Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 22 of 138
Found at i:5890817 original size:29 final size:29
Alignment explanation
Indices: 5890784--5890859 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
5890774 AATTTATAAC
*
5890784 TTTTTTATAATTTTTTGAAATTA-AAAAA
1 TTTTTTATAATTTTTTAAAATTATAAAAA
**
5890812 TTTTTTATAAATTTTAAAAAATTATAAAAA
1 TTTTTTAT-AATTTTTTAAAATTATAAAAA
*
5890842 TAATTTTATAATTTTTTA
1 T-TTTTTATAATTTTTTA
5890860 GGAATTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.21
29 12 0.31
30 13 0.33
31 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTTTTATAATTTTTTAAAATTATAAAAA
Found at i:5890823 original size:19 final size:19
Alignment explanation
Indices: 5890792--5890834 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
5890782 ACTTTTTTAT
5890792 AATTTTTTGAAA-TTAAAA
1 AATTTTTTGAAATTTAAAA
*
5890810 AATTTTTTATAAATTTTAAAA
1 AATTTTTT-GAAA-TTTAAAA
5890831 AATT
1 AATT
5890835 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
21 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTTTTTGAAATTTAAAA
Found at i:5891343 original size:23 final size:24
Alignment explanation
Indices: 5891296--5891345 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5891286 AATGGGATAA
*
5891296 AAAAATTTTAAATATTAATGTAAC
1 AAAAATTTTAAATATTAAAGTAAC
5891320 AAAAATTTTAAA-ATTTAAAG-AAC
1 AAAAATTTTAAATA-TTAAAGTAAC
5891343 AAA
1 AAA
5891346 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAAATTTTAAATATTAAAGTAAC
Found at i:5891984 original size:3 final size:3
Alignment explanation
Indices: 5891976--5892024 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5891966 TTATTGGCCC
5891976 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5892024 A
1 A
5892025 CGACTAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5894885 original size:86 final size:86
Alignment explanation
Indices: 5894731--5894978 Score: 293
Period size: 86 Copynumber: 2.9 Consensus size: 86
5894721 GCTATAAAAT
* * * * *
5894731 TGGCAAAAGATAGCCAAGAT-AAAATAAGAAGATTGTCTAT-TTTCTTTTCTTGTAAGAATGATC
1 TGGCAAAAGATAGCCAAGATAAAAACAAAAAGATTGCCTATCTAT-TTTACTTGTAAGAATGATC
* * *
5894794 TAAATAAAGATTAAGAAGTTAA
65 TAAATAAAGACTAAAAAATTAA
** * * * *
5894816 TGGCAAAAGATAGCTTAGATAAAAACAAAGAGATTGCCTATCTATTTTATTTGTAAGAATAATCC
1 TGGCAAAAGATAGCCAAGATAAAAACAAAAAGATTGCCTATCTATTTTACTTGTAAGAATGATCT
* *
5894881 AAATATAGACTAAAAAATTGA
66 AAATAAAGACTAAAAAATTAA
* * *
5894902 TGGCAAAAGATAGCCAAGATAAAAATAAAAAGATTGCCTATTTGTTTTACTTGTAAGAATGATCT
1 TGGCAAAAGATAGCCAAGATAAAAACAAAAAGATTGCCTATCTATTTTACTTGTAAGAATGATCT
*
5894967 AGATAAAGACTA
66 AAATAAAGACTA
5894979 CAAAGTTAGC
Statistics
Matches: 134, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
85 18 0.13
86 114 0.85
87 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (86 bp):
TGGCAAAAGATAGCCAAGATAAAAACAAAAAGATTGCCTATCTATTTTACTTGTAAGAATGATCT
AAATAAAGACTAAAAAATTAA
Found at i:5904352 original size:16 final size:16
Alignment explanation
Indices: 5904331--5904365 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5904321 AGATTAACTG
*
5904331 CAAACAGAAAAACTTA
1 CAAACAGAAAAACTCA
*
5904347 CAAACAGAATAACTCA
1 CAAACAGAAAAACTCA
5904363 CAA
1 CAA
5904366 GGATTTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (16 bp):
CAAACAGAAAAACTCA
Found at i:5907990 original size:2 final size:2
Alignment explanation
Indices: 5907983--5908017 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5907973 GATTATAGAA
5907983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5908018 AAGCATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5911237 original size:48 final size:46
Alignment explanation
Indices: 5911171--5911299 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 46
5911161 CATTTTGAGG
* *
5911171 TAAGCATTTTATAATTTCAAGCCTTCATTAAGAAGGAGCTTTCTTGGA
1 TAAGAATTTTA-AATTTCAAGCCTTCATTAA-AAGGAACTTTCTTGGA
* * *
5911219 TAAGAATTTTAAAGTTTCATGCTTTCCTTGAAAAGGAACTTTCTTGGA
1 TAAGAATTTTAAA-TTTCAAGCCTTCATT-AAAAGGAACTTTCTTGGA
* * *
5911267 TGAGAATTTTAAAAATTCAAGCCTTTATTAAAA
1 TAAGAATTTT-AAATTTCAAGCCTTCATTAAAA
5911300 AAAAGCTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
47 6 0.09
48 56 0.84
49 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (46 bp):
TAAGAATTTTAAATTTCAAGCCTTCATTAAAAGGAACTTTCTTGGA
Found at i:5913559 original size:20 final size:20
Alignment explanation
Indices: 5913536--5913574 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5913526 ACATGACTTT
5913536 TTTATTGAT-TTTTTGCATGA
1 TTTATT-ATATTTTTGCATGA
5913556 TTTATTATATTTTTGCATG
1 TTTATTATATTTTTGCATG
5913575 CTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.62
Consensus pattern (20 bp):
TTTATTATATTTTTGCATGA
Found at i:5913581 original size:23 final size:22
Alignment explanation
Indices: 5913527--5913588 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 22
5913517 TTATTAATTA
*
5913527 CATGACTTTTTTATTGATTTTTTG
1 CATG-CTTATTTATT-ATTTTTTG
5913551 CATG---ATTTATTATATTTTTG
1 CATGCTTATTTATTAT-TTTTTG
*
5913571 CATGCTTATTTTTTATTT
1 CATGCTTATTTATTATTT
5913589 AATATGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
22 2 0.06
23 8 0.25
24 4 0.12
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (22 bp):
CATGCTTATTTATTATTTTTTG
Found at i:5913712 original size:13 final size:14
Alignment explanation
Indices: 5913687--5913721 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5913677 ATTTGTTTGA
5913687 TTGCATGAATATTT
1 TTGCATGAATATTT
5913701 TTGCAT-AATATTT
1 TTGCATGAATATTT
5913714 TTGGCATG
1 TT-GCATG
5913722 CTTTTATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (14 bp):
TTGCATGAATATTT
Found at i:5914461 original size:11 final size:11
Alignment explanation
Indices: 5914435--5914475 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
5914425 AATTAAGTGT
*
5914435 ATAAATTTTGA
1 ATAAATTTTTA
5914446 A-AAATTTTTA
1 ATAAATTTTTA
5914456 ATAAA-TTTTA
1 ATAAATTTTTA
*
5914466 ATATATTTTT
1 ATAAATTTTT
5914476 TAGATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
ATAAATTTTTA
Found at i:5914580 original size:39 final size:39
Alignment explanation
Indices: 5914520--5914611 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
5914510 GTTTTTACAA
* *
5914520 TTTAATAAGTATTAATCAAATTTAAATTATAAA-CTATATT
1 TTTAATAAAT-TTTATCAAATTTAAATTATAAATC-ATATT
*
5914560 TTTAATAAATTTTATCAAATTTGAATTATAAATCATATT
1 TTTAATAAATTTTATCAAATTTAAATTATAAATCATATT
5914599 TTTAATAAATTTT
1 TTTAATAAATTTT
5914612 TTCATATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 38 0.79
40 10 0.21
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (39 bp):
TTTAATAAATTTTATCAAATTTAAATTATAAATCATATT
Found at i:5920024 original size:103 final size:103
Alignment explanation
Indices: 5919845--5920054 Score: 420
Period size: 103 Copynumber: 2.0 Consensus size: 103
5919835 AGGAAGTTGC
5919845 AATGGAGTTGGAGGGTCTAAGAGCAATGGCGAAGCATCCCTGGGTAAAAGATGATGTGAATTCAA
1 AATGGAGTTGGAGGGTCTAAGAGCAATGGCGAAGCATCCCTGGGTAAAAGATGATGTGAATTCAA
5919910 AGGAGACAGAATTTTTGCTTGGTGACATCTCAGGCGCT
66 AGGAGACAGAATTTTTGCTTGGTGACATCTCAGGCGCT
5919948 AATGGAGTTGGAGGGTCTAAGAGCAATGGCGAAGCATCCCTGGGTAAAAGATGATGTGAATTCAA
1 AATGGAGTTGGAGGGTCTAAGAGCAATGGCGAAGCATCCCTGGGTAAAAGATGATGTGAATTCAA
5920013 AGGAGACAGAATTTTTGCTTGGTGACATCTCAGGCGCT
66 AGGAGACAGAATTTTTGCTTGGTGACATCTCAGGCGCT
5920051 AATG
1 AATG
5920055 CTCGAGGTAC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (103 bp):
AATGGAGTTGGAGGGTCTAAGAGCAATGGCGAAGCATCCCTGGGTAAAAGATGATGTGAATTCAA
AGGAGACAGAATTTTTGCTTGGTGACATCTCAGGCGCT
Found at i:5921935 original size:20 final size:20
Alignment explanation
Indices: 5921885--5921936 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
5921875 TATATATATT
*
5921885 TTATATATTTAATAAATTAA
1 TTATATATTTAATAAATAAA
* *
5921905 TTTTTTATTTAATAATATAAA
1 TTATATATTTAATAA-ATAAA
5921926 TTATAT-TTTAA
1 TTATATATTTAA
5921937 ATTTATTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATTTAATAAATAAA
Found at i:5928994 original size:13 final size:12
Alignment explanation
Indices: 5928971--5929005 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5928961 AACATAATTT
5928971 ATTTAATAAAAAA
1 ATTTAA-AAAAAA
*
5928984 TTTTAAAAAAAA
1 ATTTAAAAAAAA
5928996 ATTTAAAAAA
1 ATTTAAAAAA
5929006 TTAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATTTAAAAAAAA
Found at i:5929789 original size:19 final size:21
Alignment explanation
Indices: 5929767--5929813 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
5929757 CTATATCAAA
5929767 AAAATAATTA-ATTT-TCTTT
1 AAAATAATTATATTTATCTTT
*
5929786 AAAAT-TTTATATTTATCTTT
1 AAAATAATTATATTTATCTTT
5929806 AAATATAA
1 AAA-ATAA
5929814 AACAAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.14
19 9 0.41
20 8 0.36
21 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATAATTATATTTATCTTT
Found at i:5933505 original size:11 final size:11
Alignment explanation
Indices: 5933472--5933508 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
5933462 TGACATCATT
5933472 TAAAAATAATA
1 TAAAAATAATA
*
5933483 TAAAATAAAATA
1 TAAAA-ATAATA
5933495 TAAAAATAATA
1 TAAAAATAATA
5933506 TAA
1 TAA
5933509 TTTATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:5940547 original size:23 final size:23
Alignment explanation
Indices: 5940521--5940565 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5940511 AATTGCTCAA
*
5940521 ACTTATAAAACGCCTTTTGTGAT
1 ACTTACAAAACGCCTTTTGTGAT
5940544 ACTTACAAAACGCCTTTTGTGA
1 ACTTACAAAACGCCTTTTGTGA
5940566 ACAAAACCCG
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:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (23 bp):
ACTTACAAAACGCCTTTTGTGAT
Found at i:5945257 original size:15 final size:13
Alignment explanation
Indices: 5945237--5945274 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5945227 AAAGTTTTTT
5945237 ATAAAAAATGATTTA
1 ATAAAAAA--ATTTA
5945252 AT-AAAAAATTTA
1 ATAAAAAAATTTA
5945264 ATAAAAAAATT
1 ATAAAAAAATT
5945275 AAATTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 8 0.36
14 5 0.23
15 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
ATAAAAAAATTTA
Found at i:5945264 original size:12 final size:12
Alignment explanation
Indices: 5945247--5945276 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5945237 ATAAAAAATG
5945247 ATTTAATAAAAA
1 ATTTAATAAAAA
5945259 ATTTAATAAAAA
1 ATTTAATAAAAA
*
5945271 AATTAA
1 ATTTAA
5945277 ATTGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:5945409 original size:14 final size:15
Alignment explanation
Indices: 5945390--5945422 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5945380 AAATTTTATC
5945390 AATATTTTAT-TAAA
1 AATATTTTATATAAA
5945404 AATA-TTTATATAAA
1 AATATTTTATATAAA
5945418 AATAT
1 AATAT
5945423 ATATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTTATATAAA
Found at i:5945419 original size:37 final size:36
Alignment explanation
Indices: 5945377--5945446 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
5945367 TATTTAACGG
* *
5945377 TAAAAAT-TTTATCAATATTTTATTAAAAATATTTATA
1 TAAAAATATATATCAA-AATTTATT-AAAATATTTATA
5945414 TAAAAATATATATCAAAATTTATTAAAATATTT
1 TAAAAATATATATCAAAATTTATTAAAATATTT
5945447 TTAAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 9 0.30
37 14 0.47
38 7 0.23
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
TAAAAATATATATCAAAATTTATTAAAATATTTATA
Found at i:5945509 original size:7 final size:7
Alignment explanation
Indices: 5945492--5945543 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
5945482 TTTCAATCTA
5945492 TTAATTTT
1 TTAA-TTT
5945500 TTAATTT
1 TTAATTT
5945507 TTAATTT
1 TTAATTT
*
5945514 TTGATTT
1 TTAATTT
5945521 TTAATTT
1 TTAATTT
*
5945528 TTGATTT
1 TTAATTT
5945535 TT-ATTT
1 TTAATTT
5945541 TTA
1 TTA
5945544 TTTAATCGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
6 6 0.15
7 30 0.75
8 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (7 bp):
TTAATTT
Found at i:5945520 original size:14 final size:14
Alignment explanation
Indices: 5945492--5945546 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
5945482 TTTCAATCTA
*
5945492 TTAATTTTTTAATTT
1 TTAA-TTTTTGATTT
5945507 TTAATTTTTGATTT
1 TTAATTTTTGATTT
5945521 TTAATTTTTGATTT
1 TTAATTTTTGATTT
5945535 TT-ATTTTT-ATTT
1 TTAATTTTTGATTT
5945547 AATCGTTCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 25 0.64
15 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (14 bp):
TTAATTTTTGATTT
Found at i:5948350 original size:17 final size:16
Alignment explanation
Indices: 5948328--5948360 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5948318 TTATCTTAAC
5948328 TTTTTTAAGTATTTTAT
1 TTTTTTAAG-ATTTTAT
5948345 TTTTTTAAGATTTTAT
1 TTTTTTAAGATTTTAT
5948361 CTTTGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTTTTAAGATTTTAT
Found at i:5949567 original size:114 final size:113
Alignment explanation
Indices: 5949368--5949578 Score: 271
Period size: 114 Copynumber: 1.9 Consensus size: 113
5949358 TTAAGTTTCA
** *
5949368 AGAATATTTTAAAATTTCAAAAGTTGTGGAGCCATACTTAAAGGAATTTTTTAAAGTTATTAAGC
1 AGAATATTTTAAAATTTCAAAAGTTGTAAAGCCATACTTAAAGGAATTTTTGAAAGTTATTAAGC
*
5949433 CTCCACTTAAATGAGCATTCATTATCAAGATTCATAAGTCCTCCAAAG
66 CTCCACTTAAAGGAGCATTCATTATCAAGATTCATAAGTCCTCCAAAG
* * * * * *
5949481 AGAATATTTTAAATTTTTAAAAGTTGTAAAGCCTTTACTTAGAGGAGGTTTTTGAAA-TTATTGA
1 AGAATATTTTAAAATTTCAAAAGTTGTAAAGCC-ATACTTAAAGGA-ATTTTTGAAAGTTATTAA
* ***
5949545 GCTTTTGCTTAAAGGAGCATTCATTATCAAGATT
64 GCCTCCACTTAAAGGAGCATTCATTATCAAGATT
5949579 TGTAAATCTT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
113 29 0.35
114 45 0.55
115 8 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (113 bp):
AGAATATTTTAAAATTTCAAAAGTTGTAAAGCCATACTTAAAGGAATTTTTGAAAGTTATTAAGC
CTCCACTTAAAGGAGCATTCATTATCAAGATTCATAAGTCCTCCAAAG
Found at i:5950136 original size:12 final size:13
Alignment explanation
Indices: 5950118--5950150 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5950108 TTTGTTTTTA
5950118 AAAAATAAGAAAT
1 AAAAATAAGAAAT
5950131 -AAAATAA-AAAT
1 AAAAATAAGAAAT
5950142 AAAAATAAG
1 AAAAATAAG
5950151 TGTTAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAATAAGAAAT
Found at i:5951324 original size:20 final size:21
Alignment explanation
Indices: 5951287--5951325 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5951277 TTTGTTTTAA
5951287 AAAATAATAAAAGGAATAAAT
1 AAAATAATAAAAGGAATAAAT
*
5951308 AAAATAA-AAAAGTAATAA
1 AAAATAATAAAAGGAATAA
5951326 CAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AAAATAATAAAAGGAATAAAT
Found at i:5957325 original size:31 final size:31
Alignment explanation
Indices: 5957290--5957352 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5957280 TTAGGATATG
5957290 AATAGTGTATATAATATCTAATGAAACCAAA
1 AATAGTGTATATAATATCTAATGAAACCAAA
5957321 AATAGTGTATATAATATCTAATGAAACCAAA
1 AATAGTGTATATAATATCTAATGAAACCAAA
5957352 A
1 A
5957353 GCCTAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
AATAGTGTATATAATATCTAATGAAACCAAA
Found at i:5958185 original size:2 final size:2
Alignment explanation
Indices: 5958178--5958215 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5958168 TAATAGCTTT
5958178 TC TC TC TC TC T- TC -C T- TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5958216 TTCCCCCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5961946 original size:2 final size:2
Alignment explanation
Indices: 5961939--5961963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5961929 TGCCATCTAA
5961939 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5961964 ATCGTATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5963936 original size:17 final size:18
Alignment explanation
Indices: 5963914--5963956 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
5963904 ACTTTAAGCC
5963914 AACAAAA-AAAAAAAAAA
1 AACAAAAGAAAAAAAAAA
*
5963931 AACAAAAGGAAAAAAAAA
1 AACAAAAGAAAAAAAAAA
5963949 AA-AAAAGA
1 AACAAAAGA
5963957 CTAAAATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (18 bp):
AACAAAAGAAAAAAAAAA
Found at i:5963962 original size:18 final size:18
Alignment explanation
Indices: 5963922--5963955 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5963912 CCAACAAAAA
5963922 AAAAAAAAAAACAAAAGG
1 AAAAAAAAAAACAAAAGG
5963940 AAAAAAAAAAA-AAAAG
1 AAAAAAAAAAACAAAAG
5963956 ACTAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAGG
Found at i:5964538 original size:14 final size:14
Alignment explanation
Indices: 5964521--5964547 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5964511 ACTTTAAGCT
5964521 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
5964535 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
5964548 CTAAAATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:5966574 original size:22 final size:24
Alignment explanation
Indices: 5966541--5966586 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
5966531 ATTAAATAAT
5966541 TAAAAAAGAAAC-AAAGT-GAAAA
1 TAAAAAAGAAACAAAAGTAGAAAA
5966563 TAAAAACA-AAACAAAAGTAGAAAA
1 TAAAAA-AGAAACAAAAGTAGAAAA
5966587 AGGGGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 6 0.29
24 5 0.24
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.09
Consensus pattern (24 bp):
TAAAAAAGAAACAAAAGTAGAAAA
Found at i:5968530 original size:6 final size:6
Alignment explanation
Indices: 5968493--5968527 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
5968483 TTTAAGCTAA
5968493 AAAAAG AAAAAG AAAAAG AAAAAG AGAAAA- AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAA
5968528 AAAGAGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5971386 original size:26 final size:22
Alignment explanation
Indices: 5971328--5971374 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5971318 TGTAGTTGAC
5971328 TACATTGAAGAATTATTGTACT
1 TACATTGAAGAATTATTGTACT
5971350 TACATTGAAGAATTATTGTACT
1 TACATTGAAGAATTATTGTACT
5971372 TAC
1 TAC
5971375 TTTTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TACATTGAAGAATTATTGTACT
Found at i:5978185 original size:20 final size:20
Alignment explanation
Indices: 5978134--5978191 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
5978124 ATTTTTATTC
5978134 ATTTTTATTTTA-AATTTTT
1 ATTTTTATTTTATAATTTTT
* *
5978153 -TATTTCATATTTATCATTTTT
1 AT-TTTTAT-TTTATAATTTTT
*
5978174 ATTTTTATTTTATGATTT
1 ATTTTTATTTTATAATTT
5978192 ATTTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 13 0.42
21 11 0.35
22 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTATTTTATAATTTTT
Found at i:5980086 original size:59 final size:56
Alignment explanation
Indices: 5980031--5980177 Score: 186
Period size: 59 Copynumber: 2.5 Consensus size: 56
5980021 AAAAAAAGTT
*
5980031 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAGTTTCCAAAAAATA
1 TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTC-AAAATCAAAATTTCC-AAAAATA
* * * *
5980090 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAGATTAAAATTTCTAAAGAATA
1 TTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATCAAAATTTCCAAA-AATA
* *
5980148 TTTTAGGGAAAAGTTAAAAGTATCAATTTT
1 TTTTTGGGAAAAGTTGAAAGTATCAATTTT
5980178 TTCTGCACAA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
57 27 0.34
58 18 0.23
59 33 0.42
60 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (56 bp):
TTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATCAAAATTTCCAAAAATA
Found at i:5980180 original size:59 final size:59
Alignment explanation
Indices: 5980038--5980177 Score: 194
Period size: 57 Copynumber: 2.4 Consensus size: 59
5980028 GTTTTTTTGA
* *
5980038 GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAGTTTCCAAAAAATATTTTTGG
1 GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAATTTCCAAAAAATATTTTTAG
* * * * *
5980097 GGAAAAGTTGAAAGTATCAATTTTCCTC-GAGATTAAAATTTCTAAAGAATA-TTTTAG
1 GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAATTTCCAAAAAATATTTTTAG
*
5980154 GGAAAAGTTAAAAGTATCAATTTT
1 GGAAAAGTTGAAAGTATCAATTTT
5980178 TTCTGCACAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 28 0.38
58 17 0.23
59 28 0.38
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (59 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAATTTCCAAAAAATATTTTTAG
Found at i:5980775 original size:16 final size:15
Alignment explanation
Indices: 5980737--5980782 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
5980727 TGTATATATG
5980737 TGTTATTATTCATTAT
1 TGTTATTATTCATT-T
5980753 TG-T-TTATTCATTT
1 TGTTATTATTCATTT
5980766 TGTTAATTATGTCATTT
1 TGTT-ATTAT-TCATTT
5980783 ATATGCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.12
14 10 0.38
15 1 0.04
16 6 0.23
17 6 0.23
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (15 bp):
TGTTATTATTCATTT
Found at i:5984084 original size:13 final size:12
Alignment explanation
Indices: 5984061--5984107 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
5984051 AAAAGTGAGC
5984061 AAAA-AGAAAAA
1 AAAAGAGAAAAA
*
5984072 AAATGATGAAAAA
1 AAAAGA-GAAAAA
5984085 AAAAGAGAAGAAA
1 AAAAGAGAA-AAA
5984098 AAAAGA-AAAA
1 AAAAGAGAAAA
5984108 TGAAAGAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
13 20 0.65
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAGAGAAAAA
Found at i:5984105 original size:23 final size:23
Alignment explanation
Indices: 5984062--5984139 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
5984052 AAAGTGAGCA
*
5984062 AAAAGAAA-AAAAATGATGAAAAA-
1 AAAAGAAAGAAAAA--AAGAAAAAT
5984085 AAAAGAGAAGAAAAAAAGAAAAAT
1 AAAAGA-AAGAAAAAAAGAAAAAT
* * *
5984109 GAAAGAAGGAAAAAATG-AAAAT
1 AAAAGAAAGAAAAAAAGAAAAAT
5984131 GAAAAGAAA
1 -AAAAGAAA
5984140 TTCAAATTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.11
23 28 0.62
24 7 0.16
25 5 0.11
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (23 bp):
AAAAGAAAGAAAAAAAGAAAAAT
Found at i:5985662 original size:42 final size:42
Alignment explanation
Indices: 5985381--5985841 Score: 742
Period size: 42 Copynumber: 11.1 Consensus size: 42
5985371 AGGATTGTCA
5985381 AGGAGCAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5985422 AGGAGCAATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
5985463 AGGAGCAATTTACTTTTTCAAAAGTCATGGTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
5985506 AGGAGCAATTTAC--TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5985546 AGGAGCAATTTAC--TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5985586 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
5985627 GGGAGCAATTTACTTTTTCAAAGTCGTCGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5985669 AGGAGCAATTTAC-TTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
5985711 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5985753 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * *
5985795 AGGAGCAATTTA-TTTTCCAAAGTCATTGAGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5985836 AGGAGC
1 AGGAGC
5985842 TTTGAAAAAA
Statistics
Matches: 397, Mismatches: 16, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
40 74 0.19
41 131 0.33
42 153 0.39
43 39 0.10
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (42 bp):
AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5985852 original size:1 final size:1
Alignment explanation
Indices: 5985846--5985942 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
5985836 AGGAGCTTTG
* * * ** * * *
5985846 AAAAAAAACAAAATAAAAAAAACAAAAAAATTAAAAAAACAAAAAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
5985911 CAAAAACAAAAAAATAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5985943 TTACCTCTGT
Statistics
Matches: 74, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:5985866 original size:8 final size:8
Alignment explanation
Indices: 5985847--5985942 Score: 108
Period size: 8 Copynumber: 11.9 Consensus size: 8
5985837 GGAGCTTTGA
5985847 AAAAAAAC
1 AAAAAAAC
*
5985855 -AAAATA-
1 AAAAAAAC
5985861 AAAAAAAC
1 AAAAAAAC
*
5985869 AAAAAAATT
1 AAAAAAA-C
5985878 AAAAAAAC
1 AAAAAAAC
5985886 AAAAAAAC
1 AAAAAAAC
5985894 AAAAAAAC
1 AAAAAAAC
5985902 AAAAAAA-
1 AAAAAAAC
5985909 AACAAAAAC
1 AA-AAAAAC
*
5985918 AAAAAAATAA
1 -AAAAAA-AC
5985928 AAAAAAAC
1 AAAAAAAC
5985936 AAAAAAA
1 AAAAAAA
5985943 TTACCTCTGT
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
7 12 0.16
8 43 0.57
9 17 0.23
10 3 0.04
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:5985880 original size:18 final size:17
Alignment explanation
Indices: 5985846--5985943 Score: 130
Period size: 16 Copynumber: 5.9 Consensus size: 17
5985836 AGGAGCTTTG
*
5985846 AAAAAA-AACAAAATAA
1 AAAAAACAAAAAAATAA
*
5985862 AAAAAACAAAAAAATTA
1 AAAAAACAAAAAAATAA
*
5985879 AAAAAACAAAAAAA-CA
1 AAAAAACAAAAAAATAA
5985895 AAAAAACAAAAAAA-AA
1 AAAAAACAAAAAAATAA
*
5985911 CAAAAACAAAAAAATAAA
1 AAAAAACAAAAAAAT-AA
5985929 AAAAAACAAAAAAAT
1 AAAAAACAAAAAAAT
5985944 TACCTCTGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
16 35 0.48
17 22 0.30
18 16 0.22
ACGTcount: A:0.87, C:0.08, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAACAAAAAAATAA
Found at i:5985882 original size:24 final size:24
Alignment explanation
Indices: 5985846--5985941 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
5985836 AGGAGCTTTG
* *
5985846 AAAAAAA-ACAAAATAAAAAAAAC
1 AAAAAAATAAAAAAAAAAAAAAAC
*
5985869 AAAAAAATTAAAAAAACAAAAAAAC
1 AAAAAAA-TAAAAAAAAAAAAAAAC
* *
5985894 AAAAAAACAAAAAAAAACAAAAAC
1 AAAAAAATAAAAAAAAAAAAAAAC
5985918 AAAAAAATAAAAAAAAACAAAAAA
1 AAAAAAATAAAAAAAAA-AAAAAA
5985942 ATTACCTCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 7 0.11
24 30 0.48
25 25 0.40
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (24 bp):
AAAAAAATAAAAAAAAAAAAAAAC
Found at i:5986241 original size:20 final size:21
Alignment explanation
Indices: 5986190--5986247 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
5986180 ATTTTTATTC
5986190 ATTTTTATTTTA-AATTTTCT
1 ATTTTTATTTTATAATTTTCT
* *
5986210 A-TTTCATATTTATCATTTT-T
1 ATTTTTAT-TTTATAATTTTCT
*
5986230 ATTTTTATTTTATGATTT
1 ATTTTTATTTTATAATTT
5986248 ATTTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 5 0.16
20 16 0.52
21 10 0.32
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTTTATTTTATAATTTTCT
Found at i:5987951 original size:15 final size:15
Alignment explanation
Indices: 5987931--5987964 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5987921 CTTTGATTAA
5987931 GAAACTCCGCAAGGC
1 GAAACTCCGCAAGGC
*
5987946 GAAACTCCGCAAGGT
1 GAAACTCCGCAAGGC
5987961 GAAA
1 GAAA
5987965 AGGGAGGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.26, T:0.09
Consensus pattern (15 bp):
GAAACTCCGCAAGGC
Found at i:5988176 original size:58 final size:58
Alignment explanation
Indices: 5988097--5988310 Score: 279
Period size: 58 Copynumber: 3.7 Consensus size: 58
5988087 AATTTTCAAA
*
5988097 AAAAAAAGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
1 AAAAAAA-TGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-TTTTC
* ** *
5988157 -AAAAAATGTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAATTTTC
* * *
5988214 AAAAAAAAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAGATTAAAATTTC
1 AAAAAAATGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAATTTTC
* * * * *
5988272 TAAAGAAT-ATTTTGGGGAAAAGTTAAAAGTATCAATTTT
1 AAAAAAATGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
5988311 TCATGCACAA
Statistics
Matches: 135, Mismatches: 18, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
57 33 0.24
58 96 0.71
59 6 0.04
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (58 bp):
AAAAAAATGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAATTTTC
Found at i:5988312 original size:116 final size:119
Alignment explanation
Indices: 5988080--5988310 Score: 355
Period size: 116 Copynumber: 2.0 Consensus size: 119
5988070 AAAAAAACAT
5988080 AAAATAAAATTTTCAAAAAAAAAAGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAA
1 AAAATAAAATTTTC-AAAAAAAAAG-TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAA
* * *
5988145 ATTAAAGTTTTCAAAAAATGTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA
64 ATTAAAATTTTCAAAAAATGATTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTA
*
5988201 AAAAT-AAATTTTC-AAAAAAAAG-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAGAT
1 AAAATAAAATTTTCAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
*
5988263 TAAAA-TTTCTAAAGAAT-ATTTTGGGGAAAAGTTAAAAGTATCAATTTT
66 TAAAATTTTC-AAAAAATGATTTTGGGGAAAAGTTAAAAGTATCAATTTT
5988311 TCATGCACAA
Statistics
Matches: 104, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
115 33 0.32
116 49 0.47
118 9 0.09
120 8 0.08
121 5 0.05
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (119 bp):
AAAATAAAATTTTCAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAT
TAAAATTTTCAAAAAATGATTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTA
Found at i:5992574 original size:20 final size:21
Alignment explanation
Indices: 5992538--5992589 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5992528 ATCGAAATTA
5992538 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
5992560 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
5992581 AT-AAATATT
1 ATAAAATATT
5992590 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:5992580 original size:21 final size:22
Alignment explanation
Indices: 5992538--5992589 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5992528 ATCGAAATTA
5992538 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
5992560 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
5992581 AT-AAATATT
1 ATAAAATATT
5992590 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:5992597 original size:30 final size:30
Alignment explanation
Indices: 5992562--5992618 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5992552 TTTAAAATAT
* * *
5992562 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATATTTA
*
5992592 AAAATATCATTATATAAATATATATAT
1 AAAATATCATTATATAAATATAAATAT
5992619 AAATAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATATTTA
Found at i:5993300 original size:15 final size:17
Alignment explanation
Indices: 5993280--5993312 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5993270 ACGTTTGAAT
5993280 TTAAATTT-T-ATTAAA
1 TTAAATTTATAATTAAA
5993295 TTAAATTTATAATTAAA
1 TTAAATTTATAATTAAA
5993312 T
1 T
5993313 AGTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTTATAATTAAA
Found at i:5993410 original size:15 final size:16
Alignment explanation
Indices: 5993382--5993417 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
5993372 TTTTTATCAT
5993382 ATTTTTTATTAAAATTA
1 ATTTTTTA-TAAAATTA
5993399 ATTTTTTA-AAAATTA
1 ATTTTTTATAAAATTA
5993414 ATTT
1 ATTT
5993418 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTATAAAATTA
Found at i:5995511 original size:8 final size:8
Alignment explanation
Indices: 5995498--5995543 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
5995488 TCATATAAAT
5995498 AATAATTA
1 AATAATTA
5995506 AATAATTA
1 AATAATTA
5995514 AATAA-TA
1 AATAATTA
5995521 AATTAA--A
1 AA-TAATTA
5995528 ATATAATTA
1 A-ATAATTA
5995537 AATAATT
1 AATAATT
5995544 TTAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 9 0.26
8 23 0.68
9 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AATAATTA
Found at i:5995526 original size:12 final size:13
Alignment explanation
Indices: 5995507--5995542 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
5995497 TAATAATTAA
5995507 ATAATTAAATAAT
1 ATAATTAAATAAT
5995520 A-AATT-AA-AAT
1 ATAATTAAATAAT
5995530 ATAATTAAATAAT
1 ATAATTAAATAAT
5995543 TTTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.20
11 6 0.30
12 6 0.30
13 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATTAAATAAT
Found at i:5995533 original size:23 final size:19
Alignment explanation
Indices: 5995493--5995542 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 19
5995483 TAGATTCATA
5995493 TAAATAATAATTAAATAAT
1 TAAATAATAATTAAATAAT
5995512 TAAATAATAAATTAAAATATAAT
1 TAAATAAT-AATT--AA-ATAAT
5995535 TAAATAAT
1 TAAATAAT
5995543 TTTAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.30
20 4 0.15
22 2 0.07
23 13 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATAATAATTAAATAAT
Found at i:5996333 original size:16 final size:17
Alignment explanation
Indices: 5996291--5996333 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5996281 TTATAAAGTT
*
5996291 ATATGTGTGTTAAAGAA
1 ATATGTTTGTTAAAGAA
*
5996308 ATTTTGTTTGTTAAAGAA
1 A-TATGTTTGTTAAAGAA
5996326 A-ATGTTTG
1 ATATGTTTG
5996334 AATCTACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
ATATGTTTGTTAAAGAA
Found at i:5999997 original size:22 final size:22
Alignment explanation
Indices: 5999972--6000025 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5999962 ATAATCACCT
* *
5999972 AATCAATATCTAATGTTCTTTA
1 AATCAATATCTAATATTCTCTA
5999994 AATCAATATCTAATATTCTCTA
1 AATCAATATCTAATATTCTCTA
6000016 AATCAATATC
1 AATCAATATC
6000026 AAATCAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.41
Consensus pattern (22 bp):
AATCAATATCTAATATTCTCTA
Found at i:6000048 original size:11 final size:11
Alignment explanation
Indices: 6000034--6000063 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6000024 TCAAATCAAT
6000034 CTAGAATATTA
1 CTAGAATATTA
6000045 CTAGAATATTA
1 CTAGAATATTA
6000056 CTAGAATA
1 CTAGAATA
6000064 ATATCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (11 bp):
CTAGAATATTA
Found at i:6007299 original size:3 final size:3
Alignment explanation
Indices: 6007293--6007327 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6007283 CTACTATTAC
6007293 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6007328 GCATAGTAAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6007391 original size:23 final size:20
Alignment explanation
Indices: 6007365--6007414 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
6007355 TAATAAAGTG
*
6007365 AAAAAAAATAAAAATTCAAAA
1 AAAAAAAAAAAAAATT-AAAA
*
6007386 CAAAAATAAAAGAAAATTAAAA
1 -AAAAA-AAAAAAAAATTAAAA
6007408 AAAAAAA
1 AAAAAAA
6007415 CTTACGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.20
22 9 0.36
23 9 0.36
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAAAAATTAAAA
Found at i:6010336 original size:59 final size:58
Alignment explanation
Indices: 6010191--6010417 Score: 267
Period size: 59 Copynumber: 3.9 Consensus size: 58
6010181 TTTGTGCAGG
*** * * * * **
6010191 AAAATTGATACTTTCAACTTTTTTTC-GAAATATTTTTTTGAAACTTTAATTTCAGGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAAA
* * ***
6010248 AAAATTGATACTTTCAATTTTTCCTCAAAAATCCATTTTTGAAAATTTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAAA
* *
6010306 AAAATTGATACTTTTCAACTTTTCCCCAAAAATATTTTTTTAAAAATTTATTTTTAAAG
1 AAAATTGATAC-TTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAAA
* *
6010365 AAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTGAAAATTTATTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAATTTATTT
6010418 CTAACAACTT
Statistics
Matches: 145, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.16
58 53 0.37
59 69 0.48
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAAA
Found at i:6010410 original size:42 final size:43
Alignment explanation
Indices: 6010364--6010448 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
6010354 TATTTTTAAA
**
6010364 GAAAATTGA-TACTTTCAACTTTTTCCT-AAAAATATTTTTTTT
1 GAAAATTGATTACTAACAAC-TTTTCCTCAAAAATATTTTTTTT
* *
6010406 GAAAATTTATTTCTAACAACTTTTCCTCAAAAATATTTTTTTT
1 GAAAATTGATTACTAACAACTTTTCCTCAAAAATATTTTTTTT
6010449 TGGAAAGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 15 0.41
43 22 0.59
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (43 bp):
GAAAATTGATTACTAACAACTTTTCCTCAAAAATATTTTTTTT
Found at i:6010462 original size:45 final size:43
Alignment explanation
Indices: 6010379--6010462 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
6010369 TTGATACTTT
*
6010379 CAACTTTTTCCTAAAAATATTTTTTTTGAAAATTTATTTCTAA
1 CAACTTTTTCCTAAAAATATTTTTTTTGAAAACTTATTTCTAA
*
6010422 CAAC-TTTTCCTCAAAAATATTTTTTTTTGGAAAGCTTATTT
1 CAACTTTTTCCT-AAAAATA-TTTTTTTT-GAAAACTTATTT
6010463 TCAAGTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 7 0.19
43 11 0.31
44 8 0.22
45 10 0.28
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (43 bp):
CAACTTTTTCCTAAAAATATTTTTTTTGAAAACTTATTTCTAA
Found at i:6010488 original size:104 final size:101
Alignment explanation
Indices: 6010321--6010507 Score: 270
Period size: 104 Copynumber: 1.8 Consensus size: 101
6010311 TGATACTTTT
*
6010321 CAACTTTTCCCCAAAAATATTTTTTTAAAAATTTATTTTTAAAGAAAATTGATACTTTCAACTTT
1 CAACTTTTCCCCAAAAATATTTTTTTAAAAACTTATTTTTAAAGAAAATTGATACTTTCAAC-TT
6010386 TTCCT-AAAAATATTTTTTTTGAAAATTTATTTCTAA
65 TTCCTCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* * * *
6010422 CAACTTTTCCTCAAAAATATTTTTTTTTGGAAAGCTTA-TTTTCAAGTAAAATTGATACTTTCAA
1 CAACTTTTCCCCAAAAATA--TTTTTTT-AAAAACTTATTTTTAAAG-AAAATTGATACTTTCAA
6010486 CTTTTCCTCAAAAATATTTTTT
62 CTTTTCCTCAAAAATATTTTTT
6010508 AGAAAGCTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
101 18 0.24
103 21 0.28
104 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.47
Consensus pattern (101 bp):
CAACTTTTCCCCAAAAATATTTTTTTAAAAACTTATTTTTAAAGAAAATTGATACTTTCAACTTT
TCCTCAAAAATATTTTTTTTGAAAATTTATTTCTAA
Found at i:6010578 original size:58 final size:59
Alignment explanation
Indices: 6010422--6010570 Score: 246
Period size: 58 Copynumber: 2.5 Consensus size: 59
6010412 TTATTTCTAA
*
6010422 CAACTTTTCCTCAAAAATATTTTTTTTTGGAAAGCTTATTTTCAAGTAAAATTGATACTTT
1 CAACTTTTCCTCAAAAATA-TTTTTTTT-GAAAGCTTATTTTCAAGAAAAATTGATACTTT
* *
6010483 CAACTTTTCCTCAAAAATA-TTTTTTAGAAAGCTTATTTTCAAGAAAAATTGATATTTT
1 CAACTTTTCCTCAAAAATATTTTTTTTGAAAGCTTATTTTCAAGAAAAATTGATACTTT
6010541 CAACTTTTCCTCAAAAATATTTTTTTTGAA
1 CAACTTTTCCTCAAAAATATTTTTTTTGAA
6010571 TTTTATTTAA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
58 49 0.59
59 15 0.18
61 19 0.23
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (59 bp):
CAACTTTTCCTCAAAAATATTTTTTTTGAAAGCTTATTTTCAAGAAAAATTGATACTTT
Found at i:6010644 original size:4 final size:4
Alignment explanation
Indices: 6010635--6010682 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
6010625 AATCTAATCT
* *
6010635 AATA AATA AATA AATA AATA AATA AAT- AATA TATA TATA AA-A AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
6010681 AA
1 AA
6010683 AAAAAAACCT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 6 0.15
4 34 0.85
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:6010674 original size:15 final size:15
Alignment explanation
Indices: 6010635--6010682 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
6010625 AATCTAATCT
6010635 AATAAATAAATAAATA
1 AATAAATAAAT-AATA
6010651 AATAAATAAATAATA
1 AATAAATAAATAATA
* * *
6010666 TATATATAAAAAATA
1 AATAAATAAATAATA
6010681 AA
1 AA
6010683 AAAAAAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:6010929 original size:16 final size:15
Alignment explanation
Indices: 6010893--6010937 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
6010883 CAGAATCCTT
6010893 TCTCCTCTTCTCTTTC
1 TCTCC-CTTCTCTTTC
*
6010909 T-TCCCTTCTTTCTTC
1 TCTCCCTTCTCT-TTC
6010924 TCTCCCTTCTCTTT
1 TCTCCCTTCTCTTT
6010938 AAAACCCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.24
15 9 0.36
16 10 0.40
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTCCCTTCTCTTTC
Found at i:6011533 original size:4 final size:4
Alignment explanation
Indices: 6011524--6011667 Score: 64
Period size: 4 Copynumber: 34.5 Consensus size: 4
6011514 AGATAAATGA
* * *
6011524 AAAT AAAT -AAT AGAT AAATT ATAAT ATAT AAAT AGAT AAAT ACTAAT
1 AAAT AAAT AAAT AAAT AAA-T A-AAT AAAT AAAT AAAT AAAT A--AAT
* * * * *
6011571 AAAT ATAT AACT AGAT AAAT AAAAT ATAT ATATT AACAT -AA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT AA-AT AAAT AAAT AAAT
* *
6011620 ATATAT TAAT AAAT AGTAAT -AAT AAAT AAAT AAAT -AAT AAAT ACAT
1 A-A-AT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
6011666 AA
1 AA
6011668 GATATAAAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 32
0.67 0.13 0.21
Matches are distributed among these distances:
3 12 0.12
4 68 0.65
5 13 0.12
6 11 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:6011535 original size:7 final size:7
Alignment explanation
Indices: 6011525--6011750 Score: 73
Period size: 7 Copynumber: 30.9 Consensus size: 7
6011515 GATAAATGAA
6011525 AATAAAT
1 AATAAAT
*
6011532 AATAGAT
1 AATAAAT
6011539 AAATTATAAT
1 -AA-TA-AAT
6011549 ATATAAAT
1 A-ATAAAT
6011557 AGATAAATACT
1 A-AT-AA-A-T
6011568 AATAAAT
1 AATAAAT
*
6011575 ATATAACT
1 A-ATAAAT
6011583 AGATAAAT
1 A-ATAAAT
6011591 -A-AAAT
1 AATAAAT
*
6011596 ATATATATT
1 A-ATA-AAT
6011605 AACATAAA-
1 AA--TAAAT
6011613 AATAAAT
1 AATAAAT
*
6011620 -ATATATT
1 AATA-AAT
6011627 AATAAAT
1 AATAAAT
*
6011634 AGT-AAT
1 AATAAAT
6011640 AATAAAT
1 AATAAAT
6011647 AAATAAAT
1 -AATAAAT
6011655 AATAAAT
1 AATAAAT
6011662 ACATAAGAT
1 A-ATAA-AT
*
6011671 -ATAAAG
1 AATAAAT
*
6011677 AAAAAAT
1 AATAAAT
6011684 -ATAAAAT
1 AAT-AAAT
6011691 AA-AAAT
1 AATAAAT
6011697 AA-AAAT
1 AATAAAT
6011703 AA-AAAT
1 AATAAAT
6011709 AA-AAAT
1 AATAAAT
*
6011715 TATAAAAT
1 AAT-AAAT
*
6011723 TATAAAAT
1 AAT-AAAT
6011731 ACA-AAAT
1 A-ATAAAT
6011738 ACA-AAAT
1 A-ATAAAT
6011745 AATAAA
1 AATAAA
6011751 AAAATAATGT
Statistics
Matches: 173, Mismatches: 18, Indels: 56
0.70 0.07 0.23
Matches are distributed among these distances:
5 4 0.02
6 39 0.23
7 53 0.31
8 51 0.29
9 16 0.09
10 8 0.05
11 2 0.01
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:6011560 original size:22 final size:22
Alignment explanation
Indices: 6011514--6011600 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 22
6011504 ATCAGATAAC
* *
6011514 AGATAAATGAAAATAAAT-AAT
1 AGATAAATTAAAATATATAAAT
*
6011535 AGATAAATTATAATATATAAAT
1 AGATAAATTAAAATATATAAAT
*
6011557 AGATAAATACTAATAAATATATAACT
1 AGATAAAT--T-A-AAATATATAAAT
6011583 AGATAAA-TAAAATATATA
1 AGATAAATTAAAATATATA
6011601 TATTAACATA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 24 0.43
22 12 0.21
23 1 0.02
24 1 0.02
25 1 0.02
26 17 0.30
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
AGATAAATTAAAATATATAAAT
Found at i:6011585 original size:26 final size:23
Alignment explanation
Indices: 6011524--6011667 Score: 85
Period size: 22 Copynumber: 6.4 Consensus size: 23
6011514 AGATAAATGA
*
6011524 AAATAAATAATAGATAAAT-TAT
1 AAATATATAATAGATAAATATAT
6011546 -AATATATAAATAGATAAATACTAAT
1 AAATATAT-AATAGATAAATA-T-AT
6011571 AAATATATAACTAGATAAATA-A-
1 AAATATATAA-TAGATAAATATAT
* *
6011593 AATATATATATTAACATAAA-A-AT
1 AA-ATATATAAT-AGATAAATATAT
* *
6011616 AAATATATATTA-ATAAATA-GT
1 AAATATATAATAGATAAATATAT
*
6011637 -AATA-ATAAATAAATAAATA-AT
1 AAATATAT-AATAGATAAATATAT
*
6011658 AAATACATAA
1 AAATATATAA
6011668 GATATAAAGA
Statistics
Matches: 102, Mismatches: 6, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
19 2 0.02
20 12 0.12
21 17 0.17
22 31 0.30
23 18 0.18
24 1 0.01
25 4 0.04
26 17 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (23 bp):
AAATATATAATAGATAAATATAT
Found at i:6011692 original size:18 final size:18
Alignment explanation
Indices: 6011647--6011757 Score: 82
Period size: 18 Copynumber: 5.7 Consensus size: 18
6011637 AATAATAAAT
6011647 AAATAAATAATAAATACATAA
1 AAATAAA-AATAAA-A-ATAA
* *
6011668 GATATAAAGA-AAAAATATA
1 -AAATAAAAATAAAAATA-A
6011687 AAATAAAAATAAAAATAA
1 AAATAAAAATAAAAATAA
6011705 AAATAAAAATTATAAAATTATA
1 AAATAAAAA-TA-AAAA-TA-A
6011727 AAATACAAAATACAAAATAA
1 AAATA-AAAATA-AAAATAA
*
6011747 TAA-AAAAATAA
1 AAATAAAAATAA
6011758 TGTAGACCTA
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.01
18 26 0.34
19 12 0.16
20 10 0.13
21 5 0.07
22 18 0.24
23 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAAAATAAAAATAA
Found at i:6011694 original size:5 final size:6
Alignment explanation
Indices: 6011647--6011757 Score: 82
Period size: 7 Copynumber: 17.0 Consensus size: 6
6011637 AATAATAAAT
* *
6011647 AAATAA ATAATAA ATACATAA GATATAA AGA-AA AAATATA AAATAA AAATAA
1 AAATAA A-AATAA A-A-ATAA -AAATAA AAATAA AAATA-A AAATAA AAATAA
6011699 AAATAA AAATAA AAATTATA AAATTATA AAATACA AAATACA AAATAA
1 AAATAA AAATAA AAA-TA-A AAA-TA-A AAATA-A AAATA-A AAATAA
*
6011747 TAA-AA AAATAA
1 AAATAA AAATAA
6011758 TGTAGACCTA
Statistics
Matches: 91, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
5 8 0.09
6 31 0.34
7 35 0.38
8 16 0.18
9 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:6012524 original size:23 final size:23
Alignment explanation
Indices: 6012496--6012545 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6012486 AATTATTAAA
6012496 AAATTTAAAAATTTGAAATCTTT
1 AAATTTAAAAATTTGAAATCTTT
* * * *
6012519 AAATTTAGATATTTTAAATTTTT
1 AAATTTAAAAATTTGAAATCTTT
6012542 AAAT
1 AAAT
6012546 ATTTAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
AAATTTAAAAATTTGAAATCTTT
Found at i:6014339 original size:22 final size:22
Alignment explanation
Indices: 6014311--6014353 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6014301 TTTAATAAAA
6014311 AATTCAAT-TAATAAATTAATAT
1 AATTCAATGTAA-AAATTAATAT
6014333 AATTCAATGTAAAAATTAATA
1 AATTCAATGTAAAAATTAATA
6014354 ATATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTCAATGTAAAAATTAATAT
Found at i:6014355 original size:54 final size:51
Alignment explanation
Indices: 6014291--6014390 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 51
6014281 AAAAATAAAT
* *
6014291 AAATAAATAATTTAATAAAAAATTCAATTAATAAATTA-ATATAATTCAATGTAA
1 AAATAAATAATAT-ATAAAAAA-T--ATTAAAAAATTATATATAATTCAATGTAA
* *
6014345 AAATTAATAATATATAAAAAATATTAAAAAATTATTTATAATTCAA
1 AAATAAATAATATATAAAAAATATTAAAAAATTATATATAATTCAA
6014391 ATTTGATCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 11 0.27
51 10 0.24
52 1 0.02
53 8 0.20
54 11 0.27
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (51 bp):
AAATAAATAATATATAAAAAATATTAAAAAATTATATATAATTCAATGTAA
Found at i:6023639 original size:29 final size:29
Alignment explanation
Indices: 6023607--6023701 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 29
6023597 TATTACATAT
*
6023607 AAATAAAATTTGAAC-TTTAATTTGTATTA
1 AAATAAAATTTTAACATTTAATTTGTA-TA
* * *
6023636 AAATAAAGTTTTAACTTTTAATTTGTATC
1 AAATAAAATTTTAACATTTAATTTGTATA
*
6023665 AAATAAAATTTTAACATTTAATTTATATA
1 AAATAAAATTTTAACATTTAATTTGTATA
6023694 TAAATAAA
1 -AAATAAA
6023702 CTTTAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
29 39 0.68
30 18 0.32
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (29 bp):
AAATAAAATTTTAACATTTAATTTGTATA
Found at i:6023648 original size:58 final size:58
Alignment explanation
Indices: 6023569--6023701 Score: 130
Period size: 58 Copynumber: 2.3 Consensus size: 58
6023559 AAATTTTATT
* * * *
6023569 ATTTTATTTAAATATATTTTTATA-TTTTTATTACATAT-AAATAAAATTTGAAC-TTTA
1 ATTTTATTAAAATAAAGTTTTA-ACTTTTAATT-CATATCAAATAAAATTTGAACATTTA
** *
6023626 ATTTGTATTAAAATAAAGTTTTAACTTTTAATTTGTATCAAATAAAATTTTAACATTTA
1 ATTT-TATTAAAATAAAGTTTTAACTTTTAATTCATATCAAATAAAATTTGAACATTTA
6023685 A-TTTATATATAAATAAA
1 ATTTTAT-TA-AAATAAA
6023702 CTTTAAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
57 11 0.17
58 40 0.63
59 12 0.19
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (58 bp):
ATTTTATTAAAATAAAGTTTTAACTTTTAATTCATATCAAATAAAATTTGAACATTTA
Found at i:6030452 original size:56 final size:56
Alignment explanation
Indices: 6030392--6030510 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 56
6030382 GAGCCCTGCA
* * *
6030392 TGCCACATTAATCTTGCTTTAAAGCTCTCACACCAATATGCCCAATGCCCCCTACG
1 TGCCACATTAATCTTGCGTTAAAGCTCCCACACCAACATGCCCAATGCCCCCTACG
** * ** * ** *
6030448 TGCCATTTTTATCTTGCGTTAAAGCTCCCATGCCAACATGCTCAATGTGCTCTACG
1 TGCCACATTAATCTTGCGTTAAAGCTCCCACACCAACATGCCCAATGCCCCCTACG
6030504 TGCCACA
1 TGCCACA
6030511 CCTCTTTTAT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.29
Consensus pattern (56 bp):
TGCCACATTAATCTTGCGTTAAAGCTCCCACACCAACATGCCCAATGCCCCCTACG
Found at i:6035835 original size:2 final size:2
Alignment explanation
Indices: 6035828--6035862 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6035818 GTGATTAGAG
*
6035828 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6035863 CGATTAGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6038931 original size:24 final size:24
Alignment explanation
Indices: 6038904--6038950 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
6038894 CCATACCCAG
6038904 AACAAAAAAAAAAAAAAAAAACAA
1 AACAAAAAAAAAAAAAAAAAACAA
* * * *
6038928 AACACAAGACAAAAAAAACAACA
1 AACAAAAAAAAAAAAAAAAAACA
6038951 CAGTCCTCGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (24 bp):
AACAAAAAAAAAAAAAAAAAACAA
Found at i:6040077 original size:15 final size:15
Alignment explanation
Indices: 6040017--6040115 Score: 91
Period size: 15 Copynumber: 6.8 Consensus size: 15
6040007 ATTCATGTTT
6040017 TAAAATCCTAAAA-T-
1 TAAAATCC-AAAACTC
*
6040031 TAAAA-CCAAACCT-
1 TAAAATCCAAAACTC
*
6040044 TAAAATCCAAAGTCTC
1 TAAAATCCAAA-ACTC
6040060 TAAAATCCAAAACTC
1 TAAAATCCAAAACTC
*
6040075 TAAAATCC-AAACCC
1 TAAAATCCAAAACTC
* * *
6040089 TTAAATCCAAACCCC
1 TAAAATCCAAAACTC
6040104 TAAAATCCAAAA
1 TAAAATCCAAAA
6040116 TCCTAAACCT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
12 3 0.04
13 8 0.11
14 22 0.31
15 28 0.39
16 11 0.15
ACGTcount: A:0.52, C:0.27, G:0.01, T:0.20
Consensus pattern (15 bp):
TAAAATCCAAAACTC
Found at i:6040122 original size:29 final size:28
Alignment explanation
Indices: 6040017--6040122 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 28
6040007 ATTCATGTTT
* *
6040017 TAAAATCCTAAAAT--TAAAACCAAACCT
1 TAAAATCC-AAAATCCTAAATCCAAACCC
* *
6040044 TAAAATCCAAAGTCTCTAAAATCCAAAACTC
1 TAAAATCCAAAATC-CT-AAATCC-AAACCC
*
6040075 TAAAATCC-AAACCCTTAAATCCAAACCCC
1 TAAAATCCAAAATCC-TAAATCCAAA-CCC
6040104 TAAAATCCAAAATCCTAAA
1 TAAAATCCAAAATCCTAAA
6040123 CCTTCCATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
26 4 0.06
27 8 0.13
28 3 0.05
29 22 0.35
30 14 0.22
31 12 0.19
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (28 bp):
TAAAATCCAAAATCCTAAATCCAAACCC
Found at i:6040190 original size:28 final size:29
Alignment explanation
Indices: 6040150--6040211 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
6040140 CTAAATTTTA
* * *
6040150 AAACCTTAAACCCTGAAATT-GAAACCCC
1 AAACCCTAAACCCTAAAATTAAAAACCCC
*
6040178 AAACCCTAAACCCTAAAATTAAAAATCCC
1 AAACCCTAAACCCTAAAATTAAAAACCCC
6040207 AAACC
1 AAACC
6040212 TTAAGATCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.48, C:0.32, G:0.03, T:0.16
Consensus pattern (29 bp):
AAACCCTAAACCCTAAAATTAAAAACCCC
Found at i:6046205 original size:1 final size:1
Alignment explanation
Indices: 6046199--6046237 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
6046189 AAGTAACTTT
* * *
6046199 AAAAAAAAAAACAAAAAAAAAAGAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6046238 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:6046227 original size:19 final size:18
Alignment explanation
Indices: 6046199--6046237 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
6046189 AAGTAACTTT
6046199 AAAAAAAAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
*
6046217 AAAAGAAAAAAAGAAAAAA
1 AAAA-AAAAAAACAAAAAA
6046236 AA
1 AA
6046238 TATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAA
Found at i:6046828 original size:16 final size:16
Alignment explanation
Indices: 6046804--6046836 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6046794 GAGGCATCAC
6046804 AAAAAAAACAAA-AAA
1 AAAAAAAACAAATAAA
6046819 AAAAACAAACAAATAAA
1 AAAAA-AAACAAATAAA
6046836 A
1 A
6046837 GTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAAAACAAATAAA
Found at i:6046843 original size:33 final size:33
Alignment explanation
Indices: 6046805--6046871 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
6046795 AGGCATCACA
*
6046805 AAAAAAACAAAAAAAAAAACAAACAAATAAAAGT
1 AAAAAAA-AAAAGAAAAAACAAACAAATAAAAGT
* * *
6046839 AAAAAAAAAAAGGAAAAATAAATAAATAAAAGT
1 AAAAAAAAAAAGAAAAAACAAACAAATAAAAGT
6046872 CATCTTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (33 bp):
AAAAAAAAAAAGAAAAAACAAACAAATAAAAGT
Found at i:6046856 original size:20 final size:20
Alignment explanation
Indices: 6046833--6046870 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6046823 ACAAACAAAT
*
6046833 AAAAGTAAA-AAAAAAAAGG
1 AAAAATAAATAAAAAAAAGG
*
6046852 AAAAATAAATAAATAAAAG
1 AAAAATAAATAAAAAAAAG
6046871 TCATCTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAATAAATAAAAAAAAGG
Found at i:6048528 original size:18 final size:18
Alignment explanation
Indices: 6048505--6048546 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6048495 ATTCGCATTC
*
6048505 TTGCATTGGCATTTACAT
1 TTGCATTGACATTTACAT
*
6048523 TTGCATTGACATTTCCAT
1 TTGCATTGACATTTACAT
*
6048541 TAGCAT
1 TTGCAT
6048547 CATTTGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (18 bp):
TTGCATTGACATTTACAT
Found at i:6048877 original size:109 final size:107
Alignment explanation
Indices: 6048681--6049012 Score: 330
Period size: 109 Copynumber: 3.0 Consensus size: 107
6048671 AAAGATCTTG
* * ***
6048681 ATTTTTAAGACCTTCTGA-CATAAATTTGATTTACGGTGTTATCCCGATTC-ATTCATTATTCTC
1 ATTTCTAAGACC-TCTGAGCATAATTTTGATTCGTGGTGTTATCCCGA-TCGATTCATTATTCTC
* * * * *
6048744 GACATGTGGTGTTGTTCCAGTCGATTCTGTAAAACCTCCAGACATT
64 GACTTGCGGTGTT-ATCCAGTCGATTCTGTAAGACCTCC-GACATA
*
6048790 ATTTCTAAGACCTCTGAGCATAATTTTGATTCGTGGTGTTATCGCGATCGATTCATTATTCTCGA
1 ATTTCTAAGACCTCTGAGCATAATTTTGATTCGTGGTGTTATCCCGATCGATTCATTATTCTCGA
* * *
6048855 CTTGCGATGTTATCCTAGTCGATTTTGTAAGACCTCCGGCATA
66 CTTGCGGTGTTATCC-AGTCGATTCTGTAAGACCTCCGACATA
* * * * *
6048898 ATTTCTGTAAGACCTCT-AGGCATGATTTCGATTCGTGATGTTATCCCGATTGATTCTTTAATT-
1 ATTTC--TAAGACCTCTGA-GCATAATTTTGATTCGTGGTGTTATCCCGATCGATTCATT-ATTC
** * *
6048961 TCGACTAACGGTGTTGTCCCAATCGATTCTGTAAGACCTCCGAGCATA
62 TCGACTTGCGGTGTTAT-CCAGTCGATTCTGTAAGACCTCCGA-CATA
6049009 ATTT
1 ATTT
6049013 TGATTCACGA
Statistics
Matches: 187, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
108 19 0.10
109 78 0.42
110 77 0.41
111 13 0.07
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (107 bp):
ATTTCTAAGACCTCTGAGCATAATTTTGATTCGTGGTGTTATCCCGATCGATTCATTATTCTCGA
CTTGCGGTGTTATCCAGTCGATTCTGTAAGACCTCCGACATA
Found at i:6048925 original size:24 final size:23
Alignment explanation
Indices: 6048875--6048926 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
6048865 TATCCTAGTC
*
6048875 GATTT-TGTAAGACCTCCGGCAT
1 GATTTCTGTAAGACCTCAGGCAT
*
6048897 AATTTCTGTAAGACCTCTAGGCAT
1 GATTTCTGTAAGACCTC-AGGCAT
6048921 GATTTC
1 GATTTC
6048927 GATTCGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 11 0.44
24 10 0.40
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (23 bp):
GATTTCTGTAAGACCTCAGGCAT
Found at i:6048965 original size:110 final size:107
Alignment explanation
Indices: 6048717--6049012 Score: 326
Period size: 110 Copynumber: 2.7 Consensus size: 107
6048707 TGATTTACGG
* * * * *
6048717 TGTTATCCCGATTCATTCATTATTCTCGACATGTGGTGTTGTTCCAGTCGATTCTGTAAAACCTC
1 TGTTATCCCGATTGATTCATTATTCTCGACTTGCGGTGTT-ATCCAGTCGATTCTGTAAGACCTC
* * * *
6048782 CAGACATTATTTCTAAGACCTCTGAGCATAATTTTGATTCGTGG
65 C-GGCATAATTTCTAAGACCTCTGAGCATAATTTCGATTCGTGA
* * * *
6048826 TGTTATCGCGATCGATTCATTATTCTCGACTTGCGATGTTATCCTAGTCGATTTTGTAAGACCTC
1 TGTTATCCCGATTGATTCATTATTCTCGACTTGCGGTGTTATCC-AGTCGATTCTGTAAGACCTC
*
6048891 CGGCATAATTTCTGTAAGACCTCT-AGGCATGATTTCGATTCGTGA
65 CGGCATAATTTC--TAAGACCTCTGA-GCATAATTTCGATTCGTGA
* ** * *
6048936 TGTTATCCCGATTGATTCTTTAATT-TCGACTAACGGTGTTGTCCCAATCGATTCTGTAAGACCT
1 TGTTATCCCGATTGATTCATT-ATTCTCGACTTGCGGTGTTAT-CCAGTCGATTCTGTAAGACCT
6049000 CCGAGCATAATTT
64 CCG-GCATAATTT
6049013 TGATTCACGA
Statistics
Matches: 157, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
108 12 0.08
109 54 0.34
110 77 0.49
111 14 0.09
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (107 bp):
TGTTATCCCGATTGATTCATTATTCTCGACTTGCGGTGTTATCCAGTCGATTCTGTAAGACCTCC
GGCATAATTTCTAAGACCTCTGAGCATAATTTCGATTCGTGA
Found at i:6049160 original size:88 final size:87
Alignment explanation
Indices: 6048900--6049187 Score: 284
Period size: 87 Copynumber: 3.3 Consensus size: 87
6048890 CCGGCATAAT
*
6048900 TTCTGTAAGACCT-CTAGGCATGA-TTTCGATTCG-TGATGTTATCCCGATTGATTCTTTAATTT
1 TTCTGTAAGACCTCCGA-GCATGATTTTCGATTCGCT-ATGTTATCCCGATTGATTCTTTAATTT
* * *
6048962 CGAC-TAACGGTGTTGTCCCAATCGA
64 CGACTTTA--GTGTTGTCCCAGTTGA
* * * * ** *
6048987 TTCTGTAAGACCTCCGAGCATAATTTT-GATTCACGATATTATCCCGATCAATTCATT-ATTCTC
1 TTCTGTAAGACCTCCGAGCATGATTTTCGATTCGCTATGTTATCCCGATTGATTCTTTAATT-TC
* *
6049050 AAC-TTACGATGTTGTCCTAGTTGA
65 GACTTTA-G-TGTTGTCCCAGTTGA
* * *
6049074 TTTTGTAAGACCTCCGAGCATGATTTTCGATTCGCTATGTTATCCTGATTGATTCTTTAATTTTG
1 TTCTGTAAGACCTCCGAGCATGATTTTCGATTCGCTATGTTATCCCGATTGATTCTTTAATTTCG
6049139 ACTTGTAGTGTTGTCCCAGTTGA
66 ACTT-TAGTGTTGTCCCAGTTGA
* * *
6049162 TTCTGTAAGACTTTCGGGCATGATTT
1 TTCTGTAAGACCTCCGAGCATGATTT
6049188 CTAAGACCTC
Statistics
Matches: 162, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
86 4 0.02
87 84 0.52
88 67 0.41
89 5 0.03
90 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (87 bp):
TTCTGTAAGACCTCCGAGCATGATTTTCGATTCGCTATGTTATCCCGATTGATTCTTTAATTTCG
ACTTTAGTGTTGTCCCAGTTGA
Found at i:6049277 original size:108 final size:111
Alignment explanation
Indices: 6049071--6049320 Score: 312
Period size: 108 Copynumber: 2.3 Consensus size: 111
6049061 TTGTCCTAGT
* * * * *
6049071 TGATTTTGTAAGACCTCCGAGCATGATTTTCGATTCGCTATGTTATCCTGATTGATTCTTTAATT
1 TGATTTTCTAAGACCTCCGAGCATGATTTTCAATTCGCTATGTTATCCTAATCGATTCATTAATT
** * *
6049136 TTGACTTGTAGTGTTGTCCCAGTTGATTCTGTAAGACTTTCGGGCA
66 TCAACTTGTAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGGGCA
*
6049182 TGA-TTTCTAAGACCTCCGAGCATAATTTT-AATTCGC-AGTGTTATCC-AATCGATTCATT-AT
1 TGATTTTCTAAGACCTCCGAGCATGATTTTCAATTCGCTA-TGTTATCCTAATCGATTCATTAAT
* * *
6049242 TCTCAACTTGTGGTGTTGTCCTAGTCGATTTTGTAAGACCTTCGGGCA
65 T-TCAACTTGTAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGGGCA
*
6049290 TGATTTTTGTAAGACCTCCGAGCATGATTTT
1 TGA-TTTTCTAAGACCTCCGAGCATGATTTT
6049321 TGTAAGACCT
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
107 3 0.03
108 52 0.43
109 14 0.12
110 48 0.40
111 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (111 bp):
TGATTTTCTAAGACCTCCGAGCATGATTTTCAATTCGCTATGTTATCCTAATCGATTCATTAATT
TCAACTTGTAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGGGCA
Found at i:6049299 original size:24 final size:24
Alignment explanation
Indices: 6049270--6049344 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
6049260 TCCTAGTCGA
*
6049270 TTTTGTAAGACCTTCGGGCATGAT
1 TTTTGTAAGACCTCCGGGCATGAT
*
6049294 TTTTGTAAGACCTCCGAGCATGAT
1 TTTTGTAAGACCTCCGGGCATGAT
*
6049318 TTTTGTAAGACCTCCAGGCATGAT
1 TTTTGTAAGACCTCCGGGCATGAT
6049342 TTT
1 TTT
6049345 GATTCGCGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (24 bp):
TTTTGTAAGACCTCCGGGCATGAT
Found at i:6049494 original size:109 final size:107
Alignment explanation
Indices: 6049297--6049566 Score: 262
Period size: 109 Copynumber: 2.5 Consensus size: 107
6049287 GCATGATTTT
* * * * *
6049297 TGTAAGACCTC-CGAGCATGATTTTTGTAAGACCTCCAGG-CATGATTTTGATTCGCGATGTTAT
1 TGTAAGACCTCAGGA-CATGA-TTTTCTAAAACCTCC-GGACATAATTTTGATTCGAGATGTTAT
* * * * * *
6049360 CTCGATCAATTCTTTAATGTTGACTTACGGTGTTGTCTCAGTCGATTC
63 CCCGATCAATTCATTAATCTCGACTT---GCGTTGTCCCAGTCGATTC
* *
6049408 TGTAAGACCTCTAGG-TATGA-TTTCTAAAACCTCTGGACATAATTTTGATTCGA-AGTGTTATC
1 TGTAAGACCTC-AGGACATGATTTTCTAAAACCTCCGGACATAATTTTGATTCGAGA-TGTTATC
* *
6049470 CCGATCGATTCATTATTCTCGACTTGCGTTGTCCCAGTCGATTC
64 CCGATCAATTCATTAATCTCGACTTGCGTTGTCCCAGTCGATTC
* * *
6049514 TGTAAGACCTCCGGACATGATTTTTGTAAGACCTCCGGACATAATTTTGATTC
1 TGTAAGACCTCAGGACATGA-TTTTCTAAAACCTCCGGACATAATTTTGATTC
6049567 ACGGTGTTGT
Statistics
Matches: 132, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
105 2 0.02
106 32 0.24
108 31 0.23
109 51 0.39
111 15 0.11
113 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (107 bp):
TGTAAGACCTCAGGACATGATTTTCTAAAACCTCCGGACATAATTTTGATTCGAGATGTTATCCC
GATCAATTCATTAATCTCGACTTGCGTTGTCCCAGTCGATTC
Found at i:6049541 original size:24 final size:24
Alignment explanation
Indices: 6049514--6049561 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6049504 CAGTCGATTC
*
6049514 TGTAAGACCTCCGGACATGATTTT
1 TGTAAGACCTCCGGACATAATTTT
6049538 TGTAAGACCTCCGGACATAATTTT
1 TGTAAGACCTCCGGACATAATTTT
6049562 GATTCACGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (24 bp):
TGTAAGACCTCCGGACATAATTTT
Found at i:6049625 original size:37 final size:37
Alignment explanation
Indices: 6049570--6049658 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
6049560 TTGATTCACG
* * *
6049570 GTGTTGTCTCAATTGATTCTTTA-TTTCTCGACTTGCA
1 GTGTTGTCCCAATCGATTCTTTACTTT-TCGACTCGCA
* *
6049607 GTGTTGTCCCGATCGATTCTTTACTTTTCGACTCGCG
1 GTGTTGTCCCAATCGATTCTTTACTTTTCGACTCGCA
6049644 GTGTTGTCCCAATCG
1 GTGTTGTCCCAATCG
6049659 TCTTTGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 42 0.93
38 3 0.07
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (37 bp):
GTGTTGTCCCAATCGATTCTTTACTTTTCGACTCGCA
Found at i:6049677 original size:39 final size:37
Alignment explanation
Indices: 6049570--6049678 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 37
6049560 TTGATTCACG
* * ** *
6049570 GTGTTGTCTCAATTGATTCTTTATTTCTCGACTTGCA
1 GTGTTGTCCCAATCGATTCTTTACGTCTCGACTCGCA
* * * *
6049607 GTGTTGTCCCGATCGATTCTTTACTTTTCGACTCGCG
1 GTGTTGTCCCAATCGATTCTTTACGTCTCGACTCGCA
* *
6049644 GTGTTGTCCCAATCGTCTTTGTTTACGTCTCGACT
1 GTGTTGTCCCAATCG--ATTCTTTACGTCTCGACT
6049679 TACGATGTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
37 44 0.76
39 14 0.24
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (37 bp):
GTGTTGTCCCAATCGATTCTTTACGTCTCGACTCGCA
Found at i:6051423 original size:15 final size:14
Alignment explanation
Indices: 6051358--6051449 Score: 66
Period size: 14 Copynumber: 6.4 Consensus size: 14
6051348 TATTCATGTT
6051358 TTAAAATCCTAAAA-
1 TTAAAATCC-AAAAC
*
6051372 TTAAAA-CCAAACC
1 TTAAAATCCAAAAC
6051385 TTAAAATCC-AAAC
1 TTAAAATCCAAAAC
6051398 TCTCCAAAATCCAAAAC
1 T-T--AAAATCCAAAAC
*
6051415 TCTAAAATCCAAACCC
1 T-TAAAATCCAAA-AC
*
6051431 TT-CAATCCAAAATC
1 TTAAAATCCAAAA-C
6051445 TTAAA
1 TTAAA
6051450 CCTTCCATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.05
13 12 0.19
14 20 0.32
15 12 0.19
16 9 0.14
17 7 0.11
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
TTAAAATCCAAAAC
Found at i:6057111 original size:146 final size:146
Alignment explanation
Indices: 6056847--6057111 Score: 404
Period size: 146 Copynumber: 1.8 Consensus size: 146
6056837 AGAGGTTTCA
* *
6056847 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTGGTGGTAGAGCTCAATCAATGTCTTTAGT
1 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
* * *
6056912 AAATGGAGAACTTTCTAAGAACTTTAGCTCATTATCAAAGGTGGAGGCTTTATTTTTTAATATTT
66 AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATTTTTTAATATTT
6056977 TATCCATTACCTCTAT
131 TATCCATTACCTCTAT
* * ** * * * *
6056993 TCATAATTCTCTAAAGTTGGCATTTTTTATCCTTTTAGTGGTTGAGCTTAATTAATGTCCTTAGT
1 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
*
6057058 AAATGGAGATCTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATT
66 AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATT
6057112 ATTTGGCTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
146 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (146 bp):
TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATTTTTTAATATTT
TATCCATTACCTCTAT
Found at i:6057124 original size:146 final size:146
Alignment explanation
Indices: 6056847--6057141 Score: 403
Period size: 146 Copynumber: 2.0 Consensus size: 146
6056837 AGAGGTTTCA
* *
6056847 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTGGTGGTAGAGCTCAATCAATGTCTTTAGT
1 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
* * * *
6056912 AAATGGAGAACTTTCTAAGAACTTTAGCTCATTATCAAAGGTGGAGGCTTTATTTTTTAATATTT
66 AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATTTTTGAATATTT
*
6056977 TATCCATTACCTCTAT
131 TATCCATTACCTCCAT
* * ** * * * *
6056993 TCATAATTCTCTAAAGTTGGCATTTTTTATCCTTTTAGTGGTTGAGCTTAATTAATGTCCTTAGT
1 TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
* **
6057058 AAATGGAGATCTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATTATTTGGCT-TT
66 AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATT-TTTGAATATT
*
6057122 TTATCCATTGCCTCCAT
130 TTATCCATTACCTCCAT
6057139 TCA
1 TCA
6057142 AGCTTCCAAA
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
146 125 0.97
147 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (146 bp):
TCATAATTCTCCAAAGTTGGCATATTGAATCCCTTTAGTGGTAGAGCTCAATCAATGTCCTTAGT
AAATGGAGAACTCTCCAAGAACTTTAGCTCATTATCAAAGGTGAAGGCTTTATTTTTGAATATTT
TATCCATTACCTCCAT
Found at i:6062200 original size:2 final size:2
Alignment explanation
Indices: 6062193--6062241 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
6062183 ATTCCTTATC
* *
6062193 AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT TT AT CAT 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
6062235 AT AT AT A
1 AT AT AT A
6062242 AATTCTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6066786 original size:18 final size:18
Alignment explanation
Indices: 6066763--6066801 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
6066753 CTAATTGTTG
6066763 ATTCATTTTCAATCAGTA
1 ATTCATTTTCAATCAGTA
*
6066781 ATTCATTTTCAATCATTA
1 ATTCATTTTCAATCAGTA
6066799 ATT
1 ATT
6066802 TGTGTGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTCATTTTCAATCAGTA
Found at i:6068035 original size:43 final size:42
Alignment explanation
Indices: 6067957--6068037 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
6067947 AAAACATAAT
* * *
6067957 AATGAAAAAATAAAATAAAATAAGACTAAAGAAGAAAAACAA
1 AATGAAAAAATAAAATAAAATAAAACAAAAAAAGAAAAACAA
*
6067999 AATGAAAATCATAACAA-AAAATAAAACAAAAAAAGAAAA
1 AATGAAAA-AATAA-AATAAAATAAAACAAAAAAAGAAAA
6068038 GTAAATACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 8 0.24
43 23 0.70
44 2 0.06
ACGTcount: A:0.75, C:0.06, G:0.07, T:0.11
Consensus pattern (42 bp):
AATGAAAAAATAAAATAAAATAAAACAAAAAAAGAAAAACAA
Found at i:6069023 original size:16 final size:16
Alignment explanation
Indices: 6069002--6069044 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
6068992 AAAATCCCAT
6069002 ATTTTTTTATTTTTGG
1 ATTTTTTTATTTTTGG
6069018 ATTTTTTTATTTTTGG
1 ATTTTTTTATTTTTGG
6069034 -TTTTTTT-TTTT
1 ATTTTTTTATTTT
6069045 ACTTTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 16 0.59
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (16 bp):
ATTTTTTTATTTTTGG
Found at i:6069130 original size:6 final size:6
Alignment explanation
Indices: 6069088--6069188 Score: 62
Period size: 6 Copynumber: 16.7 Consensus size: 6
6069078 AATAAACCAC
* * *
6069088 AAAATT AAAATC AAAA-C AAAATTTT AAAAAT ATAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAA--TT AAAATT A-AAATT AAAATT AAAATT
* * * * * * * *
6069138 AAAATC AAAATC AAGATT GAAATT AAAA-T CAAATT ACAACT CAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
6069185 AAAA
1 AAAA
6069189 ATTCTAAGCT
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
5 9 0.12
6 54 0.75
7 5 0.07
8 4 0.06
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:6069756 original size:17 final size:17
Alignment explanation
Indices: 6069711--6069759 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
6069701 AAATTTAAAT
6069711 TTTGCAAGAACTTCAGG
1 TTTGCAAGAACTTCAGG
** *
6069728 TTCACAAAAACTTCAGG
1 TTTGCAAGAACTTCAGG
6069745 TTTGCAAGAACTTCA
1 TTTGCAAGAACTTCA
6069760 AATTGGTACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (17 bp):
TTTGCAAGAACTTCAGG
Found at i:6069810 original size:17 final size:17
Alignment explanation
Indices: 6069790--6070060 Score: 91
Period size: 17 Copynumber: 16.2 Consensus size: 17
6069780 TAACAGGAAC
*
6069790 TTCAGATTTGCAAGAAT
1 TTCAGATTCGCAAGAAT
*
6069807 TTCAGGTTCGCAAGAAT
1 TTCAGATTCGCAAGAAT
* *
6069824 TTTAGATT--C-ATAA-
1 TTCAGATTCGCAAGAAT
6069837 -T---ATTCGCAAGAAT
1 TTCAGATTCGCAAGAAT
*
6069850 TTTATG-TT-GACAAGAAT
1 TTCA-GATTCG-CAAGAAT
*
6069867 TTCA-ATTTTGCAAGAAT
1 TTCAGA-TTCGCAAGAAT
* * * *
6069884 TTTAGTTTTGTAAGAATT
1 TTCAGATTCGCAAGAA-T
*
6069902 TTCAGATTCACAAGAA-
1 TTCAGATTCGCAAGAAT
* * *
6069918 CTCAAATTCACAAGAAAT
1 TTCAGATTCGCAAG-AAT
* *
6069936 TT-AGTTTCACAAGAAT
1 TTCAGATTCGCAAGAAT
* * *
6069952 TTAAAAATTTGCAAGAAT
1 TT-CAGATTCGCAAGAAT
* *
6069970 TTCATATTCGCAAAAAT
1 TTCAGATTCGCAAGAAT
* *
6069987 TTAAAGATTTGCAAGAAT
1 TT-CAGATTCGCAAGAAT
* **
6070005 TTTAGATTCATAAGAAT
1 TTCAGATTCGCAAGAAT
* * * *
6070022 TTAAAAATTTGCAAGATT
1 TT-CAGATTCGCAAGAAT
**
6070040 TTCAGATTCATAAGAAT
1 TTCAGATTCGCAAGAAT
6070057 TTCA
1 TTCA
6070061 ACTTCATCAT
Statistics
Matches: 185, Mismatches: 48, Indels: 42
0.67 0.17 0.15
Matches are distributed among these distances:
9 3 0.02
11 1 0.01
12 4 0.02
14 4 0.02
15 1 0.01
16 18 0.10
17 104 0.56
18 50 0.27
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (17 bp):
TTCAGATTCGCAAGAAT
Found at i:6069968 original size:18 final size:18
Alignment explanation
Indices: 6069945--6070037 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
6069935 TTTAGTTTCA
6069945 CAAGAATTTAAAAATTTG
1 CAAGAATTTAAAAATTTG
* * *
6069963 CAAGAATTT-CATATTCG
1 CAAGAATTTAAAAATTTG
* *
6069980 CAAAAATTTAAAGATTTG
1 CAAGAATTTAAAAATTTG
* * **
6069998 CAAGAATTT-TAGATTCA
1 CAAGAATTTAAAAATTTG
*
6070015 TAAGAATTTAAAAATTTG
1 CAAGAATTTAAAAATTTG
6070033 CAAGA
1 CAAGA
6070038 TTTTCAGATT
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
17 26 0.46
18 30 0.54
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (18 bp):
CAAGAATTTAAAAATTTG
Found at i:6070047 original size:35 final size:35
Alignment explanation
Indices: 6069890--6070058 Score: 157
Period size: 35 Copynumber: 4.9 Consensus size: 35
6069880 GAATTTTAGT
* * *
6069890 TTTGTAAGAATTTTCAGATTCACAAGAA-CT-CAAA
1 TTTGCAAG-ATTTTCAGATTCACAAGAATTTAAAAA
** * *
6069924 TTCACAAGAAATTT-AGTTTCACAAGAATTTAAAAA
1 TTTGCAAG-ATTTTCAGATTCACAAGAATTTAAAAA
* * * * *
6069959 TTTGCAAGAATTTCATATTCGCAAAAATTTAAAGA
1 TTTGCAAGATTTTCAGATTCACAAGAATTTAAAAA
*
6069994 TTTGCAAGAATTTT-AGATTCATAAGAATTTAAAAA
1 TTTGCAAG-ATTTTCAGATTCACAAGAATTTAAAAA
*
6070029 TTTGCAAGATTTTCAGATTCATAAGAATTT
1 TTTGCAAGATTTTCAGATTCACAAGAATTT
6070059 CAACTTCATC
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
33 12 0.11
34 21 0.19
35 73 0.66
36 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (35 bp):
TTTGCAAGATTTTCAGATTCACAAGAATTTAAAAA
Found at i:6070058 original size:70 final size:70
Alignment explanation
Indices: 6069928--6070058 Score: 190
Period size: 70 Copynumber: 1.9 Consensus size: 70
6069918 CTCAAATTCA
* * *
6069928 CAAGAAATTTAGTTTCACAAGAATTTAAAAATTTGCAAGAATTTCATATTCGCAAAAATTTAAAG
1 CAAGAAATTTAGATTCACAAGAATTTAAAAATTTGCAAGAATTTCAGATTCACAAAAATTTAAAG
6069993 ATTTG
66 ATTTG
* * * * *
6069998 CAAGAATTTTAGATTCATAAGAATTTAAAAATTTGCAAGATTTTCAGATTCATAAGAATTT
1 CAAGAAATTTAGATTCACAAGAATTTAAAAATTTGCAAGAATTTCAGATTCACAAAAATTT
6070059 CAACTTCATC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (70 bp):
CAAGAAATTTAGATTCACAAGAATTTAAAAATTTGCAAGAATTTCAGATTCACAAAAATTTAAAG
ATTTG
Done.