Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, 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: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 92 of 120
Found at i:12230316 original size:29 final size:30
Alignment explanation
Indices: 12230250--12230338 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
12230240 AATAATTGTG
* *
12230250 TGAATATTACTTTATTATTT-TTTCATTATT
1 TGAATATAATTTTATTATTTATTT-ATTATT
12230280 TGAATATAATTTTATT-TTTATTTATTATT
1 TGAATATAATTTTATTATTTATTTATTATT
* * *
12230309 TTAATATAATTTAATTATTTATTTTTTATT
1 TGAATATAATTTTATTATTTATTTATTATT
12230339 GTTTGGATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 23 0.44
30 29 0.56
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TGAATATAATTTTATTATTTATTTATTATT
Found at i:12230349 original size:33 final size:31
Alignment explanation
Indices: 12230264--12230353 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 31
12230254 TATTACTTTA
*
12230264 TTATTTTTTCATTATTTGAATATAATTTTATTT
1 TTATTTTTT-ATT-TTTGAATATAATTTAATTT
*
12230297 TTATTTATTA-TTTT-AATATAATTTAATTAT
1 TTATTTTTTATTTTTGAATATAATTTAATT-T
*
12230327 TTATTTTTTATTGTTTGGATATAATTT
1 TTATTTTTTATT-TTTGAATATAATTT
12230354 GATCACTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 13 0.27
30 13 0.27
31 2 0.04
32 4 0.08
33 17 0.35
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (31 bp):
TTATTTTTTATTTTTGAATATAATTTAATTT
Found at i:12236313 original size:7 final size:7
Alignment explanation
Indices: 12236301--12236326 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12236291 ATTGATGCCA
12236301 TAAGGTT
1 TAAGGTT
12236308 TAAGGTT
1 TAAGGTT
12236315 TAAGGTT
1 TAAGGTT
12236322 TAAGG
1 TAAGG
12236327 AAATTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (7 bp):
TAAGGTT
Found at i:12236596 original size:24 final size:24
Alignment explanation
Indices: 12236543--12236600 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
12236533 TTTTTCATTC
* * *
12236543 AAACATTACTTTTTAAATATAAGT
1 AAACATCACTTTTTAAAGAAAAGT
*
12236567 ATACATCA-TTTTTAAAGAAAAGT
1 AAACATCACTTTTTAAAGAAAAGT
12236590 AAAACAT-ACTT
1 -AAACATCACTT
12236601 ATTCCATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.36
Consensus pattern (24 bp):
AAACATCACTTTTTAAAGAAAAGT
Found at i:12237345 original size:62 final size:62
Alignment explanation
Indices: 12237217--12237356 Score: 155
Period size: 62 Copynumber: 2.3 Consensus size: 62
12237207 TAACGCTACA
* ** *
12237217 ATTATTATAT-TTATAAAATAATATTTGTACTATATAAATAATAATATATTATATTGTTATAT
1 ATTATTATATATTAT-AAATAATATTTATACTATATAAATAATAATATATTATATTAATAAAT
*
12237279 -TTATTAATATATTATAAATAATA-TTATATTA-ATAAATAATATAATATATTA-ATTAATAAAT
1 ATTATT-ATATATTATAAATAATATTTATACTATATAAAT-A-ATAATATATTATATTAATAAAT
12237340 ATTATTATATTATTATA
1 ATTATTATA-TATTATA
12237357 TTATTAATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
60 6 0.09
61 22 0.33
62 35 0.52
63 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (62 bp):
ATTATTATATATTATAAATAATATTTATACTATATAAATAATAATATATTATATTAATAAAT
Found at i:12237360 original size:8 final size:8
Alignment explanation
Indices: 12237338--12237362 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12237328 TAATTAATAA
12237338 ATATTATT
1 ATATTATT
12237346 ATATTATT
1 ATATTATT
12237354 ATATTATT
1 ATATTATT
12237362 A
1 A
12237363 ATAACAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATTATT
Found at i:12239605 original size:32 final size:31
Alignment explanation
Indices: 12239550--12239628 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
12239540 TAAAATGTTA
** * *
12239550 CAAATGAAATTTAAATGCATTAATATTTTAT
1 CAAATGAAATCAAAATGCATTAATAGTTTAC
12239581 CAAATGAAATCAAACATGCATTAATAGTTTAC
1 CAAATGAAATCAAA-ATGCATTAATAGTTTAC
12239613 CAAATGAAAT-AAAATG
1 CAAATGAAATCAAAATG
12239629 AAATCATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 3 0.07
31 15 0.35
32 25 0.58
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATGAAATCAAAATGCATTAATAGTTTAC
Found at i:12242135 original size:6 final size:6
Alignment explanation
Indices: 12242100--12242134 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
12242090 GTGTGTGTAA
* *
12242100 ATATAC ATATAC ATATAC ATATAT ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
12242135 TTAGATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAC
Found at i:12254938 original size:3 final size:3
Alignment explanation
Indices: 12254932--12254969 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12254922 CTACTACTAC
12254932 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12254970 TTGGCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12256106 original size:3 final size:3
Alignment explanation
Indices: 12256100--12256134 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12256090 AGAATACTAC
12256100 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12256135 TGGCCAATAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12258697 original size:18 final size:18
Alignment explanation
Indices: 12258674--12258708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12258664 AACAAGGAGT
*
12258674 ATGTGGCATTGCATAAAA
1 ATGTGGCAATGCATAAAA
*
12258692 ATGTGGTAATGCATAAA
1 ATGTGGCAATGCATAAA
12258709 GAATAAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (18 bp):
ATGTGGCAATGCATAAAA
Found at i:12265446 original size:22 final size:22
Alignment explanation
Indices: 12265400--12265463 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
12265390 AATTTAAAAT
*
12265400 TTTA-ATTAAATAAAATATTATA
1 TTTATATTAAAAAAAATA-TATA
*
12265422 TTTATATATAATAAAAATATA-A
1 TTTATAT-TAAAAAAAATATATA
12265444 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAA-AATAT
12265464 TCATTCTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.17
22 17 0.47
23 4 0.11
24 9 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTATATTAAAAAAAATATATA
Found at i:12265460 original size:17 final size:18
Alignment explanation
Indices: 12265428--12265461 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12265418 TATATTTATA
12265428 TATAATAAAAATATAATT
1 TATAATAAAAATATAATT
*
12265446 TATATTAAAAA-ATAAT
1 TATAATAAAAATATAAT
12265462 ATTCATTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAATAAAAATATAATT
Found at i:12267472 original size:21 final size:21
Alignment explanation
Indices: 12267430--12267473 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12267420 CCTTCATCTC
**
12267430 AATTCATATTCTCTTTTTAAA
1 AATTCATATTCTCTTTCAAAA
12267451 AATTCATATTCT-TTCTCAAAA
1 AATTCATATTCTCTT-TCAAAA
12267472 AA
1 AA
12267474 AATTTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTCATATTCTCTTTCAAAA
Found at i:12267872 original size:14 final size:14
Alignment explanation
Indices: 12267853--12267880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12267843 AGAGTACTAT
12267853 AACAAAAAAAAAAA
1 AACAAAAAAAAAAA
12267867 AACAAAAAAAAAAA
1 AACAAAAAAAAAAA
12267881 CTCTTATAAT
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AACAAAAAAAAAAA
Found at i:12284095 original size:2 final size:2
Alignment explanation
Indices: 12284088--12284112 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12284078 CCTACCAGAC
12284088 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
12284113 TTGCTAAGGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12284352 original size:2 final size:2
Alignment explanation
Indices: 12284345--12284386 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12284335 GTTTTGATTT
12284345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12284387 CTAGTTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12284558 original size:10 final size:10
Alignment explanation
Indices: 12284544--12284616 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
12284534 TATAATTTTG
12284544 ATTTTGATAA
1 ATTTTGATAA
*
12284554 CTTTTGATAAA
1 ATTTTGAT-AA
12284565 ATTTTGATAA
1 ATTTTGATAA
***
12284575 CCATTGATACA
1 ATTTTGATA-A
12284586 ATTTTGATAA
1 ATTTTGATAA
* *
12284596 TTTTTTATAAA
1 ATTTTGAT-AA
*
12284607 ATTTTAATAA
1 ATTTTGATAA
12284617 CCTCTTCATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
10 24 0.50
11 24 0.50
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (10 bp):
ATTTTGATAA
Found at i:12284558 original size:27 final size:27
Alignment explanation
Indices: 12284519--12284572 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12284509 ATAAGTAAAA
* * *
12284519 TTTGATAATTTTTTATATAATTTTGAT
1 TTTGATAACTTTTGATAAAATTTTGAT
12284546 TTTGATAACTTTTGATAAAATTTTGAT
1 TTTGATAACTTTTGATAAAATTTTGAT
12284573 AACCATTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.57
Consensus pattern (27 bp):
TTTGATAACTTTTGATAAAATTTTGAT
Found at i:12284570 original size:21 final size:21
Alignment explanation
Indices: 12284544--12284617 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
12284534 TATAATTTTG
12284544 ATTTTGATAACTTTTGATAAA
1 ATTTTGATAACTTTTGATAAA
** *
12284565 ATTTTGATAACCATTGATACA
1 ATTTTGATAACTTTTGATAAA
* *
12284586 ATTTTGATAATTTTTTATAAA
1 ATTTTGATAACTTTTGATAAA
*
12284607 ATTTTAATAAC
1 ATTTTGATAAC
12284618 CTCTTCATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTTTGATAACTTTTGATAAA
Found at i:12285018 original size:22 final size:22
Alignment explanation
Indices: 12284927--12285077 Score: 79
Period size: 22 Copynumber: 6.9 Consensus size: 22
12284917 GTAAAAAAAT
* * *
12284927 TTATCAATTATTGATAATTAAA
1 TTATCAATGATTTATTATTAAA
* * ** **
12284949 TTATTATTGATTTGCTATTATG
1 TTATCAATGATTTATTATTAAA
* * * *
12284971 TTATTAGTGATTTATTACTAAG
1 TTATCAATGATTTATTATTAAA
* *
12284993 TTATTAAT-ATTATATTGTTAAA
1 TTATCAATGATT-TATTATTAAA
12285015 TTATCAATGATTTATTATTAAA
1 TTATCAATGATTTATTATTAAA
* * * * **
12285037 TTAACATTGATTTACTACTATT
1 TTATCAATGATTTATTATTAAA
* *
12285059 TTATAAATGATTTACTATT
1 TTATCAATGATTTATTATT
12285078 TACTACTAAA
Statistics
Matches: 97, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 3 0.03
22 91 0.94
23 3 0.03
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (22 bp):
TTATCAATGATTTATTATTAAA
Found at i:12285100 original size:22 final size:22
Alignment explanation
Indices: 12285075--12285166 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
12285065 ATGATTTACT
**
12285075 ATTTACTACTAAATTGTTGATA
1 ATTTACTACTAAATTACTGATA
*
12285097 ATTTACTACTAAGTTACTGATA
1 ATTTACTACTAAATTACTGATA
* *
12285119 ATTTATTA-TAAAGTTA-TAATTA
1 ATTTACTACTAAA-TTACTGA-TA
* * *
12285141 ATTTACTA-TTAATTATTGATG
1 ATTTACTACTAAATTACTGATA
12285162 ATTTA
1 ATTTA
12285167 TTTTAATGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
21 14 0.25
22 43 0.75
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTTACTACTAAATTACTGATA
Found at i:12285198 original size:43 final size:44
Alignment explanation
Indices: 12285095--12285199 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 44
12285085 AAATTGTTGA
* * * *
12285095 TAATTTACTACTAAGTTACTGATAATTTATTATAAAGTTATAAT
1 TAATTTACTACTAAATTATTGATAATTTATTATAAAGATATAAC
* * * *
12285139 TAATTTACTA-TTAATTATTGATGATTTATTTTAATGAT-TAAC
1 TAATTTACTACTAAATTATTGATAATTTATTATAAAGATATAAC
*
12285181 TAATTTGCTACTAAATTAT
1 TAATTTACTACTAAATTAT
12285200 CACTTATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
42 12 0.24
43 28 0.56
44 10 0.20
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (44 bp):
TAATTTACTACTAAATTATTGATAATTTATTATAAAGATATAAC
Found at i:12285230 original size:22 final size:22
Alignment explanation
Indices: 12285190--12285232 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12285180 CTAATTTGCT
*
12285190 ACTAAATTATCACTTATTTATG
1 ACTAAATTATCACTGATTTATG
* *
12285212 ACTAAATTATTAGTGATTTAT
1 ACTAAATTATCACTGATTTAT
12285233 TGCTAAGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
ACTAAATTATCACTGATTTATG
Found at i:12285409 original size:21 final size:22
Alignment explanation
Indices: 12285376--12285653 Score: 110
Period size: 22 Copynumber: 12.6 Consensus size: 22
12285366 ACCATAATTC
* *
12285376 ACTATTAAGTTATCATTCATTT
1 ACTATTAAATTATCATTGATTT
*
12285398 A-TGTTAAATTATTCA-TGATTT
1 ACTATTAAATTA-TCATTGATTT
* * *
12285419 ATTATTAAGTTATCATTGATTA
1 ACTATTAAATTATCATTGATTT
*
12285441 ACTATTAAATTATTGA-TGATTAACT
1 ACTATTAAATTA-TCATTGATT---T
* *
12285466 ACTATTAAGTTAT-ATTAATTT
1 ACTATTAAATTATCATTGATTT
* ** *
12285487 ACT-TGTAAGTT-TCCAAAGATTA
1 ACTAT-TAAATTAT-CATTGATTT
* *
12285509 ACTGTTAAATTATCATTTATTT
1 ACTATTAAATTATCATTGATTT
* *
12285531 ACTATTAAGTTAT-TTATGATTT
1 ACTATTAAATTATCAT-TGATTT
* *
12285553 ATTATTAAATTTATCAATT-AATT
1 ACTATTAAA-TTATC-ATTGATTT
* * *
12285576 AATATTAAATTGA-AACTGATTT
1 ACTATTAAATT-ATCATTGATTT
* * *
12285598 GCTATTAAATTATCACTAATTT
1 ACTATTAAATTATCATTGATTT
* * *
12285620 A-TCATTAAGTTATTATTAATTT
1 ACT-ATTAAATTATCATTGATTT
*
12285642 ATTATT-AATTAT
1 ACTATTAAATTAT
12285654 TAATTATTAA
Statistics
Matches: 192, Mismatches: 42, Indels: 45
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.01
21 37 0.19
22 113 0.59
23 22 0.11
24 6 0.03
25 12 0.06
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.49
Consensus pattern (22 bp):
ACTATTAAATTATCATTGATTT
Found at i:12285543 original size:22 final size:22
Alignment explanation
Indices: 12285376--12285684 Score: 89
Period size: 22 Copynumber: 14.0 Consensus size: 22
12285366 ACCATAATTC
*
12285376 ACTATTAAGTTATCATTCATTT
1 ACTATTAAGTTATCATTTATTT
* * *
12285398 A-TGTTAAATTATTCA-TGATTT
1 ACTATTAAGTTA-TCATTTATTT
* * *
12285419 ATTATTAAGTTATCATTGATTA
1 ACTATTAAGTTATCATTTATTT
* * **
12285441 ACTATTAAATTATTGATGATTAACT
1 ACTATTAAGTTA-TCAT--TTATTT
*
12285466 ACTATTAAGTTAT-ATTAATTT
1 ACTATTAAGTTATCATTTATTT
*** *
12285487 ACT-TGTAAGTT-TCCAAAGATTA
1 ACTAT-TAAGTTAT-CATTTATTT
* *
12285509 ACTGTTAAATTATCATTTATTT
1 ACTATTAAGTTATCATTTATTT
12285531 ACTATTAAGTTAT--TTATGATTT
1 ACTATTAAGTTATCATT-T-ATTT
* * * *
12285553 ATTATTAAATTTATCAATTAATT
1 ACTATT-AAGTTATCATTTATTT
* * * * *
12285576 AATATTAAATTGA-AACTGATTT
1 ACTATTAAGTT-ATCATTTATTT
* * * *
12285598 GCTATTAAATTATCACTAATTT
1 ACTATTAAGTTATCATTTATTT
* *
12285620 A-TCATTAAGTTATTATTAATTT
1 ACT-ATTAAGTTATCATTTATTT
* * * *
12285642 ATTATTAA-TTATTAATTATTA
1 ACTATTAAGTTATCATTTATTT
* * *
12285663 ACTACTAAGTTGTCACTTATTT
1 ACTATTAAGTTATCATTTATTT
12285685 TTCGTTAATC
Statistics
Matches: 211, Mismatches: 55, Indels: 42
0.69 0.18 0.14
Matches are distributed among these distances:
20 4 0.02
21 48 0.23
22 120 0.57
23 23 0.11
24 2 0.01
25 14 0.07
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (22 bp):
ACTATTAAGTTATCATTTATTT
Found at i:12285623 original size:11 final size:11
Alignment explanation
Indices: 12285601--12285651 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
12285591 CTGATTTGCT
*
12285601 ATTAAATTATC
1 ATTAATTTATC
*
12285612 ACTAATTTATC
1 ATTAATTTATC
* *
12285623 ATTAAGTTATT
1 ATTAATTTATC
*
12285634 ATTAATTTATT
1 ATTAATTTATC
12285645 ATTAATT
1 ATTAATT
12285652 ATTAATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTAATTTATC
Found at i:12285659 original size:11 final size:11
Alignment explanation
Indices: 12285618--12285655 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12285608 TATCACTAAT
*
12285618 TTATCATTAAG
1 TTATTATTAAG
*
12285629 TTATTATTAAT
1 TTATTATTAAG
12285640 TTATTATTAA-
1 TTATTATTAAG
12285650 TTATTA
1 TTATTA
12285656 ATTATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (11 bp):
TTATTATTAAG
Found at i:12285663 original size:14 final size:15
Alignment explanation
Indices: 12285623--12285663 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
12285613 CTAATTTATC
12285623 ATTAAGTTATT-ATTA
1 ATTAA-TTATTAATTA
*
12285638 ATTTATTATTAATT-
1 ATTAATTATTAATTA
12285652 ATTAATTATTAA
1 ATTAATTATTAA
12285664 CTACTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTAATTATTAATTA
Found at i:12286045 original size:22 final size:22
Alignment explanation
Indices: 12285968--12286041 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
12285958 GATTAACAAT
12285968 TAAGTTATCAATTATTTAG-TAC
1 TAAGTTATCAATTATTT-GTTAC
*
12285990 TAAGTTATCAATTATTTATTAC
1 TAAGTTATCAATTATTTGTTAC
* * * *
12286012 TAAATTATGAATAATTTGTTAT
1 TAAGTTATCAATTATTTGTTAC
12286034 TAAGTTAT
1 TAAGTTAT
12286042 GAATGACTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (22 bp):
TAAGTTATCAATTATTTGTTAC
Found at i:12286210 original size:22 final size:22
Alignment explanation
Indices: 12286182--12286373 Score: 90
Period size: 22 Copynumber: 8.9 Consensus size: 22
12286172 TAAATATCTC
*
12286182 TAATTTACAACTAAATTATTAG
1 TAATTTACTACTAAATTATTAG
* *
12286204 TAATTTACTATTACATTATTAG
1 TAATTTACTACTAAATTATTAG
* *
12286226 AAATTTACTACTAAGTTA-T--
1 TAATTTACTACTAAATTATTAG
* * * * *
12286245 CAATCTACTATTAAATTATCAA
1 TAATTTACTACTAAATTATTAG
* * *
12286267 TAATTTACTATTATATTCTTA-
1 TAATTTACTACTAAATTATTAG
* * ** *
12286288 TATATTTATTATTATGTTATTAT
1 TA-ATTTACTACTAAATTATTAG
* * *
12286311 TAATTTACAACT-AATTTTTAA
1 TAATTTACTACTAAATTATTAG
* * * *
12286332 TTATTTA-TCACAAAATTATCAC
1 TAATTTACT-ACTAAATTATTAG
*
12286354 TAATTTACCACTAAATTATT
1 TAATTTACTACTAAATTATT
12286374 TATGATTCAC
Statistics
Matches: 125, Mismatches: 37, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
19 14 0.11
21 16 0.13
22 93 0.74
23 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATTTACTACTAAATTATTAG
Found at i:12286263 original size:19 final size:19
Alignment explanation
Indices: 12286231--12286267 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12286221 ATTAGAAATT
*
12286231 TACTACTAAGTTATCAATC
1 TACTACTAAATTATCAATC
*
12286250 TACTATTAAATTATCAAT
1 TACTACTAAATTATCAAT
12286268 AATTTACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (19 bp):
TACTACTAAATTATCAATC
Found at i:12286506 original size:22 final size:22
Alignment explanation
Indices: 12286426--12286528 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
12286416 GTATGATTTA
* * *
12286426 TATCAATGATTTACTATTAAGT
1 TATCAATTATTTACTACTAAAT
**
12286448 TAT--ATTGATTTACTTTTAAAT
1 TATCAATT-ATTTACTACTAAAT
* * * *
12286469 TTTCAATGAATAACTACTAAAT
1 TATCAATTATTTACTACTAAAT
*
12286491 TATCAATTATTTACTACTAATT
1 TATCAATTATTTACTACTAAAT
12286513 TAT-AATTGATTTACTA
1 TATCAATT-ATTTACTA
12286529 TTAAGTTGTT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 18 0.29
22 41 0.65
23 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (22 bp):
TATCAATTATTTACTACTAAAT
Found at i:12286546 original size:22 final size:21
Alignment explanation
Indices: 12286434--12286552 Score: 73
Period size: 22 Copynumber: 5.5 Consensus size: 21
12286424 TATATCAATG
*
12286434 ATTTACTATTAAGTTAT-ATT
1 ATTTACTATTAATTTATAATT
* *
12286454 GATTTACTTTTAAATTT-TCAATG
1 -ATTTACTATT-AATTTAT-AATT
* * * *
12286477 AATAACTACTAAATTATCAATT
1 ATTTACTATTAATTTAT-AATT
*
12286499 ATTTACTACTAATTTATAATT
1 ATTTACTATTAATTTATAATT
*
12286520 GATTTACTATTAAGTTGT-TTATT
1 -ATTTACTATTAA-TT-TATAATT
12286543 ATTTACTATT
1 ATTTACTATT
12286553 GTCAATTGAT
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
21 18 0.23
22 50 0.65
23 8 0.10
24 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTACTATTAATTTATAATT
Found at i:12286575 original size:22 final size:23
Alignment explanation
Indices: 12286550--12286640 Score: 55
Period size: 22 Copynumber: 4.1 Consensus size: 23
12286540 ATTATTTACT
12286550 ATTGTCAATTGA-TTACTATTAA
1 ATTGTCAATTGATTTACTATTAA
* * * *
12286572 ATTG-AAACTGATTTATTATTAG
1 ATTGTCAATTGATTTACTATTAA
* * * *
12286594 ATTATC-ACTCATTTGCTATTAA
1 ATTGTCAATTGATTTACTATTAA
* * *
12286616 GTTATC-ATTGATTTATTATTAA
1 ATTGTCAATTGATTTACTATTAA
12286638 ATT
1 ATT
12286641 ATCGATAATT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
21 5 0.10
22 46 0.90
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (23 bp):
ATTGTCAATTGATTTACTATTAA
Found at i:12286642 original size:22 final size:22
Alignment explanation
Indices: 12286578--12286643 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
12286568 TTAAATTGAA
*
12286578 ACTGATTTATTATTAGATTATC
1 ACTGATTTATTATTAAATTATC
* ** *
12286600 ACTCATTTGCTATTAAGTTATC
1 ACTGATTTATTATTAAATTATC
*
12286622 ATTGATTTATTATTAAATTATC
1 ACTGATTTATTATTAAATTATC
12286644 GATAATTAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (22 bp):
ACTGATTTATTATTAAATTATC
Found at i:12286661 original size:44 final size:44
Alignment explanation
Indices: 12286580--12286673 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
12286570 AAATTGAAAC
* * ** *
12286580 TGATTTATTATTAGATTATCACTCATTTGCTATTAAGTTATCAT
1 TGATTTATTATTAAATTATCACTAATTAACTACTAAGTTATCAT
12286624 TGATTTATTATTAAATTATCGA-TAATTAACTACTAAGTTATCAT
1 TGATTTATTATTAAATTATC-ACTAATTAACTACTAAGTTATCAT
*
12286668 TTATTT
1 TGATTT
12286674 TTGTTATCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (44 bp):
TGATTTATTATTAAATTATCACTAATTAACTACTAAGTTATCAT
Found at i:12286843 original size:22 final size:22
Alignment explanation
Indices: 12286774--12286857 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 22
12286764 ATTATTCTAG
* * *
12286774 ATTTACTA-AAAAGTTATCAATT
1 ATTTACTATTAAA-TTATCACTA
* * *
12286796 ATTAACTATTAAATTATCATTC
1 ATTTACTATTAAATTATCACTA
* *
12286818 ATTTACTATTTAATTATTACTA
1 ATTTACTATTAAATTATCACTA
* *
12286840 ATTTATTACTAAATTATC
1 ATTTACTATTAAATTATC
12286858 GATTATTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
22 45 0.94
23 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCACTA
Found at i:12286883 original size:20 final size:21
Alignment explanation
Indices: 12286858--12286916 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
12286848 CTAAATTATC
*
12286858 GATTATTATTAAGTTAT-ATT
1 GATTATTATTAAGTTATCAAT
*
12286878 GATTA-TATTTAAGTTTTCAAT
1 GATTATTA-TTAAGTTATCAAT
12286899 GATTACTTATTAAGTTAT
1 GATTA-TTATTAAGTTAT
12286917 TACTTATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.06
20 13 0.41
21 7 0.22
22 8 0.25
23 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
GATTATTATTAAGTTATCAAT
Found at i:12286960 original size:2 final size:2
Alignment explanation
Indices: 12286947--12286977 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12286937 ATTATTGATT
*
12286947 TA TA TA TG 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
12286978 CCAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12290845 original size:24 final size:25
Alignment explanation
Indices: 12290813--12290862 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12290803 TAAAATCAAC
* *
12290813 AATTAAAAAAA-ATGTACAAGTAAA
1 AATTAAAAAAATATGTAAAACTAAA
12290837 AATTAAAAAAATATGTAAAACTAAA
1 AATTAAAAAAATATGTAAAACTAAA
12290862 A
1 A
12290863 TAGATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (25 bp):
AATTAAAAAAATATGTAAAACTAAA
Found at i:12291187 original size:25 final size:25
Alignment explanation
Indices: 12291159--12291209 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
12291149 TAAAATCAAG
*
12291159 AATTAAAAAAATATGTACAACTAAA
1 AATTAAAAAAATATGTAAAACTAAA
*
12291184 AATTTAAAAAATATGTAAAACTAAA
1 AATTAAAAAAATATGTAAAACTAAA
12291209 A
1 A
12291210 CAGAGTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (25 bp):
AATTAAAAAAATATGTAAAACTAAA
Found at i:12291306 original size:2 final size:2
Alignment explanation
Indices: 12291301--12291342 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
12291291 AAGATAATAA
* * *
12291301 AT AT AT AT GT AC AT AT AT AT AT GT 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
12291343 TGCAGTAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12291341 original size:14 final size:14
Alignment explanation
Indices: 12291301--12291342 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
12291291 AAGATAATAA
*
12291301 ATATATATGTACAT
1 ATATATATGTATAT
12291315 ATATATATGTATAT
1 ATATATATGTATAT
*
12291329 ATATATATATATAT
1 ATATATATGTATAT
12291343 TGCAGTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:12294755 original size:93 final size:93
Alignment explanation
Indices: 12294596--12294783 Score: 376
Period size: 93 Copynumber: 2.0 Consensus size: 93
12294586 TGAAAATGAG
12294596 CCAGAAACAGAACTTGGGGATATGAATGAGCCAGCCATAGTTGGTGATGAGTCAGATGCTATTAG
1 CCAGAAACAGAACTTGGGGATATGAATGAGCCAGCCATAGTTGGTGATGAGTCAGATGCTATTAG
12294661 TTTTGAGCAGGGGGAGCAATCTTCTCTA
66 TTTTGAGCAGGGGGAGCAATCTTCTCTA
12294689 CCAGAAACAGAACTTGGGGATATGAATGAGCCAGCCATAGTTGGTGATGAGTCAGATGCTATTAG
1 CCAGAAACAGAACTTGGGGATATGAATGAGCCAGCCATAGTTGGTGATGAGTCAGATGCTATTAG
12294754 TTTTGAGCAGGGGGAGCAATCTTCTCTA
66 TTTTGAGCAGGGGGAGCAATCTTCTCTA
12294782 CC
1 CC
12294784 TGAGAGTGTT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (93 bp):
CCAGAAACAGAACTTGGGGATATGAATGAGCCAGCCATAGTTGGTGATGAGTCAGATGCTATTAG
TTTTGAGCAGGGGGAGCAATCTTCTCTA
Found at i:12297236 original size:41 final size:41
Alignment explanation
Indices: 12297191--12297273 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
12297181 TATTGTTGAG
*
12297191 AAATTATCATAATTAGTATCTCACACTCTTAAGCCAAACAT
1 AAATTATCATAATCAGTATCTCACACTCTTAAGCCAAACAT
*
12297232 AAATTATCATAATCAGTATCTCACACTCTTGAGCCAAACAT
1 AAATTATCATAATCAGTATCTCACACTCTTAAGCCAAACAT
12297273 A
1 A
12297274 TAGTACTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (41 bp):
AAATTATCATAATCAGTATCTCACACTCTTAAGCCAAACAT
Found at i:12301074 original size:16 final size:17
Alignment explanation
Indices: 12301055--12301087 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12301045 AAAATAATTT
12301055 ATTATAA-TTTTTTTTA
1 ATTATAACTTTTTTTTA
12301071 ATTATAACTTTTTTTTA
1 ATTATAACTTTTTTTTA
12301088 TAAAATAACG
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:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATAACTTTTTTTTA
Found at i:12302425 original size:2 final size:2
Alignment explanation
Indices: 12302418--12302452 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12302408 TATCCCTGAT
12302418 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12302453 AATGGCATCC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12304340 original size:21 final size:22
Alignment explanation
Indices: 12304303--12304350 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
12304293 CTTGAATTTA
12304303 ATAAAATATTATTTTTTAAAAAT
1 ATAAAATATTA-TTTTTAAAAAT
*
12304326 ATAAAATATTATTTTT-TAAAT
1 ATAAAATATTATTTTTAAAAAT
12304347 ATAA
1 ATAA
12304351 CTATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTAAAAAT
Found at i:12305005 original size:17 final size:19
Alignment explanation
Indices: 12304969--12305010 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
12304959 ATAAAAATAC
12304969 TATTATAAATAATATTTTAA
1 TATT-TAAATAATATTTTAA
12304989 TATTTAAA-AAT-TTTTAA
1 TATTTAAATAATATTTTAA
12305006 T-TTTA
1 TATTTA
12305011 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 3 0.14
19 4 0.18
20 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTAAATAATATTTTAA
Found at i:12309892 original size:15 final size:15
Alignment explanation
Indices: 12309872--12309915 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
12309862 AATTAAATTG
12309872 TATAATATTTTAAAA
1 TATAATATTTTAAAA
*
12309887 TATAATATTTAATAAA
1 TATAATATTTTA-AAA
12309903 TATGAA-ATTTTAA
1 TAT-AATATTTTAA
12309916 TTTTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TATAATATTTTAAAA
Found at i:12311819 original size:18 final size:20
Alignment explanation
Indices: 12311798--12311840 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
12311788 ATTATGATAC
*
12311798 TATTTATCAT-TAAAATA-G
1 TATTTATAATATAAAATAGG
12311816 TATTT-TAATATAAAATAGG
1 TATTTATAATATAAAATAGG
12311835 TATTTA
1 TATTTA
12311841 AAAAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTTATAATATAAAATAGG
Found at i:12312363 original size:32 final size:33
Alignment explanation
Indices: 12312271--12312396 Score: 116
Period size: 32 Copynumber: 3.9 Consensus size: 33
12312261 TTAATAAAGC
* *
12312271 AATTTTTTAAAAATGA-ATTGAAAATTTTTACTT
1 AATTTTTTTAAAATGATA-TAAAAATTTTTACTT
** ** ** *
12312304 AATAATTTTAAAA-GATATGGAGTTTTTTATTT
1 AATTTTTTTAAAATGATATAAAAATTTTTACTT
12312336 AA-TTTTTT-AAATCGATATAAAAATTTTTACTT
1 AATTTTTTTAAAAT-GATATAAAAATTTTTACTT
*
12312368 AATTTTTTTAAAATGATATAAATATTTTT
1 AATTTTTTTAAAATGATATAAAAATTTTT
12312397 CAAAATGAAT
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
30 3 0.04
31 4 0.05
32 31 0.42
33 31 0.42
34 4 0.05
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (33 bp):
AATTTTTTTAAAATGATATAAAAATTTTTACTT
Found at i:12312881 original size:23 final size:23
Alignment explanation
Indices: 12312855--12312913 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
12312845 TTTATTTTAC
12312855 TTAAAAT-TTTTAAAATATTAAT
1 TTAAAATATTTTAAAATATTAAT
* * *
12312877 ATTAAAAGTCTTTTAATATTTTAAT
1 -TTAAAA-TATTTTAAAATATTAAT
12312902 TTAAAATATTTT
1 TTAAAATATTTT
12312914 TATAGTTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 11 0.35
24 7 0.23
25 13 0.42
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAAAATATTTTAAAATATTAAT
Found at i:12313138 original size:25 final size:26
Alignment explanation
Indices: 12313080--12313139 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
12313070 TTATACTTTA
*
12313080 TATTATT-ATACATAAATATTTTTAG
1 TATTATTAATACATAAATATTATTAG
*
12313105 TATT-GTAATA-ATAAAATATTATT-G
1 TATTATTAATACAT-AAATATTATTAG
12313129 TATTATTAATA
1 TATTATTAATA
12313140 TTTTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (26 bp):
TATTATTAATACATAAATATTATTAG
Found at i:12313152 original size:33 final size:32
Alignment explanation
Indices: 12313095--12313176 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
12313085 TTATACATAA
* * * *
12313095 ATATTTTTAGTATTGTAATAATAAAATATTATT
1 ATATTATTAATATTTTAATAAT-AAATATTAAT
*
12313128 GTATTATTAATATTTTAATAATAAATATTAAT
1 ATATTATTAATATTTTAATAATAAATATTAAT
*
12313160 ATAGTATATAATATTTT
1 ATATTAT-TAATATTTT
12313177 CATTATTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 14 0.34
33 27 0.66
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (32 bp):
ATATTATTAATATTTTAATAATAAATATTAAT
Found at i:12313210 original size:15 final size:18
Alignment explanation
Indices: 12313178--12313227 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
12313168 TAATATTTTC
12313178 ATTATTATAATAATTAAT
1 ATTATTATAATAATTAAT
*
12313196 ATTATT-TAATATAATAAT
1 ATTATTATAATA-ATTAAT
* *
12313214 ACTATTTTAATAAT
1 ATTATTATAATAAT
12313228 ATAAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 17 0.63
19 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTATAATAATTAAT
Found at i:12313231 original size:19 final size:19
Alignment explanation
Indices: 12313180--12313231 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
12313170 ATATTTTCAT
* *
12313180 TATTATAATAAT-TAATAT
1 TATTTTAATAATATAATAC
12313198 TA-TTTAAT-ATAATAATAC
1 TATTTTAATAAT-ATAATAC
12313216 TATTTTAATAATATAA
1 TATTTTAATAATATAA
12313232 ATGTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.07
17 5 0.18
18 9 0.32
19 10 0.36
20 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTTAATAATATAATAC
Found at i:12316111 original size:10 final size:10
Alignment explanation
Indices: 12316093--12316131 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
12316083 TTATTTTAAA
*
12316093 ATTTATTTAT
1 ATTTGTTTAT
12316103 ATTTGTTTAT
1 ATTTGTTTAT
* *
12316113 ATTCGATTAT
1 ATTTGTTTAT
12316123 ATTTGTTTA
1 ATTTGTTTA
12316132 AGGTTTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTGTTTAT
Found at i:12316146 original size:15 final size:15
Alignment explanation
Indices: 12316117--12316173 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
12316107 GTTTATATTC
*
12316117 GATTATATTTGTTTAA
1 GATT-TATTTATTTAA
*
12316133 GGTTTATTTATTTAA
1 GATTTATTTATTTAA
*
12316148 -ATTTATTT-TATTAT
1 GATTTATTTAT-TTAA
12316162 GATTTATTTATT
1 GATTTATTTATT
12316174 ATTCATGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 1 0.03
14 10 0.29
15 19 0.56
16 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (15 bp):
GATTTATTTATTTAA
Found at i:12316174 original size:14 final size:15
Alignment explanation
Indices: 12316135--12316175 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
12316125 TTGTTTAAGG
12316135 TTTATTTATT-TAAA
1 TTTATTTATTATAAA
*
12316149 TTTATTTTATTAT-GA
1 TTTA-TTTATTATAAA
12316164 TTTATTTATTAT
1 TTTATTTATTAT
12316176 TCATGAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 11 0.46
16 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTATTTATTATAAA
Found at i:12319666 original size:27 final size:27
Alignment explanation
Indices: 12319636--12319706 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
12319626 CAATTACTGA
12319636 ATATTATATTTAATTAAA-TATAAATGT
1 ATATTATATTTAATTAAAGTATAAAT-T
* * *
12319663 ATATAATAATTAATTAAAGTATCAATT
1 ATATTATATTTAATTAAAGTATAAATT
*
12319690 ATTTTATAATTGTAATT
1 ATATTAT-ATT-TAATT
12319707 GTAGTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 22 0.63
28 8 0.23
29 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATTATATTTAATTAAAGTATAAATT
Found at i:12319846 original size:268 final size:271
Alignment explanation
Indices: 12319336--12319866 Score: 797
Period size: 268 Copynumber: 2.0 Consensus size: 271
12319326 ACAAATGAAA
* *
12319336 TAAATAATGAAATATATCAATTACTCAAATGGATACTATATTTAATTAATATAACTGTATCAAAT
1 TAAATAATGAAATACATCAATTACTCAAAT-GATA-TATATTTAATTAATATAAATGTATCAAAT
* * *
12319401 AATTAATTAGAGAATAAACTATTTTTTAATTGTAATTTTAGTATTTATTAATTTATTAATTATAT
64 AATTAATTAAAGAATAAACTATTTTATAATTGTAATTGTAGTATTTATTAATTTATTAATTATAT
*
12319466 ATTGATTGATTTAATTTGTCAAAATAAGAAATTTTTAAAATTTTAATACTTTTAATATGAATTGA
129 ATTGATTGATTTAATTTATCAAAATAAGAAATTTTTAAAATTTTAATACTTTTAATATGAATTGA
* * *
12319531 ATTAAGAATGATTTAAAATTAATAATAAAAATATAAATATAATCAATTTAGTTTTTTGAATTATA
194 ATTAAGAATAATTTAAAATTAATAATAAAAATATAAATATAATCAATTTAATTTTTTAAATTAT-
12319596 TTTTTTTATATATT
258 TTTTTTTATATATT
*
12319610 TAAAT-ATGAAATACATCAATTACT-GAAT-AT-TATATTTAATTAAATATAAATGTAT-ATAAT
1 TAAATAATGAAATACATCAATTACTCAAATGATATATATTTAATT-AATATAAATGTATCA-AAT
* * *
12319670 AATTAATTAAAGTATCAATTATTTTATAATTGTAATTGTAGTATTTATTAATTTATTAATTATAT
64 AATTAATTAAAGAATAAACTATTTTATAATTGTAATTGTAGTATTTATTAATTTATTAATTATAT
* * ** *
12319735 ATTGATTGATTTAATTTATCCAATTAA-ATTTTTTTTAAATTTTAATACTTTTAATATGAATTGA
129 ATTGATTGATTTAATTTATCAAAATAAGAAATTTTTAAAATTTTAATACTTTTAATATGAATTGA
12319799 ATTGAA-AATAATTTAAAATTAATAATAAAAATATAAATATAATCAATTTAATTTTTTAAATTAT
194 ATT-AAGAATAATTTAAAATTAATAATAAAAATATAAATATAATCAATTTAATTTTTTAAATTAT
12319863 TTTT
258 TTTT
12319867 AAATTAAAAA
Statistics
Matches: 236, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
267 4 0.02
268 104 0.44
269 100 0.42
270 2 0.01
272 3 0.01
273 18 0.08
274 5 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (271 bp):
TAAATAATGAAATACATCAATTACTCAAATGATATATATTTAATTAATATAAATGTATCAAATAA
TTAATTAAAGAATAAACTATTTTATAATTGTAATTGTAGTATTTATTAATTTATTAATTATATAT
TGATTGATTTAATTTATCAAAATAAGAAATTTTTAAAATTTTAATACTTTTAATATGAATTGAAT
TAAGAATAATTTAAAATTAATAATAAAAATATAAATATAATCAATTTAATTTTTTAAATTATTTT
TTTTATATATT
Found at i:12331072 original size:16 final size:18
Alignment explanation
Indices: 12331051--12331097 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
12331041 AATTTTTAAC
12331051 TAAAATGTAATTTT-T-T
1 TAAAATGTAATTTTCTAT
12331067 TAAAATGT-ATTTTCTAT
1 TAAAATGTAATTTTCTAT
12331084 TAAAA-GTAAATTTT
1 TAAAATGT-AATTTT
12331098 AATGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.19
16 11 0.41
17 6 0.22
18 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (18 bp):
TAAAATGTAATTTTCTAT
Found at i:12331214 original size:6 final size:6
Alignment explanation
Indices: 12331205--12331234 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12331195 ATTTGCATTG
12331205 TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT
12331235 ATTTATCTAT
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:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:12331245 original size:18 final size:17
Alignment explanation
Indices: 12331205--12331238 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12331195 ATTTGCATTG
12331205 TTATTTTTATTTTTATTT
1 TTATTTTTA-TTTTATTT
12331223 TTATTTTTA-TTTATTT
1 TTATTTTTATTTTATTT
12331239 ATCTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTATTTTTATTTTATTT
Found at i:12331245 original size:24 final size:23
Alignment explanation
Indices: 12331210--12331344 Score: 73
Period size: 24 Copynumber: 5.6 Consensus size: 23
12331200 CATTGTTATT
12331210 TTTATTT-TTATTTTTATTTTTA
1 TTTATTTATTATTTTTATTTTTA
*
12331232 TTTATTTATCTATTATTACTATTATTA
1 TTTATTTAT-TATT-TT--TATTTTTA
* * *
12331259 TTTA-TTAATATATATAATTTTTTA
1 TTTATTTATTAT-TTTTA-TTTTTA
* **
12331283 ATTATTTATCTATTAATATATTTTA
1 TTTATTTAT-TATTTTTAT-TTTTA
12331308 -TTATTTATTAATTATTTTATTTTTA
1 TTTATTTATT-A-T-TTTTATTTTTA
12331333 -TTA-TTATTATTT
1 TTTATTTATTATTT
12331345 ATCTATTAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.02
22 8 0.09
23 4 0.04
24 27 0.30
25 26 0.29
26 11 0.12
27 11 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTATTTATTATTTTTATTTTTA
Found at i:12331310 original size:55 final size:53
Alignment explanation
Indices: 12331226--12331454 Score: 242
Period size: 53 Copynumber: 4.3 Consensus size: 53
12331216 TTTATTTTTA
* * *
12331226 TTTTTATTTATTTATCTATT-AT-TACTATTA-TTATTTATTAATATATATAAT
1 TTTTTAATTATTTATCTATTAATATATTATTATTTATCTATTAATATATAT-AT
* *
12331277 TTTTTAATTATTTATCTATTAATATATT-TTA-TTATTTATTAAT-TATTTTATT
1 TTTTTAATTATTTATCTATTAATATATTATTATTTATCTATTAATATA-TATA-T
*
12331329 TTTATTATTATTATTTATCTATTAACATACATTATTATTTATCTATTAATATATAT-T
1 TTT-TTA--ATTATTTATCTATT-A-ATATATTATTATTTATCTATTAATATATATAT
* *
12331386 TTTTATTATTATTTATCTATTCATATATTATTATTTATCTATTAATATATATAT
1 TTTT-TAATTATTTATCTATTAATATATTATTATTTATCTATTAATATATATAT
12331440 TTTTT-ATT-TTTATCT
1 TTTTTAATTATTTATCT
12331455 TTTCGGTTGG
Statistics
Matches: 155, Mismatches: 9, Indels: 28
0.81 0.05 0.15
Matches are distributed among these distances:
51 29 0.19
52 26 0.17
53 36 0.23
54 5 0.03
55 28 0.18
56 2 0.01
57 11 0.07
58 3 0.02
59 13 0.08
60 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (53 bp):
TTTTTAATTATTTATCTATTAATATATTATTATTTATCTATTAATATATATAT
Found at i:12331312 original size:16 final size:16
Alignment explanation
Indices: 12331236--12331312 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 16
12331226 TTTTTATTTA
*
12331236 TTTATCTATTATTACTAT
1 TTTAT-TATTAATA-TAT
12331254 TATTATTTATTAATATAT
1 T-TTA-TTATTAATATAT
* * *
12331272 ATAATTTTTTAAT-TA-
1 TTTA-TTATTAATATAT
12331287 TTTATCTATTAATATAT
1 TTTAT-TATTAATATAT
12331304 TTTATTATT
1 TTTATTATT
12331313 TATTAATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
16 8 0.17
17 15 0.32
18 4 0.09
19 10 0.21
20 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATTATTAATATAT
Found at i:12331341 original size:83 final size:82
Alignment explanation
Indices: 12331221--12331454 Score: 229
Period size: 83 Copynumber: 2.9 Consensus size: 82
12331211 TTATTTTTAT
* * *
12331221 TTTTATT-TTTATTTATT-TATCTATTATTACTATTATTATTTATTAATATATATAATTTTTTAA
1 TTTTATTATTTATTAATTAT-TCTATTTTTATTATTATTATTTATTAATATATATAATTTTTT-A
12331284 TTATTTATCTATTAATATA
64 TTATTTATCTATTAATATA
* * *
12331303 TTTTATTATTTATTAATTATTTTATTTTTATTATTATTATTTATCTATTA-ACATACA----TTA
1 TTTTATTATTTATTAATTATTCTATTTTTATTATTATTATTTAT-TAATATATATA-ATTTTTTA
12331363 TTATTTATCTATTAATATA
64 TTATTTATCTATTAATATA
* * * *
12331382 TATTTTTTA-TTATTATTTA-TCTATTCATATATTATTATTTATCTATTAATATATAT-ATTTTT
1 T-TTTATTATTTATTAATTATTCTATT--TTTATTATTA-TTATTTATTAATATATATAATTTTT
12331444 TATT-TTTATCT
62 TATTATTTATCT
12331455 TTTCGGTTGG
Statistics
Matches: 126, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
78 5 0.04
79 31 0.25
80 21 0.17
81 10 0.08
82 14 0.11
83 39 0.31
84 6 0.05
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (82 bp):
TTTTATTATTTATTAATTATTCTATTTTTATTATTATTATTTATTAATATATATAATTTTTTATT
ATTTATCTATTAATATA
Found at i:12331413 original size:31 final size:32
Alignment explanation
Indices: 12331305--12331406 Score: 59
Period size: 31 Copynumber: 3.2 Consensus size: 32
12331295 TTAATATATT
* * *
12331305 TTATTATTTAT-TAATTATTTTATTTTTA-TTA
1 TTATTATTTATCT-ATTAATATATTATTATTTA
*
12331336 TTATTATTTATCTATTAACATACATTATTATTTA
1 TTATTATTTATCTATT-A-ATATATTATTATTTA
* * * *
12331370 TCTATTA-ATATATATT-TTTTATTATTATTTA
1 T-TATTATTTATCTATTAATATATTATTATTTA
12331401 TCTATT
1 T-TATT
12331407 CATATATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
31 32 0.56
32 2 0.04
33 7 0.12
34 11 0.19
35 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (32 bp):
TTATTATTTATCTATTAATATATTATTATTTA
Found at i:12331415 original size:22 final size:22
Alignment explanation
Indices: 12331389--12331446 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
12331379 ATATATTTTT
*
12331389 TATTATTATTTATCTATTCATA
1 TATTATTATTTATCTATTAATA
12331411 TATTATTATTTATCTATTAATA
1 TATTATTATTTATCTATTAATA
*
12331433 TATATATTTTTTAT
1 TAT-TATTATTTAT
12331447 TTTTATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 24 0.73
23 9 0.27
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATTATTTATCTATTAATA
Found at i:12332659 original size:24 final size:24
Alignment explanation
Indices: 12332631--12332707 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
12332621 ATACTATGCT
*
12332631 TGAAAAAAAAGAGAAAAAATGAAA
1 TGAAAAAAAAGAAAAAAAATGAAA
*
12332655 TGAAAAAAATGAAAAAAAATGAAA
1 TGAAAAAAAAGAAAAAAAATGAAA
* *
12332679 --AAAAAGGAA-AAAAAAAGTG-AA
1 TGAAAAA-AAAGAAAAAAAATGAAA
12332700 TGAAAAAA
1 TGAAAAAA
12332708 GAGGACTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.05
22 14 0.32
23 6 0.14
24 22 0.50
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (24 bp):
TGAAAAAAAAGAAAAAAAATGAAA
Found at i:12332676 original size:19 final size:20
Alignment explanation
Indices: 12332631--12332693 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
12332621 ATACTATGCT
12332631 TGAAAAAAAAGAGAAAAAATGAAA
1 TGAAAAAAAAG-G-AAAAA--AAA
*
12332655 TG-AAAAAAATGAAAAAAAA
1 TGAAAAAAAAGGAAAAAAAA
12332674 TGAAAAAAAAGGAAAAAAAA
1 TGAAAAAAAAGGAAAAAAAA
12332694 AGTGAATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 16 0.44
21 5 0.14
22 1 0.03
23 7 0.19
24 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (20 bp):
TGAAAAAAAAGGAAAAAAAA
Found at i:12332693 original size:10 final size:10
Alignment explanation
Indices: 12332652--12332693 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
12332642 AGAAAAAATG
12332652 AAATG-AAAA
1 AAATGAAAAA
12332661 AAATGAAAAA
1 AAATGAAAAA
12332671 AAATGAAAAA
1 AAATGAAAAA
*
12332681 AAAGGAAAAA
1 AAATGAAAAA
12332691 AAA
1 AAA
12332694 AGTGAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:12333754 original size:41 final size:41
Alignment explanation
Indices: 12333704--12333845 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 41
12333694 TTACTTTCTA
12333704 AAAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTATTTTTC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTATTTTTC
* *
12333745 AAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTGTTT-
1 AAAGTCGTTGAGCCTCTGATTAGAGGAG--TCATTTATT-TTTC
** *
12333788 -AAGTCGTTGAGTTTCTGATTAGAGGAG-CAATTTACTTTTC
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGTC-ATTTATTTTTC
*
12333828 AAAAGTCGTTGAACCTCT
1 -AAAGTCGTTGAGCCTCT
12333846 ACTTAAAGGA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
39 3 0.04
40 6 0.07
41 27 0.32
42 37 0.44
43 8 0.10
44 3 0.04
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (41 bp):
AAAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTATTTTTC
Found at i:12333827 original size:83 final size:84
Alignment explanation
Indices: 12333705--12333860 Score: 226
Period size: 83 Copynumber: 1.9 Consensus size: 84
12333695 TACTTTCTAA
* * ** *
12333705 AAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGA
1 AAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTACTTTTCAAAAGTCGTTGAACCTCTACTTAAA
12333769 GGAGCTTTATTTATTGTTT
66 GGAGCTTTATTTATTGTTT
**
12333788 AAGTCGTTGAGTTTCTGATTAGAGGAG-CAATTTACTTTTCAAAAGTCGTTGAACCTCTACTTAA
1 AAGTCGTTGAGCCTCTGATTAGAGGAGTC-ATTTACTTTTCAAAAGTCGTTGAACCTCTACTTAA
12333852 AGGAGCTTT
65 AGGAGCTTT
12333861 GATCAAAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
82 1 0.02
83 35 0.55
84 28 0.44
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (84 bp):
AAGTCGTTGAGCCTCTGATTAGAGGAGTCATTTACTTTTCAAAAGTCGTTGAACCTCTACTTAAA
GGAGCTTTATTTATTGTTT
Found at i:12334089 original size:4 final size:4
Alignment explanation
Indices: 12334073--12334239 Score: 71
Period size: 4 Copynumber: 42.8 Consensus size: 4
12334063 TATTTTTATT
* *
12334073 TTTA TTT- TTTA TTTA TTTA TCTA -TTA -TTA CTATTA -TTA TTTA TTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA
* * * * * * *
12334119 TATA -TAA TTTT TTTA ATTA TTTA TCTA TTAA TATA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * **
12334165 TTTT TTTA TTTA TTTT TATTA TTTA TCTA TTAA CATA TATTA -TTA TTTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
* * * *
12334214 TCTA TTAA TATA TATA TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
12334240 TTTTCTTTTC
Statistics
Matches: 116, Mismatches: 36, Indels: 22
0.67 0.21 0.13
Matches are distributed among these distances:
3 21 0.18
4 87 0.75
5 5 0.04
6 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:12334164 original size:31 final size:31
Alignment explanation
Indices: 12334104--12334178 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
12334094 TATTATTACT
12334104 ATTA-TTATTTATTAATATATAATTTTTTTA
1 ATTATTTATTTATTAATATATAATTTTTTTA
* *
12334134 ATTATTTATCTATTAATATAT-TTATTTTTTA
1 ATTATTTATTTATTAATATATAAT-TTTTTTA
* *
12334165 TTTTTTTATTTATT
1 ATTATTTATTTATT
12334179 TTTATTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (31 bp):
ATTATTTATTTATTAATATATAATTTTTTTA
Found at i:12335222 original size:27 final size:27
Alignment explanation
Indices: 12335192--12335281 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
12335182 TATTTTTAAG
12335192 GAAAAGTTGAAAGTATCAATTTTTCTT
1 GAAAAGTTGAAAGTATCAATTTTTCTT
* * ***
12335219 GAAAATAAGTTTTCTAAAATAT--ATTTTTGAG
1 G--AA-AAG--TT-GAAAGTATCAATTTTTCTT
12335250 GAAAAGTTGAAAGTATCAATTTTTCTT
1 GAAAAGTTGAAAGTATCAATTTTTCTT
12335277 GAAAA
1 GAAAA
12335282 TAAGTTTTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
25 6 0.13
26 2 0.04
27 12 0.27
28 3 0.07
29 4 0.09
30 3 0.07
31 7 0.16
32 2 0.04
33 6 0.13
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (27 bp):
GAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:12335226 original size:58 final size:58
Alignment explanation
Indices: 12335171--12335336 Score: 262
Period size: 58 Copynumber: 2.8 Consensus size: 58
12335161 TTAAATAAAA
*
12335171 TTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
1 TTTCTAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
* *
12335229 TTTCTAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
1 TTTCTAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
* *
12335287 TTTCTAAAAGATATTTTTGAGGAGAAAAGTTGAAAGTATCAA-TTTTCTTG
1 TTTCTAAAAAATATTTTT-AAG-GAAAAGTTGAAAGTATCAATTTTTCTTG
12335337 TATAAAAGTA
Statistics
Matches: 100, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
58 72 0.72
59 9 0.09
60 19 0.19
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (58 bp):
TTTCTAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
Found at i:12336025 original size:19 final size:19
Alignment explanation
Indices: 12335978--12336037 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
12335968 AAAAGATATT
12335978 TAATATTTTTAATAGAAAA
1 TAATATTTTTAATAGAAAA
*
12335997 TAA-ATTTTTTGGATAGAAAA
1 TAATA-TTTTT-AATAGAAAA
12336017 TAATATTTTTAATAGAAAA
1 TAATATTTTTAATAGAAAA
12336036 TA
1 TA
12336038 GTTTTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 16 0.44
21 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TAATATTTTTAATAGAAAA
Found at i:12336182 original size:26 final size:29
Alignment explanation
Indices: 12336153--12336210 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
12336143 TAACTAGTAA
12336153 ATTATGTTATAA-TAA-A-TTATAAAAAT
1 ATTATGTTATAATTAATATTTATAAAAAT
*
12336179 ATTATTTTATAATTAATATTTTATAAAAAT
1 ATTATGTTATAATTAATA-TTTATAAAAAT
12336209 AT
1 AT
12336211 ATTTGAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 11 0.41
27 3 0.11
28 1 0.04
30 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTATGTTATAATTAATATTTATAAAAAT
Found at i:12340190 original size:74 final size:74
Alignment explanation
Indices: 12340069--12340218 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
12340059 CCCAAGAAGC
*
12340069 ATGCCCTATTAACCCAGGGCAAGCCTCACAACTAGTTAATAGGAGGAATTAGTTTATCAGAAATC
1 ATGCCCTATTAACCCAGGGCAAGCCTCACAACTAGTTAACAGGAGGAATTAGTTTATCAGAAATC
12340134 AGAAAAAAG
66 AGAAAAAAG
* *
12340143 ATGCCCTATTAACCCAGGGCAGGCCTCATAACTAGTTAACAGGAGGAATTAGTTTATCAGAAATC
1 ATGCCCTATTAACCCAGGGCAAGCCTCACAACTAGTTAACAGGAGGAATTAGTTTATCAGAAATC
*
12340208 AGGAAAAAG
66 AGAAAAAAG
12340217 AT
1 AT
12340219 AAGTGTAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (74 bp):
ATGCCCTATTAACCCAGGGCAAGCCTCACAACTAGTTAACAGGAGGAATTAGTTTATCAGAAATC
AGAAAAAAG
Found at i:12346944 original size:18 final size:18
Alignment explanation
Indices: 12346886--12346951 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 18
12346876 TAAATTATTA
*
12346886 TATTTGAACATAAATAAT
1 TATTTGAAAATAAATAAT
12346904 TATTATATGATAAATAATCATAAT
1 TA-T-T-TGA-AAATAA--ATAAT
*
12346928 TATTTGAATATAAATAAAT
1 TATTTGAAAATAAAT-AAT
12346947 TATTT
1 TATTT
12346952 TTGTAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
18 4 0.10
19 9 0.23
20 6 0.15
21 6 0.15
22 6 0.15
23 1 0.03
24 7 0.18
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (18 bp):
TATTTGAAAATAAATAAT
Found at i:12348734 original size:18 final size:18
Alignment explanation
Indices: 12348711--12348749 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12348701 GAACGACGAT
12348711 AATAATAATAATGGTAGG
1 AATAATAATAATGGTAGG
*
12348729 AATAATAATGATGGTAGG
1 AATAATAATAATGGTAGG
12348747 AAT
1 AAT
12348750 GAAAAGAGCA
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:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (18 bp):
AATAATAATAATGGTAGG
Found at i:12351003 original size:8 final size:8
Alignment explanation
Indices: 12350990--12351026 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
12350980 AAATTAATTA
12350990 TATATATT
1 TATATATT
*
12350998 TATATAAT
1 TATATATT
12351006 TATATATT
1 TATATATT
*
12351014 TAAATATT
1 TATATATT
12351022 TATAT
1 TATAT
12351027 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:12351020 original size:18 final size:18
Alignment explanation
Indices: 12350976--12351020 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12350966 TAAAAATAAA
12350976 ATTTAAAT-TAATTATAT
1 ATTTAAATATAATTATAT
*
12350993 ATATT-TATATAATTATAT
1 AT-TTAAATATAATTATAT
12351011 ATTTAAATAT
1 ATTTAAATAT
12351021 TTATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAATATAATTATAT
Found at i:12351025 original size:14 final size:16
Alignment explanation
Indices: 12350976--12351044 Score: 63
Period size: 16 Copynumber: 4.3 Consensus size: 16
12350966 TAAAAATAAA
12350976 ATTTAAATTAATTATATAT
1 ATTTAAA-TAA-T-TATAT
*
12350995 ATTTATATAATTATAT
1 ATTTAAATAATTATAT
12351011 ATTTAAAT-ATT-TAT
1 ATTTAAATAATTATAT
* *
12351025 ATTTAAAAAATAATAT
1 ATTTAAATAATTATAT
12351041 -TTTA
1 ATTTA
12351045 TATTTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.23
15 9 0.20
16 15 0.34
17 1 0.02
18 3 0.07
19 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAATAATTATAT
Found at i:12351046 original size:21 final size:22
Alignment explanation
Indices: 12351016--12351067 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12351006 TATATATTTA
12351016 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12351036 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
12351058 AATATTTTAT
1 AATATTTTAT
12351068 TAATTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:12354779 original size:36 final size:36
Alignment explanation
Indices: 12354689--12354783 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
12354679 AACTAAAAGT
* * *
12354689 TCAAACATATATAATAAATCTTTCGTTCTTTCCTTT
1 TCAAACATATATAATAAATCTTTCATTCTTTCATTC
* * * * * * *
12354725 TCATATAGATGTAGTAAATCTTTTATTCTTTTATTC
1 TCAAACATATATAATAAATCTTTCATTCTTTCATTC
12354761 TCAAACATATATAATAAATCTTT
1 TCAAACATATATAATAAATCTTT
12354784 GGTTCAGCAT
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (36 bp):
TCAAACATATATAATAAATCTTTCATTCTTTCATTC
Found at i:12368910 original size:13 final size:13
Alignment explanation
Indices: 12368892--12368918 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12368882 AACATATGGC
12368892 AAGGTATCAAGAA
1 AAGGTATCAAGAA
12368905 AAGGTATCAAGAA
1 AAGGTATCAAGAA
12368918 A
1 A
12368919 TTTCAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (13 bp):
AAGGTATCAAGAA
Found at i:12378719 original size:3 final size:3
Alignment explanation
Indices: 12378711--12378736 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12378701 ATTTAACACT
12378711 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12378737 GGTCATGTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12379610 original size:17 final size:17
Alignment explanation
Indices: 12379584--12379636 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
12379574 AAAGTATATT
*
12379584 AAAATTATTAATATTTA
1 AAAATAATTAATATTTA
12379601 AAAATAATT-ATATTTTA
1 AAAATAATTAATA-TTTA
* *
12379618 ATAATATTTAATA-TTA
1 AAAATAATTAATATTTA
12379634 AAA
1 AAA
12379637 TATTATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.27
17 19 0.63
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATAATTAATATTTA
Found at i:12379639 original size:42 final size:42
Alignment explanation
Indices: 12379545--12379640 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 42
12379535 TTAATATAAC
* * *
12379545 TATTAAAACA-TTAAAAATTATTTATTATTAAAGTATATTAA
1 TATTAAAATATTTAAAAATAATTTATTATTAAAATATATTAA
* *
12379586 AATTATTAATATTTAAAAATAATTATATT-TTAATAATAT-TTAA
1 TATTA-AAATATTTAAAAATAATT-TATTATTAA-AATATATTAA
12379629 TATTAAAATATT
1 TATTAAAATATT
12379641 ATGTTAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
41 4 0.09
42 9 0.20
43 23 0.52
44 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TATTAAAATATTTAAAAATAATTTATTATTAAAATATATTAA
Found at i:12379708 original size:8 final size:8
Alignment explanation
Indices: 12379686--12379766 Score: 66
Period size: 8 Copynumber: 10.9 Consensus size: 8
12379676 TATCATTCTT
12379686 TATATT-A
1 TATATTAA
*
12379693 TTTATTAA
1 TATATTAA
12379701 TATATTAA
1 TATATTAA
12379709 TATATT-A
1 TATATTAA
*
12379716 TTTATTAA
1 TATATTAA
*
12379724 TA-A--CA
1 TATATTAA
12379729 TATATTAA
1 TATATTAA
*
12379737 TATATTAT
1 TATATTAA
*
12379745 TATAAT-A
1 TATATTAA
*
12379752 TTTATTAA
1 TATATTAA
12379760 TATATTA
1 TATATTA
12379767 TTATTTATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
5 3 0.05
6 1 0.02
7 16 0.29
8 36 0.64
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
TATATTAA
Found at i:12379769 original size:23 final size:25
Alignment explanation
Indices: 12379686--12379779 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 25
12379676 TATCATTCTT
12379686 TATATTATTTATTAATA--TATTAA
1 TATATTATTTATTAATATTTATTAA
*
12379709 TATATTATTTATTAATAACATATATTAA
1 TATATTATTTATTAAT---ATTTATTAA
12379737 TATATTA-TTA-TAATATTTATTAA
1 TATATTATTTATTAATATTTATTAA
12379760 TATATTA-TTATT--TATTTATT
1 TATATTATTTATTAATATTTATT
12379780 TATACAATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
22 8 0.12
23 34 0.53
24 1 0.02
26 5 0.08
27 3 0.05
28 13 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATTATTTATTAATATTTATTAA
Found at i:12384680 original size:2 final size:2
Alignment explanation
Indices: 12384669--12384701 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12384659 TACTAACAAT
12384669 TA TA -A 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
12384702 AACATGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12386323 original size:20 final size:20
Alignment explanation
Indices: 12386300--12386338 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12386290 TTATTATATT
12386300 AATAAAAATAATATTTTAAG
1 AATAAAAATAATATTTTAAG
* *
12386320 AATAATAATACTATTTTAA
1 AATAAAAATAATATTTTAA
12386339 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AATAAAAATAATATTTTAAG
Found at i:12386417 original size:18 final size:19
Alignment explanation
Indices: 12386383--12386421 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12386373 TTTTAAAATT
*
12386383 TTTTTATATTAATATAATA
1 TTTTAATATTAATATAATA
12386402 TTTTAATATTAA-ATAATA
1 TTTTAATATTAATATAATA
12386420 TT
1 TT
12386422 ATTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATATTAATATAATA
Found at i:12386458 original size:26 final size:26
Alignment explanation
Indices: 12386429--12386491 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
12386419 ATTATTAGAA
*
12386429 TTTAATTATTTGTGAAT-ATTAATAA-T
1 TTTAATTATTT-T-AATAATAAATAATT
12386455 TTTAATATATTTTAATAATAAATAATT
1 TTTAAT-TATTTTAATAATAAATAATT
12386482 TTTAA-TATTT
1 TTTAATTATTT
12386492 AACTAGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 8 0.24
26 14 0.42
27 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTAATTATTTTAATAATAAATAATT
Found at i:12405961 original size:33 final size:34
Alignment explanation
Indices: 12405906--12405979 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
12405896 TTAGTCGTAC
*
12405906 AATTAAACATCTAATAATGATTGGACATGTAGTA
1 AATTAAACATCTAATAATGATTGGACATGTAATA
12405940 AATTAAACATCT-ATAATGATTGGACATGTAATA
1 AATTAAACATCTAATAATGATTGGACATGTAATA
*
12405973 GATTAAA
1 AATTAAA
12405980 AAGAAAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (34 bp):
AATTAAACATCTAATAATGATTGGACATGTAATA
Found at i:12418518 original size:15 final size:15
Alignment explanation
Indices: 12418485--12418518 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12418475 ATTTTTATTT
*
12418485 TTATCATATTTAAAG
1 TTATCATATTTAAAC
*
12418500 TTATCATATTTAATC
1 TTATCATATTTAAAC
12418515 TTAT
1 TTAT
12418519 GATAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATCATATTTAAAC
Found at i:12420125 original size:25 final size:24
Alignment explanation
Indices: 12420069--12420125 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
12420059 TTCTCACATA
* *
12420069 GAAATTTTATAAAAATTTACCATTT
1 GAAAATTT-TAAAAATTTACCATTG
*
12420094 GAAAATTTTAAAAATTTCATCATTG
1 GAAAATTTTAAAAATTT-ACCATTG
*
12420119 GATAATT
1 GAAAATT
12420126 ATTATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (24 bp):
GAAAATTTTAAAAATTTACCATTG
Found at i:12420498 original size:15 final size:17
Alignment explanation
Indices: 12420480--12420519 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
12420470 TCTTCTTCTT
12420480 TTCTCTCTTTC-C-CCC
1 TTCTCTCTTTCTCTCCC
12420495 TTCTCT-TTTCTCTCCC
1 TTCTCTCTTTCTCTCCC
12420511 -TCTCTCTTT
1 TTCTCTCTTT
12420520 AAAAATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTCTCTTTCTCTCCC
Found at i:12425176 original size:33 final size:33
Alignment explanation
Indices: 12425137--12425227 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
12425127 TTATTACTTT
12425137 ATTATTTTTTCATTATTTGAATATAA-TT--TT-
1 ATTATTTTTT-ATTATTTGAATATAATTTAATTA
*
12425167 ATT-TTTATTTATTATTTTAATATAATTTAATTA
1 ATTATTT-TTTATTATTTGAATATAATTTAATTA
* *
12425200 ATTATTTTTTATTGTTTGGATATAATTT
1 ATTATTTTTTATTATTTGAATATAATTT
12425228 GATCACTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.33
30 8 0.16
32 2 0.04
33 21 0.41
34 3 0.06
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (33 bp):
ATTATTTTTTATTATTTGAATATAATTTAATTA
Found at i:12425188 original size:29 final size:30
Alignment explanation
Indices: 12425134--12425212 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
12425124 TGATTATTAC
12425134 TTTATTATTT-TTTCATTATTTGAATATAAT
1 TTTATTATTTATTT-ATTATTTGAATATAAT
*
12425164 TTTATT-TTTATTTATTATTTTAATATAAT
1 TTTATTATTTATTTATTATTTGAATATAAT
* * *
12425193 TTAATTAATTATTTTTTATT
1 TTTATTATTTATTTATTATT
12425213 GTTTGGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTATTATTTATTTATTATTTGAATATAAT
Found at i:12427007 original size:15 final size:17
Alignment explanation
Indices: 12426977--12427008 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12426967 AAGTACAAAA
12426977 GGCATAAGATTGAACAT
1 GGCATAAGATTGAACAT
12426994 GGCA-AAGA-TGAACAT
1 GGCATAAGATTGAACAT
12427009 AAATCAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (17 bp):
GGCATAAGATTGAACAT
Found at i:12428518 original size:23 final size:24
Alignment explanation
Indices: 12428492--12428575 Score: 102
Period size: 23 Copynumber: 3.5 Consensus size: 24
12428482 TATTAATATA
12428492 ATTATTAAAATATTAAAATT-TTT
1 ATTATTAAAATATTAAAATTATTT
*
12428515 ATTATTAAAATAATTGAAATTATTT
1 ATTATTAAAAT-ATTAAAATTATTT
*
12428540 ATTATTAAAAT-TTAAAATAATTAT
1 ATTATTAAAATATTAAAATTATT-T
12428564 ATT-TTAATAATA
1 ATTATTAA-AATA
12428576 ATATTTAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
23 24 0.45
24 15 0.28
25 14 0.26
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATTAAAATATTAAAATTATTT
Found at i:12428602 original size:19 final size:18
Alignment explanation
Indices: 12428567--12428611 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
12428557 TAATTATATT
12428567 TTAATAATAATATTTAATA
1 TTAA-AATAATATTTAATA
*
12428586 TTAAAATATTATATTAATA
1 TTAAAATAATAT-TTAATA
12428605 -TAAAATA
1 TTAAAATA
12428612 CTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATAATATTTAATA
Found at i:12428682 original size:20 final size:19
Alignment explanation
Indices: 12428657--12428694 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12428647 TTTAAAATGT
12428657 TTAAAATAGTATTATTATTC
1 TTAAAATAGTATT-TTATTC
*
12428677 TTAAAATATTATTTTATT
1 TTAAAATAGTATTTTATT
12428695 AATATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TTAAAATAGTATTTTATTC
Found at i:12428957 original size:44 final size:41
Alignment explanation
Indices: 12428908--12429013 Score: 117
Period size: 41 Copynumber: 2.5 Consensus size: 41
12428898 TCATATTAGG
12428908 AAAATAATATTATTATATTATTTAACATTAATTATTAAAATAAT
1 AAAATAATATTATTATATTATTT---ATTAATTATTAAAATAAT
* * *
12428952 AAAATATTATTATGTATAATA-TTATTTATTATTAAAATAAT
1 AAAATAATATTAT-TATATTATTTATTAATTATTAAAATAAT
* *
12428993 AATATAATACTATT-TATTATT
1 AAAATAATATTATTATATTATT
12429014 AAAATACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
39 4 0.08
40 2 0.04
41 27 0.51
44 14 0.26
45 6 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (41 bp):
AAAATAATATTATTATATTATTTATTAATTATTAAAATAAT
Found at i:12429039 original size:24 final size:24
Alignment explanation
Indices: 12428989--12429050 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
12428979 ATTATTAAAA
* *
12428989 TAATAATATAATACTATTTATTAT
1 TAATAATATAAAAATATTTATTAT
12429013 TAA-AATACTAAAAATATTTATGT-T
1 TAATAATA-TAAAAATATTTAT-TAT
12429037 TAATAATATAAAAA
1 TAATAATATAAAAA
12429051 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 24 0.73
25 5 0.15
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (24 bp):
TAATAATATAAAAATATTTATTAT
Found at i:12429320 original size:21 final size:20
Alignment explanation
Indices: 12429277--12429323 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
12429267 TTAAATAAAA
**
12429277 TTAAATAACAATATTTTTTG
1 TTAAATAACAATATTTTAAG
*
12429297 TTAATATAATAATATTTTAAG
1 TTAA-ATAACAATATTTTAAG
12429318 TTAAAT
1 TTAAAT
12429324 CAAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TTAAATAACAATATTTTAAG
Found at i:12439609 original size:12 final size:13
Alignment explanation
Indices: 12439589--12439633 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
12439579 ATATATAAAG
*
12439589 ATAAATTAAATA-
1 ATAATTTAAATAT
12439601 ATAATTTAAA-AT
1 ATAATTTAAATAT
12439613 ATAATTTAATATAT
1 ATAATTTAA-ATAT
12439627 ATAATTT
1 ATAATTT
12439634 CGATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 1 0.03
12 18 0.62
13 1 0.03
14 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTAAATAT
Found at i:12439997 original size:24 final size:24
Alignment explanation
Indices: 12439981--12440027 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12439971 AAATTAACAA
12439981 AAATTAAAAAAAACAAAACAAAAG
1 AAATTAAAAAAAACAAAACAAAAG
12440005 AAATTAAAAAAAA-AAAGACAAAA
1 AAATTAAAAAAAACAAA-ACAAAA
12440028 ATCAAGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.09
Consensus pattern (24 bp):
AAATTAAAAAAAACAAAACAAAAG
Found at i:12440317 original size:18 final size:19
Alignment explanation
Indices: 12440294--12440342 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
12440284 TTGACAAGAC
12440294 AAAAAAAATTTA-AAATAT
1 AAAAAAAATTTATAAATAT
*
12440312 AAAAAATATTTATTAAATAT
1 AAAAAAAATTTA-TAAATAT
12440332 ATAAAATAAAT
1 A-AAAA-AAAT
12440343 AAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
20 7 0.28
21 4 0.16
22 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAAAATTTATAAATAT
Found at i:12440329 original size:20 final size:18
Alignment explanation
Indices: 12440294--12440339 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
12440284 TTGACAAGAC
*
12440294 AAAAAAAATTTAAAATAT
1 AAAAAATATTTAAAATAT
12440312 AAAAAATATTTATTAAATAT
1 AAAAAATATTTA--AAATAT
*
12440332 ATAAAATA
1 AAAAAATA
12440340 AATAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
20 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATATTTAAAATAT
Found at i:12440556 original size:12 final size:11
Alignment explanation
Indices: 12440530--12440555 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12440520 AAAAAAGGAT
12440530 AAAAGTAAAAA
1 AAAAGTAAAAA
12440541 AAAAGTAAAAA
1 AAAAGTAAAAA
12440552 AAAA
1 AAAA
12440556 AAAGACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGTAAAAA
Found at i:12441521 original size:20 final size:19
Alignment explanation
Indices: 12441496--12441534 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12441486 GAATGGATGG
*
12441496 ATTATATTATAATTATGATA
1 ATTATATTA-AATTAAGATA
12441516 ATTATATTAAATTAAGATA
1 ATTATATTAAATTAAGATA
12441535 TTAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTATATTAAATTAAGATA
Done.