAATAA
1 AAAATAAAAT-A
*
1194469 TAAAACAAAATA
1 -AAAATAAAATA
*
1194481 AAAGTGAAAAT-
1 AAAAT-AAAATA
1194492 AAAATAAAAATAA
1 AAAAT-AAAAT-A
1194505 AAAATAAAAATA
1 AAAAT-AAAATA
* *
1194517 AAGA-AAAGTA
1 AAAATAAAATA
*
1194527 AAACAAAAAATA
1 AAA-ATAAAATA
1194539 AAAATAAAATA
1 AAAATAAAATA
*
1194550 AAGATAAAA
1 AAAATAAAA
1194559 GAATATTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
10 7 0.10
11 28 0.38
12 18 0.25
13 20 0.27
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1194503 original size:6 final size:6
Alignment explanation
Indices: 1194457--1194558 Score: 74
Period size: 6 Copynumber: 17.5 Consensus size: 6
1194447 TTATTTAAAG
* *
1194457 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTG AAAAT- AAAATA AAAATAA
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAAT-A
* *
1194505 AAAATA AAAAT- -AAAGA AAAGTA AAACA-A AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA AAAATA AAAATA AAAATA
*
1194550 AAGATA AAA
1 AAAATA AAA
1194559 GAATATTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
4 3 0.04
5 16 0.21
6 47 0.61
7 11 0.14
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1194529 original size:46 final size:48
Alignment explanation
Indices: 1194457--1194551 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 48
1194447 TTATTTAAAG
***
1194457 AAAATAAAATAATAAAACAAAATAAAAGTGAAAAT-AAAATAAAAATAA
1 AAAATAAAATAATAAAACAAAATAAAACAAAAAATAAAAAT-AAAATAA
*
1194505 AAAAT-AAA-AATAAAGA-AAAGTAAAACAAAAAATAAAAATAAAATAA
1 AAAATAAAATAATAAA-ACAAAATAAAACAAAAAATAAAAATAAAATAA
1194551 A
1 A
1194552 GATAAAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
46 27 0.66
47 9 0.22
48 5 0.12
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (48 bp):
AAAATAAAATAATAAAACAAAATAAAACAAAAAATAAAAATAAAATAA
Found at i:1194537 original size:41 final size:41
Alignment explanation
Indices: 1194457--1194550 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1194447 TTATTTAAAG
* * *
1194457 AAAATAAAATAATAAAACAAAATAAAAGTGAAAATAAAATA
1 AAAATAAAATAATAAAACAAAAGAAAAGTAAAAAAAAAATA
1194498 AAAATAAAA-AATAAAA-ATAAAGAAAAGTAAAACAAAAAATA
1 AAAATAAAATAATAAAACA-AAAGAAAAGTAAAA-AAAAAATA
1194539 AAAATAAAATAA
1 AAAATAAAATAA
1194551 AGATAAAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
39 1 0.02
40 19 0.40
41 25 0.53
42 2 0.04
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (41 bp):
AAAATAAAATAATAAAACAAAAGAAAAGTAAAAAAAAAATA
Found at i:1194560 original size:40 final size:39
Alignment explanation
Indices: 1194457--1194561 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 39
1194447 TTATTTAAAG
* * * *
1194457 AAAATAAAATAATAAAACAAAATAAAAGTGAAAATAAAATA
1 AAAATAAAAT-A-AAAATAAAAGAAAAGTAAAAAAAAAATA
1194498 AAAATAAAAAATAAAAAT-AAAGAAAAGTAAAACAAAAAATA
1 AAAAT--AAAATAAAAATAAAAGAAAAGTAAAA-AAAAAATA
*
1194539 AAAATAAAATAAAGATAAAAGAA
1 AAAATAAAATAAAAATAAAAGAA
1194562 TATTAAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 10 0.18
40 18 0.33
41 21 0.38
42 1 0.02
43 5 0.09
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (39 bp):
AAAATAAAATAAAAATAAAAGAAAAGTAAAAAAAAAATA
Found at i:1194568 original size:28 final size:25
Alignment explanation
Indices: 1194487--1194572 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 25
1194477 AATAAAAGTG
*
1194487 AAAATAAAATAAAAAT-AAAAAATA
1 AAAATAAAATAAAGATAAAAAAATA
*
1194511 AAAATAAAGA-AAAGTAAAACAAAAAATA
1 AAAATAAA-ATAAAG--ATA-AAAAAATA
*
1194539 AAAATAAAATAAAGATAAAAGAATA
1 AAAATAAAATAAAGATAAAAAAATA
*
1194564 TTAAATAAA
1 -AAAATAAA
1194573 CCTAATCTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 11 0.22
25 8 0.16
26 10 0.20
27 1 0.02
28 20 0.40
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAATAAAATAAAGATAAAAAAATA
Found at i:1195545 original size:21 final size:21
Alignment explanation
Indices: 1195486--1195677 Score: 59
Period size: 21 Copynumber: 9.1 Consensus size: 21
1195476 GATAATTAGG
*
1195486 AAAATAATAATAA-GATAAAT
1 AAAATAATAATAATAATAAAT
* *
1195506 CAACAAT-ATTATAA-GATAAAT
1 -AA-AATAATAATAATAATAAAT
*
1195527 AAAATAATAATAATAATAACAG
1 AAAATAATAATAATAATAA-AT
1195549 ATAAATAAATATATAATTAGATAAAT
1 A-AAAT-AATA-ATAA-TA-ATAAAT
1195575 AAAAATACAT-ATAA-AATAAAAT
1 -AAAATA-ATAATAATAAT-AAAT
* * **
1195597 GAAAAAAAGAA-AA-AA-AAGG
1 -AAAATAATAATAATAATAAAT
*
1195616 GAAA-AATAA-AATAA-AAAT
1 AAAATAATAATAATAATAAAT
* *
1195634 AAAATAAAAAT-ATATATTAAT
1 AAAATAATAATAATA-ATAAAT
*
1195655 -AAATAGTAATAATAAATAAAT
1 AAAATAATAATAAT-AATAAAT
1195676 AA
1 AA
1195678 TAAATACATA
Statistics
Matches: 130, Mismatches: 20, Indels: 41
0.68 0.10 0.21
Matches are distributed among these distances:
17 6 0.05
18 10 0.08
19 12 0.09
20 17 0.13
21 36 0.28
22 18 0.14
23 4 0.03
24 8 0.06
25 5 0.04
26 9 0.07
27 5 0.04
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAATAATAATAATAATAAAT
Found at i:1195678 original size:11 final size:11
Alignment explanation
Indices: 1195624--1195683 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
1195614 GGGAAAAATA
1195624 AAATAAA-AAT
1 AAATAAATAAT
1195634 AAAATAAA-AAT
1 -AAATAAATAAT
* *
1195645 ATAT-ATTAAT
1 AAATAAATAAT
1195655 AAATAGTAATAAT
1 AAATA--AATAAT
1195668 AAATAAATAAT
1 AAATAAATAAT
1195679 AAATA
1 AAATA
1195684 CATAGGATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 1 0.02
10 9 0.22
11 21 0.51
13 10 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:1195710 original size:25 final size:26
Alignment explanation
Indices: 1195666--1195721 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1195656 AATAGTAATA
* **
1195666 ATAAATAAATAATAAATACATAGGAT
1 ATAAAGAAATAATAAATACATAAAAT
*
1195692 ATAAAGAAA-AATATATACATAAAAT
1 ATAAAGAAATAATAAATACATAAAAT
1195717 ATAAA
1 ATAAA
1195722 ATACAAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (26 bp):
ATAAAGAAATAATAAATACATAAAAT
Found at i:1199269 original size:15 final size:16
Alignment explanation
Indices: 1199249--1199280 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1199239 TGTTAAGTGT
1199249 AATGAATG-AAAATGC
1 AATGAATGAAAAATGC
1199264 AATGAATGAAAAATGC
1 AATGAATGAAAAATGC
1199280 A
1 A
1199281 TGTATGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
AATGAATGAAAAATGC
Found at i:1202378 original size:14 final size:15
Alignment explanation
Indices: 1202354--1202394 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1202344 TCAGATTATT
1202354 TAAAGAAAATAAAAA
1 TAAAGAAAATAAAAA
1202369 TAAA-AAAATAAAAA
1 TAAAGAAAATAAAAA
**
1202383 GGAAGAAAATAA
1 TAAAGAAAATAA
1202395 TGATTGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (15 bp):
TAAAGAAAATAAAAA
Found at i:1202540 original size:59 final size:58
Alignment explanation
Indices: 1202414--1202747 Score: 351
Period size: 59 Copynumber: 5.7 Consensus size: 58
1202404 TTGTGTAGAA
* * *
1202414 AAAATTGATACTTTCAACTTTTCCTCAAAAAATGATTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTT-CTCCAAAAAT-A-TTTTTTGGAAAATTTATTTTTAAGG
* *
1202475 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTTATTTTTGAGG
1 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAA-ATTTATTTTTAAGG
** * *
1202534 AAAATTGATACTTTCAACTTTTC-CTCAAAAACCTTTTTT-AAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCTC-CAAAAATATTTTTTGGAAAATTTATTTTTAAGG
* * **
1202591 AAAATTAATACTTTCAACTTTT-TCCCAAAAATATTTTTT-GAAAACTTTAATTTCGA-G
1 AAAATTGATACTTTCAACTTTTCT-CCAAAAATATTTTTTGGAAAA-TTTATTTTTAAGG
* * *
1202648 AGAAATTGATACTTTCAAC-TTTCCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTTTAA-G
1 A-AAATTGATACTTTCAACTTTTCTC-CAAAAA-TATTTTTTGGAAAATTTA--TTTTTAAGG
1202709 AAAATTGATACTTTCAACTTTT-TCCCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCT-CCAAAAATATTTTTT
1202748 TTATTTTATT
Statistics
Matches: 232, Mismatches: 27, Indels: 30
0.80 0.09 0.10
Matches are distributed among these distances:
57 53 0.23
58 45 0.19
59 65 0.28
60 37 0.16
61 32 0.14
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAAATTTATTTTTAAGG
Found at i:1202593 original size:116 final size:114
Alignment explanation
Indices: 1202414--1202747 Score: 474
Period size: 116 Copynumber: 2.8 Consensus size: 114
1202404 TTGTGTAGAA
*
1202414 AAAATTGATACTTTCAACTTTTCCTCAAAAAATGATTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 AAAATTGATACTTTCAACTTTTCCTC--AAAA--ACTTTTTTTGAAAATTTATTTTTAAGAAAAA
* * *
1202479 TTGATACTTTCAAC-TTTTCTCCAAAAATATTTTTTGGAAACTTTTATTTTTGAGG
62 TTGATACTTTCAACTTTTTC-CCAAAAATATTTTTTGAAAAC-TTTAATTTCGA-G
* * *
1202534 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTAAAAATTTATTTTTAAGAAAAATTAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATTGA
1202599 TACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAG
66 TACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAG
*
1202648 AGAAATTGATACTTTCAACTTTCCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTTTAAG-AAA
1 A-AAATTGATACTTTCAACTTTTCCTCAAAAAC--TTTTTTTGAAAATTTA--TTTTTAAGAAAA
1202712 ATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
61 ATTGATACTTTCAACTTTTTCCCAAAAATATTTTTT
1202748 TTATTTTATT
Statistics
Matches: 197, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
114 2 0.01
115 39 0.20
116 61 0.31
117 19 0.10
118 42 0.21
119 8 0.04
120 26 0.13
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTAATTTCGAG
Found at i:1202771 original size:5 final size:5
Alignment explanation
Indices: 1202763--1202866 Score: 81
Period size: 5 Copynumber: 20.6 Consensus size: 5
1202753 TTATTTAAAG
*
1202763 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT AAAAT
* * * *
1202809 AAAAA AAAAGT AAAAC AAAA- AATA- AAAAT AAAAT AAAGAT AAAAT AATAT
1 AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT
*
1202859 TAAAT AAA
1 AAAAT AAA
1202867 CCTAATCTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
3 3 0.04
4 6 0.08
5 51 0.64
6 16 0.20
7 4 0.05
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1202805 original size:28 final size:28
Alignment explanation
Indices: 1202762--1202845 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 28
1202752 TTTATTTAAA
*
1202762 GAAAATAAAATAATAAAACAAAATAAAAGT
1 GAAAAT-AAA-AATAAAATAAAATAAAAGT
*
1202792 GAAAATAAAAATAAAATAAAAAAAAAGT
1 GAAAATAAAAATAAAATAAAATAAAAGT
*
1202820 -AAAACAAAAAATAAAAATAAAATAAA
1 GAAAA-TAAAAAT-AAAATAAAATAAA
1202846 GATAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.08
28 23 0.48
29 15 0.31
30 6 0.12
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (28 bp):
GAAAATAAAAATAAAATAAAATAAAAGT
Found at i:1202809 original size:11 final size:11
Alignment explanation
Indices: 1202763--1202855 Score: 98
Period size: 11 Copynumber: 8.1 Consensus size: 11
1202753 TTATTTAAAG
1202763 AAAATAAAATAA
1 AAAATAAAAT-A
*
1202775 TAAAACAAAATA
1 -AAAATAAAATA
*
1202787 AAAGTGAAAATA
1 AAAAT-AAAATA
1202799 AAAATAAAATA
1 AAAATAAAATA
1202810 AAAA-AAAAGTA
1 AAAATAAAA-TA
*
1202821 AAACAAAAAATA
1 AAA-ATAAAATA
1202833 AAAATAAAATA
1 AAAATAAAATA
*
1202844 AAGATAAAATA
1 AAAATAAAATA
1202855 A
1 A
1202856 TATTAAATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.06
11 36 0.51
12 17 0.24
13 13 0.19
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1202831 original size:34 final size:35
Alignment explanation
Indices: 1202763--1202845 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
1202753 TTATTTAAAG
***
1202763 AAAATAAAATAATAAAACAAAATAAAAGTGAAAATA
1 AAAATAAAATAA-AAAACAAAATAAAACAAAAAATA
*
1202799 AAAATAAAATAAAAAA-AAAGTAAAACAAAAAATA
1 AAAATAAAATAAAAAACAAAATAAAACAAAAAATA
1202833 AAAATAAAATAAA
1 AAAATAAAATAAA
1202846 GATAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 27 0.63
35 4 0.09
36 12 0.28
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (35 bp):
AAAATAAAATAAAAAACAAAATAAAACAAAAAATA
Found at i:1202846 original size:28 final size:26
Alignment explanation
Indices: 1202758--1202852 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 26
1202748 TTATTTTATT
*
1202758 TAAAG-AAAATAAAATAATAAAACAAAA
1 TAAAGTAAAA-AAAA-AATAAAATAAAA
*
1202785 TAAAAGTGAAAATAAAAATAAAATAAAAA
1 T-AAAGT-AAAAAAAAAATAAAAT-AAAA
*
1202814 AAAAGTAAAACAAAAAATAAAAATAAAA
1 TAAAGTAAAA-AAAAAAT-AAAATAAAA
1202842 TAAAGATAAAA
1 TAAAG-TAAAA
1202853 TAATATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 5 0.09
28 30 0.54
29 17 0.30
30 4 0.07
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (26 bp):
TAAAGTAAAAAAAAAATAAAATAAAA
Found at i:1203806 original size:25 final size:25
Alignment explanation
Indices: 1203773--1203834 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
1203763 GAAAATAATA
* *
1203773 ATAAGATAAATCAACAATATTATA-AG
1 ATAA-ATAAATAAACAATAATA-ACAG
* *
1203799 ATAAATAAAAAAATAATAATAACAG
1 ATAAATAAATAAACAATAATAACAG
1203824 ATAAATAAATA
1 ATAAATAAATA
1203835 TATAATTAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 25 0.83
26 4 0.13
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (25 bp):
ATAAATAAATAAACAATAATAACAG
Found at i:1203949 original size:28 final size:28
Alignment explanation
Indices: 1203900--1203980 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 28
1203890 GGAAAAATAA
* *
1203900 AATAAAAATATATATATTAATAAATAGT
1 AATAAAAATAAATATATAAATAAATAGT
* *
1203928 AATAATAAATAAATA-ATAAATACATAGG
1 AATAA-AAATAAATATATAAATAAATAGT
* *
1203956 ATATAAAGGA-AAATATATACATAAA
1 A-ATAAA-AATAAATATATAAATAAA
1203981 ATATAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 22 0.52
29 20 0.48
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.28
Consensus pattern (28 bp):
AATAAAAATAAATATATAAATAAATAGT
Found at i:1203993 original size:25 final size:25
Alignment explanation
Indices: 1203942--1204016 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
1203932 ATAAATAAAT
* ** **
1203942 AATAAATACATAGGATATAAAGGAA
1 AATATATACATAAAATATAAAACAA
*
1203967 AATATATACATAAAATATAAAATAA
1 AATATATACATAAAATATAAAACAA
*
1203992 AA-AT-GACA-AAAATATAAAACAA
1 AATATATACATAAAATATAAAACAA
1204014 AAT
1 AAT
1204017 TGGGCTTACC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 15 0.36
23 3 0.07
24 2 0.05
25 22 0.52
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (25 bp):
AATATATACATAAAATATAAAACAA
Found at i:1204527 original size:253 final size:253
Alignment explanation
Indices: 1204079--1204587 Score: 860
Period size: 253 Copynumber: 2.0 Consensus size: 253
1204069 GGTGTCTACA
1204079 ATATTGATGCACATATTTTATTCTCTTTTTTACAAATTTTATTAATTGTTTTATTAATTTTTATT
1 ATATTGATGCACATATTTTATTCTCTTTTTTACAAATTTTATTAATTGTTTTATTAATTTTTATT
* *
1204144 TTTGATTTAAATTTTTGAAGAAAAAATGAATTTTTATTATATTGAAGGTTTTCTATAAATATTTC
66 TTTAATTTAAATTTTTGAAGAAAAAAGGAATTTTTATTATATTGAAGGTTTTCTATAAATATTTC
*
1204209 AATATACTGACAATATTTTTTTTAAAAAAATTTTTACCTAGAGATTTCGTAAAGTATCACTACTC
131 AATACACTGACAATA-TTTTTTTAAAAAAATTTTTACCTAGAGATTTCGTAAAGTATCACTACTC
*
1204274 GAAATACTTTAAAAATCTCATCATTGGATAAAAATTT-TTTTTTCTTATTTATATTACT
195 GAAATACTTTAAAAATCCCATCATTGGATAAAAATTTCTTTTTTCTTATTTATATTACT
*
1204332 ATATTGATGCACATATTTTATTCTCTTTTTTAGAAATTTTATTAATTGTTTTATTAATTTTTATT
1 ATATTGATGCACATATTTTATTCTCTTTTTTACAAATTTTATTAATTGTTTTATTAATTTTTATT
* *
1204397 TTTAATTTAAATTTTTGAAGAAAAAAGGAATTTTTATTATATTGAAGGTTTTTTATAAATATTTT
66 TTTAATTTAAATTTTTGAAGAAAAAAGGAATTTTTATTATATTGAAGGTTTTCTATAAATATTTC
** *
1204462 AATACACTGGTAATA-TTTTTTAAAAAAATTTTCTCACCTAGGGATTTCGTAAAGTATCACTACT
131 AATACACTGACAATATTTTTTTAAAAAAATTTT-T-ACCTAGAGATTTCGTAAAGTATCACTACT
* * *
1204526 CGAAATACTTTTAAAATCCCATCATTGGATAGAATTTTCTTTTTTCTTATTTATATTACT
194 CGAAATACTTTAAAAATCCCATCATTGGATAAAAATTTCTTTTTTCTTATTTATATTACT
1204586 AT
1 AT
1204588 TTTTAATAAT
Statistics
Matches: 240, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
251 17 0.07
252 1 0.00
253 199 0.83
254 23 0.10
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (253 bp):
ATATTGATGCACATATTTTATTCTCTTTTTTACAAATTTTATTAATTGTTTTATTAATTTTTATT
TTTAATTTAAATTTTTGAAGAAAAAAGGAATTTTTATTATATTGAAGGTTTTCTATAAATATTTC
AATACACTGACAATATTTTTTTAAAAAAATTTTTACCTAGAGATTTCGTAAAGTATCACTACTCG
AAATACTTTAAAAATCCCATCATTGGATAAAAATTTCTTTTTTCTTATTTATATTACT
Found at i:1205735 original size:23 final size:23
Alignment explanation
Indices: 1205704--1205754 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1205694 ATTTATAAAG
*
1205704 TTTTTTGGGATTCAAATCTCAGA
1 TTTTCTGGGATTCAAATCTCAGA
* *
1205727 TTTTCTGGGATTCGAATCTCATA
1 TTTTCTGGGATTCAAATCTCAGA
1205750 TTTTC
1 TTTTC
1205755 AACTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (23 bp):
TTTTCTGGGATTCAAATCTCAGA
Found at i:1205920 original size:3 final size:3
Alignment explanation
Indices: 1205914--1205953 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1205904 GAAAAAAAAC
*
1205914 TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1205954 AAAAATAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1206212 original size:49 final size:49
Alignment explanation
Indices: 1206159--1206452 Score: 227
Period size: 49 Copynumber: 5.8 Consensus size: 49
1206149 ATTATAAAAA
** * *
1206159 AAAAAACTCCTTTAAGTAGAGCCTCAACAACTTTAAAAATCTCATCTTG
1 AAAAAACTCCTCCAAGCAGAGACTCAACAACTTTAAAAATCTCATCTTG
* *
1206208 AAAAAGCTCCTCTCAA-CAGAGGCTCAACAACTTTAAAAATCTCATCTTG
1 AAAAAACTCCTC-CAAGCAGAGACTCAACAACTTTAAAAATCTCATCTTG
* * * * * * *
1206257 AAAAAATTTCTCCCAGCAAAGACTCAACAATTTTAAAATTCATCATCTTA
1 AAAAAACTCCTCCAAGCAGAGACTCAACAACTTTAAAAATC-TCATCTTG
* * * ** *
1206307 AAAAAAGCTCCACTAAGCAAAGGTTCAACAACTTTAAAGAAATTCTCATTTTG
1 AAAAAA-CTCCTCCAAGCAGAGACTCAACAACTTT-AA-AAA-TCTCATCTTG
* * * *
1206360 AAAAAGCTTCTCTCAA-CAGAGACTCAATAACTTTAAAAAAATTCTCATATTG
1 AAAAAACTCCTC-CAAGCAGAGACTCAACAACTTT--AAAAA-TCTCATCTTG
* *
1206412 ACAAAGCTCCTCTC-AGCAGA-AGCTCAACAACTTTAAAAATC
1 AAAAAACTCCTC-CAAGCAGAGA-CTCAACAACTTTAAAAATC
1206453 CATATGTTCT
Statistics
Matches: 197, Mismatches: 37, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
48 2 0.01
49 73 0.37
50 20 0.10
51 22 0.11
52 60 0.30
53 18 0.09
54 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.27
Consensus pattern (49 bp):
AAAAAACTCCTCCAAGCAGAGACTCAACAACTTTAAAAATCTCATCTTG
Found at i:1206383 original size:103 final size:98
Alignment explanation
Indices: 1206176--1206452 Score: 279
Period size: 103 Copynumber: 2.7 Consensus size: 98
1206166 TCCTTTAAGT
* * * *
1206176 AGAGCCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTT
1 AGAGACTCAACAACTTTAAAAATCTCATCTTAAAAAAGCTCCACTCAACAAAGGCTCAACAACTT
* *
1206241 TAAAAATCTCATCTTGAAAAAATTTCTCCCAGC
66 TAAAAATCTCATCTTGAAAAAACTTCTCCCAAC
* * * *
1206274 AAAGACTCAACAATTTTAAAATTCATCATCTTAAAAAAAGCTCCACT-AAGCAAAGGTTCAACAA
1 AGAGACTCAACAACTTTAAAAATC-TCATCTT-AAAAAAGCTCCACTCAA-CAAAGGCTCAACAA
* * *
1206338 CTTTAAAGAAATTCTCATTTTGAAAAAGCTTCTCTCAAC
63 CTTT-AA-AAA-TCTCATCTTGAAAAAACTTCTCCCAAC
* * * * * *
1206377 AGAGACTCAATAACTTTAAAAAAATTCTCATATTGACAAAGCTCCTCTCAGCAGAA-GCTCAACA
1 AGAGACTCAACAACTTT--AAAAA-TCTCATCTTAAAAAAGCTCCACTCAACA-AAGGCTCAACA
1206441 ACTTTAAAAATC
62 ACTTTAAAAATC
1206453 CATATGTTCT
Statistics
Matches: 145, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
98 20 0.14
99 9 0.06
100 28 0.19
101 4 0.03
102 6 0.04
103 38 0.26
104 25 0.17
105 13 0.09
106 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (98 bp):
AGAGACTCAACAACTTTAAAAATCTCATCTTAAAAAAGCTCCACTCAACAAAGGCTCAACAACTT
TAAAAATCTCATCTTGAAAAAACTTCTCCCAAC
Found at i:1206392 original size:52 final size:50
Alignment explanation
Indices: 1206176--1206451 Score: 265
Period size: 52 Copynumber: 5.5 Consensus size: 50
1206166 TCCTTTAAGT
*
1206176 AGAGCCTCAACAACTTTAAAAA-TCTCATCTTGAAAAAGCTCCTCTCAAC
1 AGAGACTCAACAACTTTAAAAATTCTCATCTTGAAAAAGCTCCTCTCAAC
* ** * * *
1206225 AGAGGCTCAACAACTTTAAAAA-TCTCATCTTGAAAAAATTTCTCCCAGC
1 AGAGACTCAACAACTTTAAAAATTCTCATCTTGAAAAAGCTCCTCTCAAC
* * * *
1206274 AAAGACTCAACAA-TTTTAAAATTCATCATCTTAAAAAAAGCTCCACT-AAGC
1 AGAGACTCAACAACTTTAAAAATTC-TCATCTT-GAAAAAGCTCCTCTCAA-C
* ** * *
1206325 AAAGGTTCAACAACTTTAAAGAAATTCTCATTTTGAAAAAGCTTCTCTCAAC
1 AGAGACTCAACAACTTT-AA-AAATTCTCATCTTGAAAAAGCTCCTCTCAAC
* * * *
1206377 AGAGACTCAATAACTTTAAAAAAATTCTCATATTGACAAAGCTCCTCTCAGC
1 AGAGACTCAACAACTTT--AAAAATTCTCATCTTGAAAAAGCTCCTCTCAAC
1206429 AGA-AGCTCAACAACTTTAAAAAT
1 AGAGA-CTCAACAACTTTAAAAAT
1206452 CCATATGTTC
Statistics
Matches: 185, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
48 7 0.04
49 56 0.30
50 14 0.08
51 21 0.11
52 69 0.37
53 12 0.06
54 6 0.03
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (50 bp):
AGAGACTCAACAACTTTAAAAATTCTCATCTTGAAAAAGCTCCTCTCAAC
Found at i:1217888 original size:27 final size:27
Alignment explanation
Indices: 1217839--1217894 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1217829 TCGGTGTTTC
* *
1217839 AAAAATAATTTTCTTGATTTATTTATT
1 AAAAATAATTTTCTTAATGTATTTATT
* * *
1217866 AAAAATTATTTTTTTAATGTATTTTTT
1 AAAAATAATTTTCTTAATGTATTTATT
1217893 AA
1 AA
1217895 TGCTCAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
AAAAATAATTTTCTTAATGTATTTATT
Found at i:1222058 original size:6 final size:6
Alignment explanation
Indices: 1222048--1222085 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1222038 TAAGTCCAAA
*
1222048 TGATGA TGATGG TGATGG TGATGG TGATGG TGATGG TG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TG
1222086 TAAATTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:1222492 original size:18 final size:18
Alignment explanation
Indices: 1222429--1222491 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
1222419 TATCCACAAA
1222429 AAATGTATCATCTACCTC
1 AAATGTATCATCTACCTC
* *
1222447 AAATGTATCATTTACCAC
1 AAATGTATCATCTACCTC
* *
1222465 AAATATATC-TCCCACCTC
1 AAATGTATCAT-CTACCTC
1222483 AAATGTATC
1 AAATGTATC
1222492 TAGAATAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
17 1 0.03
18 36 0.97
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATGTATCATCTACCTC
Found at i:1222887 original size:6 final size:6
Alignment explanation
Indices: 1222876--1222903 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1222866 ATAAGAGTTT
1222876 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
1222904 TACATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:1228959 original size:16 final size:16
Alignment explanation
Indices: 1228938--1228968 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1228928 ATAATTAAAA
*
1228938 TTTAAATTCTGATAAT
1 TTTAAATTCTAATAAT
1228954 TTTAAATTCTAATAA
1 TTTAAATTCTAATAA
1228969 AAAATTATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTAAATTCTAATAAT
Found at i:1235243 original size:24 final size:21
Alignment explanation
Indices: 1235195--1235252 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1235185 AGCTGTCTCC
1235195 TCTTCTTCTTGCTTCTTTTTA
1 TCTTCTTCTTGCTTCTTTTTA
*
1235216 TCTTCTTCTTGTTTCCTTTTT-
1 TCTTCTTCTTGCTT-CTTTTTA
*
1235237 GCTTCTTCTT-CTTCTT
1 TCTTCTTCTTGCTTCTT
1235253 GCTTCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 22 0.67
22 6 0.18
ACGTcount: A:0.02, C:0.26, G:0.05, T:0.67
Consensus pattern (21 bp):
TCTTCTTCTTGCTTCTTTTTA
Found at i:1237167 original size:13 final size:14
Alignment explanation
Indices: 1237151--1237184 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1237141 AATTAAATGT
1237151 ATTAATTT-TAAAA
1 ATTAATTTATAAAA
1237164 ATTAATTTATAAAA
1 ATTAATTTATAAAA
*
1237178 TTTAATT
1 ATTAATT
1237185 AAATTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAATTTATAAAA
Found at i:1237401 original size:22 final size:22
Alignment explanation
Indices: 1237365--1237417 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1237355 ATATTTTGAG
*
1237365 TTTTATATTTAAATTTT-ATTATA
1 TTTTA-ATTAAAATTTTAATTA-A
1237388 TTTTAATTAAAATTTTAATTAA
1 TTTTAATTAAAATTTTAATTAA
*
1237410 TTTAAATT
1 TTTTAATT
1237418 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAATTAAAATTTTAATTAA
Found at i:1237409 original size:16 final size:17
Alignment explanation
Indices: 1237390--1237431 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1237380 TTATTATATT
1237390 TTAATTAAAATTTT-AA
1 TTAATTAAAATTTTAAA
*
1237406 TTAATTTAAATTTTAAA
1 TTAATTAAAATTTTAAA
1237423 TTAAATTAA
1 TT-AATTAA
1237432 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
17 4 0.18
18 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAATTTTAAA
Found at i:1237438 original size:10 final size:10
Alignment explanation
Indices: 1237421--1237490 Score: 54
Period size: 11 Copynumber: 6.6 Consensus size: 10
1237411 TTAAATTTTA
1237421 AATT-AAATT
1 AATTAAAATT
1237430 AATTAAAATTT
1 AATTAAAA-TT
*
1237441 ATTTAAAATT
1 AATTAAAATT
*
1237451 ATTTTTAATAA-T
1 A--ATTAA-AATT
1237463 AATTAAAATT
1 AATTAAAATT
1237473 AATTTAATAATT
1 AA-TTAA-AATT
1237485 AATTAA
1 AATTAA
1237491 TTGATTGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
9 6 0.12
10 13 0.25
11 17 0.33
12 13 0.25
13 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTAAAATT
Found at i:1237470 original size:22 final size:22
Alignment explanation
Indices: 1237404--1237490 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
1237394 TTAAAATTTT
*
1237404 AATTAATTTAA-ATTTTAAATT-A
1 AATTAATTTAATA-ATT-AATTAA
*
1237426 AATTAA-TTAA-AATTTATTTAA
1 AATTAATTTAATAA-TTAATTAA
*
1237447 AATTATTTTTAATAA-TAATTAA
1 AATTA-ATTTAATAATTAATTAA
1237469 AATTAATTTAATAATTAATTAA
1 AATTAATTTAATAATTAATTAA
1237491 TTGATTGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.06
21 21 0.39
22 24 0.44
23 4 0.07
24 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTAATTTAATAATTAATTAA
Found at i:1237776 original size:23 final size:24
Alignment explanation
Indices: 1237745--1237810 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
1237735 TTTTAGTGTC
* * *
1237745 AAAAAATAATATAAT-ATAATTTT
1 AAAAAATAAAAAAATAAAAATTTT
*
1237768 AAAATATAAAAAAATAAAAATTTT
1 AAAAAATAAAAAAATAAAAATTTT
* * *
1237792 AAATATTCAAAAAATAAAA
1 AAAAAATAAAAAAATAAAA
1237811 TGATAAATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAAATAAAAAAATAAAAATTTT
Found at i:1237794 original size:24 final size:24
Alignment explanation
Indices: 1237762--1237810 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1237752 AATATAATAT
1237762 AATTTTAAA-ATATAAAAAAATAAA
1 AATTTTAAATAT-TAAAAAAATAAA
*
1237786 AATTTTAAATATTCAAAAAATAAA
1 AATTTTAAATATTAAAAAAATAAA
1237810 A
1 A
1237811 TGATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AATTTTAAATATTAAAAAAATAAA
Found at i:1237809 original size:32 final size:34
Alignment explanation
Indices: 1237768--1237848 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 34
1237758 ATATAATTTT
* *
1237768 AAAATATAAAAAAATAAA-AATTTT-AAATATTC
1 AAAAAATAAAAAAATAAATAATTTTGAAATATTA
**
1237800 AAAAAATAAAATGATAAATAATTTTGAAATATTA
1 AAAAAATAAAAAAATAAATAATTTTGAAATATTA
*
1237834 AAAAAAAAGAAAAAA
1 AAAAAATA-AAAAAA
1237849 ACAGAGATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 15 0.38
33 6 0.15
34 14 0.36
35 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (34 bp):
AAAAAATAAAAAAATAAATAATTTTGAAATATTA
Found at i:1237811 original size:23 final size:23
Alignment explanation
Indices: 1237757--1237811 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1237747 AAAATAATAT
*
1237757 AATATAATTTTAAAATATAAAAA
1 AATAAAATTTTAAAATATAAAAA
*
1237780 AATAAAAATTTT-AAATATTCAAAA
1 AAT-AAAATTTTAAAATA-TAAAAA
1237804 AATAAAAT
1 AATAAAAT
1237812 GATAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAAATTTTAAAATATAAAAA
Found at i:1241631 original size:1 final size:1
Alignment explanation
Indices: 1241627--1241651 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1241617 CTTGGGGTAG
1241627 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1241652 ATACAAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1242352 original size:18 final size:18
Alignment explanation
Indices: 1242315--1242352 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1242305 ATTCACATCT
* *
1242315 TCTTCAAATTCTTCTTCC
1 TCTTCAAATTCATCTCCC
1242333 TCTTCAAATTCATCTCCC
1 TCTTCAAATTCATCTCCC
1242351 TC
1 TC
1242353 AATCACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.37, G:0.00, T:0.45
Consensus pattern (18 bp):
TCTTCAAATTCATCTCCC
Found at i:1249820 original size:21 final size:20
Alignment explanation
Indices: 1249792--1249830 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1249782 GGATCTAAGG
1249792 ATTTTTGTCCT-TCATTTTCC
1 ATTTTTGT-CTATCATTTTCC
1249812 ATTTCTTGTCTATCATTTT
1 ATTT-TTGTCTATCATTTT
1249831 TTTGGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.21, G:0.05, T:0.62
Consensus pattern (20 bp):
ATTTTTGTCTATCATTTTCC
Found at i:1251159 original size:18 final size:19
Alignment explanation
Indices: 1251131--1251170 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1251121 CAATCTTAAA
*
1251131 ATTATTAATATATGTAATT
1 ATTATTAATATATATAATT
1251150 ATTA-TAATATATATAATT
1 ATTATTAATATATATAATT
1251168 ATT
1 ATT
1251171 TTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTATTAATATATATAATT
Found at i:1258054 original size:15 final size:15
Alignment explanation
Indices: 1258034--1258072 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1258024 TTTATCAATA
*
1258034 TATTAATATATTATT
1 TATTAATATAATATT
1258049 TATTAATATAATATT
1 TATTAATATAATATT
1258064 TATATAATA
1 TAT-TAATA
1258073 AAAATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTAATATAATATT
Found at i:1274191 original size:21 final size:19
Alignment explanation
Indices: 1274167--1274221 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1274157 ATTAATTACC
*
1274167 TTTTTTATTTATGTTTTGAAA
1 TTTTTTATTTAT-TATT-AAA
*
1274188 TTTTTAATTTATTATTAAA
1 TTTTTTATTTATTATTAAA
*
1274207 TCTTTTATTTTATTA
1 TTTTTTA-TTTATTA
1274222 CATATTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 10 0.34
21 11 0.38
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTTATTTATTATTAAA
Found at i:1274193 original size:20 final size:18
Alignment explanation
Indices: 1274168--1274221 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
1274158 TTAATTACCT
*
1274168 TTTTTATTTATGTTTTGAAA
1 TTTTTATTTAT-TATT-AAA
1274188 TTTTTAATTTATTATTAAA
1 TTTTT-ATTTATTATTAAA
1274207 TCTTTTATTTTATTA
1 T-TTTTA-TTTATTA
1274222 CATATTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.17
20 19 0.63
21 6 0.20
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTATTTATTATTAAA
Found at i:1274765 original size:46 final size:46
Alignment explanation
Indices: 1274657--1274839 Score: 201
Period size: 46 Copynumber: 3.9 Consensus size: 46
1274647 TATTTAGATC
* * ** * *
1274657 TTTTTTATTTCTAAATTTTTCACAATTT-AGGTTTATTTATAAATTT
1 TTTTTTATTTTTAAATTTTTCACCATTTGA-GCCTATTTAGAAAATT
*
1274703 TCTTTTTAATTTTTAAAATTTTCACCATTTGAGCCTATTTAGAAAATT
1 T-TTTTT-ATTTTTAAATTTTTCACCATTTGAGCCTATTTAGAAAATT
* *
1274751 TTTTTTATTTTTAAATTTTTCAACATTT-AGGCCTATTTAG-AATTT
1 TTTTTTATTTTTAAATTTTTCACCATTTGA-GCCTATTTAGAAAATT
* *
1274796 TTTTTTAATTTTTAAATTTTTCATCATTTGAGTCTATTTAGAAA
1 TTTTTT-ATTTTTAAATTTTTCACCATTTGAGCCTATTTAGAAA
1274840 TTCTCTCTCT
Statistics
Matches: 118, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
45 11 0.09
46 61 0.52
47 13 0.11
48 32 0.27
49 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (46 bp):
TTTTTTATTTTTAAATTTTTCACCATTTGAGCCTATTTAGAAAATT
Found at i:1274826 original size:92 final size:94
Alignment explanation
Indices: 1274657--1274839 Score: 273
Period size: 92 Copynumber: 2.0 Consensus size: 94
1274647 TATTTAGATC
**
1274657 TTTTTTATTTCTAAATTTTTCACAATTTAGGTTTATTTATAAATTTTCTTTTTAATTTTTAAAAT
1 TTTTTTATTTCTAAATTTTTCACAATTTAGGCCTATTTATAAATTTTCTTTTTAATTTTTAAAAT
1274722 TTTCACCATTTGAGCCTATTTAGAAAATT
66 TTTCACCATTTGAGCCTATTTAGAAAATT
* * *
1274751 TTTTTTATTTTTAAATTTTTCA-ACATTTAGGCCTATTTA-GAATTTT-TTTTTAATTTTTAAAT
1 TTTTTTATTTCTAAATTTTTCACA-ATTTAGGCCTATTTATAAATTTTCTTTTTAATTTTTAAAA
* *
1274813 TTTTCATCATTTGAGTCTATTTAGAAA
65 TTTTCACCATTTGAGCCTATTTAGAAA
1274840 TTCTCTCTCT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
92 40 0.49
93 7 0.09
94 34 0.42
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (94 bp):
TTTTTTATTTCTAAATTTTTCACAATTTAGGCCTATTTATAAATTTTCTTTTTAATTTTTAAAAT
TTTCACCATTTGAGCCTATTTAGAAAATT
Found at i:1274848 original size:2 final size:2
Alignment explanation
Indices: 1274841--1274873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1274831 ATTTAGAAAT
1274841 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
1274874 TTAATCTTTG
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:1275356 original size:4 final size:4
Alignment explanation
Indices: 1275347--1275373 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1275337 TACACAAAGA
1275347 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1275374 ATACCAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1286559 original size:59 final size:56
Alignment explanation
Indices: 1286373--1286697 Score: 379
Period size: 59 Copynumber: 5.6 Consensus size: 56
1286363 TCTCGTGTAG
*
1286373 GGAAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCT-CAAAAAT-TTTTTTGAAAATTTATTTTTAA
* *
1286430 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-A-TTTTTTTGAAAATTT-ATTTTTAA
1286490 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA---TTTTTTTGAAAATTTATTTTTAA
* * *
1286549 GGAAAATTGATACTTTCAATTTTTTCCT-AAAAATATTTTTGAGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAA-CTTTTCCTCAAAAATTTTTTTGA-AAA-TTT-ATTTTTAA
* * **
1286608 AGAAAATTAATACTTTCAACTTTTCCTCAAAAACCCTTTTTG-AAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-TTTTTTTGAAAATTTATTTTTAA
* *
1286664 GAAAAATTGACACTTTCAACTTTTTCCT-AAAAAT
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAAT
1286698 ATCTTTTTTA
Statistics
Matches: 234, Mismatches: 20, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
56 36 0.15
57 38 0.16
58 19 0.08
59 78 0.33
60 63 0.27
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAAATTTATTTTTAA
Found at i:1286629 original size:118 final size:118
Alignment explanation
Indices: 1286374--1286721 Score: 505
Period size: 118 Copynumber: 3.0 Consensus size: 118
1286364 CTCGTGTAGG
*
1286374 GAAAATTGATACTTTCAACTTTT-TTCCAAAAA---TATTTTTTGAAAATTTATTTTTAAGGAAA
1 GAAAATTGATACTTTCAACTTTTCCT-CAAAAACCCT-TTTTTTGAAAATTTATTTTTAAGGAAA
* * *
1286435 ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTGATTTTCAAG
64 ATTGATACTTTCAATTTTTCCT-AAAAATATTTTTTTAGAAATTTTGATTTTCAAA
1286491 GAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGGAAAAT
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGGAAAAT
*
1286556 TGATACTTTCAATTTTTTCCTAAAAATA-TTTTTGAGAAATTTTGATTTTCAAA
66 TGATACTTTCAA-TTTTTCCTAAAAATATTTTTTTAGAAATTTTGATTTTCAAA
* *
1286609 GAAAATTAATACTTTCAACTTTTCCTCAAAAACCC--TTTTTG-AAATTTATTTTTAAGAAAAAT
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGGAAAAT
* *
1286671 TGACACTTTCAACTTTTTCCTAAAAATATCTTTTTTATAAATTTTGATTTT
66 TGATACTTTCAA-TTTTTCCTAAAAATAT-TTTTTTAGAAATTTTGATTTT
1286722 TATTTAAAGA
Statistics
Matches: 213, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
115 46 0.22
116 6 0.03
117 48 0.23
118 57 0.27
119 48 0.23
120 8 0.04
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (118 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGGAAAAT
TGATACTTTCAATTTTTCCTAAAAATATTTTTTTAGAAATTTTGATTTTCAAA
Found at i:1286761 original size:17 final size:17
Alignment explanation
Indices: 1286741--1286798 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1286731 AAAATAGAAT
1286741 AATAAAAAATAAATAAA
1 AATAAAAAATAAATAAA
* *
1286758 AATAAAGAATAAAGAAA
1 AATAAAAAATAAATAAA
*
1286775 AGTAAAACAA-AAATAAA
1 AATAAAA-AATAAATAAA
1286792 AATAAAA
1 AATAAAA
1286799 TAAAGATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 32 0.94
18 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (17 bp):
AATAAAAAATAAATAAA
Found at i:1286775 original size:27 final size:27
Alignment explanation
Indices: 1286744--1286809 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1286734 ATAGAATAAT
*
1286744 AAAAAATAAAT-AAAAATAAAGAATAA
1 AAAAAATAAAACAAAAATAAAGAATAA
*
1286770 AGAAAAGTAAAACAAAAATAAA-AATAA
1 A-AAAAATAAAACAAAAATAAAGAATAA
1286797 AATAAAGATAAAA
1 AA-AAA-ATAAAA
1286810 AGAATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 17 0.52
28 14 0.42
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.14
Consensus pattern (27 bp):
AAAAAATAAAACAAAAATAAAGAATAA
Found at i:1286781 original size:34 final size:34
Alignment explanation
Indices: 1286726--1286804 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
1286716 GATTTTTATT
1286726 TAAAGAA-AATAGAATAATAAAA-AATAAATAAAAA
1 TAAAGAATAA-AGAATAATAAAACAA-AAATAAAAA
1286760 TAAAGAATAAAGAA-AAGTAAAACAAAAATAAAAA
1 TAAAGAATAAAGAATAA-TAAAACAAAAATAAAAA
1286794 T-AA-AATAAAGA
1 TAAAGAATAAAGA
1286805 TAAAAAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
32 8 0.19
33 4 0.10
34 26 0.62
35 4 0.10
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (34 bp):
TAAAGAATAAAGAATAATAAAACAAAAATAAAAA
Found at i:1286807 original size:11 final size:11
Alignment explanation
Indices: 1286745--1286809 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
1286735 TAGAATAATA
1286745 AAAAAT-AAAT
1 AAAAATAAAAT
1286755 AAAAATAAAGAAT
1 AAAAAT-AA-AAT
* *
1286768 AAAGA-AAAGT
1 AAAAATAAAAT
1286778 AAAACA-AAAAT
1 AAAA-ATAAAAT
1286789 AAAAATAAAAT
1 AAAAATAAAAT
*
1286800 AAAGATAAAA
1 AAAAATAAAA
1286810 AGAATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
10 12 0.27
11 25 0.56
12 1 0.02
13 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1286807 original size:17 final size:17
Alignment explanation
Indices: 1286753--1286810 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1286743 TAAAAAATAA
1286753 ATAAAAATAAAGAATAAAG
1 ATAAAAAT-AA-AATAAAG
* * *
1286772 --AAAAGTAAAACAAAA
1 ATAAAAATAAAATAAAG
1286787 ATAAAAATAAAATAAAG
1 ATAAAAATAAAATAAAG
1286804 ATAAAAA
1 ATAAAAA
1286811 GAATATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 2 0.06
17 24 0.77
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (17 bp):
ATAAAAATAAAATAAAG
Found at i:1287222 original size:20 final size:20
Alignment explanation
Indices: 1287197--1287245 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1287187 GATTGAAGAT
*
1287197 TCACCGGATTCTGGGTTTTG
1 TCACCGGAATCTGGGTTTTG
*
1287217 TCACCGGAATCTGGGTTTTT
1 TCACCGGAATCTGGGTTTTG
*
1287237 TTACCGGAA
1 TCACCGGAA
1287246 GTTGGTCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (20 bp):
TCACCGGAATCTGGGTTTTG
Found at i:1287724 original size:22 final size:24
Alignment explanation
Indices: 1287693--1287746 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
1287683 AAAAAAAATC
1287693 ATAATAATCAGAT-AATCGAA-AAAA
1 ATAA-AATCAGATAAAT-GAATAAAA
1287717 A-AAAATCAGATAAATGAATAAAA
1 ATAAAATCAGATAAATGAATAAAA
1287740 ATAAAAT
1 ATAAAAT
1287747 TAACAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 11 0.41
23 10 0.37
24 6 0.22
ACGTcount: A:0.67, C:0.06, G:0.07, T:0.20
Consensus pattern (24 bp):
ATAAAATCAGATAAATGAATAAAA
Found at i:1287811 original size:17 final size:17
Alignment explanation
Indices: 1287791--1287836 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1287781 AATATTACAA
1287791 AATAATAATAATATAA-T
1 AATAATAA-AATATAACT
1287808 AATAATAAATATATAACT
1 AATAATAAA-ATATAACT
1287826 -ATAATAAAATA
1 AATAATAAAATA
1287837 CCTATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 22 0.81
18 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAAAATATAACT
Found at i:1287920 original size:10 final size:10
Alignment explanation
Indices: 1287907--1287976 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 10
1287897 AAAGATATAC
*
1287907 ACATATTAAT
1 ACATAATAAT
1287917 ACATAATAAT
1 ACATAATAAT
1287927 A-ATAAATAAAT
1 ACAT-AAT-AAT
1287938 A-ATAA-AAT
1 ACATAATAAT
1287946 ACATAA-AAT
1 ACATAATAAT
* *
1287955 ACAAAAAAAT
1 ACATAATAAT
*
1287965 A-AAAATAAT
1 ACATAATAAT
1287974 ACA
1 ACA
1287977 AGATAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
8 4 0.08
9 22 0.42
10 20 0.38
11 6 0.12
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (10 bp):
ACATAATAAT
Found at i:1287940 original size:14 final size:14
Alignment explanation
Indices: 1287791--1287942 Score: 60
Period size: 14 Copynumber: 11.4 Consensus size: 14
1287781 AATATTACAA
1287791 AATAAT-AATAATAT
1 AATAATAAATAA-AT
1287805 AATAAT-AATAAAT
1 AATAATAAATAAAT
*
1287818 -AT-ATAACTATAAT
1 AATAATAAATA-AAT
*
1287831 AA-AATACCTATAAAT
1 AATAATA--AATAAAT
* * *
1287846 ATTAACAAAAAAAT
1 AATAATAAATAAAT
1287860 GAA-AAT-AA-AAAT
1 -AATAATAAATAAAT
1287872 AA-AATAAATAAAT
1 AATAATAAATAAAT
*
1287885 -A-AATAGATAAAT
1 AATAATAAATAAAT
* * *
1287897 AA-AGATATACACAT
1 AATA-ATAAATAAAT
* *
1287911 ATTAATACAT-AAT
1 AATAATAAATAAAT
1287924 AATAATAAATAAAT
1 AATAATAAATAAAT
1287938 AATAA
1 AATAA
1287943 AATACATAAA
Statistics
Matches: 105, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
11 7 0.07
12 22 0.21
13 23 0.22
14 42 0.40
15 6 0.06
16 5 0.05
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:1289690 original size:18 final size:17
Alignment explanation
Indices: 1289663--1289696 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1289653 TAATATTGCT
1289663 CAAAAAAAGAAGGCATA
1 CAAAAAAAGAAGGCATA
1289680 CAAAAACAAGAAGGCAT
1 CAAAAA-AAGAAGGCAT
1289697 TACCTGCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.15, G:0.18, T:0.06
Consensus pattern (17 bp):
CAAAAAAAGAAGGCATA
Found at i:1292445 original size:2 final size:2
Alignment explanation
Indices: 1292438--1292468 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1292428 ACGCAACACC
1292438 TA TA 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 TA TA T
1292469 CTTGGTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1296989 original size:46 final size:46
Alignment explanation
Indices: 1296922--1297015 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
1296912 CCTTTTTTTC
* *
1296922 TTTTCTGGTAAGTAACTCTATGGTTTATTCAAATGATACGTTCCAT
1 TTTTCTGATAAGTAACTCTATGGGTTATTCAAATGATACGTTCCAT
*
1296968 TTTTCTGATAAGTAACTCTATGGGTTATTCAAATGATATGTTCCAT
1 TTTTCTGATAAGTAACTCTATGGGTTATTCAAATGATACGTTCCAT
1297014 TT
1 TT
1297016 AATATTACTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (46 bp):
TTTTCTGATAAGTAACTCTATGGGTTATTCAAATGATACGTTCCAT
Found at i:1300574 original size:24 final size:23
Alignment explanation
Indices: 1300522--1300575 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1300512 TATGCACATA
* *
1300522 AATAATCATACAAATAGATAAAT
1 AATAAACAAACAAATAGATAAAT
*
1300545 AGATAAACAAACAAATAGATATAT
1 A-ATAAACAAACAAATAGATAAAT
1300569 CAATAAA
1 -AATAAA
1300576 TAAATAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (23 bp):
AATAAACAAACAAATAGATAAAT
Found at i:1301422 original size:29 final size:28
Alignment explanation
Indices: 1301341--1301424 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
1301331 AATCTCAAAT
* **
1301341 ATTTATTTTTATTTAATTGAGTTCTTAA
1 ATTTATTTTTACTTAATTGAACTCTTAA
* * **
1301369 ATATCTATTTGTACCTAATCAAACTCTTAA
1 AT-T-TATTTTTACTTAATTGAACTCTTAA
1301399 CATTTATTTTTACTTAATTGAACTCT
1 -ATTTATTTTTACTTAATTGAACTCT
1301425 CAATTAGATG
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
28 2 0.05
29 19 0.45
30 19 0.45
31 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (28 bp):
ATTTATTTTTACTTAATTGAACTCTTAA
Found at i:1301548 original size:111 final size:111
Alignment explanation
Indices: 1301335--1301536 Score: 284
Period size: 111 Copynumber: 1.8 Consensus size: 111
1301325 ATAATTAATC
* * *
1301335 TCAAATATTTATTTTTATTTAATTGAGTTCTTAAATATCTATTTGTACCTAATCAAACTCTTAAC
1 TCAAATATTTATTTGTATTTAATTGAATTCTTAAACATCTATTTGTACCTAATCAAACTCTTAAC
* *
1301400 ATTTATTTTTACTTAATTGAACTCTCAATTAGATGGAATTGAACCT
66 ATTTATTTTTACCTAATTGAACCCTCAATTAGATGGAATTGAACCT
*
1301446 TCAAATATTTATTTGTATTTAATTGAA-TCTTTAAACATCTATTT-TCATCC-AATTAAACTCTT
1 TCAAATATTTATTTGTATTTAATTGAATTC-TTAAACATCTATTTGT-A-CCTAATCAAACTCTT
*
1301508 AAACATTTATTTTTACCTAATTGAGCCCT
63 -AACATTTATTTTTACCTAATTGAACCCT
1301537 TGTTAGATGG
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
110 3 0.04
111 50 0.62
112 27 0.34
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (111 bp):
TCAAATATTTATTTGTATTTAATTGAATTCTTAAACATCTATTTGTACCTAATCAAACTCTTAAC
ATTTATTTTTACCTAATTGAACCCTCAATTAGATGGAATTGAACCT
Found at i:1302371 original size:2 final size:2
Alignment explanation
Indices: 1302364--1302404 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1302354 TTTTTGTGCT
1302364 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1302405 AGCAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1302467 original size:16 final size:18
Alignment explanation
Indices: 1302433--1302469 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1302423 GAAATGGATT
*
1302433 TTTTTTTCATATTTATAA
1 TTTTTTTCATATATATAA
1302451 TTTTTTTCATA-AT-TAA
1 TTTTTTTCATATATATAA
1302467 TTT
1 TTT
1302470 CCTTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 1 0.06
18 11 0.61
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTTCATATATATAA
Found at i:1302525 original size:12 final size:12
Alignment explanation
Indices: 1302508--1302538 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1302498 ACAATTACGT
*
1302508 TTATTATTGTTA
1 TTATTATTGGTA
1302520 TTATTATTGGTA
1 TTATTATTGGTA
1302532 TTATTAT
1 TTATTAT
1302539 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (12 bp):
TTATTATTGGTA
Found at i:1306747 original size:2 final size:2
Alignment explanation
Indices: 1306740--1306767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1306730 TTTTCTTTTC
1306740 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
1306768 CTCTAGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1307260 original size:46 final size:46
Alignment explanation
Indices: 1307208--1307297 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
1307198 AGCCTATGTG
* *
1307208 ACAATTTCTAACTTTGATGGTAGAGTTTTAAAATTACATTAACATC
1 ACAATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACATC
* * *
1307254 ACAATTTTTAACTTTAATGGTAAAGTTTTTAAATTTCATTAACA
1 ACAATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACA
1307298 ATATGAGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (46 bp):
ACAATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACATC
Found at i:1307312 original size:2 final size:2
Alignment explanation
Indices: 1307305--1307333 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1307295 ACAATATGAG
1307305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1307334 AAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1307340 original size:2 final size:2
Alignment explanation
Indices: 1307335--1307360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1307325 ATATATATAA
1307335 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1307361 CTGATATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1311829 original size:33 final size:33
Alignment explanation
Indices: 1311787--1311852 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1311777 GATCTTTGCC
* *
1311787 AATTAAGCTAATTTATTGGTGCAAATTTATAAA
1 AATTAAGCTAACTTATTGGTACAAATTTATAAA
*
1311820 AATTAAGCTAACTTCTTGGTACAAATTTATAAA
1 AATTAAGCTAACTTATTGGTACAAATTTATAAA
1311853 TTTTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (33 bp):
AATTAAGCTAACTTATTGGTACAAATTTATAAA
Found at i:1312980 original size:21 final size:18
Alignment explanation
Indices: 1312954--1313002 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
1312944 TCTTCTCATT
1312954 TTTATTACTTATAGTTTTTA
1 TTTATTACTTA-A-TTTTTA
* *
1312974 TATTATTAATCAATTTTTA
1 T-TTATTACTTAATTTTTA
1312993 TTTATTACTT
1 TTTATTACTT
1313003 TAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.29
19 7 0.29
20 2 0.08
21 8 0.33
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATTACTTAATTTTTA
Found at i:1314394 original size:23 final size:23
Alignment explanation
Indices: 1314368--1314414 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
1314358 ATTATTTTGG
1314368 TATATTT-TATTGTATTTCGTATT
1 TATATTTATA-TGTATTTCGTATT
1314391 TATATTTATATGTATTTCGTATT
1 TATATTTATATGTATTTCGTATT
1314414 T
1 T
1314415 TTTTATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (23 bp):
TATATTTATATGTATTTCGTATT
Found at i:1314710 original size:98 final size:98
Alignment explanation
Indices: 1314595--1316084 Score: 1416
Period size: 98 Copynumber: 15.3 Consensus size: 98
1314585 CTAAAAAAGA
* * *
1314595 CTCCTCTCCGCAGAGGCTCAACAACTTTAAAAATCTTTTTTAGAAAAGCTCCTCTCAGCAGAGGG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
* *
1314660 TCAATAACTTTAAAATCCCATCTTGAAAAAGGG
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * *
1314693 TTCATCTCAGCAGAGGCTCTACAACTTTAAAAATCTCATCTT-GAAAAAGGGCTCCTCTCAGTAG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-ATTTTAG-AAAA--GCTCCTCTCAGCAG
* *
1314757 AGGCTCTACAACTTTAAAAATCTC-TTTTGAAAAA--G
62 AGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGGG
* * * * *
1314792 CTCATCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTT-GAAATAGGGCTCATTTCAACAG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-ATTTTAGAAA-A--GCTCCTCTCAGCAG
* *
1314855 AGGTTCAACAACTTTAAAATTTCAT-TTGAAAAAGGG
62 AGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * * * *
1314891 TTCCTCTCAGTAGAGGCTCTATAACTTTAAAAATC-ATTTTGGAAAAGCTCTTCTCAGCAGAGAC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
*
1314955 TCAACAACTTTAAAATCTCAT-TTTAAAACAGGG
66 TCAACAACTTTAAAATCTCATCTTGAAAA-AGGG
** * * * * * * *
1314988 CTCCTCTCAATAGAGGCTCAACAATTTTAAAATTTTATTTGAAAAAAGGCTCATCTCAGTAGAGG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAA-GCTCCTCTCAGCAGAGG
* * * *
1315053 CTCTATAACTTTAAAAATCTC-TTTTGGAAAA--G
65 CTCAACAACTTT-AAAATCTCATCTTGAAAAAGGG
* * * * *
1315085 CTCTTTTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTAAAACAAGGCTCCTCTCAGTAGA
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-ATTTTAGAA-AA-GCTCCTCTCAGCAGA
* * * *
1315149 GGCTCAACAACTTTCAAATTTTAT-TTGAAAAATGG
63 GGCTCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * *
1315184 CTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTCTTTTGGAAAAGCTCTTCTCAGCAGAGGC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
* * *
1315249 TTAACAACTTTAAAATCTCATATTGAAAAAAGG
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * * * ** *
1315282 TTTCTCTTAGCAGAGGTTCTATAACTTTAAAAATCTCGTTT-GAAAAAGCTCCTCTCACCAGAGG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAG-AAAAGCTCCTCTCAGCAGAGG
* *
1315346 CTCAACAACTTTAAAATCTTATCTTGAAAAATGG
65 CTCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * * *
1315380 CTCCTCTTAGCAGATGTTCAACAACTTTAAAAATCTCTTTTGGAAAAGCTCCTTTCAGCAGAGGC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
* *
1315445 TCAATAACTTTAAAATCTTATC-TGAAAAA--G
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * * * *
1315475 CTTCTCTCAACAGAGGTTCAACAACTTTAAAAATCTCTTTTGGAAAAGCTACTCTTAGCAGAGGC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
1315540 TCAACAACTTTAAAAT-TCATCTTG-AAAAGGG
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * * * *
1315571 CTCATTTCAGCAAAGGTTCAACAACTTT-AAAATTTCA-TTTA-AAAAGGGCTCCTCTCAGTAGA
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-ATTTTAGAAAA--GCTCCTCTCAGCAGA
* *
1315633 GGCTCTACAACTTTAAAAATCTC-TTTTGAAAAA--G
63 GGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGGG
* * *
1315667 CTCCTCTCAGCAGAGACTCAACAACTTT-AAAATCTCATCTT-GAAACAGGGCTCCTCTCAACAG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-ATTTTAGAAA-A--GCTCCTCTCAGCAG
*
1315730 AGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGAG
62 AGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* * * *
1315767 CTCCTCTCAGCAGAGGTTCAACAACTTTAAAAATCTCTTTTGGAAAAGCTGCTCTCAGCAGAGGC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
*
1315832 TCAACAACTTTAAAATCTTATC-TGAAAAA--G
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* ** * * *
1315862 CTCTTCTCAATAGAGGTTCAATAACTTTAAAAATCTCTTTTAGAAAAGCTCCTCTCAGCAGAGGC
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
** *
1315927 TCTTCAACTTTAAAAT-TTATCTTG-AAAAGGG
66 TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
** * * * * *
1315958 CTTATTTCAGCAGAGGCTCAATAACTTTAAAATATC-ATCTGA-AAAAGCTCCTCTCAACAGAGG
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-ATCTATTTTAGAAAAGCTCCTCTCAGCAGAGG
* *
1316021 CTTAACAACTTTAAAATC-CATCTTG-AAAATGG
65 CTCAACAACTTTAAAATCTCATCTTGAAAAAGGG
* *
1316053 CTCCTCTTAACAGAGGCTCAACAACTTTAAAA
1 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
1316085 TCTCATCTTC
Statistics
Matches: 1172, Mismatches: 173, Indels: 97
0.81 0.12 0.07
Matches are distributed among these distances:
94 21 0.02
95 233 0.20
96 155 0.13
97 166 0.14
98 369 0.31
99 119 0.10
100 57 0.05
101 45 0.04
102 7 0.01
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (98 bp):
CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTATTTTAGAAAAGCTCCTCTCAGCAGAGGC
TCAACAACTTTAAAATCTCATCTTGAAAAAGGG
Found at i:1314719 original size:50 final size:49
Alignment explanation
Indices: 1314588--1316093 Score: 1452
Period size: 48 Copynumber: 31.0 Consensus size: 49
1314578 TTAAAATCTA
* * * *
1314588 AAAAAGACTCCTCTCCGCAGAGGCTCAACAACTTTAAAAATCT--TTTTT
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * *
1314636 AGAAAA-GCTCCTCTCAGCAGAGGGTCAATAACTTTAAAATCCCATCTTG
1 A-AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * *
1314685 AAAAAGGGTTCATCTCAGCAGAGGCTCTACAACTTTAAAAATCTCATCTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * *
1314736 AAAAAGGGCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTC-TTTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
*
1314786 AAAAA-GCTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * * * *
1314834 AAATAGGGCTCATTTCAACAGAGGTTCAACAACTTTAAAATTTCAT-TTG
1 AAA-AAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * * * *
1314883 AAAAAGGGTTCCTCTCAGTAGAGGCTCTATAACTTTAAAA-ATCATTTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * *
1314932 GAAAA-GCTCTTCTCAGCAGAGACTCAACAACTTTAAAATCTCAT-TTT
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
** * * *
1314979 AAAACAGGGCTCCTCTCAATAGAGGCTCAACAATTTTAAAATTTTAT-TTG
1 AAAA-A-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * * *
1315029 AAAAAAGGCTCATCTCAGTAGAGGCTCTATAACTTTAAAAATCTC-TTTTG
1 -AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * * *
1315079 GAAAA-GCTCTTTTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTA
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * *
1315127 AAACAAGGCTCCTCTCAGTAGAGGCTCAACAACTTTCAAATTTTAT-TTG
1 AAA-AAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * *
1315176 AAAAATGGCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTC-TTTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * * *
1315226 GAAAA-GCTCTTCTCAGCAGAGGCTTAACAACTTTAAAATCTCATATTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * * * * *
1315274 AAAAAAGGTTTCTCTTAGCAGAGGTTCTATAACTTTAAAAATCTCGT-TTG
1 -AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* *
1315324 AAAAA-GCTCCTCTCACCAGAGGCTCAACAACTTTAAAATCTTATCTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * *
1315372 AAAAATGGCTCCTCTTAGCAGATGTTCAACAACTTTAAAAATCTC-TTTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * * *
1315422 GAAAA-GCTCCTTTCAGCAGAGGCTCAATAACTTTAAAATCTTATC-TG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * *
1315469 AAAAA-GCTTCTCTCAACAGAGGTTCAACAACTTTAAAAATCTC-TTTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * *
1315517 GAAAA-GCTACTCTTAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * * * *
1315564 AAAAGGGCTCATTTCAGCAAAGGTTCAACAACTTTAAAATTTCAT-TT-
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * *
1315611 AAAAAGGGCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTC-TTTTG
1 AAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
*
1315661 AAAAA-GCTCCTCTCAGCAGAGACTCAACAACTTTAAAATCTCATCTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* *
1315709 AAACAGGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATCTCATCTTG
1 AAA-AAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* *
1315759 AAAAAGAGCTCCTCTCAGCAGAGGTTCAACAACTTTAAAAATCTC-TTTTG
1 AAAAAG-GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
* * *
1315809 GAAAA-GCTGCTCTCAGCAGAGGCTCAACAACTTTAAAATCTTATC-TG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* ** * * *
1315856 AAAAA-GCTCTTCTCAATAGAGGTTCAATAACTTTAAAAATCTC-T-TTT
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTG
** *
1315903 AGAAAA-GCTCCTCTCAGCAGAGGCTCTTCAACTTTAAAAT-TTATCTTG
1 A-AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* ** * * *
1315951 AAAAGGGCTTATTTCAGCAGAGGCTCAATAACTTTAAAATATCATC-TG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* *
1315999 AAAAA-GCTCCTCTCAACAGAGGCTTAACAACTTTAAAATC-CATCTTG
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * *
1316046 AAAATGGCTCCTCTTAACAGAGGCTCAACAACTTTAAAATCTCATCTT
1 AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTT
1316094 CTCTCAAAAC
Statistics
Matches: 1197, Mismatches: 203, Indels: 115
0.79 0.13 0.08
Matches are distributed among these distances:
46 7 0.01
47 214 0.18
48 445 0.37
49 150 0.13
50 298 0.25
51 83 0.07
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (49 bp):
AAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
Found at i:1316867 original size:8 final size:8
Alignment explanation
Indices: 1316829--1316867 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1316819 TGAGTCATTA
*
1316829 TTTTTTAT
1 TTTTTTCT
*
1316837 TTTTTACTT
1 TTTTTTC-T
1316846 TTTTTTCT
1 TTTTTTCT
1316854 TTTTTTCT
1 TTTTTTCT
1316862 TTTTTT
1 TTTTTT
1316868 TTCAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1316868 original size:9 final size:9
Alignment explanation
Indices: 1316836--1316868 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1316826 TTATTTTTTA
*
1316836 TTTTTTACT
1 TTTTTTTCT
1316845 TTTTTTTC-
1 TTTTTTTCT
1316853 TTTTTTTCT
1 TTTTTTTCT
1316862 TTTTTTT
1 TTTTTTT
1316869 TCAAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1316870 original size:18 final size:17
Alignment explanation
Indices: 1316829--1316868 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1316819 TGAGTCATTA
*
1316829 TTTTTTATTTTTTACTT
1 TTTTTTCTTTTTTACTT
*
1316846 TTTTTTCTTTTTTTCTT
1 TTTTTTCTTTTTTACTT
1316863 TTTTTT
1 TTTTTT
1316869 TCAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTCTTTTTTACTT
Found at i:1326694 original size:33 final size:34
Alignment explanation
Indices: 1326648--1326711 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1326638 CAAAATTGAG
1326648 TTAGTGTGGTTTGAAATTTTTTTT-TTTTGTGTT
1 TTAGTGTGGTTTGAAATTTTTTTTGTTTTGTGTT
** *
1326681 TTAGTGTTTTTTGAGATTTTTTTTGTTTTGT
1 TTAGTGTGGTTTGAAATTTTTTTTGTTTTGT
1326712 TTTGTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.69
Consensus pattern (34 bp):
TTAGTGTGGTTTGAAATTTTTTTTGTTTTGTGTT
Found at i:1327186 original size:17 final size:17
Alignment explanation
Indices: 1327147--1327183 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1327137 AATTTCTTGC
1327147 TTTTTATTTTTGATTTG
1 TTTTTATTTTTGATTTG
1327164 TTTTTATTTTT-ATTT-
1 TTTTTATTTTTGATTTG
1327179 TTTTT
1 TTTTT
1327184 TTACTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 4 0.20
17 11 0.55
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (17 bp):
TTTTTATTTTTGATTTG
Found at i:1328122 original size:21 final size:18
Alignment explanation
Indices: 1328096--1328144 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
1328086 TCTTCTCATT
1328096 TTTATTACTTATATTTTTTA
1 TTTATTACTTA-A-TTTTTA
* *
1328116 TATTATTAATCAATTTTTA
1 T-TTATTACTTAATTTTTA
1328135 TTTATTACTT
1 TTTATTACTT
1328145 TAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.29
19 7 0.29
20 2 0.08
21 8 0.33
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTACTTAATTTTTA
Found at i:1329604 original size:23 final size:20
Alignment explanation
Indices: 1329563--1329620 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 20
1329553 TATTATTTTG
1329563 GTATTTTTTTATTGTATTTC
1 GTATTTTTTTATTGTATTTC
1329583 GTATTTATATTTATATGTATTTC
1 GTATTT-T-TTTAT-TGTATTTC
*
1329606 GTATTTTTTTGTTGT
1 GTATTTTTTTATTGT
1329621 TGGACAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 9 0.26
21 5 0.15
22 6 0.18
23 14 0.41
ACGTcount: A:0.17, C:0.03, G:0.12, T:0.67
Consensus pattern (20 bp):
GTATTTTTTTATTGTATTTC
Found at i:1329737 original size:61 final size:61
Alignment explanation
Indices: 1329668--1329790 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
1329658 TAAATTATAT
* *
1329668 TGGAAATATTGGATATTCCCAAATTATAATTTATTGATATGATTTACATATCAAAGATTTA
1 TGGAAATATTGGATATTCCCAAATTATAATTTATTGATATGATATACATACCAAAGATTTA
* *
1329729 TGGAAATATTGGATATTTCCAAATTATATTTTATTGATATGATATACATACCAAAGATTTA
1 TGGAAATATTGGATATTCCCAAATTATAATTTATTGATATGATATACATACCAAAGATTTA
1329790 T
1 T
1329791 CTTAATTGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (61 bp):
TGGAAATATTGGATATTCCCAAATTATAATTTATTGATATGATATACATACCAAAGATTTA
Found at i:1330495 original size:46 final size:46
Alignment explanation
Indices: 1330424--1330511 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
1330414 CCTATGTGAC
* *
1330424 AATTTCTAACTTTGATGGTAGAGTTTTAAAATTACATTAACATGAT
1 AATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACATGAT
* * *
1330470 AATTTTTAACTTTAATGGTAAAGTTTTTAAATTTCATTAACA
1 AATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACA
1330512 ATGTGAGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (46 bp):
AATTTCTAACTTTAATGGTAAAGTTTTAAAATTACATTAACATGAT
Found at i:1330554 original size:2 final size:2
Alignment explanation
Indices: 1330549--1330580 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1330539 ATAAATATAA
1330549 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1330581 CTGATATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1332054 original size:21 final size:20
Alignment explanation
Indices: 1331991--1332056 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
1331981 AGTCTCTTCT
*
1331991 CCACCACCTTCATCACCA-C
1 CCACCACCTCCATCACCATC
* *
1332010 CC-CCATCTCC-TCCACCATTA
1 CCACCACCTCCAT-CACCA-TC
1332030 CCACCACCTCCATCACCATC
1 CCACCACCTCCATCACCATC
1332050 GCCACCA
1 -CCACCA
1332057 TTTCCGTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 2 0.06
20 3 0.08
21 18 0.50
22 1 0.03
ACGTcount: A:0.24, C:0.58, G:0.02, T:0.17
Consensus pattern (20 bp):
CCACCACCTCCATCACCATC
Found at i:1344737 original size:3 final size:3
Alignment explanation
Indices: 1344676--1344714 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1344666 CATTTTAGTT
* *
1344676 TAA TAT TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1344715 ATATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1345434 original size:20 final size:20
Alignment explanation
Indices: 1345409--1345454 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1345399 GGATGGTGAA
1345409 AGAGCTATAAAGCTCTCCTC
1 AGAGCTATAAAGCTCTCCTC
*
1345429 AGAGCTCTAAAGCTCTCCTC
1 AGAGCTATAAAGCTCTCCTC
1345449 AGAGCT
1 AGAGCT
1345455 TTCTCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
AGAGCTATAAAGCTCTCCTC
Found at i:1346619 original size:25 final size:26
Alignment explanation
Indices: 1346591--1346639 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1346581 CTAGATGTTG
* *
1346591 AAAAATTAT-TAT-TAATAAATTTTC
1 AAAAAATATATATATAAGAAATTTTC
1346615 AAAAAATATATATATAAGAAATTTT
1 AAAAAATATATATATAAGAAATTTT
1346640 TAATTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAAAATATATATATAAGAAATTTTC
Found at i:1346805 original size:15 final size:15
Alignment explanation
Indices: 1346784--1346923 Score: 108
Period size: 16 Copynumber: 9.2 Consensus size: 15
1346774 TTGTAAAATC
1346784 CCCTAAAATCCAAAA
1 CCCTAAAATCCAAAA
* * *
1346799 TCCTAAAATCTGAAAC
1 CCCTAAAATC-CAAAA
*
1346815 CCCTAAAAATCTAAAA
1 CCCT-AAAATCCAAAA
* *
1346831 TCCCTTAAATCCGAAA
1 -CCCTAAAATCCAAAA
1346847 CCCTTAAAATCC-AAA
1 CCC-TAAAATCCAAAA
* *
1346862 CCCCAAAAACCAAAA
1 CCCTAAAATCCAAAA
1346877 TCCCTAAAATCC-AAA
1 -CCCTAAAATCCAAAA
*
1346892 CCCTTAAAT-CAAAA
1 CCCTAAAATCCAAAA
*
1346906 CCC-CAAATCCCAAAA
1 CCCTAAAAT-CCAAAA
1346921 CCC
1 CCC
1346924 AAACCCTAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
13 5 0.05
14 20 0.20
15 32 0.32
16 33 0.33
17 10 0.10
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.16
Consensus pattern (15 bp):
CCCTAAAATCCAAAA
Found at i:1346874 original size:14 final size:14
Alignment explanation
Indices: 1346837--1346926 Score: 65
Period size: 14 Copynumber: 6.1 Consensus size: 14
1346827 AAAATCCCTT
*
1346837 AAATCCGAAACCCTTA
1 AAATCC-AAACCC-CA
1346853 AAATCCAAACCCCA
1 AAATCCAAACCCCA
* *
1346867 AAAACCAAAATCCCTA
1 AAATCC-AAA-CCCCA
**
1346883 AAATCCAAACCCTT
1 AAATCCAAACCCCA
*
1346897 AAATCAAAACCCC-
1 AAATCCAAACCCCA
*
1346910 AAATCCCAAAACCCA
1 AAAT-CCAAACCCCA
1346925 AA
1 AA
1346927 CCCTAAAGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.07
14 28 0.46
15 14 0.23
16 15 0.25
ACGTcount: A:0.51, C:0.36, G:0.01, T:0.12
Consensus pattern (14 bp):
AAATCCAAACCCCA
Found at i:1346926 original size:51 final size:50
Alignment explanation
Indices: 1346857--1346965 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 50
1346847 CCCTTAAAAT
*
1346857 CCAAACCCCAAAAACCAAAATCCCTAAAATC-CAAACCCTTAAATCAAAACC
1 CCAAACCCCAAAAACC-AAA-CCCTAAAATCTCAAACCCTAAAATCAAAACC
* * * *
1346908 CCAAATCCCAAAACCCAAACCCTAAAGTCTTCAAACTCTAAAATCAAAACC
1 CCAAACCCCAAAAACCAAACCCTAAAATC-TCAAACCCTAAAATCAAAACC
*
1346959 CTAAACC
1 CCAAACC
1346966 TTTCATATCC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
49 9 0.18
50 3 0.06
51 37 0.76
ACGTcount: A:0.49, C:0.37, G:0.01, T:0.14
Consensus pattern (50 bp):
CCAAACCCCAAAAACCAAACCCTAAAATCTCAAACCCTAAAATCAAAACC
Found at i:1348701 original size:2 final size:2
Alignment explanation
Indices: 1348694--1348722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1348684 ATGGAGAACA
1348694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1348723 ATCCTTAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1351453 original size:13 final size:14
Alignment explanation
Indices: 1351435--1351471 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1351425 TTAAATATAC
1351435 ATAAAATAAAAT-A
1 ATAAAATAAAATGA
1351448 ATAAAATAAAATGA
1 ATAAAATAAAATGA
*
1351462 AGAAAATAAA
1 ATAAAATAAA
1351472 GAAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (14 bp):
ATAAAATAAAATGA
Found at i:1352799 original size:13 final size:13
Alignment explanation
Indices: 1352749--1352799 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1352739 ATCAAAATTT
1352749 TTTATTTTTTT-A
1 TTTATTTTTTTAA
*
1352761 TTTTTTTGATTTTAA
1 TTTATTT--TTTTAA
*
1352776 TTTAGTTTTTTAA
1 TTTATTTTTTTAA
1352789 TTTATTTTTTT
1 TTTATTTTTTT
1352800 TTTTATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 6 0.19
13 16 0.50
14 4 0.12
15 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:1353393 original size:16 final size:16
Alignment explanation
Indices: 1353338--1353395 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
1353328 TTTAAATATG
*
1353338 TATTATATTAATAAAAT
1 TATTATTTTAA-AAAAT
*
1353355 TATTA-TTT--AACAT
1 TATTATTTTAAAAAAT
1353368 T-TTAATTTTAAAAAAT
1 TATT-ATTTTAAAAAAT
1353384 TATTATTTTAAA
1 TATTATTTTAAA
1353396 CTCAATAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
12 2 0.06
13 6 0.18
14 3 0.09
16 15 0.45
17 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATTTTAAAAAAT
Found at i:1355061 original size:26 final size:25
Alignment explanation
Indices: 1355005--1355062 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
1354995 AATTTTATAC
1355005 ATTATTAATAAATTAAATAATACTAT
1 ATTATTAATAAATTAAATAATAC-AT
*
1355031 TTTATTAATAAATTAAATTAAATA-AT
1 ATTATTAATAAATTAAA-T-AATACAT
1355057 ATTATT
1 ATTATT
1355063 TTATTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 23 0.82
27 1 0.04
28 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATTAATAAATTAAATAATACAT
Found at i:1355071 original size:17 final size:17
Alignment explanation
Indices: 1355020--1355106 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
1355010 TAATAAATTA
*
1355020 AATAATACTATTTTATT
1 AATAATATTATTTTATT
**
1355037 AATAA-ATTAAATTA--
1 AATAATATTATTTTATT
1355051 AATAATATTATTTTATT
1 AATAATATTATTTTATT
* *
1355068 AATAA-ATAAATTTTA-A
1 AATAATAT-TATTTTATT
1355084 AATTAATATT-TATTTATT
1 AA-TAATATTAT-TTTATT
1355102 AATAA
1 AATAA
1355107 AATATTATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
14 5 0.09
15 7 0.13
16 11 0.21
17 26 0.49
18 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATATTATTTTATT
Found at i:1355100 original size:34 final size:31
Alignment explanation
Indices: 1355013--1355107 Score: 122
Period size: 31 Copynumber: 3.0 Consensus size: 31
1355003 ACATTATTAA
*
1355013 TAAATTAAATAATACTATTTTATTAATAAAT
1 TAAATTAAATAATATTATTTTATTAATAAAT
1355044 TAAATTAAATAATATTATTTTATTAATAAA-
1 TAAATTAAATAATATTATTTTATTAATAAAT
1355074 TAAATTTTAAAATTAATATT-TATTTATTAATAAA
1 TAAA--TT-AAA-TAATATTAT-TTTATTAATAAA
1355108 ATATTATTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
30 4 0.07
31 29 0.50
32 2 0.03
33 4 0.07
34 19 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
TAAATTAAATAATATTATTTTATTAATAAAT
Found at i:1355161 original size:26 final size:25
Alignment explanation
Indices: 1355085--1355161 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
1355075 AAATTTTAAA
* *
1355085 ATTAATATTTATTTATTAATAAAAT
1 ATTAATATTTATATATTAATAATAT
* * *
1355110 ATTATTATTTAATTTACTAATAATAT
1 ATTAATATTT-ATATATTAATAATAT
1355136 A-TAATATTTATATATTAATAATAT
1 ATTAATATTTATATATTAATAATAT
1355160 AT
1 AT
1355162 CAAATATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
24 14 0.32
25 16 0.36
26 14 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAATATTTATATATTAATAATAT
Found at i:1355168 original size:26 final size:24
Alignment explanation
Indices: 1355087--1355161 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 24
1355077 ATTTTAAAAT
*
1355087 TAATATTTATTTATTAATAAAATA
1 TAATATTTATTTATTAATAATATA
* *
1355111 TTATTATTTAATTTACTAATAATATA
1 -TAATATTT-ATTTATTAATAATATA
*
1355137 TAATATTTATATATTAATAATATA
1 TAATATTTATTTATTAATAATATA
1355161 T
1 T
1355162 CAAATATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
24 15 0.35
25 14 0.33
26 14 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATTTATTTATTAATAATATA
Found at i:1355723 original size:58 final size:57
Alignment explanation
Indices: 1355654--1355910 Score: 241
Period size: 58 Copynumber: 4.4 Consensus size: 57
1355644 TTTGTGCGGA
* *
1355654 AAAAATTGATACTTTCAACTTTTCTCTAAAAATGTTTTCTTGAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCTCTAAAAATCTTTT-TTAAAACTTTAATTTCGAG
* * **
1355712 AAAAATTGATACTTTCAACTTTTC-CTCAAAAATCTATTTTCAAAAAC-TTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCTCT-AAAAATCT-TTTT-TAAAACTTTAATTTCGAG
* * * *
1355770 AAAAATTGATAATTTCAACTTTTCCCCAAAAATATTTTTTTTAAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTT-CTCTAAAA-ATCTTTTTTAAAACTTTAATTTCGAG
* * * * **
1355829 AAAAATTGATACTTTCAA-TTTTTTCTTAAAAAAAAATATTTTTTAAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCTC-T----AAAAATCTTTTTTAAAACTTTAATTTCGAG
*
1355890 AAAAATTGATATTTTCAACTT
1 AAAAATTGATACTTTCAACTT
1355911 GAAAAATTGA
Statistics
Matches: 163, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
57 3 0.02
58 71 0.44
59 41 0.25
60 4 0.02
61 38 0.23
62 6 0.04
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCTCTAAAAATCTTTTTTAAAACTTTAATTTCGAG
Found at i:1355916 original size:22 final size:22
Alignment explanation
Indices: 1355889--1355932 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1355879 TTATTTTTAA
*
1355889 GAAAAATTGATATTTTCAACTT
1 GAAAAATTGATACTTTCAACTT
1355911 GAAAAATTGATACTTTCAACTT
1 GAAAAATTGATACTTTCAACTT
1355933 TTCTCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
GAAAAATTGATACTTTCAACTT
Found at i:1355975 original size:80 final size:82
Alignment explanation
Indices: 1355828--1355990 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 82
1355818 TTAATTTCGA
* *
1355828 GAAAAATTGATACTTTCAATTTTTTCTTAAAAAAAAATATTTTTTAAAAATTTATTTTTAAGAAA
1 GAAAAATTGATACTTTCAATCTTTTCTT-AAAAAAAATATTTTTTAAAAATTTATTTTCAAGAAA
1355893 AATTGATATTTTCAACTT
65 AATTGATATTTTCAACTT
** * *
1355911 GAAAAATTGATACTTTCAA-CTTTTC-T-CCAAAATTATTTTTTGAAAAATTTATTTTCAAGGAA
1 GAAAAATTGATACTTTCAATCTTTTCTTAAAAAAAATATTTTTT-AAAAATTTATTTTCAAGAAA
1355973 AATTGATATTTTCAACTT
65 AATTGATATTTTCAACTT
1355991 TTCTCCAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
79 12 0.16
80 36 0.49
81 1 0.01
82 5 0.07
83 19 0.26
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (82 bp):
GAAAAATTGATACTTTCAATCTTTTCTTAAAAAAAATATTTTTTAAAAATTTATTTTCAAGAAAA
ATTGATATTTTCAACTT
Found at i:1355986 original size:58 final size:60
Alignment explanation
Indices: 1355873--1356024 Score: 191
Period size: 58 Copynumber: 2.5 Consensus size: 60
1355863 AATATTTTTT
* *
1355873 AAAAATTTATTTTTAAGAAAAATTGATATTTTCAACTTGAAAAATTGATACTTTCAACTTTTCTC
1 AAAAATATATTTTT-AGAAAAATT--TATTTTCAA---GGAAAATTGATACTTTCAACTTTTCTC
1355938 C
60 C
* *
1355939 -AAAAT-TATTTTTTGAAAAATTTATTTTCAAGGAAAATTGATATTTTCAACTTTTCTCC
1 AAAAATATATTTTTAGAAAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCTCC
*
1355997 AAAAATATATTTTTAGAAAACTTTATTT
1 AAAAATATATTTTTAGAAAAATTTATTT
1356025 AAAGAAAATA
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
58 26 0.33
59 5 0.06
60 19 0.24
61 9 0.11
63 8 0.10
64 7 0.09
65 5 0.06
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (60 bp):
AAAAATATATTTTTAGAAAAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCTCC
Found at i:1356040 original size:6 final size:6
Alignment explanation
Indices: 1356029--1356108 Score: 79
Period size: 6 Copynumber: 12.3 Consensus size: 6
1356019 TTATTTAAAG
* *
1356029 AAAATAA AAATATA AAAATAA AAAATA AAAATA AAAATG AAACTA AAAATA
1 AAAAT-A AAA-ATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
*
1356080 AATAAAA ATAAATA AAAATA GAAAATA AA
1 AA-AATA A-AAATA AAAATA -AAAATA AA
1356109 TATTAAACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
6 32 0.52
7 27 0.44
8 3 0.05
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1356059 original size:27 final size:27
Alignment explanation
Indices: 1356024--1356110 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
1356014 AAACTTTATT
*
1356024 TAAAGAAAATAAAAATATAAAAATAAA
1 TAAAAAAAATAAAAATATAAAAATAAA
1356051 -AAATAAAAATAAAAATGAAACTAAAAATAAA
1 TAAA-AAAAATAAAAAT---A-TAAAAATAAA
*
1356082 TAAAAATAAATAAAAATA-GAAAATAAA
1 TAAAAA-AAATAAAAATATAAAAATAAA
1356109 TA
1 TA
1356111 TTAAACAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
26 3 0.06
27 21 0.41
29 1 0.02
30 1 0.02
31 12 0.24
32 13 0.25
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.18
Consensus pattern (27 bp):
TAAAAAAAATAAAAATATAAAAATAAA
Found at i:1356105 original size:39 final size:39
Alignment explanation
Indices: 1356028--1356105 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
1356018 TTTATTTAAA
1356028 GAAAATAAAAATATAAAAATAAAAAATAAAAATAAAAAT
1 GAAAATAAAAATATAAAAATAAAAAATAAAAATAAAAAT
* *
1356067 GAAACTAAAAATA-AATAAA-AATAAATAAAAATAGAAAAT
1 GAAAATAAAAATATAA-AAATAAAAAATAAAAATA-AAAAT
1356106 AAATATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 15 0.43
39 20 0.57
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (39 bp):
GAAAATAAAAATATAAAAATAAAAAATAAAAATAAAAAT
Found at i:1357059 original size:39 final size:41
Alignment explanation
Indices: 1357010--1357090 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
1357000 ATAAAAAATG
* *
1357010 TTAATAGATAA-TTAAAA-AAA-AATCAGATAAATAATAATA
1 TTAACAGATAACTAAAAATAAATAAT-AGATAAATAATAATA
*
1357049 TTAACAGATAACTAAAAATAAATAATAGATAAATTATAATA
1 TTAACAGATAACTAAAAATAAATAATAGATAAATAATAATA
1357090 T
1 T
1357091 ATAATCATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 10 0.28
40 5 0.14
41 18 0.50
42 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.30
Consensus pattern (41 bp):
TTAACAGATAACTAAAAATAAATAATAGATAAATAATAATA
Found at i:1357464 original size:43 final size:43
Alignment explanation
Indices: 1357368--1357746 Score: 484
Period size: 43 Copynumber: 8.9 Consensus size: 43
1357358 TTGATCAAAA
* * *
1357368 CTCCTCTAAGT-AGAGGCTCAACGACTTTG-AAGATGAATAAAA
1 CTCCTCTAA-TCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
* * *
1357410 CTCCTTTAATCAAAGGCTTAACGACTTTGAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
* *
1357453 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAGATGAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
* *
1357495 CTCCTCTAATCAGAGGCTCAATGACTTTAAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
* * *
1357538 CTCCTATAATTAGAGGCTCAACGACTTTGAAAATTAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
*
1357581 CTCATCTAATCAGAGGCTCAACGACTTTAGAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAATAAATAAAG
* * * *
1357625 CTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAGTAAGT--GG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
* *
1357666 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAAT--GG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
*
1357707 CTCATCTAATCAGAGGCTCAACGACTTTTGAAAAAGTAAA
1 CTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAA-TAAA
1357747 ATGCTCCTTG
Statistics
Matches: 298, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
41 65 0.22
42 70 0.23
43 123 0.41
44 40 0.13
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (43 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
Done.