Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 48 of 208
Found at i:18545894 original size:14 final size:14
Alignment explanation
Indices: 18545861--18545899 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18545851 TTGGCCTGTC
18545861 ATCCATTACCCATT
1 ATCCATTACCCATT
*
18545875 ACCCATTACCCATT
1 ATCCATTACCCATT
* *
18545889 TTCCATAACCC
1 ATCCATTACCC
18545900 CGCTTCCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (14 bp):
ATCCATTACCCATT
Found at i:18553019 original size:85 final size:85
Alignment explanation
Indices: 18552876--18553047 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 85
18552866 AAGATGATAA
18552876 CAAAGTATCCATTCTGAGTTCAAAAACTGCTATGGCAATAGTATGCACATATAGAAGGACAGGGT
1 CAAAGTATCCATTCTGAGTTCAAAAACTGCTATGGCAATAGTATGCACATATAGAAGGACAGGGT
18552941 AGACCAAAATATTCTCAGAT
66 AGACCAAAATATTCTCAGAT
*
18552961 CAAAGTATCCATTCTGAGTTCAAAAACTGCTATGGCAATAGTATGCACATTTAGAAGGACAGGGT
1 CAAAGTATCCATTCTGAGTTCAAAAACTGCTATGGCAATAGTATGCACATATAGAAGGACAGGGT
18553026 AGACCAAAATATTCTCAGAT
66 AGACCAAAATATTCTCAGAT
18553046 CA
1 CA
18553048 TACCATCACT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (85 bp):
CAAAGTATCCATTCTGAGTTCAAAAACTGCTATGGCAATAGTATGCACATATAGAAGGACAGGGT
AGACCAAAATATTCTCAGAT
Found at i:18601343 original size:12 final size:12
Alignment explanation
Indices: 18601310--18601349 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
18601300 AATAAAAAAA
18601310 TTTTAATAATTT
1 TTTTAATAATTT
*
18601322 TTTT--TTATTT
1 TTTTAATAATTT
18601332 TTTTAATAATTT
1 TTTTAATAATTT
18601344 TTTTAA
1 TTTTAA
18601350 AAAAATACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTAATAATTT
Found at i:18601613 original size:20 final size:20
Alignment explanation
Indices: 18601568--18601614 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
18601558 AAAAAAAAAG
*
18601568 AGAGAAAGGAGAAGAAGAGGA
1 AGAG-AAGGAGAAGAAGAAGA
* *
18601589 GGAGAAGGAGAAGGAGAAGA
1 AGAGAAGGAGAAGAAGAAGA
18601609 AGAGAA
1 AGAGAA
18601615 AAAGAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (20 bp):
AGAGAAGGAGAAGAAGAAGA
Found at i:18601804 original size:23 final size:23
Alignment explanation
Indices: 18601778--18601846 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
18601768 TGGATTAGAA
*
18601778 TTTTGTATGAATATTCTAATTTT
1 TTTTGTATGAATATTGTAATTTT
18601801 TTTTGTATGAATATTGT-A-TTT
1 TTTTGTATGAATATTGTAATTTT
*
18601822 TTTT-TATGAATATTGTAATTAT
1 TTTTGTATGAATATTGTAATTTT
18601844 TTT
1 TTT
18601847 ATAATTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 12 0.29
21 8 0.19
22 6 0.14
23 16 0.38
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (23 bp):
TTTTGTATGAATATTGTAATTTT
Found at i:18601824 original size:20 final size:20
Alignment explanation
Indices: 18601778--18601920 Score: 87
Period size: 23 Copynumber: 6.9 Consensus size: 20
18601768 TGGATTAGAA
*
18601778 TTTTGTATGAATATTCTAATTTT
1 TTTTGTATGAATATTGT-A--TT
18601801 TTTTGTATGAATATTGTATT
1 TTTTGTATGAATATTGTATT
*
18601821 TTTTTTATGAATATTGTAATT
1 TTTTGTATGAATATTGT-ATT
* *
18601842 ATTTTATAATTAA-ATTTGTATT
1 -TTTTGT-ATGAATA-TTGTATT
* * * * *
18601864 TATAGTTTTGGAT-TAGTA--
1 TTTTG-TATGAATATTGTATT
*
18601882 TTTTGTATGAATGTTGTAATT
1 TTTTGTATGAATATTGT-ATT
18601903 TTTTGTATGAATATTGTA
1 TTTTGTATGAATATTGTA
18601921 ATATTGTAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.05
18 6 0.06
19 1 0.01
20 23 0.25
21 23 0.25
22 11 0.12
23 24 0.26
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTGTATGAATATTGTATT
Found at i:18601907 original size:21 final size:21
Alignment explanation
Indices: 18601882--18602002 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
18601872 TGGATTAGTA
*
18601882 TTTTGTATGAATGTTGTAATT
1 TTTTGTATGAATATTGTAATT
18601903 TTTTGTATGAATATTGTAATATTGT
1 TTTTGTATGAATATTGT-A-A-T-T
18601928 AATTTTGTATGAATATTGTAATGT
1 --TTTTGTATGAATATTGTAAT-T
*
18601952 CGGGATATAT-TAT-AATATTGTAATT
1 -----T-TTTGTATGAATATTGTAATT
18601977 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
18601998 ATTTT
1 -TTTT
18602003 ATAATTAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.02
20 4 0.05
21 28 0.34
22 5 0.06
23 1 0.01
24 4 0.05
25 3 0.04
26 12 0.14
27 22 0.27
28 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.54
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:18602057 original size:25 final size:24
Alignment explanation
Indices: 18601990--18602074 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
18601980 TGTATGAATA
*
18601990 TTGTAATTATTTTATAATTAATTTG
1 TTGTAATTA-TTTAAAATTAATTTG
*
18602015 TTAGTAATT-TATATAAATT-ATTGTG
1 TT-GTAATTATTTA-AAATTAATT-TG
*
18602040 TGTGTAATTATTTAAAATTTAATTTA
1 T-TGTAATTATTTAAAA-TTAATTTG
18602066 TTAGTAATT
1 TT-GTAATT
18602075 TAGGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
24 6 0.12
25 19 0.40
26 20 0.42
27 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
TTGTAATTATTTAAAATTAATTTG
Found at i:18602187 original size:37 final size:37
Alignment explanation
Indices: 18602136--18602216 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
18602126 CATATAAAGT
18602136 TTATAAAAAAATTAAAAGTCATTATATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAGTCATTATATTAAAAGTTTAA
* * *
18602174 TTATAAAAAATTAAAATTTATTTTATTAAAAGTTTAA
1 TTATAAAAAATTAAAAGTCATTATATTAAAAGTTTAA
18602211 TTATAA
1 TTATAA
18602217 CTGACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (37 bp):
TTATAAAAAATTAAAAGTCATTATATTAAAAGTTTAA
Found at i:18602294 original size:15 final size:15
Alignment explanation
Indices: 18602253--18602294 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
18602243 GTTAACTCAT
*
18602253 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
18602268 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
18602284 TTAAATTTTAT
1 TTAAATTTTAT
18602295 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:18603294 original size:24 final size:23
Alignment explanation
Indices: 18603263--18603323 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
18603253 AATACTTTAT
18603263 TTTTTTCTTCTTTTCCTTCCTTC
1 TTTTTTCTTCTTTTCCTTCCTTC
*
18603286 TTTTATTCTGC--TTCCTTCCTTC
1 TTTT-TTCTTCTTTTCCTTCCTTC
*
18603308 TTATTTCTTCTGTTTC
1 TTTTTTCTTCT-TTTC
18603324 TCTAGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 5 0.16
22 14 0.45
23 4 0.13
24 8 0.26
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTTTTCTTCTTTTCCTTCCTTC
Found at i:18603426 original size:27 final size:27
Alignment explanation
Indices: 18603396--18603457 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
18603386 CTCAGTATGA
18603396 CACCAATAATGGCGCCTCCCAGATAGG
1 CACCAATAATGGCGCCTCCCAGATAGG
** * **
18603423 CACCACCATTGGCGCCTCTGAGATAGG
1 CACCAATAATGGCGCCTCCCAGATAGG
*
18603450 CGCCAATA
1 CACCAATA
18603458 CTATATATTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (27 bp):
CACCAATAATGGCGCCTCCCAGATAGG
Found at i:18607013 original size:23 final size:23
Alignment explanation
Indices: 18606969--18607011 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
18606959 GGCTATATAA
*
18606969 AAAATAAAAAAAATATAATTTAG
1 AAAATAAAAAAAATACAATTTAG
*
18606992 AAAAT-AAATAAATACAATTT
1 AAAATAAAAAAAATACAATTT
18607012 TATTAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAAAAAAATACAATTTAG
Found at i:18614663 original size:7 final size:7
Alignment explanation
Indices: 18614655--18614688 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
18614645 ATTCATTATT
*
18614655 CTTCCTT
1 CTTCCTA
18614662 CTTCCTA
1 CTTCCTA
18614669 CTTCCTA
1 CTTCCTA
18614676 CTTCCTA
1 CTTCCTA
18614683 CTTCCT
1 CTTCCT
18614689 TCACCCTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (7 bp):
CTTCCTA
Found at i:18615591 original size:18 final size:19
Alignment explanation
Indices: 18615568--18615605 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
18615558 TTAAAGTTTT
18615568 ATTTTAATATTT-TTATAC
1 ATTTTAATATTTATTATAC
*
18615586 ATTTTAATTTTTATTATAC
1 ATTTTAATATTTATTATAC
18615605 A
1 A
18615606 CACTTTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:18622651 original size:21 final size:21
Alignment explanation
Indices: 18622625--18622665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18622615 AGACGAGCAA
* *
18622625 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
18622646 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
18622666 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:18640627 original size:20 final size:20
Alignment explanation
Indices: 18640602--18640640 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18640592 TTAGGCTAGG
* *
18640602 ATAGTATATATTTATTTTAC
1 ATAGTATAAATATATTTTAC
18640622 ATAGTATAAATATATTTTA
1 ATAGTATAAATATATTTTA
18640641 AATAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
ATAGTATAAATATATTTTAC
Found at i:18641555 original size:24 final size:22
Alignment explanation
Indices: 18641507--18641555 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
18641497 TAAAGCAGAT
* *
18641507 ATATTTAGTTAAAATTCAATAA
1 ATATTTAGGTAAAATTCAAAAA
*
18641529 ATATTTAAGGTAAAATTTAAAATA
1 ATATTT-AGGTAAAATTCAAAA-A
18641553 ATA
1 ATA
18641556 GTAGAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (22 bp):
ATATTTAGGTAAAATTCAAAAA
Found at i:18642511 original size:2 final size:2
Alignment explanation
Indices: 18642504--18642537 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18642494 TCACTCCCAA
18642504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18642538 ACACACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18647696 original size:12 final size:13
Alignment explanation
Indices: 18647678--18647714 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
18647668 GGGAGGTGCT
18647678 GGTGGAAGTGGAA
1 GGTGGAAGTGGAA
18647691 -GTGGAAGT-GAA
1 GGTGGAAGTGGAA
*
18647702 GGTGGAAATGGAA
1 GGTGGAAGTGGAA
18647715 TAATAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.49, T:0.16
Consensus pattern (13 bp):
GGTGGAAGTGGAA
Found at i:18669331 original size:2 final size:2
Alignment explanation
Indices: 18669324--18669354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18669314 TCATTTATGA
18669324 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
18669355 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:18673777 original size:2 final size:2
Alignment explanation
Indices: 18673770--18673798 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18673760 TGTCAAGTTT
18673770 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 A
18673799 ATAGCATAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18678598 original size:19 final size:21
Alignment explanation
Indices: 18678560--18678598 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
18678550 AATAATTGAT
*
18678560 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
18678581 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
18678599 TTTGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:18678661 original size:3 final size:3
Alignment explanation
Indices: 18678645--18678688 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
18678635 AAAATAATAG
*
18678645 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18678689 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18678693 original size:3 final size:3
Alignment explanation
Indices: 18678687--18678721 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18678677 ATTATTATTA
18678687 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
18678722 AGTATTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:18679597 original size:18 final size:18
Alignment explanation
Indices: 18679567--18679611 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
18679557 TTGACATGGT
*
18679567 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
*
18679585 TGTTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
18679603 TGGTGGCGA
1 TGGTGGCGA
18679612 TCATTAGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.49, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:18681519 original size:30 final size:30
Alignment explanation
Indices: 18681449--18681519 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
18681439 AAAAAAATTA
18681449 CCTTTT-TTTTCTTTTTTTTCCTTCCTTTC
1 CCTTTTCTTTTCTTTTTTTTCCTTCCTTTC
*
18681478 CTCTTCTTCTTTT-TTTTTTTCTCTTCTCCTTT-
1 C-CTT-TTCTTTTCTTTTTTT-TCCT-TCCTTTC
18681510 CCTTTTCTTT
1 CCTTTTCTTT
18681520 ACTTCTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 1 0.03
30 9 0.25
31 12 0.33
32 8 0.22
33 6 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (30 bp):
CCTTTTCTTTTCTTTTTTTTCCTTCCTTTC
Found at i:18681547 original size:34 final size:37
Alignment explanation
Indices: 18681479--18681607 Score: 111
Period size: 39 Copynumber: 3.4 Consensus size: 37
18681469 CTTCCTTTCC
* * *
18681479 TCTTC-TTCTTTTTTTTTTTCTCTTCTCCTTTCCTTT
1 TCTTCTTTCTTTCTTTTTGTCTCTTCTCCTTTTCTTT
* *
18681515 TCTT-TACTTCTTTCTTTCTTTTTTCTTCTCC-TTTCATTT
1 TCTTCT--TTCTTTCTTT-TTGTCTCTTCTCCTTTTC-TTT
*
18681554 TCTTCTTTTGTCTTTCTTTTTGTCTCTTCTCCTTTCCTTT
1 TCTTC--TT-TCTTTCTTTTTGTCTCTTCTCCTTTTCTTT
18681594 TCTTTCTTTCTTTC
1 TC-TTCTTTCTTTC
18681608 CCTCTCTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
36 4 0.05
38 18 0.24
39 21 0.28
40 17 0.22
41 15 0.20
42 1 0.01
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.70
Consensus pattern (37 bp):
TCTTCTTTCTTTCTTTTTGTCTCTTCTCCTTTTCTTT
Found at i:18681786 original size:23 final size:23
Alignment explanation
Indices: 18681753--18681797 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18681743 TTTTTTGTTA
*
18681753 ATATATTTTGGTAAATAAAAAAT
1 ATATATATTGGTAAATAAAAAAT
18681776 ATATATATTGGTAAATAAAAAA
1 ATATATATTGGTAAATAAAAAA
18681798 AAGTTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (23 bp):
ATATATATTGGTAAATAAAAAAT
Found at i:18690937 original size:36 final size:36
Alignment explanation
Indices: 18690885--18690971 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
18690875 CCCAACTACT
*
18690885 GTATACGTGAACAGTACTGTATACATGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACATGAATAGTGCC
* *
18690921 GTATACGTAAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACATGAATAGTGCC
18690957 GTATACGTGAATAGT
1 GTATACGTGAATAGT
18690972 GCCGTAAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACTGTATACATGAATAGTGCC
Found at i:18690972 original size:18 final size:18
Alignment explanation
Indices: 18690885--18690977 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
18690875 CCCAACTACT
* * *
18690885 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTGCC
*
18690903 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTGCC
* * *
18690921 GTATACGTAAATAGTACT
1 GTATACGTGAATAGTGCC
18690939 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
18690957 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
18690975 GTA
1 GTA
18690978 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:18692715 original size:14 final size:14
Alignment explanation
Indices: 18692696--18692724 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18692686 TTTTTCTTTT
18692696 TGGAACAATGAAAA
1 TGGAACAATGAAAA
18692710 TGGAACAATGAAAA
1 TGGAACAATGAAAA
18692724 T
1 T
18692725 TCGAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.17
Consensus pattern (14 bp):
TGGAACAATGAAAA
Found at i:18711579 original size:24 final size:24
Alignment explanation
Indices: 18711542--18711588 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18711532 TGAGAGAATT
18711542 TTTATTTTATTTAATATCAATATA
1 TTTATTTTATTTAATATCAATATA
*
18711566 TTTATATTTA-TTAATATTAATAT
1 TTTAT-TTTATTTAATATCAATAT
18711589 TAACATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTTATTTAATATCAATATA
Found at i:18724709 original size:17 final size:17
Alignment explanation
Indices: 18724676--18724709 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18724666 AATGGAATTG
*
18724676 TAAATTTTGAGATATAA
1 TAAATTTTGAGAGATAA
*
18724693 TAAATTTTGTGAGATAA
1 TAAATTTTGAGAGATAA
18724710 GGTCAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAATTTTGAGAGATAA
Found at i:18726390 original size:32 final size:32
Alignment explanation
Indices: 18726352--18726417 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
18726342 ACTAAAGTGA
**
18726352 TTATTTTTTCTGATCATGTAGCTTTGAAATAT
1 TTATTTTTTCTGATCATACAGCTTTGAAATAT
18726384 TTATTTTTTCTGATCATACAGCTTTGAAATAT
1 TTATTTTTTCTGATCATACAGCTTTGAAATAT
18726416 TT
1 TT
18726418 GATAGGCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (32 bp):
TTATTTTTTCTGATCATACAGCTTTGAAATAT
Found at i:18728246 original size:25 final size:23
Alignment explanation
Indices: 18728217--18728291 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
18728207 AAAATTTTTA
*
18728217 ATTTTCCTATTATTGTTATTATTT
1 ATTTTTCTATTATT-TTATTATTT
18728241 ATTTTTACTATT-TTATT-TTATTTT
1 ATTTTT-CTATTATT-TTATTA-TTT
18728265 ATTTTAT-T-TTATTTTATT-TTT
1 ATTTT-TCTATTATTTTATTATTT
18728286 ATTTTT
1 ATTTTT
18728292 GCAGGAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
20 1 0.02
21 8 0.18
22 4 0.09
23 8 0.18
24 17 0.39
25 6 0.14
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (23 bp):
ATTTTTCTATTATTTTATTATTT
Found at i:18728259 original size:5 final size:5
Alignment explanation
Indices: 18728249--18728290 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
18728239 TTATTTTTAC
18728249 TATTT TATTT TATTT TATTT TATTT TATTT TATTTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT T
18728291 TGCAGGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:18732341 original size:19 final size:19
Alignment explanation
Indices: 18732318--18732361 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
18732308 AAGAACATTT
*
18732318 ATTTTT-TTTCTATTTTTA
1 ATTTTTATTTCAATTTTTA
* *
18732336 ATTTTTATTTGAATTTTTT
1 ATTTTTATTTCAATTTTTA
18732355 ATTTTTA
1 ATTTTTA
18732362 GATTGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
ATTTTTATTTCAATTTTTA
Found at i:18732448 original size:141 final size:139
Alignment explanation
Indices: 18732239--18732521 Score: 417
Period size: 141 Copynumber: 2.0 Consensus size: 139
18732229 AAATAAGGGT
* * *
18732239 TGAGAGATATTCATACTTATTTCAAAAGATTGAAGGTGACTTATTTTCTTGTTTTTAATAATAAT
1 TGAGAGATATTCATACTTATTTAAAAAAATTGAAGATGACTTATTTTCTTGTTTTTAATAATAAT
* * * *
18732304 TTTAAAGAACATTTATTTTTTTTCTATTTTTAATTTTTATTTGAA-TTTTTTATTTTTAGATTGT
66 TTTAAAGAACACTTATTTTTTTTCTATTTTTAATTTTTATTT-AATTTTTTTATTTTAAAATTAT
18732368 TTTATTGACA
130 TTTATTGACA
* *
18732378 TGAGAGATAGTTCATACTTTTTTAAAAAAAATTGAAGATGATTTATTTTCTCT-TTTTTAATAAT
1 TGAGAGATA-TTCATACTTATTT-AAAAAAATTGAAGATGACTTATTTTCT-TGTTTTTAATAAT
**
18732442 AATTTTAAAGAATGCTTATTTTTTTTCTATTTTTAATTTTTATTTAATTTTTTTATTTTAAAATT
63 AATTTTAAAGAACACTTATTTTTTTTCTATTTTTAATTTTTATTTAATTTTTTTATTTTAAAATT
18732507 ATTTTATTGACA
128 ATTTTATTGACA
18732519 TGA
1 TGA
18732522 CATATAAAAT
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
139 9 0.07
140 14 0.11
141 105 0.81
142 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (139 bp):
TGAGAGATATTCATACTTATTTAAAAAAATTGAAGATGACTTATTTTCTTGTTTTTAATAATAAT
TTTAAAGAACACTTATTTTTTTTCTATTTTTAATTTTTATTTAATTTTTTTATTTTAAAATTATT
TTATTGACA
Found at i:18753702 original size:21 final size:21
Alignment explanation
Indices: 18753678--18753717 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18753668 ATTAACAACC
18753678 ATAAAAAATACTTAAAAATAT
1 ATAAAAAATACTTAAAAATAT
* *
18753699 ATAAAAATTATTTAAAAAT
1 ATAAAAAATACTTAAAAAT
18753718 TTTAGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAAATACTTAAAAATAT
Found at i:18753721 original size:9 final size:9
Alignment explanation
Indices: 18753689--18753897 Score: 89
Period size: 9 Copynumber: 21.8 Consensus size: 9
18753679 TAAAAAATAC
18753689 TTAAAAATAT
1 TTAAAAAT-T
*
18753699 ATAAAAATTAT
1 TTAAAAA-T-T
18753710 TTAAAAATT
1 TTAAAAATT
*
18753719 TT--AGATT
1 TTAAAAATT
**
18753726 ATTAAAAAAA
1 -TTAAAAATT
18753736 TTAAAAATT
1 TTAAAAATT
* **
18753745 GTAAAAAAA
1 TTAAAAATT
**
18753754 TTAAATTTT
1 TTAAAAATT
*
18753763 TTAAATATTT
1 TTAAA-AATT
18753773 TTAAAAATAT
1 TTAAAAAT-T
*
18753783 TTTAAAATT
1 TTAAAAATT
*
18753792 TTAAAAAGCTA
1 TTAAAAA--TT
18753803 TTAAAAATT
1 TTAAAAATT
*
18753812 ATAAAACATT
1 TTAAAA-ATT
*
18753822 ATTTAAAATT
1 -TTAAAAATT
*
18753832 TTAAAAAATA
1 TT-AAAAATT
18753842 TTAAAAATT
1 TTAAAAATT
* *
18753851 GTGAAAATT
1 TTAAAAATT
18753860 ATTAAAAAATT
1 -TT-AAAAATT
**
18753871 GAAAATAATT
1 TTAAA-AATT
18753881 ATTAAAAATT
1 -TTAAAAATT
*
18753891 GTAAAAA
1 TTAAAAA
18753898 CTATGAATCA
Statistics
Matches: 147, Mismatches: 37, Indels: 31
0.68 0.17 0.14
Matches are distributed among these distances:
7 4 0.03
8 2 0.01
9 64 0.44
10 47 0.32
11 30 0.20
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (9 bp):
TTAAAAATT
Found at i:18753827 original size:40 final size:38
Alignment explanation
Indices: 18753774--18753897 Score: 142
Period size: 40 Copynumber: 3.2 Consensus size: 38
18753764 TAAATATTTT
* *
18753774 TAAAAA-TATTTTAAAATTTTAAAAAGCTATTAAAAATTA
1 TAAAAATTA-TTTAAAATTTTAAAAA-ATATTAAAAATTG
18753813 TAAAACATTATTTAAAATTTTAAAAAATATTAAAAATTG
1 TAAAA-ATTATTTAAAATTTTAAAAAATATTAAAAATTG
* * * *
18753852 TGAAAATTATTAAAAAATTGAAAATAATTATTAAAAATTG
1 TAAAAATTATTTAAAATTTTAAAA-AA-TATTAAAAATTG
18753892 TAAAAA
1 TAAAAA
18753898 CTATGAATCA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
38 16 0.22
39 22 0.30
40 34 0.46
41 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (38 bp):
TAAAAATTATTTAAAATTTTAAAAAATATTAAAAATTG
Found at i:18753890 original size:10 final size:10
Alignment explanation
Indices: 18753679--18753890 Score: 103
Period size: 10 Copynumber: 21.8 Consensus size: 10
18753669 TTAACAACCA
*
18753679 TAAAAAATACT
1 TAAAAATTA-T
18753690 TAAAAA-TAT
1 TAAAAATTAT
18753699 ATAAAAATTATT
1 -TAAAAATTA-T
18753711 TAAAAATT-T
1 TAAAAATTAT
*
18753720 T--AGATTAT
1 TAAAAATTAT
*
18753728 TAAAAA-AAT
1 TAAAAATTAT
*
18753737 TAAAAATT-G
1 TAAAAATTAT
*
18753746 TAAAAA-AAT
1 TAAAAATTAT
* *
18753755 T-AAATTTTT
1 TAAAAATTAT
* *
18753764 TAAATATTTT
1 TAAAAATTAT
18753774 TAAAAA-TATT
1 TAAAAATTA-T
*
18753784 TTAAAATT-T
1 TAAAAATTAT
*
18753793 TAAAAAGCTAT
1 TAAAAA-TTAT
18753804 TAAAAATTA-
1 TAAAAATTAT
18753813 TAAAACATTAT
1 TAAAA-ATTAT
*
18753824 TTAAAATT-T
1 TAAAAATTAT
*
18753833 TAAAAAATAT
1 TAAAAATTAT
*
18753843 TAAAAATT-G
1 TAAAAATTAT
*
18753852 TGAAAATTAT
1 TAAAAATTAT
18753862 TAAAAA--AT
1 TAAAAATTAT
18753870 TGAAAATAATTAT
1 T--AAA-AATTAT
18753883 TAAAAATT
1 TAAAAATT
18753891 GTAAAAACTA
Statistics
Matches: 152, Mismatches: 26, Indels: 47
0.68 0.12 0.21
Matches are distributed among these distances:
7 4 0.03
8 8 0.05
9 46 0.30
10 57 0.38
11 33 0.22
12 1 0.01
13 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:18754122 original size:22 final size:21
Alignment explanation
Indices: 18754096--18754228 Score: 77
Period size: 21 Copynumber: 6.6 Consensus size: 21
18754086 TTGTTAACTA
18754096 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
18754118 TTTACGATTTTTAATAATT-T
1 TTTACAATTTTTAATAATTAT
* ** * *
18754138 TATA-AAAATTAAATAA-TGT
1 TTTACAATTTTTAATAATTAT
* *
18754157 TTTATAAATTTTAATAACTT-T
1 TTTACAATTTTTAATAA-TTAT
*
18754178 TTTA-AAATTTTAA-AA-TAT
1 TTTACAATTTTTAATAATTAT
*
18754196 TTTAAACAATATTTAATAATTA-
1 TTT--ACAATTTTTAATAATTAT
18754218 -TTACAATTTTT
1 TTTACAATTTTT
18754229 TTTTATAATT
Statistics
Matches: 89, Mismatches: 12, Indels: 23
0.72 0.10 0.19
Matches are distributed among these distances:
17 1 0.01
18 5 0.06
19 22 0.25
20 24 0.27
21 26 0.29
22 9 0.10
23 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:18754179 original size:20 final size:20
Alignment explanation
Indices: 18754126--18754216 Score: 84
Period size: 20 Copynumber: 4.5 Consensus size: 20
18754116 ATTTTACGAT
18754126 TTTTAATAA-TTTTATAAAA
1 TTTTAATAATTTTTATAAAA
* *
18754145 ATTAAATAATGTTTTAT-AAA
1 TTTTAATAAT-TTTTATAAAA
18754165 TTTTAATAACTTTTT-TAAAA
1 TTTTAATAA-TTTTTATAAAA
18754185 TTTTAA-AATATTTTA-AACAA
1 TTTTAATAAT-TTTTATAA-AA
18754205 TATTTAATAATT
1 T-TTTAATAATT
18754217 ATTACAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.02
19 16 0.27
20 26 0.44
21 13 0.22
22 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (20 bp):
TTTTAATAATTTTTATAAAA
Found at i:18788089 original size:2 final size:2
Alignment explanation
Indices: 18788084--18788110 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18788074 TATCTCCCAT
18788084 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 T
18788111 TTTGTTTTCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18803885 original size:9 final size:9
Alignment explanation
Indices: 18803871--18803901 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18803861 GTTAAACGAA
18803871 TCGAGTTAT
1 TCGAGTTAT
*
18803880 TCGAGTTAA
1 TCGAGTTAT
18803889 TCGAGTTAT
1 TCGAGTTAT
18803898 TCGA
1 TCGA
18803902 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18803972 original size:9 final size:9
Alignment explanation
Indices: 18803955--18803991 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18803945 TGAGTTTTCG
18803955 AATTCGAAT
1 AATTCGAAT
*
18803964 AACTCGAAT
1 AATTCGAAT
18803973 AATTCGAAT
1 AATTCGAAT
18803982 AATTCGAAT
1 AATTCGAAT
18803991 A
1 A
18803992 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18809768 original size:23 final size:23
Alignment explanation
Indices: 18809740--18809786 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
18809730 ATTTAATTTT
18809740 TCTTTTTTT-ATGTTCTTTTAAC
1 TCTTTTTTTCATGTTCTTTTAAC
* *
18809762 TCTTTTTTTCATTTTCTTTTTAC
1 TCTTTTTTTCATGTTCTTTTAAC
18809785 TC
1 TC
18809787 CTCCCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (23 bp):
TCTTTTTTTCATGTTCTTTTAAC
Found at i:18810860 original size:24 final size:25
Alignment explanation
Indices: 18810814--18810870 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
18810804 TAAAAAGGAA
* **
18810814 AAAAAAAGTTAAATGAACATAAATG
1 AAAAAAATTTAAATGAACATAAAAC
* *
18810839 AAAAAAATTTAAAT-TACTTAAAAC
1 AAAAAAATTTAAATGAACATAAAAC
18810863 AAAAAAAT
1 AAAAAAAT
18810871 ATAGGAACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (25 bp):
AAAAAAATTTAAATGAACATAAAAC
Found at i:18812763 original size:24 final size:23
Alignment explanation
Indices: 18812688--18812770 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 23
18812678 TATTTTTTTG
18812688 TAATTAATATTATTTATAAGTATTT
1 TAATTAATATTATTTAT-A-TATTT
* *
18812713 TATTTATATATT-TTTATATA-AT
1 TAATTA-ATATTATTTATATATTT
*
18812735 AAATTAATATTATTTATATATTT
1 TAATTAATATTATTTATATATTT
18812758 GTAATTAATATTA
1 -TAATTAATATTA
18812771 GCAATGTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.10
22 13 0.27
23 3 0.06
24 12 0.25
25 10 0.21
26 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATTAATATTATTTATATATTT
Found at i:18819167 original size:21 final size:22
Alignment explanation
Indices: 18819141--18819190 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
18819131 ATTAAAAAAC
* *
18819141 TCAATTAATTGATTA-TAATTT
1 TCAATTAATTAATCACTAATTT
*
18819162 TTAATT-ATTAATCACTAATTT
1 TCAATTAATTAATCACTAATTT
18819183 TCAATTAA
1 TCAATTAA
18819191 AAAACTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (22 bp):
TCAATTAATTAATCACTAATTT
Found at i:18819174 original size:55 final size:55
Alignment explanation
Indices: 18819113--18819223 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
18819103 CAAAGATTAA
*
18819113 ATTAATCACTAATTTTCGATTAAAAAACTCAATTAATTGATTATAATTTTTAATT
1 ATTAATCACTAATTTTCAATTAAAAAACTCAATTAATTGATTATAATTTTTAATT
18819168 ATTAATCACTAATTTTCAATTAAAAAACTCAATTAATTGATTATAATTTTTAATT
1 ATTAATCACTAATTTTCAATTAAAAAACTCAATTAATTGATTATAATTTTTAATT
18819223 A
1 A
18819224 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (55 bp):
ATTAATCACTAATTTTCAATTAAAAAACTCAATTAATTGATTATAATTTTTAATT
Found at i:18820944 original size:13 final size:13
Alignment explanation
Indices: 18820928--18820965 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
18820918 TTTAAACCAA
18820928 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
18820941 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
18820954 ACTTTTCAAAAG
1 ACTTTTCAAAAG
18820966 TAATGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:18823140 original size:16 final size:16
Alignment explanation
Indices: 18823119--18823149 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18823109 CTCCTACTTC
18823119 CGTTTCTAACTCATCA
1 CGTTTCTAACTCATCA
18823135 CGTTTCTAACTCATC
1 CGTTTCTAACTCATC
18823150 CACATGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (16 bp):
CGTTTCTAACTCATCA
Found at i:18827854 original size:29 final size:29
Alignment explanation
Indices: 18827795--18827853 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
18827785 TTTGGTTTAC
* *
18827795 TGTGCAGTTTTATATATAAACTTTAATTT
1 TGTGCAATTTTATATAGAAACTTTAATTT
* *
18827824 TGTGCAATTTTATATAAGAAATTTTGATTT
1 TGTGCAATTTTATAT-AGAAACTTTAATTT
18827854 GATCTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATATAGAAACTTTAATTT
Found at i:18838896 original size:18 final size:18
Alignment explanation
Indices: 18838873--18838908 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18838863 ATTAAGTTGG
*
18838873 AAATCATTTATTAGTATA
1 AAATCATATATTAGTATA
18838891 AAATCATATATTAGTATA
1 AAATCATATATTAGTATA
18838909 CAATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
AAATCATATATTAGTATA
Found at i:18839094 original size:22 final size:22
Alignment explanation
Indices: 18839069--18839110 Score: 50
Period size: 22 Copynumber: 1.9 Consensus size: 22
18839059 TTTTCAAGTA
*
18839069 TTTTTAATTT-TATATTTAATAC
1 TTTTTATTTTATA-ATTTAATAC
*
18839091 TTTTTGTTTTATAATTTAAT
1 TTTTTATTTTATAATTTAAT
18839111 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
22 15 0.88
23 2 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTATAATTTAATAC
Found at i:18839278 original size:7 final size:7
Alignment explanation
Indices: 18839266--18839291 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18839256 AAAAGTGTAT
18839266 ATTTAAA
1 ATTTAAA
18839273 ATTTAAA
1 ATTTAAA
18839280 ATTTAAA
1 ATTTAAA
18839287 ATTTA
1 ATTTA
18839292 CTTTAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:18848737 original size:23 final size:23
Alignment explanation
Indices: 18848696--18848767 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
18848686 TACGATACAT
*
18848696 AAGTGCCTG-AA-ACGACACACG
1 AAGTGCCTGAAATACGACACACA
*
18848717 AAGTGCCTGAAATACGACACATA
1 AAGTGCCTGAAATACGACACACA
* *
18848740 AAGTGCCTGAAATATGACACATA
1 AAGTGCCTGAAATACGACACACA
18848763 AAGTG
1 AAGTG
18848768 TTTGATCGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 9 0.20
22 2 0.04
23 35 0.76
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
AAGTGCCTGAAATACGACACACA
Found at i:18848945 original size:17 final size:17
Alignment explanation
Indices: 18848925--18848957 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18848915 TCATATTTTT
*
18848925 CATTTGATTCAATTTCA
1 CATTTCATTCAATTTCA
18848942 CATTTCATTCAATTTC
1 CATTTCATTCAATTTC
18848958 GATAAGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (17 bp):
CATTTCATTCAATTTCA
Found at i:18850603 original size:5 final size:5
Alignment explanation
Indices: 18850593--18850664 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
18850583 TGTTAAAAAA
* *
18850593 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
18850639 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
18850665 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:18850646 original size:19 final size:19
Alignment explanation
Indices: 18850622--18850664 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
18850612 ATTATGTTTT
18850622 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
18850641 TATATTATATTATATTATA
1 TATATTATATTATATTATA
18850660 TATAT
1 TATAT
18850665 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:18850695 original size:16 final size:16
Alignment explanation
Indices: 18850674--18850706 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18850664 TACATAAAAC
*
18850674 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
18850690 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
18850706 A
1 A
18850707 CAGAATAGAA
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:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:18851695 original size:46 final size:44
Alignment explanation
Indices: 18851635--18851749 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
18851625 ACAGGACAGA
* *
18851635 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
18851681 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
18851725 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
18851750 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:18851730 original size:44 final size:45
Alignment explanation
Indices: 18851635--18851768 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
18851625 ACAGGACAGA
* *
18851635 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
18851681 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
18851725 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
18851769 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:18853204 original size:101 final size:101
Alignment explanation
Indices: 18853027--18853242 Score: 326
Period size: 101 Copynumber: 2.1 Consensus size: 101
18853017 TGCCATAATT
* * * * **
18853027 CAGTTATGGTGTTATCATCAGAATGCCATAGCCCATCTATGGTCTTATATATAAACATTGCCATG
1 CAGTTATGGTCTTACCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAACACCGCCATG
18853092 GTCTAACCATGGTCTTACGTTCATAGTGTCATAACC
66 GTCTAACCATGGTCTTACGTTCATAGTGTCATAACC
* *
18853128 CATTTATGGTCTTACCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAACACCGTCATG
1 CAGTTATGGTCTTACCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAACACCGCCATG
*
18853193 GT-TCAATCATGGTCTTACGTTCATAGTGTCATAACC
66 GTCT-AACCATGGTCTTACGTTCATAGTGTCATAACC
*
18853229 TAGTTATGGTCTTA
1 CAGTTATGGTCTTA
18853243 TCCGTCAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 102 0.99
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (101 bp):
CAGTTATGGTCTTACCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAACACCGCCATG
GTCTAACCATGGTCTTACGTTCATAGTGTCATAACC
Found at i:18857670 original size:58 final size:58
Alignment explanation
Indices: 18857600--18857714 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
18857590 ATAGGGGTTG
* *
18857600 AGTACTAGAAATAGAAAAAATGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAAT
1 AGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAAT
**
18857658 AGTACCAGAAATATCAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
1 AGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAA
18857715 GAGAGGCGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (58 bp):
AGTACCAGAAATAGAAAAAAGGAGGCTAATCGAATCAGGAAATGCTTAACCGAAAAAT
Found at i:18863574 original size:101 final size:101
Alignment explanation
Indices: 18863394--18863584 Score: 247
Period size: 101 Copynumber: 1.9 Consensus size: 101
18863384 GAATTGATGG
* * * * * ** * * *
18863394 ATAAGACCATGGTTGGACCATGGCAATGTTTAAATGTACGGCCATAGTTGGGCTATGGCATTTTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAACTGAGCTATGACATTCTA
*
18863459 ATGAAAAGATCATAACTAAGTTATGGCACCTTGAGC
66 ATGAAAAGACCATAACTAAGTTATGGCACCTTGAGC
*
18863495 ATAAGACCATGGTTGGACCATGACAATATATATATGTAAGACCATAACTGAGCTATGACATTCTA
1 ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAACTGAGCTATGACATTCTA
* * *
18863560 ATGATAAGACCATAATTAGGTTATG
66 ATGAAAAGACCATAACTAAGTTATG
18863585 ACACTACAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (101 bp):
ATAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAACTGAGCTATGACATTCTA
ATGAAAAGACCATAACTAAGTTATGGCACCTTGAGC
Found at i:18863585 original size:33 final size:33
Alignment explanation
Indices: 18863528--18863605 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
18863518 CAATATATAT
* *
18863528 ATGTAAGACCATAACTGAGCTATGACA-TTCTA
1 ATGTAAGACCATAACTGAGCTATGACACTACAA
* *
18863560 ATGATAAGACCATAA-TTAGGTTATGACACTACAA
1 ATG-TAAGACCATAACTGA-GCTATGACACTACAA
18863594 ATGTAAGACCAT
1 ATGTAAGACCAT
18863606 GACAGGGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 5 0.13
33 28 0.72
34 6 0.15
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (33 bp):
ATGTAAGACCATAACTGAGCTATGACACTACAA
Found at i:18878384 original size:28 final size:26
Alignment explanation
Indices: 18878323--18878393 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 26
18878313 ATTTATTAAT
*
18878323 TATTTATAATGTTAATCATTTAAACAA
1 TATTTATAAT-TTAATAATTTAAACAA
* *
18878350 GATTTTATTAATTTAATAATTTAAAACTA
1 TA-TTTA-TAATTTAATAATTT-AAACAA
*
18878379 TATTTACAAATTTAA
1 TATTTA-TAATTTAA
18878394 AAGATAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.03
28 24 0.69
29 10 0.29
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (26 bp):
TATTTATAATTTAATAATTTAAACAA
Found at i:18881082 original size:25 final size:26
Alignment explanation
Indices: 18881054--18881114 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
18881044 GAATATGCTG
18881054 AGAAGAGAAG-ATGAAGAACAGAAGA
1 AGAAGAGAAGAATGAAGAACAGAAGA
**
18881079 AGAA-A-AAGGAATGAAGAATGGAAGA
1 AGAAGAGAA-GAATGAAGAACAGAAGA
18881104 AGAAGAAGAAG
1 AGAAG-AGAAG
18881115 GAGCCTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 21 0.72
27 2 0.07
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.33, T:0.05
Consensus pattern (26 bp):
AGAAGAGAAGAATGAAGAACAGAAGA
Found at i:18881199 original size:18 final size:17
Alignment explanation
Indices: 18881176--18881209 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
18881166 TTTGCAACAC
18881176 AAGGGGAAGGGAGAAGGG
1 AAGGGGAAGGGA-AAGGG
18881194 AAGGGGAAGGGAAAGG
1 AAGGGGAAGGGAAAGG
18881210 TTAAAGGGGA
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:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGAAAGGG
Found at i:18882304 original size:22 final size:23
Alignment explanation
Indices: 18882276--18882345 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 23
18882266 CGGAACTAAG
*
18882276 TTATCAATATTT-TAATGTA-ATT
1 TTATCAAT-TTTATAATCTATATT
18882298 TTATCAATTTTATAATCTATATT
1 TTATCAATTTTATAATCTATATT
* *
18882321 TTAT--ATTTTATATTTTATATT
1 TTATCAATTTTATAATCTATATT
18882342 TTAT
1 TTAT
18882346 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 22 0.51
22 14 0.33
23 7 0.16
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (23 bp):
TTATCAATTTTATAATCTATATT
Found at i:18882325 original size:7 final size:7
Alignment explanation
Indices: 18882304--18882350 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
18882294 AATTTTATCA
18882304 ATTTTAT
1 ATTTTAT
* *
18882311 AATCTAT
1 ATTTTAT
18882318 ATTTTAT
1 ATTTTAT
18882325 ATTTTAT
1 ATTTTAT
18882332 ATTTTAT
1 ATTTTAT
18882339 ATTTTAT
1 ATTTTAT
18882346 ATTTT
1 ATTTT
18882351 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTTAT
Found at i:18883422 original size:20 final size:20
Alignment explanation
Indices: 18883373--18883410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18883363 GTCTAAAAAA
*
18883373 TTATACTTTTTAAAATGAAT
1 TTATACTTTTTAAAAAGAAT
*
18883393 TTATATTTTTTAAAAAGA
1 TTATACTTTTTAAAAAGA
18883411 TTTCTAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATACTTTTTAAAAAGAAT
Found at i:18884353 original size:64 final size:64
Alignment explanation
Indices: 18884259--18884380 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
18884249 GTATACTCCA
* *
18884259 ACTGATCTAATAGTCACTCTATTGTTTCTAGGCAATTCTCAGCAATTTCGGGTTCTGTACTCTG
1 ACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTGTACTCTG
18884323 ACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTGT
1 ACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTGT
18884381 GCCTTTCATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (64 bp):
ACTGATCTAATAGTCACTCTACTGTTTCTAGGCAATACTCAGCAATTTCGGGTTCTGTACTCTG
Found at i:18886227 original size:18 final size:20
Alignment explanation
Indices: 18886186--18886225 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18886176 GATAGAATTG
* *
18886186 TTATTCTTATAAAATAGAAT
1 TTATACTTAAAAAATAGAAT
18886206 TTATACTTAAAAAATA-AAT
1 TTATACTTAAAAAATAGAAT
18886225 T
1 T
18886226 ATCATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TTATACTTAAAAAATAGAAT
Found at i:18909105 original size:22 final size:22
Alignment explanation
Indices: 18909072--18909136 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
18909062 CTCCAATTAT
*
18909072 TAGCACATTAGTGCTCTCTGTA
1 TAGCACTTTAGTGCTCTCTGTA
* * *
18909094 TAGTACTTTAGTGTTCTTTGTA
1 TAGCACTTTAGTGCTCTCTGTA
18909116 TAGCACTTTAGTGCTCTCTGT
1 TAGCACTTTAGTGCTCTCTGT
18909137 TTAATAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (22 bp):
TAGCACTTTAGTGCTCTCTGTA
Found at i:18911445 original size:41 final size:40
Alignment explanation
Indices: 18911400--18911497 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 40
18911390 GCTTAGAGCT
*
18911400 TAGCAGGCTTATTGCCGATGAAACACTTCAGACAAAATGTC
1 TAGCAGGCTTAATGCCGATGAAACA-TTCAGACAAAATGTC
* * * * *
18911441 TAGCAGGCTTAATGCCGGTGAAATATTTAGACTATATGTC
1 TAGCAGGCTTAATGCCGATGAAACATTCAGACAAAATGTC
18911481 TAGCAGGC-TAAGTGCCG
1 TAGCAGGCTTAA-TGCCG
18911498 GTGTACTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.06
40 25 0.50
41 22 0.44
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (40 bp):
TAGCAGGCTTAATGCCGATGAAACATTCAGACAAAATGTC
Found at i:18915654 original size:22 final size:21
Alignment explanation
Indices: 18915619--18915659 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18915609 GCGATGGATA
18915619 CGGGTTAGAGGTGTTACAAAT
1 CGGGTTAGAGGTGTTACAAAT
*
18915640 CGGGTATAGGGGTGTTACAA
1 CGGGT-TAGAGGTGTTACAA
18915660 CGCCATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.10, G:0.37, T:0.27
Consensus pattern (21 bp):
CGGGTTAGAGGTGTTACAAAT
Found at i:18933294 original size:3 final size:3
Alignment explanation
Indices: 18933272--18933309 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
18933262 TACTATGACT
* *
18933272 TTA TTA CTA TTA TCA TTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18933310 CTGTACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:18933585 original size:16 final size:16
Alignment explanation
Indices: 18933552--18933585 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18933542 TATTGTACAC
**
18933552 ATATATATGTATTTGA
1 ATATATATGTATGCGA
18933568 ATATATATGTATGCGA
1 ATATATATGTATGCGA
18933584 AT
1 AT
18933586 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:18935033 original size:3 final size:3
Alignment explanation
Indices: 18935025--18935074 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
18935015 TAAATGAACA
* * *
18935025 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18935073 AA
1 AA
18935075 ATTTGTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18936031 original size:21 final size:23
Alignment explanation
Indices: 18936007--18936051 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
18935997 GTTTGCAGGT
*
18936007 GAGCAGTTG-GGCGATGG-CAGA
1 GAGCAGGTGCGGCGATGGTCAGA
*
18936028 GAGCAGGTGCGGCGCTGGTCAGA
1 GAGCAGGTGCGGCGATGGTCAGA
18936051 G
1 G
18936052 GCGGTGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.20, C:0.18, G:0.49, T:0.13
Consensus pattern (23 bp):
GAGCAGGTGCGGCGATGGTCAGA
Found at i:18936041 original size:22 final size:22
Alignment explanation
Indices: 18936007--18936058 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
18935997 GTTTGCAGGT
*
18936007 GAGCAGTTGGGCGATGG-CAGA
1 GAGCAGGTGGGCGATGGTCAGA
*
18936028 GAGCAGGTGCGGCGCTGGTCAGA
1 GAGCAGGTG-GGCGATGGTCAGA
18936051 G-GC-GGTGG
1 GAGCAGGTGG
18936059 CAGGGGGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 9 0.33
23 5 0.19
ACGTcount: A:0.17, C:0.17, G:0.52, T:0.13
Consensus pattern (22 bp):
GAGCAGGTGGGCGATGGTCAGA
Found at i:18936650 original size:30 final size:30
Alignment explanation
Indices: 18936614--18936672 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
18936604 TCATGTTTTT
*
18936614 ATGAAATTCAAGTACCAAAATGAACTTAAA
1 ATGAAATTCAAGTACCAAAATAAACTTAAA
* **
18936644 ATGAAATTTAAGTATTAAAATAAACTTAA
1 ATGAAATTCAAGTACCAAAATAAACTTAA
18936673 TTATTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (30 bp):
ATGAAATTCAAGTACCAAAATAAACTTAAA
Found at i:18936677 original size:18 final size:18
Alignment explanation
Indices: 18936639--18936685 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
18936629 CAAAATGAAC
*
18936639 TTAAAATGAAATTTAAGTA
1 TTAAAAT-AAACTTAAGTA
*
18936658 TTAAAATAAACTTAATTA
1 TTAAAATAAACTTAAGTA
*
18936676 TTAAATTAAA
1 TTAAAATAAA
18936686 ATACGGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
TTAAAATAAACTTAAGTA
Found at i:18944716 original size:50 final size:50
Alignment explanation
Indices: 18944604--18945097 Score: 664
Period size: 50 Copynumber: 9.7 Consensus size: 50
18944594 ATTTGGGTAA
* *
18944604 AGAGATCCCATGCAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
18944660 AGAGGTCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
18944710 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
18944760 AGAGGTCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
18944810 AGGGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
18944860 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
18944911 AGAGGTCCCATATAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
18944961 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
18945011 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
18945062 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
18945098 TTTAGCATGT
Statistics
Matches: 398, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
50 230 0.58
51 123 0.31
53 3 0.01
55 2 0.01
56 40 0.10
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:18944913 original size:151 final size:151
Alignment explanation
Indices: 18944604--18945097 Score: 738
Period size: 151 Copynumber: 3.2 Consensus size: 151
18944594 ATTTGGGTAA
*
18944604 AGAGATCCCATGCAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGATCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATGAGAGGTCCC
** * * * * **
18944669 ATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGT
60 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGT
*
18944733 CTGGGACATGACATTGGCACCGAGATG
125 CTGGGACATGGCATTGGCACCGAGATG
* *
18944760 AGAGGTCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGGGGTCCCCCGTAA
1 AGAGATCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
18944825 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
66 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
18944890 CATGGCATTGGCACCGAGATG
131 CATGGCATTGGCACCGAGATG
* ** *
18944911 AGAGGTCCCATATAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
1 AGAGATCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
18944976 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
66 GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
* *
18945041 CATGGCATGGGCACCGATATG
131 CATGGCATTGGCACCGAGATG
* *
18945062 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGCAAGACCATGTCTGGGACATGGC
18945098 TTTAGCATGT
Statistics
Matches: 314, Mismatches: 22, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
150 48 0.15
151 192 0.61
152 29 0.09
153 3 0.01
155 2 0.01
156 40 0.13
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (151 bp):
AGAGATCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAA
GACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGA
CATGGCATTGGCACCGAGATG
Found at i:18945043 original size:26 final size:26
Alignment explanation
Indices: 18945014--18945094 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
18945004 CGATATGAGA
18945014 ACATCCCATGTAAGACCATGTCTGGG
1 ACATCCCATGTAAGACCATGTCTGGG
** * * *
18945040 ACATGGCATG--GGCACC--GATATGAGA
1 ACATCCCATGTAAG-ACCATG-TCTG-GG
18945065 ACATCCCATGTAAGACCATGTCTGGG
1 ACATCCCATGTAAGACCATGTCTGGG
18945091 ACAT
1 ACAT
18945095 GGCTTTAGCA
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 12 0.32
26 16 0.42
27 4 0.11
28 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (26 bp):
ACATCCCATGTAAGACCATGTCTGGG
Found at i:18946539 original size:11 final size:11
Alignment explanation
Indices: 18946517--18946557 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
18946507 AACTAATCCT
18946517 CTCTCAAATTTC
1 CTCTC-AATTTC
18946529 CTCTCAATTTC
1 CTCTCAATTTC
* *
18946540 CTCTTAATTTG
1 CTCTCAATTTC
18946551 CTCTCAA
1 CTCTCAA
18946558 ATTATAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.22, C:0.32, G:0.02, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:18948060 original size:19 final size:19
Alignment explanation
Indices: 18948019--18948061 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18948009 AGCTTTAATG
* *
18948019 TTTTTTTTGTTAATTTTAC
1 TTTTTTTAGTTAATTTGAC
18948038 TTTTTTTAGTTAAATTTGA-
1 TTTTTTTAGTT-AATTTGAC
18948057 TTTTT
1 TTTTT
18948062 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTTAGTTAATTTGAC
Found at i:18966367 original size:22 final size:21
Alignment explanation
Indices: 18966336--18966376 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18966326 CATGGCTTGC
*
18966336 ATTTGGATGTGTTCTTATTTAA
1 ATTTGAATGTGTTC-TATTTAA
18966358 ATTTGAATGTGTTCTATTT
1 ATTTGAATGTGTTCTATTT
18966377 TGACATGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (21 bp):
ATTTGAATGTGTTCTATTTAA
Found at i:18967833 original size:12 final size:12
Alignment explanation
Indices: 18967816--18967842 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18967806 AGAAAATTTT
18967816 AACAATATGATA
1 AACAATATGATA
18967828 AACAATATGATA
1 AACAATATGATA
18967840 AAC
1 AAC
18967843 CTTGTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (12 bp):
AACAATATGATA
Found at i:18967954 original size:21 final size:21
Alignment explanation
Indices: 18967928--18967967 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18967918 GTATTTAGTA
18967928 GAGCGTAAAAATAGAAAGATT
1 GAGCGTAAAAATAGAAAGATT
18967949 GAGCGTAAAAATAGAAAGA
1 GAGCGTAAAAATAGAAAGA
18967968 AAAAAATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.25, T:0.15
Consensus pattern (21 bp):
GAGCGTAAAAATAGAAAGATT
Found at i:18970132 original size:49 final size:48
Alignment explanation
Indices: 18970077--18970180 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 48
18970067 TCATGTGTTA
* * *
18970077 TAATTTTATACAGTGTT-GAGTTTTTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCCA-TTTTT-ATTCATGATATTAAACTCAATTT
*
18970126 TAATTTTATAAAGTGTTCCCATTTTTATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTT-CCATTTTTATTCATGATATTAAACTCAATTT
18970175 TAATTT
1 TAATTT
18970181 GTTTTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 43 0.88
50 5 0.10
51 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (48 bp):
TAATTTTATAAAGTGTTCCATTTTTATTCATGATATTAAACTCAATTT
Found at i:18971456 original size:26 final size:26
Alignment explanation
Indices: 18971418--18971558 Score: 86
Period size: 26 Copynumber: 5.5 Consensus size: 26
18971408 AAGTAGATTA
18971418 TAAATTATA-TTTAATAATAATTATT
1 TAAATTATATTTTAATAATAATTATT
*
18971443 TAAATTATATTTT-ATAGT-ATTA--
1 TAAATTATATTTTAATAATAATTATT
* * *
18971465 TATATTATGATTTTAGT-A-AATTCATA
1 TAAATTAT-ATTTTAATAATAATT-ATT
* * *
18971491 TAAGA--ATATTTAATATTAAGAATTTTAT
1 TAA-ATTATATTT--TAATAATAATTAT-T
18971519 TAAATTATA-TTTAATAATAATTATTT
1 TAAATTATATTTTAATAATAATTA-TT
18971545 TAAATTATATTTTA
1 TAAATTATATTTTA
18971559 TAGTATTATA
Statistics
Matches: 88, Mismatches: 11, Indels: 32
0.67 0.08 0.24
Matches are distributed among these distances:
22 7 0.08
23 8 0.09
24 10 0.11
25 15 0.17
26 27 0.31
27 9 0.10
28 9 0.10
29 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (26 bp):
TAAATTATATTTTAATAATAATTATT
Found at i:18971566 original size:15 final size:15
Alignment explanation
Indices: 18971548--18971577 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18971538 ATTATTTTAA
*
18971548 ATTATATTTTATAGT
1 ATTATATATTATAGT
18971563 ATTATATATTATAGT
1 ATTATATATTATAGT
18971578 TTTAGTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTATATATTATAGT
Found at i:18971646 original size:26 final size:26
Alignment explanation
Indices: 18971511--18971647 Score: 85
Period size: 26 Copynumber: 5.5 Consensus size: 26
18971501 TAATATTAAG
* *
18971511 AATTTTATTAAATTATATTTAATAAT
1 AATTATATTAAATTATATTTAATAAC
* * *
18971537 AATTATTTTAAATTATATTTTAT-AG
1 AATTATATTAAATTATATTTAATAAC
* *
18971562 TATTATA-T--ATTATAGTTTTAGT-A-
1 AATTATATTAAATTATA--TTTAATAAC
*
18971585 AATTCATA-TAAGA--ATATTTATTAAC
1 AATT-ATATTAA-ATTATATTTAATAAC
*
18971610 AATTTTATTAAATTATATTTAATAAC
1 AATTATATTAAATTATATTTAATAAC
*
18971636 AATTATGTTAAA
1 AATTATATTAAA
18971648 ATATGATTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 22
0.70 0.11 0.18
Matches are distributed among these distances:
22 6 0.07
23 8 0.09
24 14 0.16
25 16 0.19
26 41 0.48
27 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
AATTATATTAAATTATATTTAATAAC
Found at i:18971676 original size:102 final size:100
Alignment explanation
Indices: 18971418--18971647 Score: 385
Period size: 102 Copynumber: 2.3 Consensus size: 100
18971408 AAGTAGATTA
18971418 TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
1 TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
*
18971483 AATTCATATAAGAATATTTAATATTAAGAATTTTAT
66 AATTCATATAAGAATATTT-ATATTAACAATTTTAT
18971519 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTAT-AGTTTTAG
1 TAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA-TTTTAG
18971583 TAAATTCATATAAGAATA-TT-TATTAACAATTTTAT
64 TAAATTCATATAAGAATATTTATATTAACAATTTTAT
*
18971618 TAAATTATATTTAATAACAATTATGTTAAA
1 TAAATTATATTTAATAATAATTAT-TTAAA
18971648 ATATGATTAA
Statistics
Matches: 124, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
98 1 0.01
99 41 0.33
101 26 0.21
102 56 0.45
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (100 bp):
TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
AATTCATATAAGAATATTTATATTAACAATTTTAT
Found at i:18971834 original size:39 final size:43
Alignment explanation
Indices: 18971781--18971882 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 43
18971771 TTTCCTTATG
* * *
18971781 CTATTACACATCTATTC-T-ATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCATCATTCAACCAAACAAAAGAATTAC
*
18971821 C-ATTACGCCTCTATTCCATTCCATTCAACCAAGCAAAAGAATTAC
1 CTATTACGCCTCTATT-CA-T-CATTCAACCAAACAAAAGAATTAC
18971866 CTATTACGCCTCTATTC
1 CTATTACGCCTCTATTC
18971883 CATTACACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
39 12 0.24
40 2 0.04
42 1 0.02
44 17 0.33
45 5 0.10
46 14 0.27
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.29
Consensus pattern (43 bp):
CTATTACGCCTCTATTCATCATTCAACCAAACAAAAGAATTAC
Found at i:18971849 original size:44 final size:46
Alignment explanation
Indices: 18971794--18971886 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
18971784 TTACACATCT
* *
18971794 ATTCTATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
*
18971838 ATTCCATTCAACCAAGCAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
18971884 ATT
1 ATT
18971887 ACACTTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 21 0.48
45 4 0.09
46 19 0.43
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:18972853 original size:20 final size:21
Alignment explanation
Indices: 18972808--18972853 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
18972798 GGTTTTCTAG
18972808 GATTTTTTATTTTAGTGTTTA
1 GATTTTTTATTTTAGTGTTTA
* *
18972829 CATTTTTTATTTTA-TTTTTA
1 GATTTTTTATTTTAGTGTTTA
18972849 GATTT
1 GATTT
18972854 AAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.70
Consensus pattern (21 bp):
GATTTTTTATTTTAGTGTTTA
Found at i:18974994 original size:25 final size:25
Alignment explanation
Indices: 18974954--18975046 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
18974944 CCCATATGAG
*
18974954 CATATAATCAGGAAGCTCTTTCGAGC
1 CATATAA-CGGGAAGCTCTTTCGAGC
* * *
18974980 CATATAACGGAAAGCTCATGT-AAGC
1 CATATAACGGGAAGCTC-TTTCGAGC
** *
18975005 TGTATAACGGGAAGCTCTTGCGAGC
1 CATATAACGGGAAGCTCTTTCGAGC
* *
18975030 CAAATATCGGGAAGCTC
1 CATATAACGGGAAGCTC
18975047 AAGAAAGCCA
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
24 1 0.02
25 41 0.80
26 9 0.18
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (25 bp):
CATATAACGGGAAGCTCTTTCGAGC
Found at i:18975325 original size:11 final size:11
Alignment explanation
Indices: 18975308--18975345 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
18975298 TTTTTAATCA
18975308 AATATATATTT
1 AATATATATTT
* *
18975319 TATATATATTA
1 AATATATATTT
18975330 AATATATATTT
1 AATATATATTT
18975341 AATAT
1 AATAT
18975346 GGGTCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:18975332 original size:22 final size:22
Alignment explanation
Indices: 18975277--18975345 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
18975267 TAACCCGAAT
*
18975277 TATATATTAAATAT-TTTTTTA
1 TATATATTAAATATATATTTTA
* * *
18975298 TTTTTAATCAAATATATATTTTA
1 TATAT-ATTAAATATATATTTTA
*
18975321 TATATATTAAATATATATTTAA
1 TATATATTAAATATATATTTTA
18975343 TAT
1 TAT
18975346 GGGTCGGGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.08
22 26 0.68
23 9 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATTAAATATATATTTTA
Found at i:18975516 original size:25 final size:25
Alignment explanation
Indices: 18975482--18975531 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
18975472 ATCACCTCTA
*
18975482 GTGAGAGCCAAGTATCGGGAAGCTC
1 GTGAGAGCCAAATATCGGGAAGCTC
*
18975507 GTGAGAGCCAAATATCGGGACGCTC
1 GTGAGAGCCAAATATCGGGAAGCTC
18975532 ATAAAAGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (25 bp):
GTGAGAGCCAAATATCGGGAAGCTC
Found at i:18977816 original size:11 final size:11
Alignment explanation
Indices: 18977800--18977833 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
18977790 CGCTTACAAT
18977800 AATAATAATTA
1 AATAATAATTA
18977811 AATAATAATTA
1 AATAATAATTA
18977822 AATAATTAATTA
1 AATAA-TAATTA
18977834 GTATTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAATAATTA
Found at i:19000284 original size:33 final size:36
Alignment explanation
Indices: 19000247--19000327 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 36
19000237 ATGGTTATAT
19000247 TTAAATATTTAAAATATAATT-TATTTATT-C-TAA
1 TTAAATATTTAAAATATAATTATATTTATTGCTTAA
**
19000280 TTAAAT-TTTGTAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT-ATATTTATTGCTTAA
19000315 --AAATATTTAAAAT
1 TTAAATATTTAAAAT
19000328 TTATATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
31 6 0.16
32 5 0.13
33 18 0.47
34 6 0.16
35 3 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (36 bp):
TTAAATATTTAAAATATAATTATATTTATTGCTTAA
Found at i:19000540 original size:13 final size:13
Alignment explanation
Indices: 19000524--19000589 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
19000514 TTTAAACTAA
19000524 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
19000537 ACTTCTT-AAAAAC
1 ACTT-TTCAAAAAC
* * ***
19000550 ACATTTCTACGTC
1 ACTTTTCAAAAAC
19000563 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
*
19000576 AATTTTCAAAAAC
1 ACTTTTCAAAAAC
19000589 A
1 A
19000590 TTCTCAAACT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 2 0.05
13 36 0.90
14 2 0.05
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:19016631 original size:23 final size:23
Alignment explanation
Indices: 19016605--19016649 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19016595 AAATTAATTA
*
19016605 TGTAATATCCCGAAAATTACTAT
1 TGTAATACCCCGAAAATTACTAT
19016628 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAATTACTA
19016650 CAGTAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAT
Found at i:19016655 original size:23 final size:23
Alignment explanation
Indices: 19016606--19016655 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
19016596 AATTAATTAT
* **
19016606 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTACA
19016629 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
19016652 GTAA
1 GTAA
19016656 GAAAGTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTACA
Found at i:19018526 original size:46 final size:46
Alignment explanation
Indices: 19018459--19018552 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
19018449 ACAATGCTAT
19018459 AACTCAGTATAGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATAGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
* **
19018505 AACTCAGTATGGTTTTTTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATAGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
19018551 AA
1 AA
19018553 TTTGCCATGG
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:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (46 bp):
AACTCAGTATAGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:19021921 original size:24 final size:25
Alignment explanation
Indices: 19021889--19021940 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
19021879 TGATCGAGAT
* *
19021889 GCTCCGAAGAGCA-TTTAATGGGAA
1 GCTCCGAAGAACACTATAATGGGAA
*
19021913 GCTCGGAAGAACACTATAATGGGAA
1 GCTCCGAAGAACACTATAATGGGAA
19021938 GCT
1 GCT
19021941 TGAAAAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (25 bp):
GCTCCGAAGAACACTATAATGGGAA
Found at i:19024297 original size:17 final size:17
Alignment explanation
Indices: 19024277--19024314 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19024267 AATAATTTAA
*
19024277 AATATAAACATTAATAT
1 AATATAAAAATTAATAT
*
19024294 AATATAAAAATTATTAT
1 AATATAAAAATTAATAT
19024311 AATA
1 AATA
19024315 AATAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAAAAATTAATAT
Found at i:19025197 original size:16 final size:15
Alignment explanation
Indices: 19025172--19025202 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
19025162 AATTATTAAA
19025172 ATAATAATTATAATT
1 ATAATAATTATAATT
19025187 ATAAGTAATTATAATT
1 ATAA-TAATTATAATT
19025203 CTTTGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAATAATTATAATT
Found at i:19025281 original size:16 final size:17
Alignment explanation
Indices: 19025260--19025300 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
19025250 AATTAATTGT
19025260 AATTATATAAT-TAAAA
1 AATTATATAATCTAAAA
19025276 AATTATATAATCTAAAA
1 AATTATATAATCTAAAA
*
19025293 AATAATAT
1 AATTATAT
19025301 TACTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTATATAATCTAAAA
Found at i:19025618 original size:20 final size:19
Alignment explanation
Indices: 19025573--19025621 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
19025563 ATTTAGTTAA
19025573 AATT-AATATAAATAATTT
1 AATTAAATATAAATAATTT
* *
19025591 ATAATAAATACTAAGTAATTT
1 A-ATTAAATA-TAAATAATTT
19025612 AATTAAATAT
1 AATTAAATAT
19025622 TTAGTAGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 11 0.44
21 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTAAATATAAATAATTT
Found at i:19025620 original size:24 final size:23
Alignment explanation
Indices: 19025560--19025620 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 23
19025550 TAAATAATTT
* *
19025560 GTAATTTAGTTAAAATTAATATAA
1 GTAATTTAATT-AAATAAATATAA
*
19025584 ATAATTT-A-T-AATAAATACTAA
1 GTAATTTAATTAAATAAATA-TAA
19025605 GTAATTTAATTAAATA
1 GTAATTTAATTAAATA
19025621 TTTAGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 2 0.07
23 1 0.03
24 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
GTAATTTAATTAAATAAATATAA
Done.