Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 4 of 31
Found at i:940354 original size:25 final size:25
Alignment explanation
Indices: 940299--940354 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
940289 TCTCATATAT
*
940299 TTTTAAAATTTTTTATTAATTTAAA
1 TTTTAAAATTTTTTATAAATTTAAA
*
940324 TATTAAAATATTTTTA-AAATATT-AA
1 TTTTAAAAT-TTTTTATAAAT-TTAAA
940349 TTTTAA
1 TTTTAA
940355 CGCCATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTAAAATTTTTTATAAATTTAAA
Found at i:941661 original size:34 final size:34
Alignment explanation
Indices: 941618--941686 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
941608 AAATTGAACA
*
941618 TCCAATTTGTCTTAATAGAGTGCTCAATGCCAGT
1 TCCAATTTGTCTTAATAGAGTGCTCAATACCAGT
*
941652 TCCAATTTGTCTTAATAGAGTGCTCGATACCAGT
1 TCCAATTTGTCTTAATAGAGTGCTCAATACCAGT
941686 T
1 T
941687 AGCTTGTGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (34 bp):
TCCAATTTGTCTTAATAGAGTGCTCAATACCAGT
Found at i:943335 original size:52 final size:52
Alignment explanation
Indices: 943255--943359 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
943245 ACACTTGACT
943255 TTTATATCTTATATAATCAAAGCCTGAGATAACAGAGTCATAGTTGAATGGC
1 TTTATATCTTATATAATCAAAGCCTGAGATAACAGAGTCATAGTTGAATGGC
*
943307 TTTATATCTTATATAATCAAAGCTTGAGATAACAGAGTCATAGTTGAATGGC
1 TTTATATCTTATATAATCAAAGCCTGAGATAACAGAGTCATAGTTGAATGGC
943359 T
1 T
943360 CTGTAAGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (52 bp):
TTTATATCTTATATAATCAAAGCCTGAGATAACAGAGTCATAGTTGAATGGC
Found at i:953071 original size:2 final size:2
Alignment explanation
Indices: 953064--953096 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
953054 ATCTATCAAC
953064 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 A
953097 GATAGAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:953446 original size:21 final size:20
Alignment explanation
Indices: 953400--953447 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
953390 TAAATTTGAA
*
953400 TTATTTTAAATTCAGATTAT
1 TTATTTTAAATTCAAATTAT
*
953420 TAATTTTGAAA-TCAAATTAAT
1 TTATTTT-AAATTCAAATT-AT
953441 TTATTTT
1 TTATTTT
953448 TTACTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (20 bp):
TTATTTTAAATTCAAATTAT
Found at i:954194 original size:22 final size:24
Alignment explanation
Indices: 954162--954211 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
954152 ATATTATATT
* *
954162 ATATTTTTATTTA-AT-TTTTAAA
1 ATATTTATATTTATATATATTAAA
954184 ATATTTATATTTATATATATTAAA
1 ATATTTATATTTATATATATTAAA
954208 ATAT
1 ATAT
954212 AAATGTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.50
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTATATTTATATATATTAAA
Found at i:956203 original size:2 final size:2
Alignment explanation
Indices: 956190--956219 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
956180 GCATGCATGC
*
956190 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
956220 CTACACCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:956742 original size:2 final size:2
Alignment explanation
Indices: 956735--956772 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
956725 TATTCAAGAA
*
956735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
956773 TTGTCCCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:967667 original size:2 final size:2
Alignment explanation
Indices: 967660--967701 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
967650 CGGGTGATTG
967660 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
967702 GAGAGAGAGA
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:967745 original size:2 final size:2
Alignment explanation
Indices: 967740--967776 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
967730 ATATATATAT
967740 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
967777 TAAAAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:969137 original size:20 final size:19
Alignment explanation
Indices: 969114--969170 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
969104 TTAAAAAATA
969114 TAAATATTAATATAAATTTT
1 TAAATATTAAT-TAAATTTT
* *
969134 TAAATAGTAATTAAAGCTTT
1 TAAATATTAATTAAA-TTTT
*
969154 TAAAT-TAAATTAAATTT
1 TAAATATTAATTAAATTT
969171 GATTCAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 18 0.58
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TAAATATTAATTAAATTTT
Found at i:972421 original size:21 final size:22
Alignment explanation
Indices: 972386--972430 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
972376 TAATCAAAAT
972386 TTTTATTACTTTTTAATATATA
1 TTTTATTACTTTTTAATATATA
*
972408 TTTTATTA-TTTTTAATTTATA
1 TTTTATTACTTTTTAATATATA
972429 TT
1 TT
972431 GAAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTACTTTTTAATATATA
Found at i:972437 original size:22 final size:21
Alignment explanation
Indices: 972390--972438 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
972380 CAAAATTTTT
**
972390 ATTACTTTTTAATATATATTTT
1 ATTA-TTTTTAATATATATTAA
*
972412 ATTATTTTTAATTTATATTGAA
1 ATTATTTTTAATATATATT-AA
972434 ATTAT
1 ATTAT
972439 CAATTTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTATTTTTAATATATATTAA
Found at i:972494 original size:25 final size:26
Alignment explanation
Indices: 972440--972494 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
972430 TGAAATTATC
* *
972440 AATTTGAGTTTGAGTTCAATATAAAT
1 AATTTGAGTTTGAATTCAATATAAAG
*
972466 AATTTG-GTTTGAAATTGAATA-AAAG
1 AATTTGAGTTTG-AATTCAATATAAAG
972491 AATT
1 AATT
972495 GAACTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (26 bp):
AATTTGAGTTTGAATTCAATATAAAG
Found at i:972773 original size:19 final size:21
Alignment explanation
Indices: 972725--972774 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
972715 TATTTTTATT
*
972725 ATATTTTAAAATAAAAATATA
1 ATATTTTAAAACAAAAATATA
* *
972746 ATTTTTTAAAACAATAA-A-A
1 ATATTTTAAAACAAAAATATA
972765 ATATTTTAAA
1 ATATTTTAAA
972775 CTTTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 1 0.04
21 14 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATTTTAAAACAAAAATATA
Found at i:977520 original size:2 final size:2
Alignment explanation
Indices: 977513--977542 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
977503 TGTAAATCAA
*
977513 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
977543 GCAAGCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:990459 original size:13 final size:13
Alignment explanation
Indices: 990441--990467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
990431 AATGTTAGTT
990441 TTATAAACTTATG
1 TTATAAACTTATG
990454 TTATAAACTTATG
1 TTATAAACTTATG
990467 T
1 T
990468 CCAAATACAT
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:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTATAAACTTATG
Found at i:992929 original size:17 final size:16
Alignment explanation
Indices: 992890--992930 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
992880 TTATGGGTAT
992890 AAAATATAAATATAAA
1 AAAATATAAATATAAA
*
992906 AATAATATAAATACTATA
1 AA-AATATAAATA-TAAA
992924 AAAATAT
1 AAAATAT
992931 TTATGTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAATATAAA
Found at i:996267 original size:2 final size:2
Alignment explanation
Indices: 996260--996291 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
996250 GCAAATGCGA
996260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
996292 GTGAAGAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:998453 original size:20 final size:21
Alignment explanation
Indices: 998428--998468 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
998418 TTTGAAAAAG
* *
998428 AAAATATTTAA-ATAAATATA
1 AAAATAATTAATAAAAATATA
998448 AAAATAATTAATAAAAATATA
1 AAAATAATTAATAAAAATATA
998469 TTACGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATAATTAATAAAAATATA
Found at i:1004845 original size:21 final size:24
Alignment explanation
Indices: 1004809--1004870 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 24
1004799 AATTATTATT
* *
1004809 TATTAATAAAAAATATTATTTAAA
1 TATTAATATAAAATATTATATAAA
1004833 T-TTAAT-T-AAATA-TATATAAA
1 TATTAATATAAAATATTATATAAA
1004853 TATTAATATAAAATATTA
1 TATTAATATAAAATATTA
1004871 AAAATTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 8 0.25
21 10 0.31
22 1 0.03
23 10 0.31
24 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTAATATAAAATATTATATAAA
Found at i:1005452 original size:14 final size:14
Alignment explanation
Indices: 1005433--1005461 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1005423 ACATCAGCAG
1005433 ATAATAAAAGATGA
1 ATAATAAAAGATGA
1005447 ATAATAAAAGATGA
1 ATAATAAAAGATGA
1005461 A
1 A
1005462 CTGATTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
ATAATAAAAGATGA
Found at i:1005529 original size:19 final size:18
Alignment explanation
Indices: 1005504--1005562 Score: 82
Period size: 19 Copynumber: 3.2 Consensus size: 18
1005494 TTAAATTATA
1005504 TATAATTAAATAAAATAT
1 TATAATTAAATAAAATAT
*
1005522 TATCAATTACATATAAATAT
1 TAT-AATTAAATA-AAATAT
*
1005542 TATAATTATATAAAATAT
1 TATAATTAAATAAAATAT
1005560 TAT
1 TAT
1005563 TTTTACACGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.32
19 16 0.43
20 9 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATTAAATAAAATAT
Found at i:1005619 original size:11 final size:11
Alignment explanation
Indices: 1005603--1005661 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1005593 ATTTTTCACT
1005603 AAAATTATATA
1 AAAATTATATA
*
1005614 AAAATTGTATA
1 AAAATTATATA
*
1005625 AAATTTAATTATA
1 AAAATT-A-TATA
1005638 AAAA-TATATA
1 AAAATTATATA
*
1005648 AATATTAATATA
1 AAAATT-ATATA
1005660 AA
1 AA
1005662 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 7 0.18
11 17 0.44
12 8 0.21
13 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AAAATTATATA
Found at i:1005647 original size:23 final size:23
Alignment explanation
Indices: 1005602--1005661 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1005592 AATTTTTCAC
*
1005602 TAAA-ATT-ATATAAAAATTGTA
1 TAAATATTAATATAAAAATTATA
1005623 TAAA-ATTTAATTATAAAAA-TATA
1 TAAATA-TTAA-TATAAAAATTATA
1005646 TAAATATTAATATAAA
1 TAAATATTAATATAAA
1005662 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 5 0.15
22 8 0.24
23 12 0.35
24 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAATATTAATATAAAAATTATA
Found at i:1005663 original size:34 final size:34
Alignment explanation
Indices: 1005602--1005678 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
1005592 AATTTTTCAC
* *
1005602 TAAAATTATATAAAAATTGTATAAAATTTAATTA
1 TAAAAATATATAAAAATTATATAAAATTTAATTA
* * *
1005636 TAAAAATATATAAATATTA-ATATAAATTTATTTT
1 TAAAAATATATAAAAATTATATA-AAATTTAATTA
1005670 TAAAAATAT
1 TAAAAATAT
1005679 TTTAACAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
TAAAAATATATAAAAATTATATAAAATTTAATTA
Found at i:1005773 original size:19 final size:19
Alignment explanation
Indices: 1005745--1005790 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1005735 AATTATAACG
1005745 TAATAAAAATACATAAATA
1 TAATAAAAATACATAAATA
* *
1005764 TAATATAAATATATAAAT-
1 TAATAAAAATACATAAATA
1005782 TAA-AAAAAT
1 TAATAAAAAT
1005791 TTCTCTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.21
18 3 0.12
19 16 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAAAAATACATAAATA
Found at i:1006329 original size:21 final size:20
Alignment explanation
Indices: 1006283--1006331 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1006273 TTAAGGTAAA
1006283 TATTTATTAAATTTAAAATT
1 TATTTATTAAATTTAAAATT
*
1006303 TAATTTATTTAATTTATATAA-T
1 T-ATTTATTAAATTTA-A-AATT
1006325 TATTTAT
1 TATTTAT
1006332 AAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 3 0.12
23 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTATTAAATTTAAAATT
Found at i:1006679 original size:50 final size:50
Alignment explanation
Indices: 1006604--1006801 Score: 265
Period size: 50 Copynumber: 4.0 Consensus size: 50
1006594 GATTTGGTGG
*
1006604 TCTTCACCAACCTTTGACGATCGAGAGAAGTGGTCGTAATTATTGACTAT
1 TCTTCACCAACCTTTGACAATCGAGAGAAGTGGTCGTAATTATTGACTAT
* *
1006654 TCTTCACCAACCTTTGACAATCGAGAG-AGATGGTCTTAATTATTAACTAT
1 TCTTCACCAACCTTTGACAATCGAGAGAAG-TGGTCGTAATTATTGACTAT
* * *
1006704 TCTTCACCAACCTTTAACAATCGAGA-AAGGTGGTCATAATTGTTGACTAT
1 TCTTCACCAACCTTTGACAATCGAGAGAA-GTGGTCGTAATTATTGACTAT
* * * * *
1006754 TCTTCATCAACCTTTGACAATAGAGAGAGGTGGGCGTAATTGTTGACT
1 TCTTCACCAACCTTTGACAATCGAGAGAAGTGGTCGTAATTATTGACT
1006802 CTAAGCAACT
Statistics
Matches: 131, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
49 2 0.02
50 127 0.97
51 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (50 bp):
TCTTCACCAACCTTTGACAATCGAGAGAAGTGGTCGTAATTATTGACTAT
Found at i:1011321 original size:50 final size:50
Alignment explanation
Indices: 1011253--1011450 Score: 263
Period size: 50 Copynumber: 4.0 Consensus size: 50
1011243 GATTTAGTGG
* * ** *
1011253 TCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTGTTGATTAT
1 TCTTCACTAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACTAT
* * *
1011303 TCTTCACTAACTTTTGACAATCGAGAGAAGTGGTCGTAATTATTGACTAT
1 TCTTCACTAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACTAT
* *
1011353 TCTTCACAAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTAACTAT
1 TCTTCACTAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACTAT
* * *
1011403 TCTTTA-TCAACCTTTGACAATAGAGAGAGGTGGGCGTAATTGTTGACT
1 TCTTCACT-AACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACT
1011451 CTAAGCAACT
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 131 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (50 bp):
TCTTCACTAACCTTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACTAT
Found at i:1017021 original size:24 final size:24
Alignment explanation
Indices: 1016989--1017039 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1016979 AAACAAAAAC
1016989 AAAAACAAAAATAATAATATCATT
1 AAAAACAAAAATAATAATATCATT
1017013 AAAAACAAAAATAATAATATCATT
1 AAAAACAAAAATAATAATATCATT
1017037 AAA
1 AAA
1017040 TTTTTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAAACAAAAATAATAATATCATT
Found at i:1017247 original size:2 final size:2
Alignment explanation
Indices: 1017240--1017265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1017230 TGAGAAAGGA
1017240 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1017266 TGAAGGGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1017531 original size:20 final size:20
Alignment explanation
Indices: 1017416--1017558 Score: 61
Period size: 19 Copynumber: 7.4 Consensus size: 20
1017406 TAAATAAAAA
*
1017416 TAATATTATTTTAATATATT
1 TAATATTATTTTATTATATT
* * * *
1017436 TTATCATAAATATATTATATT
1 TAAT-ATTATTTTATTATATT
* *
1017457 T-ATATAATTTT-TAATATAT
1 TAATATTATTTTATTATAT-T
*
1017476 TAATA--ATTTTAATAT-TT
1 TAATATTATTTTATTATATT
*
1017493 TAATATTATATT-TTATATT
1 TAATATTATTTTATTATATT
*
1017512 T--TATTATATTTAATATTATT
1 TAATATTAT-TTTATTA-TATT
* * *
1017532 AAATTTTATTTT-TTATTTT
1 TAATATTATTTTATTATATT
*
1017551 TTATATTA
1 TAATATTA
1017559 ATATTTTAAA
Statistics
Matches: 90, Mismatches: 21, Indels: 25
0.66 0.15 0.18
Matches are distributed among these distances:
17 12 0.13
18 16 0.18
19 27 0.30
20 14 0.16
21 16 0.18
22 5 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATATTATTTTATTATATT
Found at i:1017542 original size:37 final size:35
Alignment explanation
Indices: 1017483--1017568 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 35
1017473 TATTAATAAT
1017483 TTTAATATTTTAATATTATATTTTATATTTTATTATA
1 TTTAATATTTTAA-ATTATATTTTATATTTT-TTATA
* *
1017520 TTTAATATTATTAAATTTTATTTTTTATTTTTTATA
1 TTTAATATT-TTAAATTATATTTTATATTTTTTATA
1017556 -TTAATATTTTAAA
1 TTTAATATTTTAAA
1017569 ATTAAAATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 5 0.11
35 8 0.17
36 5 0.11
37 24 0.52
38 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (35 bp):
TTTAATATTTTAAATTATATTTTATATTTTTTATA
Found at i:1017547 original size:29 final size:28
Alignment explanation
Indices: 1017482--1017558 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
1017472 ATATTAATAA
* *
1017482 TTTTAATATTTTAATATTATATTTTATAT
1 TTTTTATA-TTTAATATTATAATTTATAT
1017511 TTTATTATATTTAATATTATTAAATTT-TAT
1 TTT-TTATATTTAATATTA-T-AATTTATAT
* *
1017541 TTTTTATTTTTTATATTA
1 TTTTTATATTTAATATTA
1017559 ATATTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 26 0.63
30 11 0.27
31 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTTATATTTAATATTATAATTTATAT
Found at i:1017565 original size:20 final size:20
Alignment explanation
Indices: 1017446--1017566 Score: 77
Period size: 17 Copynumber: 5.7 Consensus size: 20
1017436 TTATCATAAA
1017446 TATATTATATTTATATAATTTTT
1 TATATTATATTT-TAT-A-TTTT
1017469 AATATATTAATAATTTTAATATTTT
1 --TATATT-AT-ATTTT-ATATTTT
*
1017494 AATATTATATTTTATA--TT
1 TATATTATATTTTATATTTT
* *
1017512 T-TATTATATTTAATATTAT
1 TATATTATATTTTATATTTT
* * *
1017531 TAAATTTTATTTTTTATTTTT
1 TATATTATATTTTATA-TTTT
1017552 TATATTAATATTTTA
1 TATATT-ATATTTTA
1017567 AAATTAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
17 13 0.17
18 2 0.03
19 2 0.03
20 13 0.17
21 13 0.17
22 8 0.11
23 5 0.07
25 10 0.13
26 4 0.05
27 6 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTATATTTTATATTTT
Found at i:1017977 original size:24 final size:23
Alignment explanation
Indices: 1017925--1017983 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1017915 TAAAATGAGT
*
1017925 TAAAT-ATATATAATTATATATTA
1 TAAATAATAT-TAATTAAATATTA
1017948 -ATAATAATATTAATATAAATATTA
1 TA-AATAATATTAAT-TAAATATTA
*
1017972 TAAATAAAATTA
1 TAAATAATATTA
1017984 TAGACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 7 0.23
24 21 0.70
25 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATAATATTAATTAAATATTA
Found at i:1022335 original size:3 final size:3
Alignment explanation
Indices: 1022327--1022361 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1022317 ATCAAAAGCA
1022327 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1022362 AAGCTTAAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1023300 original size:14 final size:14
Alignment explanation
Indices: 1023281--1023308 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1023271 AAGCCCTATA
1023281 AATTTAATTCAAGT
1 AATTTAATTCAAGT
1023295 AATTTAATTCAAGT
1 AATTTAATTCAAGT
1023309 TGGCTTCTTT
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTTAATTCAAGT
Found at i:1024475 original size:30 final size:29
Alignment explanation
Indices: 1024374--1024481 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 29
1024364 ATTTTTATTA
*
1024374 TATTTAATTAAATTTTAAAAATATTATTTT
1 TATTTAATTAAATCTT-AAAATATTATTTT
* * * *
1024404 TATCTGATTAAGTCATTTAAATATTATTTT
1 TATTTAATTAAATC-TTAAAATATTATTTT
1024434 TATTTAATTAAACTCTTAAAATATTATTTT
1 TATTTAATTAAA-TCTTAAAATATTATTTT
*
1024464 TATTTGATTAAATTCTTA
1 TATTTAATTAAA-TCTTA
1024482 TTTTATTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 61 0.94
31 4 0.06
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (29 bp):
TATTTAATTAAATCTTAAAATATTATTTT
Found at i:1027064 original size:15 final size:15
Alignment explanation
Indices: 1027044--1027072 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1027034 TAAATTAAAA
1027044 AATTTATTTTTTATT
1 AATTTATTTTTTATT
1027059 AATTTATTTTTTAT
1 AATTTATTTTTTAT
1027073 AAATATACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
AATTTATTTTTTATT
Found at i:1027313 original size:3 final size:3
Alignment explanation
Indices: 1027305--1027344 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1027295 GTATTTTATG
1027305 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1027345 CTGACCAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1028214 original size:24 final size:25
Alignment explanation
Indices: 1028165--1028214 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1028155 TTTAAATTTT
* *
1028165 TATTTAAAAATTTATATTTAACTTA
1 TATTTAAAAATTTAAATATAACTTA
*
1028190 TATTTAAAATTTTAAATATAA-TTA
1 TATTTAAAAATTTAAATATAACTTA
1028214 T
1 T
1028215 GAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTAAAAATTTAAATATAACTTA
Found at i:1029327 original size:139 final size:137
Alignment explanation
Indices: 1029077--1029346 Score: 495
Period size: 139 Copynumber: 2.0 Consensus size: 137
1029067 TTCAGAGCTG
1029077 AACTGCTGATCAAATCATCATGCCAAAGGGGACCAAGAATAGTTAAAGCACTGGCACTTGGGTGA
1 AACTGCTGATCAAATCATCATGCCAAAGGGGACCAAGAATAGTTAAAGCACTGGCACTTGGGTGA
*
1029142 GCCTCCAGAGGTTGAAAACGGTTGCAGAGTACGTACAGTATGGTGGCCACAAAATGACCCAAAAA
66 GCCTCCAGAGGTTGAAAACGGTTGCAGAGTACGTACAGCATGGTGGCCACAAAATGA--CAAAAA
1029207 AAAAAAATC
129 AAAAAAATC
*
1029216 AACTGCTGATCAAATCATCATGCCAAAGGGGACCAAGAATAGTTGAAGCACTGGCACTTGGGTGA
1 AACTGCTGATCAAATCATCATGCCAAAGGGGACCAAGAATAGTTAAAGCACTGGCACTTGGGTGA
*
1029281 GCCTCCAGAGGTTGAAGACGGTTGCAGAGTACGTACAGCATGGTGGCCACAAAATGACAAAAAAA
66 GCCTCCAGAGGTTGAAAACGGTTGCAGAGTACGTACAGCATGGTGGCCACAAAATGACAAAAAAA
1029346 A
131 A
1029347 TGATTGTGTA
Statistics
Matches: 128, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
137 9 0.07
139 119 0.93
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (137 bp):
AACTGCTGATCAAATCATCATGCCAAAGGGGACCAAGAATAGTTAAAGCACTGGCACTTGGGTGA
GCCTCCAGAGGTTGAAAACGGTTGCAGAGTACGTACAGCATGGTGGCCACAAAATGACAAAAAAA
AAAAATC
Found at i:1029861 original size:4 final size:4
Alignment explanation
Indices: 1029852--1029878 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1029842 CTTGAAGCTT
1029852 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1029879 TAATCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1030638 original size:14 final size:14
Alignment explanation
Indices: 1030621--1030654 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1030611 TTTAAAAAAT
1030621 AATTTTAAAATTTA
1 AATTTTAAAATTTA
*
1030635 AATTTTAATATTTA
1 AATTTTAAAATTTA
1030649 AATTTT
1 AATTTT
1030655 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTTAAAATTTA
Found at i:1030968 original size:24 final size:24
Alignment explanation
Indices: 1030933--1030978 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1030923 AATAAAATAT
1030933 TACATATTATATGATATATTTAAA
1 TACATATTATATGATATATTTAAA
* *
1030957 TACA-ATTAATATTATATTTTTA
1 TACATATT-ATATGATATATTTA
1030979 CTGTATACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TACATATTATATGATATATTTAAA
Found at i:1033577 original size:2 final size:2
Alignment explanation
Indices: 1033534--1033566 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1033524 GCCCAAAAGC
1033534 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 A
1033567 ACGACTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1036898 original size:20 final size:23
Alignment explanation
Indices: 1036873--1036924 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1036863 AACACAACAT
*
1036873 TAAAAATTAAT-T-AAA-AAATA
1 TAAAAATAAATATGAAATAAATA
1036893 TAAAAAATAAATATGAAATAAATA
1 T-AAAAATAAATATGAAATAAATA
1036917 TAAAAATA
1 TAAAAATA
1036925 TAAACAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 9 0.33
22 1 0.04
23 10 0.37
24 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAATAAATATGAAATAAATA
Found at i:1036944 original size:32 final size:33
Alignment explanation
Indices: 1036886--1036953 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
1036876 AAATTAATTA
1036886 AAAAATATAAAAAATAAATATGAAATA-AATAT
1 AAAAATATAAAAAATAAATATGAAATATAATAT
** *
1036918 AAAAATATAAACAAATATTTAT-AAATATTATAT
1 AAAAATATAAA-AAATAAATATGAAATATAATAT
1036951 AAA
1 AAA
1036954 TTTATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAAATATAAAAAATAAATATGAAATATAATAT
Found at i:1038571 original size:13 final size:13
Alignment explanation
Indices: 1038553--1038577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1038543 TATTTTAAAT
1038553 AATAAAAAATATA
1 AATAAAAAATATA
1038566 AATAAAAAATAT
1 AATAAAAAATAT
1038578 GAATTCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAAAAATATA
Found at i:1038680 original size:26 final size:24
Alignment explanation
Indices: 1038637--1038704 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
1038627 TATACATAAA
1038637 ATAAAATAAATTATTAATATGTAAAAAAT
1 ATAAAA-AAA-TA-TAATAT-T-AAAAAT
**
1038666 ATAAAAAAATATAATATTTTAAAT
1 ATAAAAAAATATAATATTAAAAAT
1038690 ATAAAAAAATA-AATA
1 ATAAAAAAATATAATA
1038705 CAAACATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 4 0.11
24 15 0.41
25 1 0.03
26 6 0.16
27 2 0.05
28 3 0.08
29 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
ATAAAAAAATATAATATTAAAAAT
Found at i:1039575 original size:51 final size:51
Alignment explanation
Indices: 1039508--1039607 Score: 200
Period size: 51 Copynumber: 2.0 Consensus size: 51
1039498 AATTGGGTAA
1039508 ATATTCATGAATTGAAATAAAACACGAACAAGATATAAATATAAATTTTCT
1 ATATTCATGAATTGAAATAAAACACGAACAAGATATAAATATAAATTTTCT
1039559 ATATTCATGAATTGAAATAAAACACGAACAAGATATAAATATAAATTTT
1 ATATTCATGAATTGAAATAAAACACGAACAAGATATAAATATAAATTTT
1039608 TTCAAAATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (51 bp):
ATATTCATGAATTGAAATAAAACACGAACAAGATATAAATATAAATTTTCT
Found at i:1040017 original size:31 final size:32
Alignment explanation
Indices: 1039951--1040045 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 32
1039941 TTTTTTCTCC
* * *
1039951 TATATATAAAATAAATTA-TACATA-ACAATATA
1 TATACATAAAATAAATTATTA-ATATATAA-AAA
1039983 TATA-ATAAAATAAATTATTAATATATAAAAA
1 TATACATAAAATAAATTATTAATATATAAAAA
*
1040014 TATACA-AAAATATAATATTTTAA-ATATAAAAA
1 TATACATAAAATA-AAT-TATTAATATATAAAAA
1040046 ATTATAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
31 28 0.51
32 22 0.40
33 5 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (32 bp):
TATACATAAAATAAATTATTAATATATAAAAA
Found at i:1040055 original size:16 final size:16
Alignment explanation
Indices: 1039981--1040059 Score: 61
Period size: 16 Copynumber: 4.8 Consensus size: 16
1039971 CATAACAATA
1039981 TATATAATA-AAATAAAT
1 TATA-AATATAAA-AAAT
*
1039998 TATTAATATATAAAAAT
1 TATAAATATA-AAAAAT
* * * *
1040015 ATACAAAAATATAATAT
1 -TATAAATATAAAAAAT
*
1040032 TTTAAATATAAAAAAT
1 TATAAATATAAAAAAT
1040048 TATAAATATAAA
1 TATAAATATAAA
1040060 CACATAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
16 26 0.55
17 12 0.26
18 9 0.19
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAATATAAAAAAT
Found at i:1040087 original size:13 final size:13
Alignment explanation
Indices: 1040069--1040116 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
1040059 ACACATAAAA
1040069 TTTTTTTCTTTCC
1 TTTTTTTCTTTCC
*
1040082 TTTTTTT-TTTTC
1 TTTTTTTCTTTCC
*
1040094 TTTTCTTTCTTTCT
1 TTTT-TTTCTTTCC
1040108 TTCTTTTTC
1 TT-TTTTTC
1040117 AGCAAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.28
13 10 0.34
14 9 0.31
15 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:1040091 original size:17 final size:17
Alignment explanation
Indices: 1040069--1040113 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1040059 ACACATAAAA
*
1040069 TTTTTTTCTTTCCTTTT
1 TTTTTTTCTTTCCTTTC
*
1040086 TTTTTTTCTTTTCTTTC
1 TTTTTTTCTTTCCTTTC
*
1040103 TTTCTTTCTTT
1 TTTTTTTCTTT
1040114 TTCAGCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCCTTTC
Found at i:1043705 original size:5 final size:5
Alignment explanation
Indices: 1043695--1043719 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1043685 TTTAATTATC
1043695 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
1043720 ATTTTTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:1044078 original size:15 final size:16
Alignment explanation
Indices: 1044057--1044100 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1044047 TATGATTATT
1044057 TATTTATTTTTTAAAA
1 TATTTATTTTTTAAAA
*
1044073 -ATTTATATATTTAAAA
1 TATTTAT-TTTTTAAAA
1044089 TATTATATTTTT
1 TATT-TATTTTT
1044101 ATTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 6 0.26
18 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATTTTTTAAAA
Found at i:1044097 original size:14 final size:13
Alignment explanation
Indices: 1044078--1044128 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1044068 TAAAAATTTA
1044078 TATATTTAAAATAT
1 TATATTT-AAATAT
* *
1044092 TATATTTTTATTAT
1 TATA-TTTAAATAT
1044106 TATATTTAAATA-
1 TATATTTAAATAT
1044118 TATA-TTAAATA
1 TATATTTAAATA
1044129 AAAATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 7 0.22
12 4 0.12
13 6 0.19
14 12 0.38
15 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATATTTAAATAT
Found at i:1044939 original size:20 final size:20
Alignment explanation
Indices: 1044882--1044939 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1044872 GAAGTAAATT
* *
1044882 ATAAAATATATAAATGATAA
1 ATAAAATATTTAAATTATAA
*
1044902 ATAAAATATTTAATTTATAA
1 ATAAAATATTTAAATTATAA
1044922 A-AAAATATTTATAATTAT
1 ATAAAATATTTA-AATTAT
1044940 TATTCAGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAATATTTAAATTATAA
Found at i:1045655 original size:32 final size:32
Alignment explanation
Indices: 1045619--1045684 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1045609 ATACTTAATT
*
1045619 ATTTACTATATATCCATTA-TTAATAGT-TTATA
1 ATTTA-TATA-ATACATTATTTAATAGTATTATA
*
1045651 ATTTATATAATACTTTATTTAATAGTATTATA
1 ATTTATATAATACATTATTTAATAGTATTATA
1045683 AT
1 AT
1045685 ATATCTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.20
31 12 0.40
32 12 0.40
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTTATATAATACATTATTTAATAGTATTATA
Found at i:1045719 original size:20 final size:20
Alignment explanation
Indices: 1045680--1045719 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1045670 TAATAGTATT
* * *
1045680 ATAATATATCTTATATTATA
1 ATAATATATATTAAACTATA
1045700 ATAATATATATTAAACTATA
1 ATAATATATATTAAACTATA
1045720 CATACAAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATATATATTAAACTATA
Found at i:1047072 original size:18 final size:17
Alignment explanation
Indices: 1047045--1047083 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1047035 ATCTATATTA
1047045 ATATAATTATATATAGT
1 ATATAATTATATATAGT
* *
1047062 ATATAATTTATGTATATT
1 ATATAA-TTATATATAGT
1047080 ATAT
1 ATAT
1047084 CAGGTACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATATAATTATATATAGT
Found at i:1048679 original size:18 final size:20
Alignment explanation
Indices: 1048654--1048697 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1048644 TCAAAAAGGT
* *
1048654 TTTTTTTTTTTTTCTTTCTA
1 TTTTTTATTTCTTCTTTCTA
1048674 TTTTTTAGTTTCTTCTTTCTA
1 TTTTTTA-TTTCTTCTTTCTA
1048695 TTT
1 TTT
1048698 ATGCTAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTATTTCTTCTTTCTA
Found at i:1051955 original size:19 final size:19
Alignment explanation
Indices: 1051931--1051969 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1051921 AATACATAAA
*
1051931 TAAATTTATAAATGTGATC
1 TAAATTTATAAATGCGATC
1051950 TAAATTTATAAATGCGATC
1 TAAATTTATAAATGCGATC
1051969 T
1 T
1051970 GTCTTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (19 bp):
TAAATTTATAAATGCGATC
Found at i:1061546 original size:2 final size:2
Alignment explanation
Indices: 1061539--1061579 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1061529 GGCTTTTCTT
* *
1061539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1061580 TTGGGGGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1061815 original size:22 final size:22
Alignment explanation
Indices: 1061790--1061831 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1061780 TACAATTACG
* *
1061790 TACATGCATATACATATATAAA
1 TACATGCAAATAAATATATAAA
*
1061812 TACATGTAAATAAATATATA
1 TACATGCAAATAAATATATA
1061832 CATGTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (22 bp):
TACATGCAAATAAATATATAAA
Found at i:1063848 original size:16 final size:16
Alignment explanation
Indices: 1063801--1063849 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1063791 AAATTAATAT
* *
1063801 TTAAATTTTAAATTTA
1 TTAAATTATAAATTAA
*
1063817 TTAATTGTATAAATTAA
1 TTAAAT-TATAAATTAA
*
1063834 TTAAATTATATATTAA
1 TTAAATTATAAATTAA
1063850 ATTTCAAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAATTATAAATTAA
Found at i:1063959 original size:2 final size:2
Alignment explanation
Indices: 1063952--1063981 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1063942 TCCATGCTTA
1063952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1063982 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1065060 original size:2 final size:2
Alignment explanation
Indices: 1065022--1065046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1065012 AAAAGTAAGG
1065022 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
1065047 CGTTCGTATA
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:1066150 original size:17 final size:17
Alignment explanation
Indices: 1066128--1066161 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1066118 GAATTAAAAT
1066128 TTATATAATATAAATTA
1 TTATATAATATAAATTA
*
1066145 TTATATAATATATATTA
1 TTATATAATATAAATTA
1066162 CAATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATATAATATAAATTA
Found at i:1066202 original size:19 final size:19
Alignment explanation
Indices: 1066178--1066223 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1066168 TTATTTTTAT
*
1066178 AATATATTAAAAATATATA
1 AATATAATAAAAATATATA
**
1066197 AATATAATACGAATATATA
1 AATATAATAAAAATATATA
1066216 AATTATAA
1 AA-TATAA
1066224 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATAATAAAAATATATA
Found at i:1066818 original size:15 final size:17
Alignment explanation
Indices: 1066788--1066819 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1066778 CCCTCCCCCC
1066788 CCAAAAGACTATAATAA
1 CCAAAAGACTATAATAA
1066805 CCAAAA-AC-ATAATAA
1 CCAAAAGACTATAATAA
1066820 TAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.62, C:0.19, G:0.03, T:0.16
Consensus pattern (17 bp):
CCAAAAGACTATAATAA
Found at i:1067220 original size:2 final size:2
Alignment explanation
Indices: 1067207--1067250 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
1067197 TAACAAAGGG
* * *
1067207 AT AT AT AC AT AT AT AT AT AT AT TT AT AT AT AT TT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1067250 A
1 A
1067251 AGTTACTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1077582 original size:2 final size:2
Alignment explanation
Indices: 1077575--1077604 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1077565 GATGCTGGTA
1077575 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1077605 GCCCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1078634 original size:29 final size:29
Alignment explanation
Indices: 1078602--1078686 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
1078592 TGGGAAAGTT
* * *
1078602 TTTAAAT-TTTTTCATTTTATTTAAGTAAA
1 TTTAAATATTTTT-ATTGTAATTAAATAAA
*
1078631 TTTATATATTTTTATTGTAATTAAATAAA
1 TTTAAATATTTTTATTGTAATTAAATAAA
*
1078660 -TT-ATTATTTTTAATTTGT-ATTAAATAA
1 TTTAAATATTTTT-A-TTGTAATTAAATAA
1078687 GTTTTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.15
28 12 0.26
29 23 0.49
30 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTAAATATTTTTATTGTAATTAAATAAA
Found at i:1078681 original size:28 final size:27
Alignment explanation
Indices: 1078609--1078696 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
1078599 GTTTTTAAAT
*
1078609 TTTTTCATTT-TATTTAAGTAAATTTATATA
1 TTTTT-ATTTGTA-TTAAATAAA-TTAT-TA
1078639 TTTTTA-TTGTAATTAAATAAATTATTA
1 TTTTTATTTGT-ATTAAATAAATTATTA
* *
1078666 TTTTTAATTTGTATTAAATAAGTTTTTA
1 TTTTT-ATTTGTATTAAATAAATTATTA
1078694 TTT
1 TTT
1078697 AAAATAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.14
28 24 0.47
29 14 0.27
30 6 0.12
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTTATTTGTATTAAATAAATTATTA
Found at i:1078767 original size:22 final size:23
Alignment explanation
Indices: 1078737--1078800 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
1078727 TATTTAGATA
1078737 TAAATTAAAAATAAAATTTTATT
1 TAAATTAAAAATAAAATTTTATT
*
1078760 T-AATTAAAAGTTAAAA-TTTATT
1 TAAATTAAAA-ATAAAATTTTATT
1078782 TAAATGT-AAAATAAAATTT
1 TAAAT-TAAAAATAAAATTT
1078801 AAAGATTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 20 0.57
23 14 0.40
24 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAATTAAAAATAAAATTTTATT
Found at i:1078796 original size:29 final size:30
Alignment explanation
Indices: 1078764--1078832 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1078754 TTTATTTAAT
*
1078764 TAAAAGTTAAA-ATTTATTTAAATGTAAAA
1 TAAAAGTTAAAGATTTATTTAAATATAAAA
* * *
1078793 TAAAATTTAAAGATTTGTTTAAATATAAAT
1 TAAAAGTTAAAGATTTATTTAAATATAAAA
1078823 TAAAAGTTAA
1 TAAAAGTTAA
1078833 TTGTTTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (30 bp):
TAAAAGTTAAAGATTTATTTAAATATAAAA
Found at i:1078884 original size:26 final size:25
Alignment explanation
Indices: 1078845--1078945 Score: 84
Period size: 26 Copynumber: 4.0 Consensus size: 25
1078835 GTTTATATGG
*
1078845 TTAAAAGTTAAAAATTATAAATTTAT
1 TTAAAA-TTAAAAAATATAAATTTAT
**
1078871 TTAAAATTAAAAAATAATAAAAATAT
1 TTAAAATTAAAAAAT-ATAAATTTAT
*
1078897 ATTCAAATGTAATAAAA-ATAAATTTAT
1 -TTAAAAT-TAA-AAAATATAAATTTAT
1078924 TT-AAA-T-AAAAATATAAAATTTA
1 TTAAAATTAAAAAATAT-AAATTTA
1078946 AGATTTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.06
22 3 0.05
23 8 0.13
25 11 0.17
26 16 0.25
27 14 0.22
28 3 0.05
29 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (25 bp):
TTAAAATTAAAAAATATAAATTTAT
Found at i:1085838 original size:31 final size:31
Alignment explanation
Indices: 1085800--1085862 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1085790 CATACAGGAA
*
1085800 TTCAGTTGCCAAGTTAGTTTTAAACTTTGAT
1 TTCAGTTGCCAAGTTAGTCTTAAACTTTGAT
1085831 TTCAGTTGCCAAGTTAGTCTTAAACTTTGAT
1 TTCAGTTGCCAAGTTAGTCTTAAACTTTGAT
1085862 T
1 T
1085863 CTCTCTGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (31 bp):
TTCAGTTGCCAAGTTAGTCTTAAACTTTGAT
Found at i:1087840 original size:11 final size:11
Alignment explanation
Indices: 1087811--1087883 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 11
1087801 TTGATTATTA
*
1087811 TTATAATATAT
1 TTATATTATAT
1087822 TT-TA-TATAT
1 TTATATTATAT
1087831 TTATATTATA-
1 TTATATTATAT
*
1087841 TTATATTTTA-
1 TTATATTATAT
*
1087851 AT-TATT-T-T
1 TTATATTATAT
*
1087859 TTATATCATAT
1 TTATATTATAT
*
1087870 TTATATTAAAT
1 TTATATTATAT
1087881 TTA
1 TTA
1087884 AAATTATAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 2 0.04
9 14 0.28
10 15 0.30
11 19 0.38
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1087844 original size:18 final size:18
Alignment explanation
Indices: 1087823--1087877 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 18
1087813 ATAATATATT
1087823 TTATATATTTATATTATA
1 TTATATATTTATATTATA
*
1087841 TTATAT-TTTA-ATTATT
1 TTATATATTTATATTATA
* *
1087857 TTTTATA-TCATATTTATA
1 TTATATATTTATA-TTATA
1087875 TTA
1 TTA
1087878 AATTTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.41
17 5 0.17
18 12 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATATTTATATTATA
Found at i:1087845 original size:25 final size:24
Alignment explanation
Indices: 1087808--1087875 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
1087798 TGATTGATTA
*
1087808 TTATTATAATATATTTTATATATT
1 TTATTATATTATATTTTATATATT
1087832 TATATTATATTATATTTTA-ATTATT
1 T-TATTATATTATATTTTATA-TATT
*
1087857 TT-TTATATCATA-TTTATAT
1 TTATTATATTATATTTTATAT
1087876 TAAATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 5 0.13
23 10 0.26
24 3 0.08
25 21 0.54
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATATTATATTTTATATATT
Found at i:1088174 original size:33 final size:31
Alignment explanation
Indices: 1088129--1088206 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 31
1088119 TTATGTTTAA
* *
1088129 AATATTTTATATTTATATAATTTTTAAATTGAT
1 AATAATTTATATTTATATAA-ATTTAAATT-AT
1088162 AATAATTTATA-TTATATAAATTTAAATTAT
1 AATAATTTATATTTATATAAATTTAAATTAT
1088192 --T-ATTTATATTTATAT
1 AATAATTTATATTTATAT
1088207 TGTATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.17
28 7 0.17
30 2 0.05
31 8 0.19
32 8 0.19
33 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
AATAATTTATATTTATATAAATTTAAATTAT
Found at i:1088183 original size:15 final size:15
Alignment explanation
Indices: 1088141--1088191 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1088131 TATTTTATAT
*
1088141 TTATATAATTTTTAAA
1 TTATATAA-ATTTAAA
*
1088157 TTGATA-ATAATTTATA
1 TT-ATATA-AATTTAAA
1088173 TTATATAAATTTAAA
1 TTATATAAATTTAAA
1088188 TTAT
1 TTAT
1088192 TATTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 14 0.48
16 11 0.38
17 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTATATAAATTTAAA
Found at i:1088711 original size:12 final size:12
Alignment explanation
Indices: 1088694--1088727 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1088684 TCTTTCCGGT
1088694 CATCCTTCTTGC
1 CATCCTTCTTGC
*
1088706 CATCCTTCTTGT
1 CATCCTTCTTGC
1088718 CATCCTTCTT
1 CATCCTTCTT
1088728 CTCCTCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.38, G:0.06, T:0.47
Consensus pattern (12 bp):
CATCCTTCTTGC
Found at i:1088735 original size:12 final size:12
Alignment explanation
Indices: 1088693--1088736 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1088683 ATCTTTCCGG
1088693 TCATCCTTCTTGC
1 TCATCCTTCTT-C
*
1088706 -CATCCTTCTTG
1 TCATCCTTCTTC
1088717 TCATCCTTCTTC
1 TCATCCTTCTTC
*
1088729 TCCTCCTT
1 TCATCCTT
1088737 TGCAGCCCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.41, G:0.05, T:0.48
Consensus pattern (12 bp):
TCATCCTTCTTC
Found at i:1092444 original size:15 final size:15
Alignment explanation
Indices: 1092421--1092450 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1092411 GTGATACTTG
1092421 TCTTCACTTTTACAA
1 TCTTCACTTTTACAA
*
1092436 TCTTTACTTTTACAA
1 TCTTCACTTTTACAA
1092451 CAACAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTTCACTTTTACAA
Found at i:1095956 original size:18 final size:20
Alignment explanation
Indices: 1095914--1095961 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 20
1095904 TTCATTAGTC
1095914 TTAATACTAAAAATATATTATA
1 TTAATA-TAAAAATATA-TATA
1095936 TTAATATAAAAATA-A-ATA
1 TTAATATAAAAATATATATA
1095954 TTAATATA
1 TTAATATA
1095962 TTATTGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.42
20 1 0.04
21 8 0.31
22 6 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATATAAAAATATATATA
Found at i:1097528 original size:16 final size:16
Alignment explanation
Indices: 1097507--1097548 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1097497 ATTTTACTAT
1097507 TTATTATATTATTTTA
1 TTATTATATTATTTTA
* *
1097523 TTATTAAAATATTTTA
1 TTATTATATTATTTTA
1097539 -TATTAATATT
1 TTATT-ATATT
1097549 TATATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTATATTATTTTA
Found at i:1097583 original size:24 final size:22
Alignment explanation
Indices: 1097530--1097608 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
1097520 TTATTATTAA
**
1097530 AATATTTTATATTAATATTTAT
1 AATATTTTATATTAATATAAAT
1097552 -ATATTTTTATAATTAAATATAAAT
1 AATA-TTTTAT-ATT-AATATAAAT
* *
1097576 AATATTTTATTTTTATTATTAAAT
1 AATATTTTA-TATTAATA-TAAAT
*
1097600 AATAATTTA
1 AATATTTTA
1097609 GATATCATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 3 0.07
22 6 0.13
23 6 0.13
24 27 0.59
25 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTTTATATTAATATAAAT
Found at i:1098008 original size:22 final size:22
Alignment explanation
Indices: 1097983--1098035 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1097973 AAATTAAATT
* * *
1097983 AATATTGATCATAAATTTTATA
1 AATATTAAACATAAATTTGATA
1098005 AATATTAAACATAAATTTGATA
1 AATATTAAACATAAATTTGATA
*
1098027 ATTATTAAA
1 AATATTAAA
1098036 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
AATATTAAACATAAATTTGATA
Found at i:1098791 original size:19 final size:18
Alignment explanation
Indices: 1098769--1098825 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
1098759 AAAAATAATT
1098769 AATAATATTTAAATATTTA
1 AATAATA-TTAAATATTTA
*
1098788 AATATTAATTAAATA-TTA
1 AATAAT-ATTAAATATTTA
* *
1098806 AATGATATGAAAT-TTTA
1 AATAATATTAAATATTTA
1098823 AAT
1 AAT
1098826 TTTATATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 12 0.38
18 7 0.22
19 12 0.38
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
AATAATATTAAATATTTA
Found at i:1100026 original size:19 final size:18
Alignment explanation
Indices: 1099998--1100035 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1099988 AAAAAATATT
*
1099998 AATTTCATTTTTATATTTA
1 AATTTAATTTTTA-ATTTA
1100017 AATTTAATTTTTAATTTA
1 AATTTAATTTTTAATTTA
1100035 A
1 A
1100036 TTTGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTAATTTTTAATTTA
Found at i:1100463 original size:2 final size:2
Alignment explanation
Indices: 1100456--1100488 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1100446 GGTCAGAATG
1100456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1100489 TGGTGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1103886 original size:15 final size:16
Alignment explanation
Indices: 1103860--1103890 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1103850 TTCGTTTATC
1103860 ATTTATATTAAATATT
1 ATTTATATTAAATATT
1103876 ATTTA-ATTAAATATT
1 ATTTATATTAAATATT
1103891 TTAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATATTAAATATT
Found at i:1104015 original size:25 final size:25
Alignment explanation
Indices: 1103982--1104048 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
1103972 AATAAGATTT
*
1103982 AAATTAAATTATT-TTTTAATTATAA
1 AAATAAAATTATTATTTTAATT-TAA
* *
1104007 AAATAAAATTTTTATTTTTATTTAA
1 AAATAAAATTATTATTTTAATTTAA
1104032 AACTATAAAA-TATTATT
1 AA--ATAAAATTATTATT
1104049 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 16 0.46
26 13 0.37
27 6 0.17
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATAAAATTATTATTTTAATTTAA
Found at i:1104592 original size:19 final size:18
Alignment explanation
Indices: 1104570--1104608 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1104560 ATTTTAAAAT
1104570 ATTTTAAATAAAATTTTAA
1 ATTTTAAATAAAA-TTTAA
*
1104589 ATTTTAAATTAAATTTAA
1 ATTTTAAATAAAATTTAA
1104607 AT
1 AT
1104609 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTAAATAAAATTTAA
Found at i:1111692 original size:2 final size:2
Alignment explanation
Indices: 1111685--1111711 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1111675 AATGAAATCC
1111685 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 A
1111712 GGGTTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1126220 original size:46 final size:46
Alignment explanation
Indices: 1126160--1126252 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
1126150 CATCCACAAT
* *
1126160 ACCTGCAGATAATGGAGTATATTCCTACAAACTCATTTTAAGCCTA
1 ACCTGCAGAAAATGGAGTATATTCCTACAAACTCATTTGAAGCCTA
*
1126206 ACCTGCAGAAAATGGAGTATATTCCTACAAGCTCATTTGAAGCCTA
1 ACCTGCAGAAAATGGAGTATATTCCTACAAACTCATTTGAAGCCTA
1126252 A
1 A
1126253 AAACTCAGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (46 bp):
ACCTGCAGAAAATGGAGTATATTCCTACAAACTCATTTGAAGCCTA
Found at i:1128878 original size:17 final size:18
Alignment explanation
Indices: 1128844--1128881 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1128834 ATTTAAATTG
*
1128844 ATATATAATTTATTTTATA
1 ATATAAAATTTA-TTTATA
1128863 ATATAAAATTTA-TTATA
1 ATATAAAATTTATTTATA
1128880 AT
1 AT
1128882 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAAAATTTATTTATA
Found at i:1129573 original size:21 final size:21
Alignment explanation
Indices: 1129550--1129591 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1129540 TATCGTATAT
*
1129550 AAATTTAATTTAATTTTATGTA
1 AAATTT-ATTTAATTATATGTA
1129572 AAATTTATTTAATTATATGT
1 AAATTTATTTAATTATATGT
1129592 TAGTTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
AAATTTATTTAATTATATGTA
Found at i:1129687 original size:22 final size:25
Alignment explanation
Indices: 1129661--1129708 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1129651 TTGATTATAC
1129661 TAATAAA-A-TAAAAAAA-ATCTTA
1 TAATAAAGATTAAAAAAATATCTTA
1129683 TAATAAATGATTAAAAAAATATCTTA
1 TAATAAA-GATTAAAAAAATATCTTA
1129709 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
24 1 0.05
25 8 0.36
26 6 0.27
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
TAATAAAGATTAAAAAAATATCTTA
Found at i:1130251 original size:17 final size:18
Alignment explanation
Indices: 1130207--1130254 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1130197 AATTAATATC
1130207 TTATATTATTTTTATTTAA
1 TTATATTATTTTTA-TTAA
*
1130226 TTAAATTATTTTTA-TAA
1 TTATATTATTTTTATTAA
*
1130243 TTATTTTATTTT
1 TTATATTATTTT
1130255 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
19 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTATTTTTATTAA
Found at i:1130273 original size:27 final size:27
Alignment explanation
Indices: 1130239--1130294 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1130229 AATTATTTTT
* * *
1130239 ATAATTATTTTATTTTATTTTTATATA
1 ATAATTATTGTATTATAATTTTATATA
*
1130266 ATAATTATTGTATTATAATTTTATTTA
1 ATAATTATTGTATTATAATTTTATATA
1130293 AT
1 AT
1130295 TTTAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATAATTATTGTATTATAATTTTATATA
Found at i:1130282 original size:41 final size:41
Alignment explanation
Indices: 1130207--1130285 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
1130197 AATTAATATC
*
1130207 TTATATTATTTTTATTTAATTAAATTATTTTTATAATTATT
1 TTATATTATTTTTATATAATTAAATTATTTTTATAATTATT
*
1130248 TTATTTTATTTTTATATAA-T-AATTATTGTATTATAATT
1 TTATATTATTTTTATATAATTAAATTATT-T-TTATAATT
1130286 TTATTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.21
40 2 0.06
41 25 0.74
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (41 bp):
TTATATTATTTTTATATAATTAAATTATTTTTATAATTATT
Found at i:1139913 original size:2 final size:2
Alignment explanation
Indices: 1139906--1139937 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1139896 CATTATTTAT
*
1139906 TA TA TA TA TA CA 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
1139938 ATTCTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1142627 original size:22 final size:22
Alignment explanation
Indices: 1142601--1142665 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 22
1142591 TTTCATCTCA
1142601 ATTTTTTTTTTAATTTTTATTT
1 ATTTTTTTTTTAATTTTTATTT
*
1142623 A---TTTTTTTACTTTTT-TTT
1 ATTTTTTTTTTAATTTTTATTT
*
1142641 ATTTTGTGTTTTAATTTTTTATTT
1 ATTTT-TTTTTTAA-TTTTTATTT
1142665 A
1 A
1142666 GTGCATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 4 0.12
19 13 0.38
21 1 0.03
22 7 0.21
23 5 0.15
24 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (22 bp):
ATTTTTTTTTTAATTTTTATTT
Found at i:1143705 original size:11 final size:11
Alignment explanation
Indices: 1143689--1143731 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1143679 ATTAAATTAA
1143689 TATATTTATAT
1 TATATTTATAT
*
1143700 TATATTTGTAT
1 TATATTTATAT
1143711 TAT-TTTATAT
1 TATATTTATAT
1143721 CTATATCTTAT
1 -TATAT-TTAT
1143732 TTTAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.22
11 16 0.59
12 1 0.04
13 4 0.15
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1143732 original size:21 final size:21
Alignment explanation
Indices: 1143693--1143732 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1143683 AATTAATATA
*
1143693 TTTATATTATATTTGTATTAT
1 TTTATATTATATCTGTATTAT
1143714 TTTATATCTATATCT-TATT
1 TTTATAT-TATATCTGTATT
1143733 TTAAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATATTATATCTGTATTAT
Found at i:1144940 original size:22 final size:22
Alignment explanation
Indices: 1144916--1144975 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
1144906 AATAAGATAT
1144916 AAAATAATTAAAATATAAAATTA
1 AAAATAA-TAAAATATAAAATTA
*
1144939 AAAATAATATAATATAAATATATA
1 AAAATAATAAAATATAAA-AT-TA
* *
1144963 AATATGATAAAAT
1 AAAATAATAAAAT
1144976 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 10 0.32
23 9 0.29
24 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATAATAAAATATAAAATTA
Found at i:1144974 original size:33 final size:32
Alignment explanation
Indices: 1144914--1145026 Score: 92
Period size: 33 Copynumber: 3.6 Consensus size: 32
1144904 TTAATAAGAT
*
1144914 ATAAAATAAT-TAAA-ATATAAA-AT-TAAAA
1 ATAATATAATATAAATATATAAATATATAAAA
1144942 ATAATATAATATAAATATATAAATATGATAAAA
1 ATAATATAATATAAATATATAAATAT-ATAAAA
* * * * *
1144975 TTTATTTAAAATAAAT-TATTAATATATAAAA
1 ATAATATAATATAAATATATAAATATATAAAA
*
1145006 ATTTATATGAATATATAATAT
1 A-TAATAT-AATATA-AATAT
1145027 TTTAAATCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
28 9 0.13
29 4 0.06
30 7 0.10
31 8 0.12
32 13 0.19
33 22 0.33
34 3 0.04
35 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (32 bp):
ATAATATAATATAAATATATAAATATATAAAA
Found at i:1146795 original size:21 final size:22
Alignment explanation
Indices: 1146727--1146796 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 22
1146717 TTATTTTATT
1146727 ATTTATAATAATATTAAAATTAATA
1 ATTTATAAT--TATTAAAA-TAATA
* *
1146752 TTTATATAATTAAATTTAAATAA-A
1 ATT-TATAATT--ATTAAAATAATA
1146776 ATTTATAATTATTAAAATAAT
1 ATTTATAATTATTAAAATAAT
1146797 TTAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
21 9 0.24
23 7 0.19
24 4 0.11
25 5 0.14
26 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTATAATTATTAAAATAATA
Found at i:1147217 original size:3 final size:3
Alignment explanation
Indices: 1147209--1147244 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1147199 AAGAAAATAA
1147209 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
1147245 TAATTTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1148494 original size:7 final size:8
Alignment explanation
Indices: 1148473--1148519 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1148463 TAAAATAAAT
1148473 TATTAATA
1 TATTAATA
1148481 TATTAATA
1 TATTAATA
1148489 -ATTAATA
1 TATTAATA
*
1148496 TTTTAAATA
1 TATT-AATA
*
1148505 TAATTAAAA
1 T-ATTAATA
1148514 TATTAA
1 TATTAA
1148520 AAATAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 15 0.45
9 9 0.27
10 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TATTAATA
Found at i:1148507 original size:18 final size:18
Alignment explanation
Indices: 1148485--1148531 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1148475 TTAATATATT
* *
1148485 AATAATTAATATTTTAAA
1 AATAATTAAAATATTAAA
*
1148503 TATAATTAAAATATTAAA
1 AATAATTAAAATATTAAA
1148521 AATAA-TAAAAT
1 AATAATTAAAAT
1148532 TTTGTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATTAAAATATTAAA
Found at i:1151369 original size:20 final size:20
Alignment explanation
Indices: 1151344--1151412 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
1151334 ATTATTAAAT
1151344 ATATTTATTAAAAATATTAC
1 ATATTTATTAAAAATATTAC
* * * * *
1151364 ATATTTATCATAATTACGTAAATT
1 ATATTTATTAAAAATA--T-TA-C
1151388 ATATTTATTAAAAATATTAC
1 ATATTTATTAAAAATATTAC
1151408 ATATT
1 ATATT
1151413 CATGTCATGC
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 18 0.51
21 1 0.03
22 2 0.06
23 1 0.03
24 13 0.37
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (20 bp):
ATATTTATTAAAAATATTAC
Found at i:1152498 original size:3 final size:3
Alignment explanation
Indices: 1152490--1152516 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1152480 AAGAAAATGA
1152490 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1152517 TAATTTAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.