Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 38 of 109
Found at i:5837269 original size:2 final size:2
Alignment explanation
Indices: 5837262--5837295 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5837252 CACTTTTATC
5837262 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5837296 TACTTACATT
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):
CT
Found at i:5838682 original size:18 final size:17
Alignment explanation
Indices: 5838659--5838703 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
5838649 ATTTATTTTG
*
5838659 AATTTTATTTTAATTATT
1 AATTTTATTTTAA-TATA
5838677 AA--TT-TTTTAATATA
1 AATTTTATTTTAATATA
5838691 AATTTTATTTTAA
1 AATTTTATTTTAA
5838704 AAGATAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 5 0.22
15 6 0.26
16 4 0.17
17 6 0.26
18 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATTTTAATATA
Found at i:5839062 original size:20 final size:20
Alignment explanation
Indices: 5839027--5839072 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5839017 AGATTCATAT
*
5839027 TTTTCGACGTAATTTCTCAA
1 TTTTCGACGTAATTTCCCAA
** *
5839047 TTTTCGACGTTGTTTCCCAG
1 TTTTCGACGTAATTTCCCAA
5839067 TTTTCG
1 TTTTCG
5839073 GTAAAACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (20 bp):
TTTTCGACGTAATTTCCCAA
Found at i:5839415 original size:12 final size:12
Alignment explanation
Indices: 5839379--5839415 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5839369 CATTCTTTGG
5839379 TATTT-TTATTT
1 TATTTATTATTT
5839390 TATTTATT-TATT
1 TATTTATTAT-TT
5839402 TATTTATTATTT
1 TATTTATTATTT
5839414 TA
1 TA
5839416 GCATGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 16 0.70
13 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTATTATTT
Found at i:5839619 original size:8 final size:8
Alignment explanation
Indices: 5839601--5839677 Score: 104
Period size: 8 Copynumber: 9.5 Consensus size: 8
5839591 ATATTTTTTT
5839601 AAATA-AA
1 AAATATAA
5839608 AAATATAA
1 AAATATAA
5839616 AAATAATAA
1 AAAT-ATAA
5839625 AAATATAA
1 AAATATAA
5839633 AAATA-ATA
1 AAATATA-A
5839641 AAATATAA
1 AAATATAA
5839649 AAATAATAA
1 AAAT-ATAA
*
5839658 AAACATAA
1 AAATATAA
5839666 AAATATAA
1 AAATATAA
5839674 AAAT
1 AAAT
5839678 TTTGGCATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
7 6 0.10
8 41 0.65
9 16 0.25
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATATAA
Found at i:5839628 original size:17 final size:17
Alignment explanation
Indices: 5839606--5839677 Score: 121
Period size: 17 Copynumber: 4.4 Consensus size: 17
5839596 TTTTTAAATA
5839606 AAAAATATAAAAATAAT
1 AAAAATATAAAAATAAT
5839623 AAAAATATAAAAATAAT
1 AAAAATATAAAAATAAT
5839640 -AAAATATAAAAATAAT
1 AAAAATATAAAAATAAT
*
5839656 AAAAACATAAAAAT-AT
1 AAAAATATAAAAATAAT
5839672 AAAAAT
1 AAAAAT
5839678 TTTGGCATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
16 23 0.44
17 29 0.56
ACGTcount: A:0.76, C:0.01, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATATAAAAATAAT
Found at i:5839677 original size:33 final size:32
Alignment explanation
Indices: 5839601--5839677 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 32
5839591 ATATTTTTTT
*
5839601 AAATAAAAAATATAAAAATAATAAAAATATAA
1 AAATAAAAAATATAAAAATAATAAAAACATAA
5839633 AAATAATAAAATATAAAAATAATAAAAACATAA
1 AAATAA-AAAATATAAAAATAATAAAAACATAA
5839666 AAATATAAAAAT
1 AAATA-AAAAAT
5839678 TTTGGCATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 6 0.14
33 35 0.83
34 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (32 bp):
AAATAAAAAATATAAAAATAATAAAAACATAA
Found at i:5840073 original size:49 final size:48
Alignment explanation
Indices: 5840018--5840114 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
5840008 TTTCCAAGAA
* * *
5840018 AAAAAAAGAATTTATAAATAGATCTAAATAGTGAAAAATTTAGAAATTTCG
1 AAAAAAA-AA-TTATAAATAGACCCAAATAGTAAAAAATTTA-AAATTTCG
* *
5840069 AAAAAAAAATTCTAAATAGACCCAAATTGTAAAAAATTTAAAATTT
1 AAAAAAAAATTATAAATAGACCCAAATAGTAAAAAATTTAAAATTT
5840115 TCAAAAGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 6 0.15
49 26 0.63
50 2 0.05
51 7 0.17
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (48 bp):
AAAAAAAAATTATAAATAGACCCAAATAGTAAAAAATTTAAAATTTCG
Found at i:5841220 original size:50 final size:50
Alignment explanation
Indices: 5841164--5841272 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
5841154 GTATCTATAT
*
5841164 CATTTTCATATCATTCCATTTTATGCATCATTTTCATCCTCATGTTTTAA
1 CATTTTCATATCATTCCATTTTATGCATCATTTTCATCATCATGTTTTAA
* ** *
5841214 CATTTTCATATCTTTTTATTTTATGCATCATTTTCATGATCATGTTTTAA
1 CATTTTCATATCATTCCATTTTATGCATCATTTTCATCATCATGTTTTAA
*
5841264 CATTATCAT
1 CATTTTCAT
5841273 TTGCATCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (50 bp):
CATTTTCATATCATTCCATTTTATGCATCATTTTCATCATCATGTTTTAA
Found at i:5850780 original size:17 final size:17
Alignment explanation
Indices: 5850737--5850790 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
5850727 AAGAAAAGAG
5850737 AAAACAAAAGGAAAAAGAAT
1 AAAA-AAAA-GAAAAA-AAT
* *
5850757 GAAAAAATGAAAAAAAT
1 AAAAAAAAGAAAAAAAT
5850774 AAAAAAAAGAAGAAAAA
1 AAAAAAAAGAA-AAAAA
5850791 CTCAAGGCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 12 0.41
18 11 0.38
19 3 0.10
20 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAT
Found at i:5851891 original size:43 final size:43
Alignment explanation
Indices: 5851793--5852200 Score: 429
Period size: 43 Copynumber: 9.6 Consensus size: 43
5851783 ATGATTGTCA
* * *
5851793 AGGAGCATTTTATTTTTCCAAAGTTGTGG-TGCCTTTATTTAG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
** * * *
5851835 AAAAGTAATTTATTTTTCCAAAGTTGTGGTTGCCTTTGTTTGG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* * *
5851878 AGGAGCAAATTA-TTTT-CAAAGTTGTGGTTACCTCTATTTAG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* *
5851919 ATGAGCAATTTATTTTTTTCAAAGTTGTGGTTGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* * * * *
5851963 AGAAGTAATTTATTTTTTCAAAAGTTGTTG-AGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* ** *
5852006 ATGAGCAATTTATTTTTTTAAAGTTGTAGTTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* *
5852049 ATGAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* * *
5852092 AGGAGTAA--T-TTTTTCCAAAGTTGTGGTTGCTTTTGTTTAG
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* * * *
5852132 AGGAGCAATTTATTTTT-CGAAGTTGTAG-TGCCTCTATTTAA
1 AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
* *
5852173 ATGAGCAATTTATTATTTTCAAAGTTGT
1 AGGAGCAATTTATT-TTTCCAAAGTTGT
5852201 TGTACCTTTG
Statistics
Matches: 308, Mismatches: 48, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
40 35 0.11
41 54 0.18
42 56 0.18
43 116 0.38
44 47 0.15
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.45
Consensus pattern (43 bp):
AGGAGCAATTTATTTTTCCAAAGTTGTGGTTGCCTCTGTTTAG
Found at i:5852827 original size:15 final size:14
Alignment explanation
Indices: 5852807--5852838 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
5852797 TTTTTAAAAA
5852807 TTTTTTGGTAAATTT
1 TTTTTTGG-AAATTT
5852822 TTTTTTGGAAATTT
1 TTTTTTGGAAATTT
5852836 TTT
1 TTT
5852839 GGAAAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (14 bp):
TTTTTTGGAAATTT
Found at i:5853516 original size:8 final size:8
Alignment explanation
Indices: 5853503--5853543 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
5853493 TATTTTCAAA
5853503 ATAAAAAT
1 ATAAAAAT
5853511 ATAAAAAT
1 ATAAAAAT
*
5853519 AATAAAAAC
1 -ATAAAAAT
5853528 ATAAAAAT
1 ATAAAAAT
5853536 ATAAAAAT
1 ATAAAAAT
5853544 TTTGGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
ATAAAAAT
Found at i:5853524 original size:17 final size:17
Alignment explanation
Indices: 5853502--5853543 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
5853492 TTATTTTCAA
5853502 AATAAAAATATAAAAAT
1 AATAAAAATATAAAAAT
*
5853519 AATAAAAACATAAAAAT
1 AATAAAAATATAAAAAT
5853536 -ATAAAAAT
1 AATAAAAAT
5853544 TTTGGAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAATATAAAAAT
Found at i:5853628 original size:26 final size:24
Alignment explanation
Indices: 5853568--5853629 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
5853558 CAAATTACCT
*
5853568 AATGATGAGATTCTTAGAAATTTCA
1 AATGA-GAAATTCTTAGAAATTTCA
* *
5853593 AATGATAAATTCTTAAGAAATCTTTA
1 AATGAGAAATTCTT-AGAAAT-TTCA
*
5853619 GATGAGAAATT
1 AATGAGAAATT
5853630 TCTTCTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 12 0.40
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (24 bp):
AATGAGAAATTCTTAGAAATTTCA
Found at i:5855881 original size:12 final size:11
Alignment explanation
Indices: 5855846--5855922 Score: 50
Period size: 12 Copynumber: 6.5 Consensus size: 11
5855836 TGTGAAAATT
5855846 TTTAATTAAATAA
1 TTTAA-TAAA-AA
*
5855859 TTTAATTAAAA
1 TTTAATAAAAA
5855870 TTATAATAAAAA
1 TT-TAATAAAAA
*
5855882 TTTAAATTTATAAA
1 TTT-AA--TAAAAA
*
5855896 TTT-AT-GAAA
1 TTTAATAAAAA
5855905 TTTAATAAAAAA
1 TTTAAT-AAAAA
5855917 TTTAAT
1 TTTAAT
5855923 GATATGTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
9 6 0.12
10 3 0.06
11 5 0.10
12 25 0.48
13 5 0.10
14 8 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
TTTAATAAAAA
Found at i:5855935 original size:21 final size:22
Alignment explanation
Indices: 5855893--5855942 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
5855883 TTAAATTTAT
*
5855893 AAATTT-ATGAAATTTAATAAA
1 AAATTTAATGAAATGTAATAAA
*
5855914 AAATTTAATGATATGTAA-AAA
1 AAATTTAATGAAATGTAATAAA
*
5855935 ATATTTAA
1 AAATTTAA
5855943 AATATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTTAATGAAATGTAATAAA
Found at i:5856846 original size:2 final size:2
Alignment explanation
Indices: 5856833--5856868 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5856823 TTTATTGATA
*
5856833 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5856869 AGTGAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5858214 original size:21 final size:22
Alignment explanation
Indices: 5858190--5858230 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5858180 ATAAAATATA
*
5858190 TATTTATTA-TTTTATTAAATT
1 TATTTATAATTTTTATTAAATT
5858211 TATTTATAATTTTTATTAAA
1 TATTTATAATTTTTATTAAA
5858231 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTATAATTTTTATTAAATT
Found at i:5864287 original size:29 final size:29
Alignment explanation
Indices: 5864220--5864289 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
5864210 TATTTTTATT
* *
5864220 AAAAAATTAATAAATTTAAAATTATAATG
1 AAAAAATTAATAAAATTAAAATTATAATA
* *
5864249 ATAAATTTAATAAAATTAAAA-TATAATA
1 AAAAAATTAATAAAATTAAAATTATAATA
5864277 ACAAAAATTAATA
1 A-AAAAATTAATA
5864290 TTAATCTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAAAATTAATAAAATTAAAATTATAATA
Found at i:5865612 original size:19 final size:20
Alignment explanation
Indices: 5865590--5865631 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5865580 AAATTTATTT
5865590 ATTATATTA-AATTAAT-AAA
1 ATTATATTACAA-TAATCAAA
*
5865609 ATTATTTTACAATAATCAAA
1 ATTATATTACAATAATCAAA
5865629 ATT
1 ATT
5865632 TGATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTATATTACAATAATCAAA
Found at i:5865613 original size:26 final size:28
Alignment explanation
Indices: 5865552--5865615 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
5865542 AATTTTATTT
*
5865552 AAATTATTTATTAATATATTATATAATA
1 AAATTATTTATTAATATATAATATAATA
5865580 AAATTTATTTATT-ATAT-TAA-ATTAATA
1 AAA-TTATTTATTAATATATAATA-TAATA
5865607 AAATTATTT
1 AAATTATTT
5865616 TACAATAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.21
27 10 0.30
28 7 0.21
29 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATTATTTATTAATATATAATATAATA
Found at i:5869378 original size:23 final size:23
Alignment explanation
Indices: 5869348--5869393 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5869338 GGTCCCCCTT
*
5869348 TTCAAATTACAGCAACTATCCAC
1 TTCAAATTAAAGCAACTATCCAC
5869371 TTCAAATTAAAGCAACTATCCAC
1 TTCAAATTAAAGCAACTATCCAC
5869394 CTAACATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.26
Consensus pattern (23 bp):
TTCAAATTAAAGCAACTATCCAC
Found at i:5873647 original size:371 final size:368
Alignment explanation
Indices: 5873029--5873798 Score: 904
Period size: 371 Copynumber: 2.1 Consensus size: 368
5873019 GAATAATATC
* * * **
5873029 TCACAAATGTGTGAACTGTGACAGGAAGATTGATCCGAGACACCGGAAGAGTGAATGCCCGAGTT
1 TCACAAAGGTATGAACCGTGACAGGAAGGCTGATCCGAGACACCGGAAGAGTGAATGCCCGAGTT
* * * * *** *
5873094 TCGGAGCCGCGCGGGTTCGAAGTTTAAGTCTCGACTTGTGACAAATGGTATCAGAGCCAGCCCTA
66 CCGGAGCCGCGCAGGTTCGAAGCTTAAGTCTCAACCCATGACAAATGATATCAGAGCCAGCCCTA
* * * * * *
5873159 AATCGTTCCACACCAAGCGCTTCTAGAGAGATAGGTATGGTGGCCAACCTCCATGACGAAGACGT
131 AACCGTTCCACACCAAGCGCCTCGAGAGAGATAGGCAAGGTAGCCAACCTCCATGACGAAGACGT
* * *
5873224 CATGATGTTAGGTGGAAGAGAATGTTACAGACCTAAGAAAAAGTCATGAATCTCACATCGAACAT
196 CACGAAGTTAGGTGGAAGAGAATGTCACAGACCTAAGAAAAAGTCATGAATCTCACATCGAACAT
* * **
5873289 AATAAGAAGGTCACTGAGATATAAAAATGTTCATACCACCTCTTTCT-TGTGAGATGCCTTTTGT
261 AATAAGAAGGTCACTGAGATATAAAAAGGTTCACACCACCTCTTTCTGT-TGAGACACCTTTTGT
* *
5873353 AGGATAAAACCGTGAGGCC-A-GAGGGGGTCAGAGAGGACAATACCT
325 AGGACAAAACCGTGAGGCCAATGA-GGGCT-AGAGAGGACAATA-CT
* * * *
5873398 T-ACAAGGGTATGAACCGTGACAGGAAGGCTGATCCGAGACATCGGAAGGGTGAATGCCCGGGTT
1 TCACAAAGGTATGAACCGTGACAGGAAGGCTGATCCGAGACACCGGAAGAGTGAATGCCCGAGTT
* * ***
5873462 CCGG-GCCGTGCAGGTTCGAAGCTTAAGTCTCAACCCATGACAAATGATATCAGAGTCAGTTTTA
66 CCGGAGCCGCGCAGGTTCGAAGCTTAAGTCTCAACCCATGACAAATGATATCAGAGCCAGCCCTA
* * * * * *
5873526 AACCGTTCGATCCACGTCAAGCTCCTCGAGGGAGGTAGGCAAGGTAGCCAGCCTCCATGA-TAAG
131 AACCGTTCCA--CAC--CAAGCGCCTCGAGAGAGATAGGCAAGGTAGCCAACCTCCATGACGAAG
* * * * *
5873590 AGCGTCACGAAGTTAGGTGGAGGAGAATGTCACGGACCTAAGGAAGAGTCTTGAATCTCACATCG
192 A-CGTCACGAAGTTAGGTGGAAGAGAATGTCACAGACCTAAGAAAAAGTCATGAATCTCACATCG
* * * * *
5873655 AACATAATAAGAGGGTCACTGGGGTATAAAAGGGTTCACACCACCTCTTTCTGTTGAGGCACCTT
256 AACATAATAAGAAGGTCACTGAGATATAAAAAGGTTCACACCACCTCTTTCTGTTGAGACACCTT
* *
5873720 TTGTAGGACAAAACTGTGAGGCCAATGAGGGCTAGAGCGGACAATACT
321 TTGTAGGACAAAACCGTGAGGCCAATGAGGGCTAGAGAGGACAATACT
* *
5873768 TCACAAAGGTGTGAACCGTGACAAGAAGGCT
1 TCACAAAGGTATGAACCGTGACAGGAAGGCT
5873799 CCTACAAAAT
Statistics
Matches: 334, Mismatches: 58, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
367 56 0.17
368 57 0.17
369 4 0.01
370 7 0.02
371 202 0.60
372 6 0.02
373 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (368 bp):
TCACAAAGGTATGAACCGTGACAGGAAGGCTGATCCGAGACACCGGAAGAGTGAATGCCCGAGTT
CCGGAGCCGCGCAGGTTCGAAGCTTAAGTCTCAACCCATGACAAATGATATCAGAGCCAGCCCTA
AACCGTTCCACACCAAGCGCCTCGAGAGAGATAGGCAAGGTAGCCAACCTCCATGACGAAGACGT
CACGAAGTTAGGTGGAAGAGAATGTCACAGACCTAAGAAAAAGTCATGAATCTCACATCGAACAT
AATAAGAAGGTCACTGAGATATAAAAAGGTTCACACCACCTCTTTCTGTTGAGACACCTTTTGTA
GGACAAAACCGTGAGGCCAATGAGGGCTAGAGAGGACAATACT
Found at i:5873882 original size:97 final size:97
Alignment explanation
Indices: 5873713--5873904 Score: 271
Period size: 97 Copynumber: 2.0 Consensus size: 97
5873703 TTCTGTTGAG
* *
5873713 GCACCTTTTGTAGGACAAAACTGTGAGGCCAATGAGGGCTAGAGCGGACAATACTTCACAAAGGT
1 GCACCTTTTGTAGGACAAAACTGTGAGGCCAATGAGGGCTAAAGCGGACAATACCTCACAAAGGT
* *
5873778 GTGAACCGTGACAAGAAGGCTCCTACAAAATT
66 GTAAACCGTGACAAGAAAGCTCCTACAAAATT
* *
5873810 GCACCTTTTGTAGGATAAAA-TCGTGAGGCCAAT-AGGGGTCAAAGCGGACAATACCTCACAAAG
1 GCACCTTTTGTAGGACAAAACT-GTGAGGCCAATGAGGGCT-AAAGCGGACAATACCTCACAAAG
* * *
5873873 GTGTAAACCGTGATAGGAAAGCTTCTACAAAA
64 GTGTAAACCGTGACAAGAAAGCTCCTACAAAA
5873905 CCGTGAGGCC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 6 0.07
97 78 0.93
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (97 bp):
GCACCTTTTGTAGGACAAAACTGTGAGGCCAATGAGGGCTAAAGCGGACAATACCTCACAAAGGT
GTAAACCGTGACAAGAAAGCTCCTACAAAATT
Found at i:5873966 original size:75 final size:75
Alignment explanation
Indices: 5873826--5873966 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 75
5873816 TTTGTAGGAT
* * ** *
5873826 AAAATCGTGAGGCCAATAGGGGTCAAAGCGGACAATACCTCACAAAGGTGTAAACCGTGATAGGA
1 AAAACCGTGAGGCCAAGAGGGACCAAAGCGGACAATACCTCACAAAGGTGTAAACCGTGACAGGA
5873891 AAGCTTCTAC
66 AAGCTTCTAC
* * * *
5873901 AAAACCGTGAGGCCAAGAGGGACCAAAGTGGACAATACCTCACAAGGGTGTGAACTGTGACAGGA
1 AAAACCGTGAGGCCAAGAGGGACCAAAGCGGACAATACCTCACAAAGGTGTAAACCGTGACAGGA
5873966 A
66 A
5873967 GGCTGATCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.15
Consensus pattern (75 bp):
AAAACCGTGAGGCCAAGAGGGACCAAAGCGGACAATACCTCACAAAGGTGTAAACCGTGACAGGA
AAGCTTCTAC
Found at i:5874275 original size:95 final size:97
Alignment explanation
Indices: 5874110--5874298 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 97
5874100 GTGAGGCACT
* * * * *
5874110 TTTTGTATGATAAAATCGTGAGGTCAATGGGGGTCAGAGCGGACAATACCTCACAAAGGTGTGAA
1 TTTTGTAGGACAAAACCGTGAGGTCAATGGGGGCCAGAGCGGACAATACCTCACAAAAGTGTGAA
*
5874175 CCGTGACAGGAAGGCTCCTACAAAACCGTATC
66 CCGTGACAAGAAGGCTCCTACAAAACCGTATC
*
5874207 TTTTGTAGGACAAAACCGTGAGGTCAAT-GGGGCCAGAGC-GACATTACCTCACAAAAGTGTGAA
1 TTTTGTAGGACAAAACCGTGAGGTCAATGGGGGCCAGAGCGGACAATACCTCACAAAAGTGTGAA
5874270 CCGTGACAAGAAGGCTCCTACAAAACCGT
66 CCGTGACAAGAAGGCTCCTACAAAACCGT
5874299 GAGGCCAAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
95 50 0.59
96 10 0.12
97 25 0.29
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (97 bp):
TTTTGTAGGACAAAACCGTGAGGTCAATGGGGGCCAGAGCGGACAATACCTCACAAAAGTGTGAA
CCGTGACAAGAAGGCTCCTACAAAACCGTATC
Found at i:5877805 original size:41 final size:41
Alignment explanation
Indices: 5877746--5877829 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
5877736 GTCTCATCGC
* *
5877746 TGAAAGATATTTTTGTATGGAAGCATC-ATCCATAG-CTATAA
1 TGAAAGATATTTTCGTATGAAAGCATCGA-CCAT-GCCTATAA
*
5877787 TGAAAGTTATTTTCGTATGAAAGCATCGACCATGCCTATAA
1 TGAAAGATATTTTCGTATGAAAGCATCGACCATGCCTATAA
5877828 TG
1 TG
5877830 TATTAACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 36 0.95
42 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (41 bp):
TGAAAGATATTTTCGTATGAAAGCATCGACCATGCCTATAA
Found at i:5881489 original size:6 final size:6
Alignment explanation
Indices: 5881478--5881507 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5881468 AAGAAAATGG
5881478 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
5881508 AAGTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GTTTGA
Found at i:5881768 original size:29 final size:29
Alignment explanation
Indices: 5881726--5881785 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5881716 AAGTTTGTCA
5881726 TCTCTTTTGAGTACTTGTTTCTATTTTTT
1 TCTCTTTTGAGTACTTGTTTCTATTTTTT
5881755 TCTCTTTTGAGTACTTGTTTCTATTTTTT
1 TCTCTTTTGAGTACTTGTTTCTATTTTTT
5881784 TC
1 TC
5881786 AATTGATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.65
Consensus pattern (29 bp):
TCTCTTTTGAGTACTTGTTTCTATTTTTT
Found at i:5886115 original size:24 final size:25
Alignment explanation
Indices: 5886088--5886136 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5886078 TTTTCACCTA
*
5886088 TGAATTTTATAAAAATTT-ATCATT
1 TGAAATTTATAAAAATTTCATCATT
* *
5886112 TGAAATTTCTATAAATTTCATCATT
1 TGAAATTTATAAAAATTTCATCATT
5886137 GGATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (25 bp):
TGAAATTTATAAAAATTTCATCATT
Found at i:5886118 original size:185 final size:186
Alignment explanation
Indices: 5885839--5886180 Score: 462
Period size: 185 Copynumber: 1.8 Consensus size: 186
5885829 CAATTACTTT
*
5885839 TATTGAAACTTTCATCTAAATTATTGTACTATTTGAGACAAATTTAGAAAAAAATTTCACCTAAA
1 TATTGAAACTTTCATCTAAATTATTGTACCATTTGAGACAAATTTAGAAAAAAATTTCACCTAAA
* **
5885904 AAATTCTTAAAAAATTTACCATTTGAAATTTCTAAAAATCTCATCCTTCAATAATTTGTATTTAA
66 AAATTCTTAAAAAATTTACCATTTGAAATTTCTAAAAATCTCATCATTCAATAATTAATATTT-A
*
5885969 TT-CCAAAATTTTTATATTTTA-TATTTTTTTGTTTGAAGATAAATATTAATTATTGG
130 TTCCCAAAATATTTAT-TTTTATTATTTTTTTGTTTGAAGATAAATATTAATTATTGG
* * *
5886025 TATTGAAACTTT-TTCTAAATTATT-TCACCATTTGAGACACATTTAGACAAAAATTTTCACCT-
1 TATTGAAACTTTCATCTAAATTATTGT-ACCATTTGAGACAAATTTAGA-AAAAAATTTCACCTA
** * * * **
5886087 ATGAATT-TTATAAAAATTTATCATTTGAAATTTCTATAAATTTCATCATTGGATAATTAATATT
64 AAAAATTCTTA-AAAAATTTACCATTTGAAATTTCTAAAAATCTCATCATTCAATAATTAATATT
5886151 TATTCCCAAAATATTTATTTTTATTATTTT
128 TATTCCCAAAATATTTATTTTTATTATTTT
5886181 ATTTTTTATA
Statistics
Matches: 136, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
184 12 0.09
185 99 0.73
186 25 0.18
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (186 bp):
TATTGAAACTTTCATCTAAATTATTGTACCATTTGAGACAAATTTAGAAAAAAATTTCACCTAAA
AAATTCTTAAAAAATTTACCATTTGAAATTTCTAAAAATCTCATCATTCAATAATTAATATTTAT
TCCCAAAATATTTATTTTTATTATTTTTTTGTTTGAAGATAAATATTAATTATTGG
Found at i:5887077 original size:15 final size:14
Alignment explanation
Indices: 5887057--5887100 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
5887047 ATCAATCAAA
5887057 AAATAATAGTAATAT
1 AAATAATAGTAA-AT
5887072 AAATAATAGTAAAT
1 AAATAATAGTAAAT
* *
5887086 -AATAAAAATAAAT
1 AAATAATAGTAAAT
5887099 AA
1 AA
5887101 TAAACGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 3 0.12
15 12 0.46
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AAATAATAGTAAAT
Found at i:5887086 original size:10 final size:9
Alignment explanation
Indices: 5887066--5887148 Score: 55
Period size: 9 Copynumber: 9.0 Consensus size: 9
5887056 AAAATAATAG
5887066 TAATATAAA
1 TAATATAAA
5887075 TAATAGTAAA
1 TAATA-TAAA
*
5887085 TAATAAAAA
1 TAATATAAA
5887094 TAAATAATAAA
1 T-AAT-ATAAA
* *
5887105 CGAA-AAAAA
1 -TAATATAAA
* *
5887114 CAAATAAAAA
1 -TAATATAAA
5887124 TAATATAAA
1 TAATATAAA
5887133 TAA-ATAAA
1 TAATATAAA
5887141 TAA-ATAAA
1 TAATATAAA
5887149 ATGAACCCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
8 13 0.21
9 26 0.42
10 17 0.27
11 6 0.10
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
TAATATAAA
Found at i:5887097 original size:13 final size:13
Alignment explanation
Indices: 5887081--5887148 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 13
5887071 TAAATAATAG
5887081 TAAATAATAAAAA
1 TAAATAATAAAAA
5887094 TAAATAATAAACGAA
1 TAAATAATAAA--AA
*
5887109 -AAA-AACAAATAA
1 TAAATAATAAA-AA
*
5887121 -AAATAATATAAA
1 TAAATAATAAAAA
*
5887133 TAAATAA-ATAAA
1 TAAATAATAAAAA
5887145 TAAA
1 TAAA
5887149 ATGAACCCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
12 16 0.34
13 26 0.55
14 3 0.06
15 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:5887100 original size:4 final size:4
Alignment explanation
Indices: 5887070--5887148 Score: 56
Period size: 4 Copynumber: 19.2 Consensus size: 4
5887060 TAATAGTAAT
* * * *
5887070 ATAA ATAA TAGTAA ATAA TAAAA ATAA AT-A ATAA ACGAA AAAA ACAA
1 ATAA ATAA -A-TAA ATAA -ATAA ATAA ATAA ATAA A-TAA ATAA ATAA
5887117 AT-A A-AA ATAA TATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA A
5887149 ATGAACCCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
3 7 0.11
4 39 0.64
5 12 0.20
6 3 0.05
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:5887141 original size:23 final size:24
Alignment explanation
Indices: 5887067--5887144 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 24
5887057 AAATAATAGT
* *
5887067 AATATAAATAATAGTAAATAATAAA
1 AATAAAAATAATACTAAATAA-AAA
*
5887092 AATAAATAATAA-ACGAAA-AAAACA
1 AATAAA-AATAATACTAAATAAAA-A
*
5887116 AATAAAAATAATA-TAAATAAATA
1 AATAAAAATAATACTAAATAAAAA
5887139 AATAAA
1 AATAAA
5887145 TAAAATGAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 17 0.39
24 13 0.30
25 9 0.20
26 5 0.11
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (24 bp):
AATAAAAATAATACTAAATAAAAA
Found at i:5896430 original size:15 final size:14
Alignment explanation
Indices: 5896409--5896442 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5896399 ATTATCTGAA
5896409 AAAATAAATTTATT
1 AAAATAAATTTATT
5896423 ACAAAT-AATTTATT
1 A-AAATAAATTTATT
5896437 AAAATA
1 AAAATA
5896443 TATTACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATAAATTTATT
Found at i:5897877 original size:8 final size:8
Alignment explanation
Indices: 5897866--5897907 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
5897856 CATTATATTT
5897866 TATTTTAA
1 TATTTTAA
*
5897874 TATTTTAT
1 TATTTTAA
*
5897882 TATTATATA
1 TATTTTA-A
5897891 TATTTTAA
1 TATTTTAA
5897899 TATTTTAA
1 TATTTTAA
5897907 T
1 T
5897908 TACTTGCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTTAA
Found at i:5897878 original size:13 final size:13
Alignment explanation
Indices: 5897860--5897905 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
5897850 TTATTACATT
5897860 ATATTTTATTTTA
1 ATATTTTATTTTA
5897873 ATATTTTATTATT-
1 ATATTTTATT-TTA
*
5897886 ATA-TATATTTTA
1 ATATTTTATTTTA
5897898 ATATTTTA
1 ATATTTTA
5897906 ATTACTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 16 0.57
14 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTTTATTTTA
Found at i:5897909 original size:26 final size:26
Alignment explanation
Indices: 5897857--5897905 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5897847 AAATTATTAC
*
5897857 ATTATATTTTATTTTAATATTTTATT
1 ATTATATTATATTTTAATATTTTATT
5897883 ATTATA-TATATTTTAATATTTTA
1 ATTATATTATATTTTAATATTTTA
5897906 ATTACTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTATATTATATTTTAATATTTTATT
Found at i:5898446 original size:14 final size:14
Alignment explanation
Indices: 5898427--5898454 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5898417 ATCTCAAGGT
5898427 TTTAAGATTTTTTA
1 TTTAAGATTTTTTA
5898441 TTTAAGATTTTTTA
1 TTTAAGATTTTTTA
5898455 ATTACATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTAAGATTTTTTA
Found at i:5899736 original size:3 final size:3
Alignment explanation
Indices: 5899728--5899759 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5899718 TTCCCACTTT
5899728 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5899760 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5899766 original size:3 final size:3
Alignment explanation
Indices: 5899760--5899806 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
5899750 AATAATAATA
*
5899760 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TTT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5899805 TA
1 TA
5899807 ATCGTTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5901042 original size:2 final size:2
Alignment explanation
Indices: 5901035--5901065 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5901025 ACAACCCTTT
5901035 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
5901066 TTCTCTCGAG
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:5905585 original size:19 final size:19
Alignment explanation
Indices: 5905563--5905600 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5905553 TTCTAAAAAC
* *
5905563 AAAAAAAATAAATAAAAGG
1 AAAAAAAAAAAAAAAAAGG
5905582 AAAAAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAAAAGG
5905601 GATTTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAGG
Found at i:5906908 original size:11 final size:10
Alignment explanation
Indices: 5906892--5906917 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5906882 TAAAATAAAG
5906892 TTTTTTTTTC
1 TTTTTTTTTC
5906902 TTTTTTTTTC
1 TTTTTTTTTC
5906912 TTTTTT
1 TTTTTT
5906918 GAAATAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5908198 original size:29 final size:28
Alignment explanation
Indices: 5908137--5908195 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
5908127 CTACAACAAC
*
5908137 AATTCAATATTTATTTTTTTCAAAATAAA
1 AATTCAATATTTA-TGTTTTCAAAATAAA
*
5908166 AATTCAATATTTA-GTTTTCAATATTAAA
1 AATTCAATATTTATGTTTTCAA-AATAAA
5908194 AA
1 AA
5908196 ATTTAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 7 0.26
29 13 0.48
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTCAATATTTATGTTTTCAAAATAAA
Found at i:5915766 original size:21 final size:21
Alignment explanation
Indices: 5915733--5915778 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5915723 TGATAAGTAT
* *
5915733 AATTAAATAAAAATAATACAA
1 AATTAAATAAAAATAAGAAAA
5915754 AATT-AATAAAAAATAAGAAAA
1 AATTAAAT-AAAAATAAGAAAA
5915775 AATT
1 AATT
5915779 TTTTTATCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AATTAAATAAAAATAAGAAAA
Found at i:5916618 original size:10 final size:10
Alignment explanation
Indices: 5916603--5916628 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5916593 AAAATTATCC
5916603 TTTTAATAAA
1 TTTTAATAAA
5916613 TTTTAATAAA
1 TTTTAATAAA
5916623 TTTTAA
1 TTTTAA
5916629 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:5919877 original size:41 final size:41
Alignment explanation
Indices: 5919822--5919907 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
5919812 TTCAAAAAAT
5919822 AAAATTTTTGATATATGGTATTCTGATTTTTTTAATTTTTA
1 AAAATTTTTGATATATGGTATTCTGATTTTTTTAATTTTTA
5919863 AAAATTTTTGATATATGGTATTCTGATTTTTTTAATTTTTA
1 AAAATTTTTGATATATGGTATTCTGATTTTTTTAATTTTTA
5919904 AAAA
1 AAAA
5919908 GGTTCAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (41 bp):
AAAATTTTTGATATATGGTATTCTGATTTTTTTAATTTTTA
Found at i:5928067 original size:48 final size:49
Alignment explanation
Indices: 5927956--5928110 Score: 154
Period size: 49 Copynumber: 3.2 Consensus size: 49
5927946 TTTTAAAAAG
* * * *** *
5927956 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAGTTTTTTTTCAAGATGAAT
1 TTTAAAGTTGTTAAGCCTATGCTTAGAAGAACCTTTGTTCAAGATGAAT
* *
5928005 TTTAAAGTTATTAAGCCTATGCTTAGAAGAACCTTTGTT-AAGGTGAAT
1 TTTAAAGTTGTTAAGCCTATGCTTAGAAGAACCTTTGTTCAAGATGAAT
* * * *
5928053 TTTAAAGTTGTTAAGCCTCTACTTA-TAGAAGCTTT-TTCGAAGATGAATT
1 TTTAAAGTTGTTAAGCCTATGCTTAGAAGAACCTTTGTTC-AAGATGAA-T
5928102 TTTAAAGTT
1 TTTAAAGTT
5928111 ATTCAACCAG
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
46 2 0.02
47 8 0.09
48 37 0.42
49 41 0.47
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (49 bp):
TTTAAAGTTGTTAAGCCTATGCTTAGAAGAACCTTTGTTCAAGATGAAT
Found at i:5929482 original size:21 final size:21
Alignment explanation
Indices: 5929439--5929482 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5929429 TGATAAGTAT
* *
5929439 AATTAAATAAAAATAATACAA
1 AATTAAATAAAAATAAGAAAA
5929460 AATT-AATAAAAAATAAGAAAA
1 AATTAAAT-AAAAATAAGAAAA
5929481 AA
1 AA
5929483 AAATTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AATTAAATAAAAATAAGAAAA
Found at i:5931533 original size:29 final size:30
Alignment explanation
Indices: 5931465--5931533 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
5931455 ATGACATCTA
* *
5931465 AACTATAATAAAATGTTTAATGTGATATTTG
1 AACTATAA-AAAATGTTTAATGTAATACTTG
* * *
5931496 AATTTTAAAAACT-TTTAATGTAATACTTG
1 AACTATAAAAAATGTTTAATGTAATACTTG
5931525 AACTATAAA
1 AACTATAAA
5931534 TATATTAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 21 0.68
30 4 0.13
31 6 0.19
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.41
Consensus pattern (30 bp):
AACTATAAAAAATGTTTAATGTAATACTTG
Found at i:5931695 original size:28 final size:29
Alignment explanation
Indices: 5931634--5931715 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
5931624 AAAATTCATG
* *
5931634 ATTCAAGTATCATATTAAAATTTTTTAAA
1 ATTCAAATATCATATTAAAATTTTGTAAA
* *
5931663 ATTCAAATATCATTTTTAAATTTTGT-AA
1 ATTCAAATATCATATTAAAATTTTGTAAA
*
5931691 ATTCAAATACCATATTAAAAATTTT
1 ATTCAAATATCATATT-AAAATTTT
5931716 ATTATAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 16 0.36
29 29 0.64
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTCAAATATCATATTAAAATTTTGTAAA
Found at i:5933045 original size:2 final size:2
Alignment explanation
Indices: 5933032--5933067 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5933022 ATGAAGAACC
*
5933032 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5933068 AAGGGTCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5936450 original size:31 final size:31
Alignment explanation
Indices: 5936389--5936452 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5936379 TATAAAATAT
*
5936389 TTAATATGATACTTTATTATAAATTTATTAA
1 TTAATATGATACTTTATTATAAATTAATTAA
* * *
5936420 TTAATATGAT-GTTTATTTTTAATATAATTAA
1 TTAATATGATACTTTATTATAAAT-TAATTAA
5936451 TT
1 TT
5936453 TTAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (31 bp):
TTAATATGATACTTTATTATAAATTAATTAA
Found at i:5939462 original size:17 final size:17
Alignment explanation
Indices: 5939440--5939506 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
5939430 GTCCAGGAAA
5939440 AAATATGAAATACATAT
1 AAATATGAAATACATAT
* *
5939457 AAATATAAAATACGAAAT
1 AAATATGAAATAC-ATAT
*
5939475 ACATAT-AAAT--ATA-
1 AAATATGAAATACATAT
*
5939488 AAATACGAAATACA-AT
1 AAATATGAAATACATAT
5939504 AAA
1 AAA
5939507 AATATAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 1 0.03
16 4 0.10
17 16 0.41
18 8 0.21
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (17 bp):
AAATATGAAATACATAT
Found at i:5939473 original size:24 final size:24
Alignment explanation
Indices: 5939439--5939515 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
5939429 TGTCCAGGAA
*
5939439 AAAATATGAAATACATATAAATAT
1 AAAATACGAAATACATATAAATAT
5939463 AAAATACGAAATACATATAAATAT
1 AAAATACGAAATACATATAAATAT
*
5939487 AAAATACGAAATACAATAAAAATAT
1 AAAATACGAAATAC-ATATAAATAT
5939512 AAAA
1 AAAA
5939516 AATAATACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 37 0.74
25 13 0.26
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAATACGAAATACATATAAATAT
Found at i:5939529 original size:19 final size:19
Alignment explanation
Indices: 5939501--5939546 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5939491 TACGAAATAC
5939501 AATA-AAAATATAAA-AAA
1 AATACAAAATATAAACAAA
*
5939518 TAATACAAAATATAAACCAA
1 -AATACAAAATATAAACAAA
5939538 AATACAAAA
1 AATACAAAA
5939547 AAAAACAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 19 0.76
20 2 0.08
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (19 bp):
AATACAAAATATAAACAAA
Found at i:5942329 original size:11 final size:11
Alignment explanation
Indices: 5942313--5942351 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5942303 ATAATACTAA
5942313 AAAAAAAAAAC
1 AAAAAAAAAAC
*
5942324 AAAAAAAACAC
1 AAAAAAAAAAC
* *
5942335 TAAAAAAAAAT
1 AAAAAAAAAAC
5942346 AAAAAA
1 AAAAAA
5942352 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.87, C:0.08, G:0.00, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:5950514 original size:11 final size:12
Alignment explanation
Indices: 5950476--5950506 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
5950466 ATATTTTGCT
5950476 TAAAAAAAAAAG
1 TAAAAAAAAAAG
5950488 -AAAAAAAAAAG
1 TAAAAAAAAAAG
5950499 TAAAAAAA
1 TAAAAAAA
5950507 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.87, C:0.00, G:0.06, T:0.06
Consensus pattern (12 bp):
TAAAAAAAAAAG
Found at i:5950515 original size:8 final size:8
Alignment explanation
Indices: 5950476--5950517 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
5950466 ATATTTTGCT
5950476 TAAAAAAA
1 TAAAAAAA
5950484 -AAAGAAAA
1 TAAA-AAAA
*
5950492 -AAAAAAG
1 TAAAAAAA
5950499 TAAAAAAA
1 TAAAAAAA
5950507 TAAAAAAA
1 TAAAAAAA
5950515 TAA
1 TAA
5950518 TGACTCATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
TAAAAAAA
Found at i:5951415 original size:47 final size:47
Alignment explanation
Indices: 5951253--5951867 Score: 597
Period size: 47 Copynumber: 12.9 Consensus size: 47
5951243 TTGAGAAAAG
*
5951253 ATGAGATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCCCTTTT-TAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG--CTTTTCTAA
* ** *
5951301 GAT-AAATTTTAAAGTCATTGAGCCTCTGCTGAGAGGAGCCTTTT-T-C
1 -ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCTAA
* **
5951347 A--AGACTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTCTAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* * *
5951392 ATGAGATTTTAAAGTCGTTGAGCCTCTACTGAGAGGAGTTTTTCTAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* * *
5951439 ATGAGATTTTAATTAAAGTTGTTGAGCCTCTGCTGAGATGACCTTTTTTAA
1 ATGAGA--TT--TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* * *
5951490 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTGAAAGGAGCTTTTCCAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* *
5951537 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTG-GAAGGAGCTTTTCCAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAG-AGGAGCTTTTCTAA
* * *
5951584 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAACTTTTCCAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* * * *
5951631 ATGAGATTTTTAAAGTTGTTGAGTCTCTGCTAAGAGGAGCTTTTTTTA
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* *
5951679 A--A-ATTTTAAAGTTGTTGAACCTCTACTGAGAGGAGCTTTT-TGAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCT-AA
* * *
5951723 ATGAGATTTTCAAAGTTGTTGAGCTTCTGCTGAGAGGAATCTTTTTTAGA
1 ATGAGATTTT-AAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTCTA-A
* * * ** * * *
5951773 TTTTAAATTCCCAAAAGTTGTTGAGCCTCTGTTAAGAGGAACTTTT-TAA
1 -ATGAGATT--TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
* *
5951822 GATGAAATTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTT
1 -ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTT
5951868 TCAGATTTTA
Statistics
Matches: 476, Mismatches: 66, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.01
44 65 0.14
45 3 0.01
46 2 0.00
47 184 0.39
48 114 0.24
49 23 0.05
50 6 0.01
51 50 0.11
52 23 0.05
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (47 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCTAA
Found at i:5951539 original size:145 final size:142
Alignment explanation
Indices: 5951253--5951867 Score: 596
Period size: 145 Copynumber: 4.3 Consensus size: 142
5951243 TTGAGAAAAG
* * *
5951253 ATGAGATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCCCTTTTT--AAGAT-A-AATTTTAAA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG---TTTTTCCAA-ATGAGATTTTTAAA
** * * *
5951314 GTCATTGAGCCTCTGCTGAGAGGAGCC-TTTTT-CA--AGACTTTAAAGTTGTTGAGCCTCTATT
62 GTTGTTGAGCCTCTGCTGAGAGGA-CCTTTTTTAAATGAGATTTTAAAGTTGTTGAGCCTCTGTT
*
5951375 GAGAGGAGCTTTTCTAA
126 AAGAGGAGCTTTTCTAA
* *
5951392 ATGAGATTTTAAAGTCGTTGAGCCTCTACTGAGAGGAGTTTTTCTAAATGAGATTTTAATTAAAG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGTTTTTCCAAATGAGA-TTT--TTAAAG
*
5951457 TTGTTGAGCCTCTGCTGAGATGACCTTTTTTAAATGAGATTTTAAAGTTGTTGAGCCTCTGTTGA
63 TTGTTGAGCCTCTGCTGAGAGGACCTTTTTTAAATGAGATTTTAAAGTTGTTGAGCCTCTGTT-A
*
5951522 A-AGGAGCTTTTCCAA
127 AGAGGAGCTTTTCTAA
** *
5951537 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTG-GAAGGAGCTTTTCCAAATGAGA-TTTTAAAGTT
1 ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAG-AGGAGTTTTTCCAAATGAGATTTTTAAAGTT
* * ** * *
5951600 GTTGAGCCTCTGCTGAGATGAACTTTTCCAAATGAGATTTTTAAAGTTGTTGAGTCTCTGCTAAG
65 GTTGAGCCTCTGCTGAGAGGACCTTTTTTAAATGAGA-TTTTAAAGTTGTTGAGCCTCTGTTAAG
* *
5951665 AGGAGCTTTTTTTA
129 AGGAGCTTTTCTAA
* * *
5951679 A--A-ATTTTAAAGTTGTTGAACCTCTACTGAGAGGAGCTTTTT-GAAATGAGATTTTCAAAGTT
1 ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-TTTTTCCAAATGAGATTTTTAAAGTT
* * * * * **
5951740 GTTGAGCTTCTGCTGAGAGGAATCTTTTTTAGATTTTAAATTCCCAAAAGTTGTTGAGCCTCTGT
65 GTTGAGCCTCTGCTGAGAGG-ACCTTTTTTA-A-ATGAGATT--TTAAAGTTGTTGAGCCTCTGT
*
5951805 TAAGAGGAACTTTT-TAA
125 TAAGAGGAGCTTTTCTAA
* * *
5951822 GATGAAATTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTT
1 -ATGAGA-TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGT-TTTT
5951868 TCAGATTTTA
Statistics
Matches: 399, Mismatches: 48, Indels: 49
0.80 0.10 0.10
Matches are distributed among these distances:
136 5 0.01
137 2 0.01
138 3 0.01
139 72 0.18
140 35 0.09
141 53 0.13
142 68 0.17
143 8 0.02
144 32 0.08
145 84 0.21
146 2 0.01
147 2 0.01
148 33 0.08
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (142 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGTTTTTCCAAATGAGATTTTTAAAGTTG
TTGAGCCTCTGCTGAGAGGACCTTTTTTAAATGAGATTTTAAAGTTGTTGAGCCTCTGTTAAGAG
GAGCTTTTCTAA
Found at i:5951718 original size:92 final size:93
Alignment explanation
Indices: 5951253--5951868 Score: 582
Period size: 92 Copynumber: 6.5 Consensus size: 93
5951243 TTGAGAAAAG
* * * * **
5951253 ATGAGATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCCCTTTTTAAGATAAATTTTAAAGTCA
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTTAA-AGAGATTTTAAAGTTG
*
5951318 TTGAGCCTCTGCTGAGAGGAGCCTTTTTC--
64 TTGAGCCTCTGCTGAGAGGAG-CTTTTCCAA
* ** * *
5951347 A--AGACTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTCTAAATGAGATTTTAAAGTCGT
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAA-GAGATTTTAAAGTTGT
* * *
5951410 TGAGCCTCTACTGAGAGGAGTTTTTCTAA
65 TGAGCCTCTGCTGAGAGGAGCTTTTCCAA
* *
5951439 ATGAGATTTTAATTAAAGTTGTTGAGCCTCTGCTGAGATGACCTTTTTTAAATGAGATTTTAAAG
1 ATGAGA--TT--TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAA-GAGATTTTAAAG
* *
5951504 TTGTTGAGCCTCTGTTGAAAGGAGCTTTTCCAA
61 TTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAA
* **
5951537 ATGAGATTTTAAAGTTGTTGAGCCTCTGTTG-GAAGGAGCTTTTCCAAATGAGATTTTAAAGTTG
1 ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAG-AGGAGCTTTTTTAAA-GAGATTTTAAAGTTG
* *
5951601 TTGAGCCTCTGCTGAGATGAACTTTTCCAA
64 TTGAGCCTCTGCTGAGAGGAGCTTTTCCAA
* * *
5951631 ATGAGATTTTTAAAGTTGTTGAGTCTCTGCTAAGAGGAGCTTTTTTTAA-A-ATTTTAAAGTTGT
1 ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAAGAGATTTTAAAGTTGT
* * **
5951694 TGAACCTCTACTGAGAGGAGCTTTTTGAA
65 TGAGCCTCTGCTGAGAGGAGCTTTTCCAA
* * ** * **
5951723 ATGAGATTTTCAAAGTTGTTGAGCTTCTGCTGAGAGGAATCTTTTTTAGATTTTAAATTCCCAAA
1 ATGAGATTTT-AAAGTTGTTGAGCCTCTGCTGAGAGG-AGCTTTTTTA-A--AGAGATT--TTAA
* * * *
5951788 AGTTGTTGAGCCTCTGTTAAGAGGAACTTTT-TAA
59 AGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAA
* *
5951822 GATGAAATTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTTT
1 -ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTT
5951869 CAGATTTTAA
Statistics
Matches: 434, Mismatches: 64, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
90 5 0.01
91 43 0.10
92 97 0.22
93 10 0.02
94 86 0.20
95 34 0.08
96 4 0.01
97 1 0.00
98 84 0.19
99 3 0.01
100 63 0.15
101 4 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (93 bp):
ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAAGAGATTTTAAAGTTGTT
GAGCCTCTGCTGAGAGGAGCTTTTCCAA
Found at i:5951791 original size:52 final size:51
Alignment explanation
Indices: 5951730--5951901 Score: 190
Period size: 52 Copynumber: 3.4 Consensus size: 51
5951720 GAAATGAGAT
* *
5951730 TTTC-AAAGTTGTTGAGCTTCTGCTGAGAGGAATCTTTTTTAGATTTTAAA
1 TTTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAATCTTTTTAAGATTTTAAA
* * * *
5951780 TTCCCAAAAGTTGTTGAGCCTCTGTTAAGAGGAA-CTTTTTAAGA--TGAAA
1 TT-TCAAAAGTTGTTGAGCCTCTGCTGAGAGGAATCTTTTTAAGATTTTAAA
** * * *
5951829 TTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTTTCAGATTTTAAA
1 TTTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAATCTTTTTAAGATTTTAAA
*
5951880 TTTTCAAAAGTTGTCGAGCCTC
1 -TTTCAAAAGTTGTTGAGCCTC
5951902 AAGTGAGAGG
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
48 24 0.25
49 15 0.15
50 2 0.02
51 14 0.14
52 42 0.43
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (51 bp):
TTTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAATCTTTTTAAGATTTTAAA
Found at i:5951800 original size:192 final size:188
Alignment explanation
Indices: 5951253--5951868 Score: 577
Period size: 192 Copynumber: 3.2 Consensus size: 188
5951243 TTGAGAAAAG
* * * * *
5951253 ATGAGA-TTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCCCTTTTTAAGATAAATTTTAAAGTC
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTTAA-AGAGATTTTAAAGTT
* * * * * * * *
5951317 ATTGAGCCTCTGCTGAGAGGAGCCTTTTTC--A--AGACTTTAAAGTTGTTGAGCCTCT-ATTGA
64 GTTGAACCTCTACTGAAAGGAG-CTTTTCCAAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGGA
* * ** * * **
5951377 GAGGAGCTTTTCTAAATGAGATTTTAAAGTCGTTGAGCCTCTACTGAGAGGAGTTTTTCTAA
128 -AGGAGCTTTTCCAAATGAAATTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAACTTTTCTAA
* *
5951439 ATGAGATTTTAATTAAAGTTGTTGAGCCTCTGCTGAGATGACCTTTTTTAAATGAGATTTTAAAG
1 ATGAGA-TTT--TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAA-GAGATTTTAAAG
* ** *
5951504 TTGTTGAGCCTCTGTTGAAAGGAGCTTTTCCAAATGAGATTTTAAAGTTGTTGAGCCTCTGTTGG
62 TTGTTGAACCTCTACTGAAAGGAGCTTTTCCAAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGG
* ** * *
5951569 AAGGAGCTTTTCCAAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGATGAACTTTTCCAA
127 AAGGAGCTTTTCCAAATGAAATTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAACTTTTCTAA
* * *
5951631 ATGAGATTTTTAAAGTTGTTGAGTCTCTGCTAAGAGGAGCTTTTTTTAA-A-ATTTTAAAGTTGT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAAGAGATTTTAAAGTTGT
* ** *
5951694 TGAACCTCTACTGAGAGGAGCTTTTTGAAATGAGATTTTCAAAGTTGTTGAGCTTCTGCT-GAGA
66 TGAACCTCTACTGAAAGGAGCTTTTCCAAATGAGATTTT-AAAGTTGTTGAGCCTCTGCTGGA-A
* ** * * * *
5951758 GGAATCTTTTTTAGATTTTAAATTCCCAAAAGTTGTTGAGCCTCTGTTAAGAGGAACTTTT-TAA
129 GG-AGCTTTTCCA-A-ATGAAATT--CAAAAGTTGTTGAGCCTCTGCTGAGAGGAACTTTTCTAA
* *
5951822 GATGAAATTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTTT
1 -ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTT
5951869 CAGATTTTAA
Statistics
Matches: 361, Mismatches: 50, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
186 54 0.15
187 22 0.06
188 16 0.04
189 74 0.20
190 33 0.09
191 5 0.01
192 148 0.41
193 9 0.02
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (188 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAAAGAGATTTTAAAGTTGT
TGAACCTCTACTGAAAGGAGCTTTTCCAAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGGAAGG
AGCTTTTCCAAATGAAATTCAAAAGTTGTTGAGCCTCTGCTGAGAGGAACTTTTCTAA
Found at i:5951881 original size:51 final size:50
Alignment explanation
Indices: 5951589--5951901 Score: 215
Period size: 48 Copynumber: 6.4 Consensus size: 50
5951579 TCCAAATGAG
* * * * *
5951589 ATTTT-AAAGTTGTTGAGCCTCTGCTGAGATGAACTTTTCCAA-A--TGAG
1 ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGATCTTTT-TAAGATTTTAA
* * * * *
5951636 ATTTTTAAAGTTGTTGAGTCTCTGCTAAGAGGAGC-TTTT----TTTAAA
1 ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGATCTTTTTAAGATTTTAA
* * * * *
5951681 ATTTT-AAAGTTGTTGAACCTCTACTGAGAGGAGCTTTTTGAA-A--TGAG
1 ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGATCTTTTT-AAGATTTTAA
* * *
5951728 ATTTTCAAAGTTGTTGAGCTTCTGCTGAGAGGAATCTTTTTTAGATTTTAA
1 ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGG-ATCTTTTTAAGATTTTAA
** * * * *
5951779 ATTCCCAAAAGTTGTTGAGCCTCTGTTAAGAGGAACTTTTTAAGA--TGAA
1 ATT-TTAAAAGTTGTTGAGCCTCTGCTGAGAGGATCTTTTTAAGATTTTAA
* * *
5951828 ATTTTTAAAGTTGTTGTGCCTCTGCTGAGAGGAGTCTTTTTCAGATTTTAA
1 ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGA-TCTTTTTAAGATTTTAA
*
5951879 ATTTTCAAAAGTTGTCGAGCCTC
1 ATTTT-AAAAGTTGTTGAGCCTC
5951902 AAGTGAGAGG
Statistics
Matches: 207, Mismatches: 41, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
44 25 0.12
45 11 0.05
47 15 0.07
48 73 0.35
49 23 0.11
51 23 0.11
52 37 0.18
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (50 bp):
ATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGATCTTTTTAAGATTTTAA
Found at i:5952034 original size:7 final size:7
Alignment explanation
Indices: 5952022--5952082 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
5952012 TTGTCCAAAA
5952022 AAAATAT
1 AAAATAT
5952029 AAAATACAT
1 AAAAT--AT
5952038 ATAAATAT
1 A-AAATAT
*
5952046 AAAATAC
1 AAAATAT
5952053 AAAATACAT
1 AAAAT--AT
5952062 ATAAATAT
1 A-AAATAT
*
5952070 AAAATAC
1 AAAATAT
5952077 AAAATA
1 AAAATA
5952083 CAATAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 26 0.58
8 6 0.13
9 5 0.11
10 8 0.18
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATAT
Found at i:5952045 original size:17 final size:17
Alignment explanation
Indices: 5952023--5952089 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
5952013 TGTCCAAAAA
5952023 AAATATAAAATACATAT
1 AAATATAAAATACATAT
*
5952040 AAATATAAAATACAAAAT
1 AAATATAAAATAC-ATAT
*
5952058 ACATAT-AAAT--ATA-
1 AAATATAAAATACATAT
*
5952071 AAATACAAAATACA-AT
1 AAATATAAAATACATAT
5952087 AAA
1 AAA
5952090 AAAATACCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 1 0.03
16 4 0.10
17 17 0.43
18 8 0.20
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATATAAAATACATAT
Found at i:5952047 original size:6 final size:6
Alignment explanation
Indices: 5952023--5952072 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
5952013 TGTCCAAAAA
* * *
5952023 AAATAT AAA-AT ACATAT AAATAT AAA-AT ACAAAAT ACATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT A-AATAT AAATAT AAATAT
5952070 AAA
1 AAA
5952073 ATACAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
5 7 0.19
6 26 0.72
7 3 0.08
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (6 bp):
AAATAT
Found at i:5952056 original size:24 final size:24
Alignment explanation
Indices: 5952022--5952089 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
5952012 TTGTCCAAAA
*
5952022 AAAATATAAAATACATATAAATAT
1 AAAATACAAAATACATATAAATAT
5952046 AAAATACAAAATACATATAAATAT
1 AAAATACAAAATACATATAAATAT
5952070 AAAATACAAAATACA-ATAAA
1 AAAATACAAAATACATATAAA
5952090 AAAATACCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 5 0.12
24 38 0.88
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATACAAAATACATATAAATAT
Found at i:5952083 original size:7 final size:7
Alignment explanation
Indices: 5952040--5952119 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
5952030 AAATACATAT
*
5952040 AAATATA
1 AAATACA
5952047 AAATACA
1 AAATACA
5952054 AAATACATA
1 AAATAC--A
*
5952063 TAAATATA
1 -AAATACA
5952071 AAATACA
1 AAATACA
5952078 AAATACA
1 AAATACA
5952085 ATAA-A-A
1 A-AATACA
*
5952091 AAATACC
1 AAATACA
5952098 AAA-A-A
1 AAATACA
* *
5952103 TAATATA
1 AAATACA
5952110 AAATACA
1 AAATACA
5952117 AAA
1 AAA
5952120 AAAAATAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
5 4 0.07
6 5 0.09
7 39 0.68
8 3 0.05
9 1 0.02
10 5 0.09
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATACA
Found at i:5952110 original size:22 final size:20
Alignment explanation
Indices: 5952019--5952119 Score: 80
Period size: 24 Copynumber: 4.7 Consensus size: 20
5952009 AATTTGTCCA
*
5952019 AAAAAAATATAAAATACATAT
1 AAAAAAATACAAAATACA-AT
5952040 AAATATAAAATACAAAATACATAT
1 -AA-A-AAAATACAAAATACA-AT
5952064 AAATATAAAATACAAAATACAAT
1 -AA-A-AAAATACAAAATACAAT
*
5952087 AAAAAAATACCAAAA-ATAAT
1 AAAAAAATA-CAAAATACAAT
*
5952107 -ATAAAATACAAAA
1 AAAAAAATACAAAA
5952120 AAAAATAGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.07
19 7 0.10
20 10 0.14
21 6 0.08
22 4 0.05
23 3 0.04
24 38 0.52
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAAATACAAAATACAAT
Found at i:5954597 original size:31 final size:31
Alignment explanation
Indices: 5954554--5954618 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
5954544 TGAAATTTAG
* *
5954554 TTACTTGAATGAAATTTGAAATTTAATCTTT
1 TTACTTGAATGAAATTTAAAATTTAATCTCT
5954585 TTACTT-ATATGAAATTTAAAATTTAATCTCT
1 TTACTTGA-ATGAAATTTAAAATTTAATCTCT
5954616 TTA
1 TTA
5954619 ATGCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
TTACTTGAATGAAATTTAAAATTTAATCTCT
Found at i:5955652 original size:30 final size:30
Alignment explanation
Indices: 5955589--5955663 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
5955579 AAGTTTTTAA
* * * *
5955589 AAATTTAAAATATTTTTAAATTAGAAGGACT
1 AAATTTTAAAT-TTTATAAAGTAGAAAGACT
*
5955620 AAATTTTAAATTTTATAAAGTAGAAAGTCT
1 AAATTTTAAATTTTATAAAGTAGAAAGACT
*
5955650 AAATTTTAATTTTT
1 AAATTTTAAATTTT
5955664 TTACGAGTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 28 0.74
31 10 0.26
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (30 bp):
AAATTTTAAATTTTATAAAGTAGAAAGACT
Found at i:5982193 original size:14 final size:13
Alignment explanation
Indices: 5982162--5982208 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
5982152 TAATTATAAT
5982162 TTAAAAAATTTTA
1 TTAAAAAATTTTA
*
5982175 ATAAAAAATTTATA
1 TTAAAAAATTT-TA
*
5982189 TTAAATATATTTTA
1 TTAAA-AAATTTTA
5982203 TTAAAA
1 TTAAAA
5982209 TTAATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 11 0.38
14 13 0.45
15 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAAAAATTTTA
Found at i:5982520 original size:26 final size:28
Alignment explanation
Indices: 5982463--5982522 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
5982453 TATTATGTTA
* * *
5982463 ATTAATAAATTTATAATTTAAATATTAT
1 ATTAAAAAATTTATAATTTAAATATCAC
*
5982491 ATTAAAAAATTTA-AA-TTATATATCAC
1 ATTAAAAAATTTATAATTTAAATATCAC
5982517 ATTAAA
1 ATTAAA
5982523 TATTTTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.50
27 2 0.07
28 12 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAAAAAATTTATAATTTAAATATCAC
Found at i:5983284 original size:17 final size:17
Alignment explanation
Indices: 5983262--5983342 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
5983252 TAAAGTATTA
5983262 ATTTTTTAATATAAAAT
1 ATTTTTTAATATAAAAT
5983279 A-TTTTTAATATAAAAT
1 ATTTTTTAATATAAAAT
*
5983295 ATTATTTAATAT----T
1 ATTTTTTAATATAAAAT
5983308 A-TTTTTAATATAAAAT
1 ATTTTTTAATATAAAAT
*
5983324 ATTTTTTAAAATAAAAT
1 ATTTTTTAATATAAAAT
5983341 AT
1 AT
5983343 AAAATTAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
12 9 0.16
13 2 0.04
16 18 0.33
17 26 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTTTAATATAAAAT
Found at i:5983916 original size:14 final size:15
Alignment explanation
Indices: 5983888--5983921 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5983878 ATTTCAAAAG
5983888 TTAA-TCAATCGAAT
1 TTAATTCAATCGAAT
5983902 TTAATTCAATC-AAT
1 TTAATTCAATCGAAT
5983916 TTAATT
1 TTAATT
5983922 AATTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAATTCAATCGAAT
Found at i:5983959 original size:18 final size:17
Alignment explanation
Indices: 5983944--5983977 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5983934 AATTAAATAA
5983944 TAAATTATA-TTTAAAT
1 TAAATTATATTTTAAAT
*
5983960 TATATTATATTTTAAAT
1 TAAATTATATTTTAAAT
5983977 T
1 T
5983978 CTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTATATTTTAAAT
Found at i:5986987 original size:17 final size:19
Alignment explanation
Indices: 5986961--5986998 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5986951 GCTTGATCCA
5986961 TTTTCATTTTCC-TTTTCT
1 TTTTCATTTTCCTTTTTCT
5986979 TTTTC-TTTTCCTTTTTCT
1 TTTTCATTTTCCTTTTTCT
5986997 TT
1 TT
5986999 CGTTGGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCATTTTCCTTTTTCT
Found at i:5986996 original size:12 final size:12
Alignment explanation
Indices: 5986961--5986998 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5986951 GCTTGATCCA
* *
5986961 TTTTCATTTTCC
1 TTTTCCTTTTTC
5986973 TTTT-CTTTTTC
1 TTTTCCTTTTTC
5986984 TTTTCCTTTTTC
1 TTTTCCTTTTTC
5986996 TTT
1 TTT
5986999 CGTTGGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCCTTTTTC
Found at i:5993938 original size:14 final size:15
Alignment explanation
Indices: 5993919--5993949 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5993909 AATGTAAAAA
5993919 TTTTTAATT-TTAAT
1 TTTTTAATTATTAAT
5993933 TTTTTAATTATTAAT
1 TTTTTAATTATTAAT
5993948 TT
1 TT
5993950 CAATTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATTATTAAT
Found at i:5996937 original size:181 final size:181
Alignment explanation
Indices: 5996632--5996994 Score: 645
Period size: 181 Copynumber: 2.0 Consensus size: 181
5996622 GCATGTTATT
*
5996632 AGGAATTCCCACCATCACTTCAATATCTGTCCCAGTAAGAGCTGTCATAGTCCCCTCATTGTACT
1 AGGAATTCCCACCATCACTTCAATATCTGTCCCAGTAAGAGCTGTCATAATCCCCTCATTGTACT
** *
5996697 CGAAAGGCTTCAACTTATCAAACCCATTATCTCTCAGCATTTTCACCACCTTGTTTGGAGGGAGT
66 CGAAAACCTTCAACTTATCAAACCCATTATCTCTCAGCATTTTCACCACCTTATTTGGAGGGAGT
* *
5996762 TGGTGGGTAGCCAGGGTTCCCCAGTTCACTCCAACACTATTTCCATTTGGA
131 TGGTGGCTAGCCAGGGTTCCCCAGATCACTCCAACACTATTTCCATTTGGA
5996813 AGGAATTCCCACCATCACTTCAATATCTGTCCCAGTAAGAGCTGTCATAATCCCCTCATTGTACT
1 AGGAATTCCCACCATCACTTCAATATCTGTCCCAGTAAGAGCTGTCATAATCCCCTCATTGTACT
*
5996878 CGAAAACCTTCGACTTATCAAACCCATTATCTCTCAGCATTTTCACCACCTTATTTGGAGGGAGT
66 CGAAAACCTTCAACTTATCAAACCCATTATCTCTCAGCATTTTCACCACCTTATTTGGAGGGAGT
* *
5996943 TGGTGGCTAGCCGGGGTTCCCCGGATCACTCCAACACTATTTCCATTTGGA
131 TGGTGGCTAGCCAGGGTTCCCCAGATCACTCCAACACTATTTCCATTTGGA
5996994 A
1 A
5996995 CCAGAATCGT
Statistics
Matches: 173, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 173 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (181 bp):
AGGAATTCCCACCATCACTTCAATATCTGTCCCAGTAAGAGCTGTCATAATCCCCTCATTGTACT
CGAAAACCTTCAACTTATCAAACCCATTATCTCTCAGCATTTTCACCACCTTATTTGGAGGGAGT
TGGTGGCTAGCCAGGGTTCCCCAGATCACTCCAACACTATTTCCATTTGGA
Found at i:5998992 original size:12 final size:12
Alignment explanation
Indices: 5998975--5998999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5998965 ATCATATTCT
5998975 AGAGAAAAAAAA
1 AGAGAAAAAAAA
5998987 AGAGAAAAAAAA
1 AGAGAAAAAAAA
5998999 A
1 A
5999000 AGGAAGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAAAA
Found at i:5999163 original size:3 final size:3
Alignment explanation
Indices: 5999155--5999187 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5999145 ATAAAATTTC
5999155 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5999188 TGATATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5999487 original size:3 final size:3
Alignment explanation
Indices: 5999479--5999523 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
5999469 AAAGGCCTTT
5999479 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5999524 GCGTCTTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6007480 original size:11 final size:11
Alignment explanation
Indices: 6007455--6007488 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6007445 TCTAAACACC
6007455 AAAAATTAAATA
1 AAAAATTAAA-A
*
6007467 AAAAAGTAAAA
1 AAAAATTAAAA
6007478 AAAAATTAAAA
1 AAAAATTAAAA
6007489 TTAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATTAAAA
Found at i:6008371 original size:21 final size:20
Alignment explanation
Indices: 6008346--6008393 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
6008336 TTTGAACTTG
*
6008346 AATTTTTTTAAATTTAAATTT
1 AATTTTTGTAAATTT-AATTT
*
6008367 TATTTCTTGTAAATTTAATTT
1 AATTT-TTGTAAATTTAATTT
6008388 AATTTT
1 AATTTT
6008394 AAGTTCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
AATTTTTGTAAATTTAATTT
Found at i:6011086 original size:16 final size:19
Alignment explanation
Indices: 6011051--6011088 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
6011041 AAGAATATTT
6011051 AAATAATTTTATTTATAAA
1 AAATAATTTTATTTATAAA
6011070 AAAT-ATTTT-TTTA-AAA
1 AAATAATTTTATTTATAAA
6011086 AAA
1 AAA
6011089 GTGAAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 4 0.21
18 5 0.26
19 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATAATTTTATTTATAAA
Found at i:6011087 original size:17 final size:19
Alignment explanation
Indices: 6011051--6011088 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
6011041 AAGAATATTT
*
6011051 AAATAATTTTATTTATAAA
1 AAATAATTTTATTTAAAAA
6011070 AAAT-ATTTT-TTTAAAAA
1 AAATAATTTTATTTAAAAA
6011087 AA
1 AA
6011089 GTGAAAGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATAATTTTATTTAAAAA
Found at i:6011184 original size:3 final size:3
Alignment explanation
Indices: 6011176--6011207 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6011166 CAGAAATCAA
*
6011176 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6011208 GATATGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6017284 original size:30 final size:30
Alignment explanation
Indices: 6017250--6017313 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
6017240 TTCTATTTCA
* *
6017250 AATTGAATCCTCAAACATTTATTTTCATCC
1 AATTGAACCCTCAAACATTTATTTTCAACC
* *
6017280 AATTGAACCCTTATACATTTATTTTCAACC
1 AATTGAACCCTCAAACATTTATTTTCAACC
6017310 AATT
1 AATT
6017314 AAGCACAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTGAACCCTCAAACATTTATTTTCAACC
Found at i:6021453 original size:21 final size:21
Alignment explanation
Indices: 6021427--6021472 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6021417 TCCGAAATTA
6021427 ATAAAATA-TATATTTTAAAAT
1 ATAAAATATTAT-TTTTAAAAT
*
6021448 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
6021469 ATAA
1 ATAA
6021473 TTATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:6026389 original size:19 final size:19
Alignment explanation
Indices: 6026340--6026378 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6026330 AGCTTGATTA
6026340 TGTCATGCCATGGTGATGG
1 TGTCATGCCATGGTGATGG
6026359 TGTCATGCCATGGTGATGG
1 TGTCATGCCATGGTGATGG
6026378 T
1 T
6026379 TGTATTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.36, T:0.33
Consensus pattern (19 bp):
TGTCATGCCATGGTGATGG
Found at i:6027457 original size:3 final size:3
Alignment explanation
Indices: 6027449--6027474 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6027439 TATTAATTGA
6027449 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6027475 AGAAGGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6031016 original size:2 final size:2
Alignment explanation
Indices: 6031004--6031049 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
6030994 TCGTCTCTGC
* **
6031004 AT AT AT GT AT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6031046 AT AT
1 AT AT
6031050 GAGTAGGATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6032516 original size:35 final size:35
Alignment explanation
Indices: 6032436--6032521 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 35
6032426 ATTTTTTTTA
*
6032436 AAAATAATTTAATAAAAAATTTAAATTAATAAATTG
1 AAAAT-ATTTAATAAAAAATTTAAAATAATAAATTG
6032472 ATAAA-ATTTAATATAAAAA-TTAATAATAATAAA-T-
1 A-AAATATTTAATA-AAAAATTTAA-AATAATAAATTG
6032506 AAAATTATTTAA-AAAA
1 AAAA-TATTTAATAAAA
6032522 TTATTTACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
33 6 0.14
34 2 0.05
35 19 0.43
36 14 0.32
37 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAATATTTAATAAAAAATTTAAAATAATAAATTG
Found at i:6032603 original size:13 final size:12
Alignment explanation
Indices: 6032558--6032630 Score: 53
Period size: 13 Copynumber: 6.2 Consensus size: 12
6032548 ATTAATTTAA
*
6032558 TTATAAAAAT-T
1 TTATTAAAATAT
* *
6032569 TTATTAATATTT
1 TTATTAAAATAT
6032581 TTATTAAAAATAT
1 TTATT-AAAATAT
6032594 TTATATAAAATAT
1 TTAT-TAAAATAT
* *
6032607 ATA-TCAAA-AT
1 TTATTAAAATAT
*
6032617 TTATTAAAAAAT
1 TTATTAAAATAT
6032629 TT
1 TT
6032631 TAAAATTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 4 0.08
11 16 0.33
12 10 0.20
13 18 0.37
14 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (12 bp):
TTATTAAAATAT
Found at i:6032841 original size:34 final size:34
Alignment explanation
Indices: 6032803--6032872 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
6032793 CGTGGGACAC
6032803 GACACGCGCGGTAGAAATAAGGTCAGACACAAAA
1 GACACGCGCGGTAGAAATAAGGTCAGACACAAAA
* * *
6032837 GACACGTGGGGTAGAAATGAGGTCAGACACAAAA
1 GACACGCGCGGTAGAAATAAGGTCAGACACAAAA
6032871 GA
1 GA
6032873 AACCGTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.30, T:0.10
Consensus pattern (34 bp):
GACACGCGCGGTAGAAATAAGGTCAGACACAAAA
Found at i:6033098 original size:13 final size:14
Alignment explanation
Indices: 6033071--6033104 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
6033061 TGAATTTAAT
6033071 ATTTAAAAAATAAA
1 ATTTAAAAAATAAA
*
6033085 ATTTTAAAAA-AAA
1 ATTTAAAAAATAAA
6033098 ATTTAAA
1 ATTTAAA
6033105 TTTTTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTTAAAAAATAAA
Found at i:6033262 original size:18 final size:18
Alignment explanation
Indices: 6033235--6033286 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
6033225 TAAAGAAATT
6033235 ATTAAAAATTTATAAAAA
1 ATTAAAAATTTATAAAAA
*
6033253 ATTTAAAATTTATAAAAA
1 ATTAAAAATTTATAAAAA
*
6033271 ATTAAAAATTTTTAAA
1 ATTAAAAATTTATAAA
6033287 TTAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAAATTTATAAAAA
Found at i:6033287 original size:26 final size:26
Alignment explanation
Indices: 6033247--6033296 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6033237 TAAAAATTTA
*
6033247 TAAAAAATTTAAAATTTATAAAAAAT
1 TAAAAAATTTAAAATTAATAAAAAAT
* *
6033273 TAAAAATTTTTAAATTAATAAAAA
1 TAAAAAATTTAAAATTAATAAAAA
6033297 TAATCAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAAAATTTAAAATTAATAAAAAAT
Found at i:6033321 original size:13 final size:13
Alignment explanation
Indices: 6033303--6033327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6033293 AAAATAATCA
6033303 AAATATTTTTTTG
1 AAATATTTTTTTG
6033316 AAATATTTTTTT
1 AAATATTTTTTT
6033328 TAATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AAATATTTTTTTG
Found at i:6034413 original size:22 final size:22
Alignment explanation
Indices: 6034379--6034428 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6034369 TTTATTTAAT
6034379 AAAA-AATTAATTGATAAATAA
1 AAAATAATTAATTGATAAATAA
* * *
6034400 CAAATAATTTATTGATTAATAA
1 AAAATAATTAATTGATAAATAA
6034422 AAAATAA
1 AAAATAA
6034429 GTCACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAATAATTAATTGATAAATAA
Found at i:6034532 original size:23 final size:22
Alignment explanation
Indices: 6034505--6034667 Score: 110
Period size: 23 Copynumber: 7.5 Consensus size: 22
6034495 TTATTTACTT
6034505 ATAAATAATATTATAATATATTA
1 ATAAATAATA-TATAATATATTA
** * *
6034528 ATAAATGTTATATTATATATAA
1 ATAAATAATATATAATATATTA
*
6034550 AT-AA-AATA-ATATTATATTA
1 ATAAATAATATATAATATATTA
* *
6034569 ATTAAT-AT-TGTAATATATTA
1 ATAAATAATATATAATATATTA
*
6034589 ATAAATAATATACTATTA-ATATA
1 ATAAATAATATA-TAATATAT-TA
*
6034612 ATATATTAATA-A-ACAT-TATTA
1 ATA-AATAATATATA-ATATATTA
* *
6034633 AGAAATAATATTATAATAAATTA
1 ATAAATAATA-TATAATATATTA
6034656 ATAAATAATATA
1 ATAAATAATATA
6034668 AAAATAATAA
Statistics
Matches: 106, Mismatches: 20, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
19 10 0.09
20 26 0.25
21 9 0.08
22 23 0.22
23 32 0.30
24 6 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAAATAATATATAATATATTA
Found at i:6034544 original size:20 final size:20
Alignment explanation
Indices: 6034511--6034680 Score: 96
Period size: 20 Copynumber: 8.2 Consensus size: 20
6034501 ACTTATAAAT
6034511 AATATTATAATATATTAATA
1 AATATTATAATATATTAATA
* *
6034531 AATGTTATATTATATATAAATA
1 AATATTATA--ATATATTAATA
* * *
6034553 AA-ATAATATTATATTAATT
1 AATATTATAATATATTAATA
*
6034572 AATATTGTAATATATTAATA
1 AATATTATAATATATTAATA
* * *
6034592 AATAATATACTAT-TAATATA
1 AATATTATAATATATTA-ATA
* *
6034612 ATATATTAATAAACATTATTAAGAAA
1 A-ATATT-AT-AATA-TATT-A-ATA
*
6034638 TAATATTATAATAAATTAATA
1 -AATATTATAATATATTAATA
* *
6034659 AATAATATAA-A-AATAATA
1 AATATTATAATATATTAATA
6034677 AATA
1 AATA
6034681 GTTTTATTTT
Statistics
Matches: 113, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
18 10 0.09
19 13 0.12
20 44 0.39
21 10 0.09
22 15 0.13
23 5 0.04
24 4 0.04
25 3 0.03
26 8 0.07
27 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATTATAATATATTAATA
Found at i:6034549 original size:41 final size:41
Alignment explanation
Indices: 6034505--6034661 Score: 120
Period size: 41 Copynumber: 3.7 Consensus size: 41
6034495 TTATTTACTT
6034505 ATAAATAATATTATAATATATTAATAAATGTTATATTATAT-
1 ATAAATAATATTATAATATATTAATAAAT-TTATATTATATA
* * * * * *
6034546 ATAAATAAAATAATATTATATTAATTAATATTGTAATATATTA
1 ATAAATAATATTATAATATATTAATAAAT-TTATATTATA-TA
* * ** *
6034589 ATAAATAATATACTATTAATATAATATATTAATAAACATTAT-TA
1 ATAAATAATAT--TA-TAATATATTA-ATAAATTTATATTATATA
* *
6034633 AGAAATAATATTATAATAAATTAATAAAT
1 ATAAATAATATTATAATATATTAATAAAT
6034662 AATATAAAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
40 5 0.06
41 41 0.46
42 3 0.03
43 10 0.11
44 12 0.13
45 1 0.01
46 12 0.13
47 6 0.07
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (41 bp):
ATAAATAATATTATAATATATTAATAAATTTATATTATATA
Found at i:6034614 original size:31 final size:30
Alignment explanation
Indices: 6034516--6034624 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 30
6034506 TAAATAATAT
*
6034516 TATAATATATTAATAAAT-GT-TATATTATA
1 TATAATATATTAATAAATAATATATATTA-A
* *
6034545 TATAA-ATA-AAAT-AATATTATATTAATTAA
1 TATAATATATTAATAAATAATATA-T-ATTAA
6034574 TATTGTAATATATTAATAAATAATATACTATTAA
1 TA---TAATATATTAATAAATAATATA-TATTAA
6034608 TATAATATATTAATAAA
1 TATAATATATTAATAAA
6034625 CATTATTAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
26 3 0.05
27 4 0.06
28 5 0.08
29 9 0.14
30 4 0.06
31 15 0.23
32 3 0.05
33 3 0.05
34 10 0.15
35 9 0.14
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (30 bp):
TATAATATATTAATAAATAATATATATTAA
Found at i:6034656 original size:36 final size:34
Alignment explanation
Indices: 6034608--6034676 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
6034598 ATACTATTAA
* *
6034608 TATAATATATTAATAAACATTATTAAGAAATAATAT
1 TATAATAAATTAATAAACAATA-TAA-AAATAATAT
*
6034644 TATAATAAATTAATAAATAATATAAAAATAATA
1 TATAATAAATTAATAAACAATATAAAAATAATA
6034677 AATAGTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 8 0.27
35 3 0.10
36 19 0.63
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (34 bp):
TATAATAAATTAATAAACAATATAAAAATAATAT
Found at i:6034673 original size:23 final size:23
Alignment explanation
Indices: 6034629--6034674 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6034619 AATAAACATT
* *
6034629 ATTAAGAAATAATATTATAATAA
1 ATTAAGAAATAATATAAAAATAA
*
6034652 ATTAATAAATAATATAAAAATAA
1 ATTAAGAAATAATATAAAAATAA
6034675 TAAATAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTAAGAAATAATATAAAAATAA
Found at i:6034762 original size:16 final size:16
Alignment explanation
Indices: 6034670--6034797 Score: 60
Period size: 15 Copynumber: 8.2 Consensus size: 16
6034660 ATAATATAAA
*
6034670 AATAATAAATAGTTTT
1 AATAATAAATAATTTT
**
6034686 -ATTTTAAAT-ATTTT
1 AATAATAAATAATTTT
*
6034700 AATATTAAATATTATTATT
1 AATAATAAATA--ATT-TT
*
6034719 AA-AATATAATTATTTTT
1 AATAATA-AA-TAATTTT
*
6034736 GAA-AATTAATAATTTT
1 -AATAATAAATAATTTT
6034752 AATAATAAATAA-TTT
1 AATAATAAATAATTTT
* *
6034767 --CAAT--AT-ACTTT
1 AATAATAAATAATTTT
6034778 AATAATAAATAATTTT
1 AATAATAAATAATTTT
6034794 AATA
1 AATA
6034798 GTTGTATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
10 1 0.01
11 5 0.06
13 6 0.07
14 4 0.05
15 22 0.26
16 22 0.26
17 4 0.05
18 13 0.15
19 6 0.07
20 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AATAATAAATAATTTT
Found at i:6034912 original size:14 final size:15
Alignment explanation
Indices: 6034893--6034921 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6034883 TTTTAATTCA
6034893 AAAAATT-ATTTTTT
1 AAAAATTCATTTTTT
6034907 AAAAATTCATTTTTT
1 AAAAATTCATTTTTT
6034922 TACTAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAAATTCATTTTTT
Found at i:6035235 original size:65 final size:65
Alignment explanation
Indices: 6035120--6035249 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
6035110 AGTAAGTCAA
*
6035120 GTCACGTGGCTAAATCCATCTGGCCACGTTATTGACCTGTACGCCGAATTTCTTCAGGTACGGGT
1 GTCACGTGGCTAAATCCATCTGGCCACGTTATTGACCTGTACGCCAAATTTCTTCAGGTACGGGT
* * *
6035185 GTCACGTGGCTAAATCCGTCTGGCCACGTTATTGACTTGTAGGCCAAATTTCTTCAGGTACGGGT
1 GTCACGTGGCTAAATCCATCTGGCCACGTTATTGACCTGTACGCCAAATTTCTTCAGGTACGGGT
6035250 ATCTTCCGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (65 bp):
GTCACGTGGCTAAATCCATCTGGCCACGTTATTGACCTGTACGCCAAATTTCTTCAGGTACGGGT
Found at i:6042073 original size:17 final size:16
Alignment explanation
Indices: 6042031--6042076 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
6042021 ATTAAAATGG
*
6042031 ATTTTTTTAATTTTTT
1 ATTTTTTTAATTTTAT
6042047 ATTATTTTTAATTTTAAT
1 ATT-TTTTTAATTTT-AT
*
6042065 ATTTATTTAATT
1 ATTTTTTTAATT
6042077 CAATTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 19 0.73
18 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTTAATTTTAT
Found at i:6042211 original size:7 final size:7
Alignment explanation
Indices: 6042200--6042252 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 7
6042190 AAAATAAAAA
6042200 TAATTAT
1 TAATTAT
*
6042207 AAATT-T
1 TAATTAT
6042213 TAATTAT
1 TAATTAT
6042220 TAATTAAT
1 TAATT-AT
6042228 TAATTAAT
1 TAATT-AT
6042236 TAA-TAT
1 TAATTAT
6042242 TAA-TAT
1 TAATTAT
6042248 TAATT
1 TAATT
6042253 GTAATGAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 16 0.39
7 12 0.29
8 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TAATTAT
Found at i:6043034 original size:42 final size:42
Alignment explanation
Indices: 6042955--6043069 Score: 105
Period size: 42 Copynumber: 2.7 Consensus size: 42
6042945 ATATTTTTAT
* * **
6042955 ATATTATATTAAT-AAAATTAT-TATTTAATATTTTAATTTGAA
1 ATATTA-ATTAATAAAAATAATATATTT-ATATTATAATTAAAA
6042997 ATATTAATTCAATAAAAATAATATATTTATA-TATAATTAAAA
1 ATATTAATT-AATAAAAATAATATATTTATATTATAATTAAAA
6043039 ATA-TAATTTATATTAAAAATAATAT-TTTATA
1 ATATTAA-TTA-A-TAAAAATAATATATTTATA
6043070 AATACTACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
41 7 0.11
42 29 0.46
43 22 0.35
44 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
ATATTAATTAATAAAAATAATATATTTATATTATAATTAAAA
Found at i:6043055 original size:18 final size:19
Alignment explanation
Indices: 6043032--6043069 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6043022 TTTATATATA
6043032 ATTAAAAAT-ATAATTTAT
1 ATTAAAAATAATAATTTAT
*
6043050 ATTAAAAATAATATTTTAT
1 ATTAAAAATAATAATTTAT
6043069 A
1 A
6043070 AATACTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAAAATAATAATTTAT
Done.