Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1399
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: 214408
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 1 of 2
Found at i:426 original size:20 final size:20
Alignment explanation
Indices: 379--453 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
369 AAAAAGACAT
*
379 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
398 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
419 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
439 AATGTATCGATACAT
1 AATGTATCGATACAT
454 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:447 original size:40 final size:39
Alignment explanation
Indices: 376--453 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
366 GGTAAAAAGA
* *
376 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
415 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
454 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:701 original size:42 final size:42
Alignment explanation
Indices: 652--768 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
642 TGGTGTCTAC
* *
652 AGGAGGGATGATAGGAGGAGAGACAAGAGAGATAGTAGAGAT
1 AGGAGGGATGATAGGAGGAGAGACAAGAGAGATAATAGAGAG
* *
694 ATGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGAGAG
1 AGGAGGGATGATAGGAGGAGAGACAAGAGAGATAATAGAGAG
*
736 AGGAGGGATGATAGGAGGAGGAGAGAAGA-AGAT
1 AGGAGGGATGATAGGAGGA-GAGACAAGAGAGAT
769 GGAAGAGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 60 0.90
43 7 0.10
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (42 bp):
AGGAGGGATGATAGGAGGAGAGACAAGAGAGATAATAGAGAG
Found at i:739 original size:18 final size:18
Alignment explanation
Indices: 712--761 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
702 TGATAGGAGG
*
712 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
730 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
748 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
762 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:6002 original size:16 final size:16
Alignment explanation
Indices: 5977--6021 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
5967 CCTAATATCG
* *
5977 AAAATGATCTAATCTC
1 AAAATAATCTAAACTC
5993 AAAATAATCTAAACTC
1 AAAATAATCTAAACTC
*
6009 AAAATAATTTAAA
1 AAAATAATCTAAA
6022 ATTGAAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (16 bp):
AAAATAATCTAAACTC
Found at i:6664 original size:11 final size:11
Alignment explanation
Indices: 6650--6768 Score: 50
Period size: 11 Copynumber: 10.5 Consensus size: 11
6640 GCATTATTAT
6650 TATTATATTTA
1 TATTATATTTA
*
6661 TATTATTTTTA
1 TATTATATTTA
*
6672 TTTTAT-TATTA
1 TATTATAT-TTA
*
6683 TATTATAATTTT
1 TATTAT-ATTTA
*
6695 TAAATATATTTA
1 T-ATTATATTTA
*
6707 TGAGTT-TAAATTA
1 T-A-TTAT-ATTTA
6720 TATTATATTT-
1 TATTATATTTA
*
6730 TAATAT-TTTA
1 TATTATATTTA
*
6740 -ATTATTTTTTTA
1 TATTA--TATTTA
*
6752 TATCATATTTAA
1 TATTATATTT-A
6764 TATTA
1 TATTA
6769 CTTAATTTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
9 6 0.08
10 6 0.08
11 33 0.41
12 21 0.26
13 14 0.17
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTATATTTA
Found at i:6704 original size:18 final size:18
Alignment explanation
Indices: 6679--6730 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
6669 TTATTTTATT
6679 ATTATATTATAATTTTTAA
1 ATTATATTAT-ATTTTTAA
*
6698 A-TATATT-TATGAGTTTAA
1 ATTATATTATAT--TTTTAA
6716 ATTATATTATATTTT
1 ATTATATTATATTTT
6731 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
16 2 0.07
17 1 0.04
18 14 0.52
19 7 0.26
20 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTATATTATATTTTTAA
Found at i:8290 original size:16 final size:16
Alignment explanation
Indices: 8269--8300 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8259 ACTTGCACAA
8269 ATACACTAAATCTAAT
1 ATACACTAAATCTAAT
8285 ATACACTAAATCTAAT
1 ATACACTAAATCTAAT
8301 CCACCTACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACACTAAATCTAAT
Found at i:10185 original size:21 final size:20
Alignment explanation
Indices: 10146--10185 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10136 ATTAAAATAT
*
10146 AAAACAACACAAAATGACAA
1 AAAACAACAAAAAATGACAA
*
10166 AAAATAACAAAAATATGACA
1 AAAACAACAAAAA-ATGACA
10186 CAAATATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAACAACAAAAAATGACAA
Found at i:10558 original size:2 final size:2
Alignment explanation
Indices: 10551--10579 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10541 GATCAGTCAC
10551 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10580 ATGTTAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19757 original size:53 final size:53
Alignment explanation
Indices: 19693--19809 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
19683 ATTTTTAAAT
** * *
19693 ATTTATTATTTAGCTTTAAATTATTT-TTATAAATAATATATTTAGATATTTAA
1 ATTTATTATTTAAATTTAAATTATTTGTT-TAAATAATAAATTTAAATATTTAA
** *
19746 ATTTATTATTTAAATTTGTATTATTTGTTTATATAATAAATTTAAATATTTAA
1 ATTTATTATTTAAATTTAAATTATTTGTTTAAATAATAAATTTAAATATTTAA
*
19799 TTTTATTATTT
1 ATTTATTATTT
19810 TTTATTTGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 53 0.96
54 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (53 bp):
ATTTATTATTTAAATTTAAATTATTTGTTTAAATAATAAATTTAAATATTTAA
Found at i:21793 original size:21 final size:21
Alignment explanation
Indices: 21750--21794 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21740 GATGAAATAA
* *
21750 TTAATATAAGTTATAATATTT
1 TTAATATAACTTATAATAATT
**
21771 TTAATATAACTTATTTTAATT
1 TTAATATAACTTATAATAATT
21792 TTA
1 TTA
21795 TACCAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAATATAACTTATAATAATT
Found at i:22296 original size:46 final size:45
Alignment explanation
Indices: 22227--22322 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 45
22217 ATATTCGTAT
* ** * * *
22227 TTAAACTAATTAAAATTGGTTATTGCTAGTACAACTGAATATATA
1 TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
* * *
22272 CTTAAACCAATTGAAATTAATTATTATTAATACAATTAAATATATA
1 -TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
22318 TTAAA
1 TTAAA
22323 TTCATTTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
45 5 0.12
46 36 0.88
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (45 bp):
TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
Found at i:22465 original size:46 final size:46
Alignment explanation
Indices: 22336--22471 Score: 164
Period size: 46 Copynumber: 3.0 Consensus size: 46
22326 ATTTTTAGAC
* * ** * *
22336 TAATTAAAATTTATCAATAAGCGTACAATTGAATATACACTTAAAT
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
**
22382 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTCGAG
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
* ** *
22428 TAATTAAAATTAATCATTATTTTTACAATTGAATATATAATTAA
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAA
22472 TGTTACTACA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (46 bp):
TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
Found at i:23463 original size:29 final size:29
Alignment explanation
Indices: 23396--23474 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
23386 TGAAATTGCA
23396 AAATGATCTTAGTTCATAAAAAATAACCT
1 AAATGATCTTAGTTCATAAAAAATAACCT
* * *
23425 AAATAATCTTAGATT-ATGAAAAATAA-TT
1 AAATGATCTTAG-TTCATAAAAAATAACCT
*
23453 AAATGATTCTTACATTCATAAA
1 AAATGA-TCTTA-GTTCATAAA
23475 GTTACATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
28 6 0.15
29 28 0.70
30 6 0.15
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (29 bp):
AAATGATCTTAGTTCATAAAAAATAACCT
Found at i:23509 original size:29 final size:29
Alignment explanation
Indices: 23470--23553 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
23460 TCTTACATTC
*
23470 ATAAAGTTACATAAAAGTCTCTAAAAT-A
1 ATAAAATTACATAAAAGTCTCTAAAATGA
* *
23498 ATGCAAATTACA-AAAATGATCT-TAAAATGT
1 AT-AAAATTACATAAAA-G-TCTCTAAAATGA
* *
23528 ATAAAATTACATAAAAGCCCCTAAAA
1 ATAAAATTACATAAAAGTCTCTAAAA
23554 CATGATAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
28 7 0.16
29 28 0.64
30 9 0.20
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (29 bp):
ATAAAATTACATAAAAGTCTCTAAAATGA
Found at i:23564 original size:58 final size:58
Alignment explanation
Indices: 23470--23640 Score: 204
Period size: 58 Copynumber: 3.0 Consensus size: 58
23460 TCTTACATTC
* * * * * * *
23470 ATAAAGTTACATAAAAGTCTCTAAAATAATGCAAATTAC-AAAAATGATCTTAAAATGT
1 ATAAAATTACATAAAAGCCCCTAAAA-CATGAAAATTACTTAAAATGAGCTTAAAATGT
23528 ATAAAATTACATAAAAGCCCCTAAAACATGATAAATT-CTTAAAATGAGCTTAAAATGT
1 ATAAAATTACATAAAAGCCCCTAAAACATGA-AAATTACTTAAAATGAGCTTAAAATGT
* * * *
23586 ATGAAATTATATAAAA-CCCTTAAAACATGAAAAATACTTAAAATGAGCTTAAAAT
1 ATAAAATTACATAAAAGCCCCTAAAACATGAAAATTACTTAAAATGAGCTTAAAAT
23641 ACTTAAAATT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
56 4 0.04
57 36 0.36
58 59 0.60
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (58 bp):
ATAAAATTACATAAAAGCCCCTAAAACATGAAAATTACTTAAAATGAGCTTAAAATGT
Found at i:23581 original size:29 final size:29
Alignment explanation
Indices: 23549--23639 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
23539 TAAAAGCCCC
23549 TAAAACATGATAAATTCTTAAAATGAGCT
1 TAAAACATGATAAATTCTTAAAATGAGCT
* **
23578 T-AAA-ATGTATGAAATTATATAAAA--CCCT
1 TAAAACATG-AT-AAATTCT-TAAAATGAGCT
* *
23606 TAAAACATGAAAAATACTTAAAATGAGCT
1 TAAAACATGATAAATTCTTAAAATGAGCT
23635 TAAAA
1 TAAAA
23640 TACTTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
27 8 0.17
28 13 0.28
29 18 0.38
30 8 0.17
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.29
Consensus pattern (29 bp):
TAAAACATGATAAATTCTTAAAATGAGCT
Found at i:23638 original size:11 final size:9
Alignment explanation
Indices: 23616--23649 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
23606 TAAAACATGA
23616 AAAATACTT
1 AAAATACTT
23625 AAAATGAGCTT
1 AAAAT-A-CTT
23636 AAAATACTT
1 AAAATACTT
23645 AAAAT
1 AAAAT
23650 TGCATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAATACTT
Found at i:24332 original size:12 final size:13
Alignment explanation
Indices: 24310--24342 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
24300 TATGAAGTTT
24310 TAAATAAAAATTA
1 TAAATAAAAATTA
24323 TAAA-AAAAATTA
1 TAAATAAAAATTA
24335 -AAATAAAA
1 TAAATAAAA
24343 CATTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 12 0.63
13 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAAAATTA
Found at i:24539 original size:12 final size:13
Alignment explanation
Indices: 24524--24556 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
24514 TTTCCCTTTA
24524 TTTTTTTCTC-TT
1 TTTTTTTCTCATT
24536 TTTTTTTCTCATT
1 TTTTTTTCTCATT
24549 TTTCTTTT
1 TTT-TTTT
24557 ATGGTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 5 0.26
14 4 0.21
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTCATT
Found at i:26590 original size:20 final size:19
Alignment explanation
Indices: 26565--26609 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
26555 TAAAATCAAT
*
26565 TTTTTATTAATTTAATATAA
1 TTTTTATTAATTAAAT-TAA
*
26585 TTTTTATTGATTAAATTAA
1 TTTTTATTAATTAAATTAA
26604 TTTTTA
1 TTTTTA
26610 CTAAGTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATTAATTAAATTAA
Found at i:28008 original size:17 final size:16
Alignment explanation
Indices: 27982--28049 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
27972 AAAAAATATT
* *
27982 AATAACTTAAACTCGAA
1 AATAATTTAAACT-TAA
*
27999 AATAATTTAAATTTAA
1 AATAATTTAAACTTAA
*
28015 AATAATCTAAACTTAA
1 AATAATTTAAACTTAA
*
28031 AATTATTTAAACTTAA
1 AATAATTTAAACTTAA
28047 AAT
1 AAT
28050 GAATCGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
16 33 0.75
17 11 0.25
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (16 bp):
AATAATTTAAACTTAA
Found at i:28018 original size:16 final size:16
Alignment explanation
Indices: 27997--28097 Score: 78
Period size: 16 Copynumber: 6.3 Consensus size: 16
27987 CTTAAACTCG
27997 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
* *
28013 AAAATAATCTAAACTT
1 AAAATAATTTAAATTT
* *
28029 AAAATTATTTAAACTT
1 AAAATAATTTAAATTT
** *
28045 AAAATGAA-TCGAATCT
1 AAAAT-AATTTAAATTT
* *
28061 AAAATGATTTAAATTC
1 AAAATAATTTAAATTT
* * *
28077 GAAATAATCTAAATCT
1 AAAATAATTTAAATTT
28093 AAAAT
1 AAAAT
28098 TATTCGAACC
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 1 0.02
16 61 0.97
17 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:28039 original size:32 final size:32
Alignment explanation
Indices: 27997--28101 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
27987 CTTAAACTCG
*
27997 AAAATAATTTAAATTTAAAATAATCTAAACTT
1 AAAATTATTTAAATTTAAAATAATCTAAACTT
* * *
28029 AAAATTATTTAAACTTAAAATGAATCGAATC-T
1 AAAATTATTTAAATTTAAAAT-AATCTAAACTT
* **
28061 AAAATGATTTAAATTCGAAATAATCTAAA-TCT
1 AAAATTATTTAAATTTAAAATAATCTAAACT-T
28093 AAAATTATT
1 AAAATTATT
28102 CGAACCTATA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 6 0.10
32 46 0.78
33 7 0.12
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (32 bp):
AAAATTATTTAAATTTAAAATAATCTAAACTT
Found at i:28096 original size:48 final size:46
Alignment explanation
Indices: 28044--28143 Score: 110
Period size: 48 Copynumber: 2.1 Consensus size: 46
28034 TATTTAAACT
* * *
28044 TAAAATGAATCGAATCTAAAATGATTTAAATTCGAAATAATCTAAATC
1 TAAAATGAATCGAACCTAAAATGA-TTAAACTCGAAA-AATCTAAATA
* * * * *
28092 TAAAATTATTCGAACCTATAATTATTAAACTCGATAAATCTAAATA
1 TAAAATGAATCGAACCTAAAATGATTAAACTCGAAAAATCTAAATA
28138 TAAAAT
1 TAAAAT
28144 TTAATTGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 15 0.34
47 10 0.23
48 19 0.43
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (46 bp):
TAAAATGAATCGAACCTAAAATGATTAAACTCGAAAAATCTAAATA
Found at i:28299 original size:16 final size:16
Alignment explanation
Indices: 28280--28318 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28270 AATTCAAATA
*
28280 TAAAATTAAATTAACT
1 TAAAATTAAAATAACT
*
28296 TAAAATTAAAATAATT
1 TAAAATTAAAATAACT
28312 TAAAATT
1 TAAAATT
28319 TTAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTAAAATAACT
Found at i:30273 original size:1 final size:1
Alignment explanation
Indices: 30267--30291 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30257 TCATTACACC
30267 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
30292 AACCTACCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:34635 original size:152 final size:149
Alignment explanation
Indices: 34326--34625 Score: 518
Period size: 152 Copynumber: 2.0 Consensus size: 149
34316 AGAATGTGGC
34326 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
1 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
*
34391 TAATATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATTTTTTTTTTTTTGT
66 T-ATATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAA--TATTTTTTTTTGT
34456 TCATAAGATTAGGAAATTAAAT
128 TCATAAGATTAGGAAATTAAAT
34478 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTA-TT
1 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
* *
34542 T-TA-ATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAGATTAGGAA-ATTTTTTTTTGTTTA
66 TATATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATATTTTTTTTTGTTCA
34604 TAAGATTAGGAAATTAAAT
131 TAAGATTAGGAAATTAAAT
34623 CTT
1 CTT
34626 CATTTTTTTT
Statistics
Matches: 145, Mismatches: 3, Indels: 7
0.94 0.02 0.05
Matches are distributed among these distances:
145 35 0.24
148 43 0.30
149 2 0.01
151 3 0.02
152 62 0.43
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (149 bp):
CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
TATATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATATTTTTTTTTGTTCA
TAAGATTAGGAAATTAAAT
Found at i:35257 original size:20 final size:20
Alignment explanation
Indices: 35229--35275 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
35219 TATTAAATTA
*
35229 AATTTAAATAAAATTTT-TTT
1 AATTAAAAT-AAATTTTATTT
35249 AATTAAAATAAATTTTATTT
1 AATTAAAATAAATTTTATTT
35269 AACTTAA
1 AA-TTAA
35276 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 13 0.54
21 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAAATAAATTTTATTT
Found at i:35290 original size:15 final size:18
Alignment explanation
Indices: 35261--35297 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
35251 TTAAAATAAA
35261 TTTTATTTAACTTAAT-T
1 TTTTATTTAACTTAATAT
35278 TTTTATTT-A-TTAATAT
1 TTTTATTTAACTTAATAT
35294 TTTT
1 TTTT
35298 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 8 0.42
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTTAACTTAATAT
Found at i:38669 original size:2 final size:2
Alignment explanation
Indices: 38662--38692 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38652 CCACAATGCA
*
38662 AT AT AT AT AC 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 A
38693 ATTTTGTTCG
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38725 original size:13 final size:14
Alignment explanation
Indices: 38707--38754 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
38697 TGTTCGAATA
38707 AATAATTT-ATTTT
1 AATAATTTAATTTT
38720 AATAATTTAATTTT
1 AATAATTTAATTTT
* **
38734 AAT-TTTTAATTAA
1 AATAATTTAATTTT
38747 AATAATTT
1 AATAATTT
38755 TTTATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATAATTTAATTTT
Found at i:39313 original size:22 final size:22
Alignment explanation
Indices: 39288--39329 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39278 TAAAAAAATT
39288 TTAAAATATTTT-TATATTAATA
1 TTAAAATATTTTATA-ATTAATA
*
39310 TTAATATATTTTATAATTAA
1 TTAAAATATTTTATAATTAA
39330 ATAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATATTTTATAATTAATA
Found at i:39336 original size:21 final size:20
Alignment explanation
Indices: 39291--39336 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
39281 AAAAATTTTA
39291 AAATATTTTTATATTAATAT
1 AAATATTTTTATATTAATAT
*
39311 TAATATATTTTATAATTAA-AT
1 AAATAT-TTTTAT-ATTAATAT
39332 AAATA
1 AAATA
39337 AAAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTTTATATTAATAT
Found at i:39976 original size:18 final size:18
Alignment explanation
Indices: 39934--39977 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
39924 AAATATTAAA
39934 ATATAAAAATATTTTTAT
1 ATATAAAAATATTTTTAT
* *
39952 ATTTAAATATATTTTTA-
1 ATATAAAAATATTTTTAT
39969 ATAATAAAA
1 AT-ATAAAA
39978 TAAGCTTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAAAAATATTTTTAT
Found at i:39978 original size:19 final size:18
Alignment explanation
Indices: 39936--39979 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
39926 ATATTAAAAT
39936 ATAAAA-ATATTTTTATA
1 ATAAAATATATTTTTATA
* *
39953 TTTAAATATATTTTTAATA
1 ATAAAATATATTTTT-ATA
39972 ATAAAATA
1 ATAAAATA
39980 AGCTTTCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.19
18 8 0.38
19 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAAAATATATTTTTATA
Found at i:40231 original size:33 final size:32
Alignment explanation
Indices: 40168--40231 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 32
40158 ATTTTTAAAT
* * * **
40168 TAAAATAATATATTTTTATTTAAATTTAATTA
1 TAAAATAATAAATATTTATCTAAAAATAATTA
40200 TAAAATATATAAATATTTATCTAAAAATAATT
1 TAAAATA-ATAAATATTTATCTAAAAATAATT
40232 TTTCAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAATAATAAATATTTATCTAAAAATAATTA
Found at i:41890 original size:2 final size:2
Alignment explanation
Indices: 41883--41920 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
41873 GTGACGTGAG
*
41883 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41921 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:41929 original size:14 final size:16
Alignment explanation
Indices: 41883--41929 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
41873 GTGACGTGAG
*
41883 TATATATATATATATATA
1 TATATATAAATA-ATA-A
41901 TATATATAAATAATAA
1 TATATATAAATAATAA
41917 TATA-ATAAA-AATA
1 TATATATAAATAATA
41930 TTTTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 5 0.18
17 3 0.11
18 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAAATAATAA
Found at i:41947 original size:30 final size:31
Alignment explanation
Indices: 41913--41994 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 31
41903 TATATAAATA
41913 ATAATATAATAAAAATATTTTAA-AATTTAT
1 ATAATATAATAAAAATATTTTAATAATTTAT
* * * * *
41943 ATAATATAA-ATAATTAATATAATAATTTTT
1 ATAATATAATAAAAATATTTTAATAATTTAT
*
41973 ATAAAAT-AT-AAAATATTTTAAT
1 ATAATATAATAAAAATATTTTAAT
41995 CATAATAATA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATATAATAAAAATATTTTAATAATTTAT
Found at i:41974 original size:32 final size:35
Alignment explanation
Indices: 41938--42018 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
41928 TATTTTAAAA
*
41938 TTTATATAATAT-AAATA-ATTAAT-ATAATAATT
1 TTTATAAAATATAAAATATATTAATCATAATAATT
* *
41970 TTTATAAAATATAAAATATTTTAATCATAATAATA
1 TTTATAAAATATAAAATATATTAATCATAATAATT
* *
42005 ATAATAAAATATAA
1 TTTATAAAATATAA
42019 TACAAATCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.27
33 5 0.12
34 5 0.12
35 20 0.49
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
TTTATAAAATATAAAATATATTAATCATAATAATT
Found at i:41976 original size:21 final size:21
Alignment explanation
Indices: 41943--42010 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
41933 TAAAATTTAT
**
41943 ATAATATAAATAATTAATATA
1 ATAATATTTATAATTAATATA
*
41964 ATAATTTTTATAA--AATATA
1 ATAATATTTATAATTAATATA
41983 A-AATATTT-TAATCATAATAATA
1 ATAATATTTATAAT--TAAT-ATA
42005 ATAATA
1 ATAATA
42011 AAATATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 7 0.19
21 13 0.35
22 4 0.11
23 4 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATTTATAATTAATATA
Found at i:41988 original size:39 final size:40
Alignment explanation
Indices: 41894--41988 Score: 97
Period size: 43 Copynumber: 2.3 Consensus size: 40
41884 ATATATATAT
*
41894 ATATATATATATATAAATAATAATATAATAAAAATATTTTAAA
1 ATATATA-AAATATAAATAATAATATAAT--AAATATTTTAAA
* *
41937 ATTTATATAATATAAATAATTAATATAAT-AAT-TTTTATAA
1 ATATATAAAATATAAATAA-TAATATAATAAATATTTTA-AA
41977 A-ATATAAAATAT
1 ATATATAAAATAT
41989 TTTAATCATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
39 14 0.31
40 6 0.13
42 10 0.22
43 15 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
ATATATAAAATATAAATAATAATATAATAAATATTTTAAA
Found at i:42279 original size:16 final size:16
Alignment explanation
Indices: 42258--42288 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42248 GTTTGGAGGA
*
42258 TTATTTTTTATTTTTT
1 TTATTTATTATTTTTT
42274 TTATTTATTATTTTT
1 TTATTTATTATTTTT
42289 ATTGTTATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTATTTATTATTTTTT
Found at i:42534 original size:14 final size:14
Alignment explanation
Indices: 42514--42599 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
42504 ATATTATGAC
42514 ATATT-TATTAAAT
1 ATATTATATTAAAT
*
42527 ATATTTTATT--A-
1 ATATTATATTAAAT
*
42538 ATCTTAT-TTAAAT
1 ATATTATATTAAAT
*
42551 ATACTATATTAAAT
1 ATATTATATTAAAT
* **
42565 TTATTATATTATTTTT
1 ATATTATATTA--AAT
42581 ATATT-TATTAAAT
1 ATATTATATTAAAT
42594 ATATTA
1 ATATTA
42600 AATTTATATC
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 2 0.04
13 16 0.30
14 19 0.35
15 5 0.09
16 5 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTATATTAAAT
Found at i:42598 original size:24 final size:24
Alignment explanation
Indices: 42514--42599 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
42504 ATATTATGAC
42514 ATATTTATTAAATATATT-TTATT
1 ATATTTATTAAATATATTATTATT
*
42537 A-ATCTTATTTAAATATACTA-TATT
1 ATAT-TTA-TTAAATATATTATTATT
* *
42561 AAATTTA-T---TATATTATTTTT
1 ATATTTATTAAATATATTATTATT
42581 ATATTTATTAAATATATTA
1 ATATTTATTAAATATATTA
42600 AATTTATATC
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
19 6 0.12
20 9 0.18
21 1 0.02
22 3 0.06
23 4 0.08
24 25 0.50
25 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTATTAAATATATTATTATT
Found at i:43803 original size:24 final size:27
Alignment explanation
Indices: 43752--43806 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43742 AAAATATAAC
*
43752 TTTTTATAATATTTAATAATTAAAATT
1 TTTTTATAATATTAAATAATTAAAATT
*
43779 TTTTTATAA-A-TAAATAATT-ATATT
1 TTTTTATAATATTAAATAATTAAAATT
43803 TTTT
1 TTTT
43807 AATTTACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 8 0.31
26 1 0.04
27 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATTAAATAATTAAAATT
Found at i:44156 original size:13 final size:14
Alignment explanation
Indices: 44128--44154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44118 CAATATTTTG
44128 TAAATTTTTTTAAA
1 TAAATTTTTTTAAA
44142 TAAATTTTTTTAA
1 TAAATTTTTTTAA
44155 TATATGGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATTTTTTTAAA
Found at i:44904 original size:22 final size:20
Alignment explanation
Indices: 44878--44930 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
44868 AACAATATGA
44878 AAATTTAAATGATCTAAATAATT
1 AAATTTAAAT-ATCT-AA-AATT
*
44901 -AATTAAAAATATCTAAAATT
1 AAATT-TAAATATCTAAAATT
44921 AAATTTAAAT
1 AAATTTAAAT
44931 CTAAATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 8 0.31
23 4 0.15
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTTAAATATCTAAAATT
Found at i:44961 original size:16 final size:16
Alignment explanation
Indices: 44942--44982 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
44932 TAAATTGATT
44942 TAATTTTAAAATTCAA
1 TAATTTTAAAATTCAA
44958 TAA-TTT-AAATTCAA
1 TAATTTTAAAATTCAA
*
44972 AATATTTTAAA
1 TA-ATTTTAAA
44983 TCTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 6 0.29
17 2 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTTAAAATTCAA
Found at i:44989 original size:15 final size:16
Alignment explanation
Indices: 44956--44998 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
44946 TTTAAAATTC
44956 AATAATTTAAATTCAA
1 AATAATTTAAATTCAA
* *
44972 AATATTTTAAA-TCTA
1 AATAATTTAAATTCAA
*
44987 AATAATTCAAAT
1 AATAATTTAAAT
44999 ATTAAATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATTTAAATTCAA
Found at i:46120 original size:32 final size:32
Alignment explanation
Indices: 46047--46120 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
46037 AATATTTTTA
* * * *
46047 TTTAAATTTATTTATAAAAGTATTTTTAAATT
1 TTTAAATTAATTTATAAAAATATATTTAAACT
**
46079 TTTTTATTAATTTATAAATAATA-ATTTAAACT
1 TTTAAATTAATTTATAAA-AATATATTTAAACT
46111 TTTAAATTAA
1 TTTAAATTAA
46121 ACTTTATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 30 0.91
33 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTAAATTAATTTATAAAAATATATTTAAACT
Found at i:47247 original size:209 final size:207
Alignment explanation
Indices: 46971--47346 Score: 495
Period size: 209 Copynumber: 1.8 Consensus size: 207
46961 ATTTATTCGA
* * * * *
46971 TTTGATTTAGCTAATTTCAATAAAATTTCATTAAGCAAATCGATTTAAATATGTGTGATCAATTG
1 TTTGATTTAGCCAATTTCAAAAAAAATTCATTAAGCAAATAGATTTAAATATATGTGATCAATTG
* * * * * * *
47036 ATTTGTAGTTTTTTATTTTTTAAACTAAACAAACCCATCTATATTATCTTTATCAAATCTATAAC
66 ATTTGCAGTTTTTTATTTTTCAAACCAAAC-AACCCAACTATATTAGC-TTACCAAATCCATAAC
* * **
47101 TATTTTACTTAATTTCATAAGCCCAAAATAAAACACAAACAGACACAACCAACCAAACCAAACTA
129 TATATTACTCAATTTCATAAAACCAAAATAAAACACAAACAGACACAACCAACCAAACCAAACTA
47166 ATTAATTTTGGTTG
194 ATTAATTTTGGTTG
* * *
47180 TTTGATTTAGCCAATTTCAAAAAAAATTCCTTAAGCGAATTAG-TTTAAATATAT-TTATTCAAT
1 TTTGATTTAGCCAATTTCAAAAAAAATTCATTAAGC-AAATAGATTTAAATATATGTGA-TCAAT
* *
47243 TGATTTGCAGTTTTTTATTTTTCAAACCAAACAACCCAACTATATTAGCTTACCCAATCCATAAT
64 TGATTTGCAGTTTTTTATTTTTCAAACCAAACAACCCAACTATATTAGCTTACCAAATCCATAAC
* *
47308 TATATTACTCAATTTCATAAAATCAAAATAAAACTCAAA
129 TATATTACTCAATTTCATAAAACCAAAATAAAACACAAA
47347 TCGGTATAAT
Statistics
Matches: 142, Mismatches: 23, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
207 45 0.32
208 17 0.12
209 76 0.54
210 4 0.03
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (207 bp):
TTTGATTTAGCCAATTTCAAAAAAAATTCATTAAGCAAATAGATTTAAATATATGTGATCAATTG
ATTTGCAGTTTTTTATTTTTCAAACCAAACAACCCAACTATATTAGCTTACCAAATCCATAACTA
TATTACTCAATTTCATAAAACCAAAATAAAACACAAACAGACACAACCAACCAAACCAAACTAAT
TAATTTTGGTTG
Found at i:47745 original size:22 final size:22
Alignment explanation
Indices: 47719--47774 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
47709 TTATTGATTA
47719 TAATATTAAAATATTTT-TATAT
1 TAATATTAAAATATTTTATA-AT
* *
47741 TAATATTTATATATTTTATAAT
1 TAATATTAAAATATTTTATAAT
*
47763 TAA-ATAAAAATA
1 TAATATTAAAATA
47775 AAAATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 20 0.71
23 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTAAAATATTTTATAAT
Found at i:48496 original size:13 final size:14
Alignment explanation
Indices: 48478--48525 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
48468 TGTTTCAATA
48478 AATAATTT-ATTTT
1 AATAATTTAATTTT
48491 AATAATTTAATTTT
1 AATAATTTAATTTT
* **
48505 AAT-TTTTAATTAA
1 AATAATTTAATTTT
48518 AATAATTT
1 AATAATTT
48526 TTTGTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATAATTTAATTTT
Found at i:48501 original size:18 final size:19
Alignment explanation
Indices: 48459--48504 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
48449 CAAAATATAT
48459 ATTTAATTTTGTTTCAATA
1 ATTTAATTTTGTTTCAATA
*
48478 A-ATAATTTAT-TTT-AATA
1 ATTTAATTT-TGTTTCAATA
48495 ATTTAATTTT
1 ATTTAATTTT
48505 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTAATTTTGTTTCAATA
Found at i:49078 original size:21 final size:23
Alignment explanation
Indices: 49054--49098 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
49044 TAATAAAAAA
49054 ATTAAAATATTTTA-TATT-AAT
1 ATTAAAATATTTTATTATTGAAT
*
49075 ATTAATATATTTTATTATTGAAT
1 ATTAAAATATTTTATTATTGAAT
49098 A
1 A
49099 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTAAAATATTTTATTATTGAAT
Found at i:49479 original size:16 final size:16
Alignment explanation
Indices: 49446--49512 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
49436 CCCAATCCCA
* *
49446 AATCCGAAATAACTTG
1 AATCCGAAATGACCTG
** *
49462 AATTTGAAATGATCTG
1 AATCCGAAATGACCTG
49478 AATCCGAAATGACCTG
1 AATCCGAAATGACCTG
*
49494 AA-CTCGAAATTACCTG
1 AATC-CGAAATGACCTG
49510 AAT
1 AAT
49513 AATTAACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.03
16 39 0.98
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (16 bp):
AATCCGAAATGACCTG
Found at i:49503 original size:32 final size:32
Alignment explanation
Indices: 49446--49512 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
49436 CCCAATCCCA
* * * *
49446 AATCCGAAATAACTTGAATTTGAAATGATCTG
1 AATCCGAAATAACCTGAACTCGAAATGACCTG
* *
49478 AATCCGAAATGACCTGAACTCGAAATTACCTG
1 AATCCGAAATAACCTGAACTCGAAATGACCTG
49510 AAT
1 AAT
49513 AATTAACCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (32 bp):
AATCCGAAATAACCTGAACTCGAAATGACCTG
Found at i:50601 original size:16 final size:16
Alignment explanation
Indices: 50565--50595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50555 CCCGATTGAT
50565 TCGAACCCGAAATAAC
1 TCGAACCCGAAATAAC
*
50581 TCGAACTCGAAATAA
1 TCGAACCCGAAATAA
50596 TCCGAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (16 bp):
TCGAACCCGAAATAAC
Found at i:50607 original size:53 final size:53
Alignment explanation
Indices: 50498--50607 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 53
50488 ACCAGAATAC
* * *
50498 TAAACCCGATTAACCCGAATCCAAAATAACTCGAACTCGATTAACCCGAGTGT
1 TAAACCCGATTAACCCGAACCCAAAATAACTCGAACTCGAATAACCCGAATGT
* ** * *
50551 TAAACCCGATTGATTCGAACCCGAAATAACTCGAACTCGAAATAATCCGAAT-T
1 TAAACCCGATTAACCCGAACCCAAAATAACTCGAACTCG-AATAACCCGAATGT
50604 TAAA
1 TAAA
50608 ATGACTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 39 0.81
54 9 0.19
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (53 bp):
TAAACCCGATTAACCCGAACCCAAAATAACTCGAACTCGAATAACCCGAATGT
Found at i:51102 original size:16 final size:16
Alignment explanation
Indices: 51064--51103 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
51054 TATTCATTCA
*
51064 ATAAATTTAATTTAAT
1 ATAAATTTAAGTTAAT
* *
51080 TTGAATTTAAGTTAAT
1 ATAAATTTAAGTTAAT
51096 ATAAATTT
1 ATAAATTT
51104 TTAATAATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
ATAAATTTAAGTTAAT
Found at i:52448 original size:22 final size:22
Alignment explanation
Indices: 52423--52464 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52413 CTCAAAATAT
*
52423 GATTTTTAGATTT-TTAAATTGA
1 GATTTTGA-ATTTATTAAATTGA
52445 GATTTTGAATTTATTAAATT
1 GATTTTGAATTTATTAAATT
52465 TTAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (22 bp):
GATTTTGAATTTATTAAATTGA
Found at i:53252 original size:32 final size:31
Alignment explanation
Indices: 53182--53262 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
53172 ATGATATATA
**
53182 AAATTATTA-ATAATAT-AATAAAAATATTTT
1 AAATT-TTATATAATATAAATAAAAATATAAT
* *
53212 AAAATTTATATAATATAAATAATTAATATAAT
1 AAATTTTATATAATATAAATAA-AAATATAAT
*
53244 AAATTTTATAAAATATAAA
1 AAATTTTATATAATATAAA
53263 ATACTAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 3 0.07
30 11 0.26
31 5 0.12
32 23 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATTTTATATAATATAAATAAAAATATAAT
Found at i:53271 original size:32 final size:32
Alignment explanation
Indices: 53211--53271 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
53201 AAAAATATTT
* *
53211 TAAAATTTATATAATATAAATAATTAATATAA
1 TAAAATTTATAAAATATAAATAACTAATATAA
*
53243 TAAATTTTATAAAATATAAA-ATACTAATA
1 TAAAATTTATAAAATATAAATA-ACTAATA
53272 CAAATCGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAATTTATAAAATATAAATAACTAATATAA
Found at i:53881 original size:28 final size:27
Alignment explanation
Indices: 53849--53922 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
53839 ACATCGTAAA
*
53849 TATATTTATTAATTTTATTTAAATTTAT
1 TATATTTATT-ATTTTATTTAAATATAT
53877 TATA-TTATT-TTTATATTATTAAATATAT
1 TATATTTATTATTT-TA-T-TTAAATATAT
*
53905 TAAATTTA-TATTTTATTT
1 TATATTTATTATTTTATTT
53923 TTTTGTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
25 3 0.08
26 4 0.10
27 7 0.18
28 19 0.49
29 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TATATTTATTATTTTATTTAAATATAT
Found at i:53942 original size:26 final size:26
Alignment explanation
Indices: 53906--53960 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
53896 TAAATATATT
* *
53906 AAATTTATATTT-TATTTTTTTGTTTA
1 AAATTTATATTTATATATATTT-TTTA
*
53932 AAATTTTTATTTATATATATTTTTTA
1 AAATTTATATTTATATATATTTTTTA
53958 AAA
1 AAA
53961 AATCAACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
AAATTTATATTTATATATATTTTTTA
Found at i:54522 original size:10 final size:10
Alignment explanation
Indices: 54507--54532 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54497 TCATGACTTA
54507 TATTTATAAT
1 TATTTATAAT
54517 TATTTATAAT
1 TATTTATAAT
54527 TATTTA
1 TATTTA
54533 ATTCATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATAAT
Found at i:56752 original size:11 final size:11
Alignment explanation
Indices: 56738--56763 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56728 TTAAAAATTA
56738 AAAATTAAAAT
1 AAAATTAAAAT
56749 AAAATTAAAAT
1 AAAATTAAAAT
56760 AAAA
1 AAAA
56764 AATTACATAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:56766 original size:18 final size:18
Alignment explanation
Indices: 56731--56764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56721 AATTTAATTA
*
56731 AAAATTAAAAATTAAAAT
1 AAAATTAAAAATAAAAAT
56749 AAAATT-AAAATAAAAA
1 AAAATTAAAAATAAAAA
56765 ATTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAAAAATAAAAAT
Found at i:57146 original size:9 final size:9
Alignment explanation
Indices: 57121--57196 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
57111 AGATAAAAAA
57121 ATTATATTT
1 ATTATATTT
57130 A-TATTATTT
1 ATTA-TATTT
*
57139 ATTATATTAG
1 ATTATATT-T
57149 ATTATATTTT
1 ATTATA-TTT
*
57159 AATTATTTTT
1 -ATTATATTT
*
57169 A-TAAATTT
1 ATTATATTT
*
57177 ATTATTTTT
1 ATTATATTT
*
57186 TTTAT-TTT
1 ATTATATTT
57194 ATT
1 ATT
57197 TTATATAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
8 13 0.25
9 21 0.40
10 11 0.21
11 7 0.13
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (9 bp):
ATTATATTT
Found at i:57194 original size:17 final size:17
Alignment explanation
Indices: 57153--57196 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
57143 TATTAGATTA
57153 TATTTTAATTATTTTTAT
1 TATTTT-ATTATTTTTAT
* * *
57171 AAATTTATTATTTTTTT
1 TATTTTATTATTTTTAT
57188 TATTTTATT
1 TATTTTATT
57197 TTATATAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTATTATTTTTAT
Found at i:59931 original size:11 final size:11
Alignment explanation
Indices: 59917--59946 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59907 AATCAAAAAC
59917 TAATTTTTTTA
1 TAATTTTTTTA
*
59928 TAATTTTTTTT
1 TAATTTTTTTA
59939 TAATTTTT
1 TAATTTTT
59947 ATAAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:60164 original size:14 final size:14
Alignment explanation
Indices: 60145--60178 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
60135 ATTGTAATAC
60145 ATAATATTTTTAAA
1 ATAATATTTTTAAA
60159 ATAATATTTTTAAA
1 ATAATATTTTTAAA
60173 ATAATA
1 ATAATA
60179 ATGTGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATATTTTTAAA
Found at i:60180 original size:17 final size:15
Alignment explanation
Indices: 60139--60178 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
60129 AATTTGATTG
60139 TAATACATAATATTTT
1 TAATA-ATAATATTTT
60155 TAA-AATAATATTTT
1 TAATAATAATATTTT
60169 TAA-AATAATA
1 TAATAATAATA
60179 ATGTGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 20 0.83
15 1 0.04
16 3 0.12
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATAATATTTT
Found at i:60235 original size:14 final size:15
Alignment explanation
Indices: 60145--60241 Score: 64
Period size: 14 Copynumber: 6.5 Consensus size: 15
60135 ATTGTAATAC
*
60145 ATAATATTT-TTAAA
1 ATAATATTTATTATA
*
60159 ATAATATTT-TTAAA
1 ATAATATTTATTATA
60173 ATAATAATGTGATATTATA
1 ATAAT-AT-T--TATTATA
60192 ATAAT-TTTATTA-A
1 ATAATATTTATTATA
60205 AT-AT-TTAATATTATA
1 ATAATATT--TATTATA
60220 ATAATATTTATT-TA
1 ATAATATTTATTATA
*
60234 ATGATATT
1 ATAATATT
60242 AACAAAGAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
12 4 0.06
13 3 0.04
14 38 0.54
15 9 0.13
16 4 0.06
17 3 0.04
18 1 0.01
19 9 0.13
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATAATATTTATTATA
Found at i:60531 original size:13 final size:13
Alignment explanation
Indices: 60513--60668 Score: 58
Period size: 13 Copynumber: 11.8 Consensus size: 13
60503 GTTAGATACC
60513 TTATATATTTATA
1 TTATATATTTATA
*
60526 TTATAT-TAATATA
1 TTATATAT-TTATA
* *
60539 TTTTTATATATAATA
1 -TTATATAT-TTATA
*
60554 TT-TATTTTTA-A
1 TTATATATTTATA
* *
60565 ATAT-TATATATA
1 TTATATATTTATA
*
60577 TTATATATATATA
1 TTATATATTTATA
60590 TTA-ATAATTTATA
1 TTATAT-ATTTATA
*
60603 TTATGTAAATTTAATATA
1 TTA--TATA-TT--TATA
*
60621 TTAATATATTAATA
1 TT-ATATATTTATA
* *
60635 TTAAATTTTTATA
1 TTATATATTTATA
60648 TT-TA-A-TTATA
1 TTATATATTTATA
*
60658 TTTTATATTTA
1 TTATATATTTA
60669 AAGTTGTCGA
Statistics
Matches: 107, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
10 7 0.07
11 8 0.07
12 12 0.11
13 47 0.44
14 12 0.11
15 6 0.06
16 5 0.05
17 3 0.03
18 6 0.06
19 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:60554 original size:23 final size:21
Alignment explanation
Indices: 60514--60666 Score: 82
Period size: 19 Copynumber: 7.7 Consensus size: 21
60504 TTAGATACCT
60514 TATATATTTATATTATATTAA
1 TATATATTTATATTATATTAA
60535 TATAT-TTT-TA-TATA-TAA
1 TATATATTTATATTATATTAA
* * *
60552 TATTTATTTTTA-AATATT-A
1 TATATATTTATATTATATTAA
60571 TATATATTATATATATATATT-A
1 TATATATT-TATAT-TATATTAA
* *
60593 -ATA-ATTTATATTATGTAAA
1 TATATATTTATATTATATTAA
*
60612 TTTAATATATTA-A-TATATTAA
1 TAT-ATAT-TTATATTATATTAA
* *
60633 TATTAAATTTTTA-TAT-TTAA
1 TA-TATATTTATATTATATTAA
60653 T-TATATTTTATATT
1 TATATA-TTTATATT
60667 TAAAGTTGTC
Statistics
Matches: 102, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
17 7 0.07
18 14 0.14
19 26 0.25
20 19 0.19
21 23 0.23
22 10 0.10
23 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TATATATTTATATTATATTAA
Found at i:60628 original size:26 final size:28
Alignment explanation
Indices: 60515--60635 Score: 89
Period size: 26 Copynumber: 4.5 Consensus size: 28
60505 TAGATACCTT
*
60515 ATATATT-TATAT-TATATTAATATATTTTT
1 ATATATTATATATATAT-TTAATATA--TTA
* * *
60544 ATATATAATATTTATTTTTAA-ATATTA
1 ATATATTATATATATATTTAATATATTA
60571 TATATATTATATATATATATTAATA-ATT-
1 -ATATATTATATATATAT-TTAATATATTA
*
60599 -TATATTATGTA-A-ATTTAATATATTA
1 ATATATTATATATATATTTAATATATTA
60624 ATATATTA-ATAT
1 ATATATTATATAT
60636 TAAATTTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
23 6 0.08
24 5 0.07
25 3 0.04
26 17 0.23
27 2 0.03
28 14 0.19
29 16 0.22
30 9 0.12
31 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
ATATATTATATATATATTTAATATATTA
Found at i:60646 original size:45 final size:45
Alignment explanation
Indices: 60521--60650 Score: 128
Period size: 45 Copynumber: 2.9 Consensus size: 45
60511 CCTTATATAT
**
60521 TTATATTATATTAATATATTTTTATATATAATATTTAT-TTTTAAATA
1 TTATA-TATATTAATATATTAATAT-TA-AATATTTATATTTTAAATA
60568 TTATATATATT-ATATA-TATATATT-AATAATTTATATTATGTAAAT-
1 TTATATATATTAATATATTA-ATATTAAAT-ATTTATATT-T-TAAATA
*
60613 TTA-ATATATTAATATATTAATATTAAATTTTTATATTT
1 TTATATATATTAATATATTAATATTAAATATTTATATTT
60651 AATTATATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
42 3 0.04
43 6 0.08
44 12 0.17
45 30 0.42
46 16 0.22
47 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (45 bp):
TTATATATATTAATATATTAATATTAAATATTTATATTTTAAATA
Found at i:61774 original size:16 final size:16
Alignment explanation
Indices: 61753--61784 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61743 TAGAATAGAA
61753 TAATTTAATAAAAATT
1 TAATTTAATAAAAATT
*
61769 TAATTTAATAATAATT
1 TAATTTAATAAAAATT
61785 AAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAATAAAAATT
Found at i:61810 original size:45 final size:43
Alignment explanation
Indices: 61757--61840 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 43
61747 ATAGAATAAT
61757 TTAATAAAAATTTAATT-TAATAATAATTAAAAATAATTTTAAGA
1 TTAAT-AAAATTTAATTGTAATAATAATTAAAAA-AATTTTAAGA
* * **
61801 TTAACTAAAATTTTATTGTATTTTTAATTAAAAAAATTTT
1 TTAA-TAAAATTTAATTGTAATAATAATTAAAAAAATTTT
61841 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
44 20 0.59
45 14 0.41
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
TTAATAAAATTTAATTGTAATAATAATTAAAAAAATTTTAAGA
Found at i:62521 original size:12 final size:13
Alignment explanation
Indices: 62502--62534 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
62492 TTTATTTTTT
62502 TATTTTAATTTAA
1 TATTTTAATTTAA
*
62515 T-TTTTAATTTGA
1 TATTTTAATTTAA
62527 TATTTTAA
1 TATTTTAA
62535 AAAATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TATTTTAATTTAA
Found at i:67257 original size:18 final size:18
Alignment explanation
Indices: 67236--67273 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
67226 AAGCTGAGTG
67236 ATAAAATTTAATAAAAAA
1 ATAAAATTTAATAAAAAA
*
67254 ATAAAATTTAATAATAAA
1 ATAAAATTTAATAAAAAA
67272 AT
1 AT
67274 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAATTTAATAAAAAA
Found at i:68832 original size:21 final size:21
Alignment explanation
Indices: 68806--68851 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
68796 ATTTAAATTG
*
68806 ATTTAA-ATTATTATTTATTTA
1 ATTTAATAATATT-TTTATTTA
*
68827 ATTTAATAATATTTTTATTTT
1 ATTTAATAATATTTTTATTTA
68848 ATTT
1 ATTT
68852 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTAATAATATTTTTATTTA
Found at i:68973 original size:6 final size:5
Alignment explanation
Indices: 68929--68969 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
68919 AATTTAAGTT
68929 ATTAA ATTAA ATTAA ATTAA ATTTAA ATTTAAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA A-TTAA A-TT-AA ATTAA ATT
68970 TAAAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 21 0.62
6 10 0.29
7 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATTAA
Found at i:68977 original size:7 final size:6
Alignment explanation
Indices: 68930--68973 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
68920 ATTTAAGTTA
*
68930 TTAAA- TTAAA- TTAAA- TTAAAT TTAAAT TTAAAA TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
68974 ATTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:82287 original size:16 final size:16
Alignment explanation
Indices: 82266--82304 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
82256 ATCATTTTTT
*
82266 TTAATATTAATATATA
1 TTAATATTAACATATA
*
82282 TTAATATTAACATATT
1 TTAATATTAACATATA
82298 TTAATAT
1 TTAATAT
82305 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATATTAACATATA
Found at i:82762 original size:16 final size:17
Alignment explanation
Indices: 82735--82768 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
82725 AAAGTATTAA
*
82735 AAATATTAAATTTTTTT
1 AAATATTAAATTTATTT
82752 AAATA-TAAATTTATTT
1 AAATATTAAATTTATTT
82768 A
1 A
82769 TATTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTAAATTTATTT
Found at i:83191 original size:17 final size:16
Alignment explanation
Indices: 83156--83188 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83146 TTTTAAAAAC
*
83156 TTATTAT-AAATTTAA
1 TTATTATAAAAATTAA
83171 TTATTATAAAAATTAA
1 TTATTATAAAAATTAA
83187 TT
1 TT
83189 TATATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATAAAAATTAA
Found at i:85200 original size:14 final size:15
Alignment explanation
Indices: 85173--85218 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
85163 TAATAAAAAA
85173 TTATTAATATAATTTT
1 TTATT-ATATAATTTT
85189 TTATTATA-AATTTT
1 TTATTATATAATTTT
85203 TTATTATCAT-ATTTT
1 TTATTAT-ATAATTTT
85218 T
1 T
85219 CTATACTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.46
15 10 0.36
16 5 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTATATAATTTT
Found at i:87140 original size:18 final size:17
Alignment explanation
Indices: 87103--87153 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
87093 AAACGTATCG
87103 TAAAA-AATTAAAAT-A
1 TAAAATAATTAAAATAA
87118 TAAAATAATATAAAATAA
1 TAAAATAAT-TAAAATAA
*
87136 TAAAATTATTTAAAATAA
1 TAAAA-TAATTAAAATAA
87154 ATTTGTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 5 0.16
16 3 0.10
17 6 0.19
18 14 0.45
19 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATAATTAAAATAA
Found at i:91281 original size:28 final size:28
Alignment explanation
Indices: 91239--91401 Score: 77
Period size: 28 Copynumber: 5.6 Consensus size: 28
91229 ATATATGGTT
91239 ATATAAATATAATATATATAATAATTAAA
1 ATAT-AATATAATATATATAATAATTAAA
**
91268 ATATAATATAATAT-TAATAATTTTTTAAA
1 ATATAATATAATATAT-ATAA-TAATTAAA
* *
91297 ATTTATACAATATAA-AT-TATTATTATATAAA
1 A--TAT--AATATAATATATATAATAAT-TAAA
* * * *
91328 A-ATTTATATAA-ATATAAAATATTTTAA
1 ATA-TAATATAATATATATAATAATTAAA
* * *
91355 ATATAATTATAACATA-ATAAAATATTTAA
1 ATATAA-TATAATATATATAATA-ATTAAA
91384 ATATAATATGAATATATA
1 ATATAATAT-AATATATA
91402 AATTATCAAC
Statistics
Matches: 104, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
27 15 0.14
28 33 0.32
29 31 0.30
30 4 0.04
31 11 0.11
32 3 0.03
33 7 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
ATATAATATAATATATATAATAATTAAA
Found at i:91283 original size:18 final size:18
Alignment explanation
Indices: 91249--91284 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
91239 ATATAAATAT
91249 AATATATATAATAATTAA
1 AATATATATAATAATTAA
91267 AATATAATATAAT-ATTAA
1 AATAT-ATATAATAATTAA
91285 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATATATAATAATTAA
Found at i:91285 original size:11 final size:12
Alignment explanation
Indices: 91239--91286 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
91229 ATATATGGTT
91239 ATATAA-ATATA
1 ATATAATATATA
91250 ATAT-ATATAATA
1 ATATAATAT-ATA
*
91262 AT-TAAAATATA
1 ATATAATATATA
91273 ATATAATAT-TA
1 ATATAATATATA
91284 ATA
1 ATA
91287 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 17 0.55
12 13 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAATATATA
Found at i:91357 original size:16 final size:17
Alignment explanation
Indices: 91293--91360 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
91283 AATAATTTTT
91293 TAAAAT-TTA-TACAATA
1 TAAAATATTATTA-AATA
* *
91309 TAAATTATTATTATATA
1 TAAAATATTATTAAATA
91326 -AAAAT-TTATATAAATA
1 TAAAATATTAT-TAAATA
91342 TAAAATATT-TTAAATA
1 TAAAATATTATTAAATA
91358 TAA
1 TAA
91361 TTATAACATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.09
16 23 0.53
17 12 0.28
18 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATTATTAAATA
Found at i:91375 original size:30 final size:27
Alignment explanation
Indices: 91334--91404 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 27
91324 TAAAAATTTA
91334 TATAAATATAAAATATTTTAAATATAAT
1 TATAAATATAAAATA-TTTAAATATAAT
91362 TATAACATAATAAAATATTTAAATATAA-
1 TATAA-AT-ATAAAATATTTAAATATAAT
*
91390 TATGAATATATAAAT
1 TATAAATATA-AAAT
91405 TATCAACGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 3 0.08
27 6 0.15
28 9 0.23
29 13 0.33
30 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
TATAAATATAAAATATTTAAATATAAT
Found at i:92539 original size:18 final size:18
Alignment explanation
Indices: 92513--92555 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
92503 TATAATTTTA
*
92513 AAATTTATATTTACACAT
1 AAATGTATATTTACACAT
*
92531 AAATGTATATTTATACAT
1 AAATGTATATTTACACAT
*
92549 ATATGTA
1 AAATGTA
92556 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
AAATGTATATTTACACAT
Found at i:93187 original size:15 final size:15
Alignment explanation
Indices: 93154--93195 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
93144 TCTTAATATT
* * *
93154 AATATATATATATAT
1 AATATATATTTAAAA
93169 AATATATATTTAAAA
1 AATATATATTTAAAA
93184 AATA-ATATTTAA
1 AATATATATTTAA
93196 TCGATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATATTTAAAA
Found at i:93753 original size:13 final size:13
Alignment explanation
Indices: 93735--93760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
93725 ATTTTTATGT
93735 TAATATTATATAA
1 TAATATTATATAA
93748 TAATATTATATAA
1 TAATATTATATAA
93761 AACAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATTATATAA
Found at i:94570 original size:2 final size:2
Alignment explanation
Indices: 94563--94602 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
94553 AGATCTCTTC
94563 AT AT AT AT 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 AT AT AT AT
94603 TTTGTCGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95947 original size:15 final size:14
Alignment explanation
Indices: 95904--95961 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
95894 TATTTAAATA
*
95904 TAAAAATATA-ATT
1 TAAATATATATATT
* *
95917 TATATAAATA-ATT
1 TAAATATATATATT
95930 TAAATATATATATAT
1 TAAATATATATAT-T
*
95945 TAAATGTATATATT
1 TAAATATATATATT
95959 TAA
1 TAA
95962 CATTCATCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 18 0.49
14 6 0.16
15 13 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATATATATT
Found at i:102328 original size:19 final size:19
Alignment explanation
Indices: 102293--102331 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
102283 TATTAAATTT
*
102293 AATAATATATTTTATAATA
1 AATAATATATTTAATAATA
102312 AATAATA-ATATTAATAATA
1 AATAATATAT-TTAATAATA
102331 A
1 A
102332 CTAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:107800 original size:12 final size:11
Alignment explanation
Indices: 107785--107824 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
107775 AGATTTGAAA
107785 ATTTATTTTATT
1 ATTTATTTTA-T
107797 ATTTATTTTAT
1 ATTTATTTTAT
107808 ATTTAATATTTAT
1 ATTT-AT-TTTAT
107821 ATTT
1 ATTT
107825 TTATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.19
12 12 0.46
13 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTATTTTAT
Found at i:107817 original size:18 final size:17
Alignment explanation
Indices: 107786--107820 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
107776 GATTTGAAAA
*
107786 TTTATTTTATTATTTAT
1 TTTATTTTAATATTTAT
107803 TTTATATTTAATATTTAT
1 TTTAT-TTTAATATTTAT
107821 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTAATATTTAT
Found at i:109686 original size:20 final size:19
Alignment explanation
Indices: 109657--109698 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
109647 AAAACCTTAA
109657 AAAAACTAAAACAAATAAGAG
1 AAAAACTAAAA-AAATAA-AG
109678 AAAAA-TAAAAAAATAAAG
1 AAAAACTAAAAAAATAAAG
109696 AAA
1 AAA
109699 GTTTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 5 0.24
21 5 0.24
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAACTAAAAAAATAAAG
Found at i:110497 original size:16 final size:16
Alignment explanation
Indices: 110466--110516 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 16
110456 AAGATTATAT
110466 AATATAAATATAATAAAA
1 AATATAAATATAAT--AA
*
110484 AATAATAAATATAATAT
1 AAT-ATAAATATAATAA
110501 AATATAAATAT-ATAA
1 AATATAAATATAATAA
110516 A
1 A
110517 TATTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 4 0.13
16 8 0.27
17 4 0.13
18 3 0.10
19 11 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATAAATATAATAA
Found at i:110515 original size:24 final size:24
Alignment explanation
Indices: 110461--110519 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
110451 ATGGTAAGAT
110461 TATAT-AATATAAATATAATAAAA
1 TATATAAATATAAATATAATAAAA
*
110484 AATAATAAATAT-AATATAATATAAA
1 TAT-ATAAATATAAATATAATA-AAA
110509 TATATAAATAT
1 TATATAAATAT
110520 TTTAACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 19 0.61
25 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TATATAAATATAAATATAATAAAA
Found at i:110601 original size:20 final size:20
Alignment explanation
Indices: 110564--110601 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
110554 AAATTTATAT
**
110564 AAATTAAAATATTTTAAATA
1 AAATTAAAATATAATAAATA
110584 AAATTAAAATATAATAAA
1 AAATTAAAATATAATAAA
110602 ATATATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTAAAATATAATAAATA
Found at i:110661 original size:13 final size:15
Alignment explanation
Indices: 110581--110740 Score: 78
Period size: 16 Copynumber: 10.1 Consensus size: 15
110571 AATATTTTAA
110581 ATAAAAT-TAAAATAT
1 ATAAAATAT-AAATAT
110596 AATAAAATATATAA-AT
1 -ATAAAATATA-AATAT
110612 ATTAAACGAATATAATATAT
1 A-T-AA--AATATAA-ATAT
110632 ATAAAATATAAATAT
1 ATAAAATATAAATAT
*
110647 ATAAAATAT-GA-AT
1 ATAAAATATAAATAT
* * *
110660 ATAAATTTTAAAATTT
1 ATAAAATAT-AAATAT
110676 ATAAAATATAAAT-T
1 ATAAAATATAAATAT
* *
110690 ATTAATATATTAAAATTT
1 A-TAAAATA-T-AAATAT
110708 ATATAAATATTAAATAT
1 ATA-AAATA-TAAATAT
* * *
110725 TTTAAATATAATTAT
1 ATAAAATATAAATAT
110740 A
1 A
110741 AATATTTAAG
Statistics
Matches: 114, Mismatches: 14, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
13 9 0.08
14 3 0.03
15 31 0.27
16 32 0.28
17 17 0.15
18 11 0.10
19 8 0.07
20 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAAAATATAAATAT
Found at i:111459 original size:20 final size:22
Alignment explanation
Indices: 111413--111460 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
111403 CTTTTTTATC
*
111413 TATTTTTTTCTGTTATTTTGTC
1 TATTTTTTTCTGTTATTTTGTA
*
111435 T-TTTTTTT-TTTTATTTT-TA
1 TATTTTTTTCTGTTATTTTGTA
111454 TATTTTT
1 TATTTTT
111461 ATTTAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
20 13 0.57
21 7 0.30
22 1 0.04
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (22 bp):
TATTTTTTTCTGTTATTTTGTA
Found at i:111585 original size:43 final size:44
Alignment explanation
Indices: 111500--111585 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 44
111490 TACAATTATT
** *
111500 TAATAAATATTAAAAAATTAATTAATTATATTTATTTTTACTAAA
1 TAATAAATATTAAAAAATTAA-TAATTATATTTAAATATACTAAA
*
111545 TAATAAATTATTAAAATATTAA-AA-TATATTTAAATATACTA
1 TAATAAA-TATTAAAAAATTAATAATTATATTTAAATATACTA
111586 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 14 0.39
44 2 0.06
45 7 0.19
46 13 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (44 bp):
TAATAAATATTAAAAAATTAATAATTATATTTAAATATACTAAA
Found at i:111918 original size:29 final size:29
Alignment explanation
Indices: 111886--111964 Score: 158
Period size: 29 Copynumber: 2.7 Consensus size: 29
111876 TTTAAGGATA
111886 AAAATAATAATATTTTAATAAATATTTTT
1 AAAATAATAATATTTTAATAAATATTTTT
111915 AAAATAATAATATTTTAATAAATATTTTT
1 AAAATAATAATATTTTAATAAATATTTTT
111944 AAAATAATAATATTTTAATAA
1 AAAATAATAATATTTTAATAA
111965 TTAAATTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AAAATAATAATATTTTAATAAATATTTTT
Found at i:111920 original size:15 final size:15
Alignment explanation
Indices: 111902--111950 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
111892 ATAATATTTT
111902 AATAAATATTTTTAA
1 AATAAATATTTTTAA
111917 AAT-AATAATATTTT--
1 AATAAAT-AT-TTTTAA
111931 AATAAATATTTTTAA
1 AATAAATATTTTTAA
111946 AATAA
1 AATAA
111951 TAATATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 13 0.45
16 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATATTTTTAA
Found at i:111922 original size:18 final size:17
Alignment explanation
Indices: 111886--111959 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
111876 TTTAAGGATA
111886 AAAATAATAATA-TTTT
1 AAAATAATAATATTTTT
111902 --AAT-A-AATATTTTT
1 AAAATAATAATATTTTT
111915 AAAATAATAATA-TTTT
1 AAAATAATAATATTTTT
111931 --AAT-A-AATATTTTT
1 AAAATAATAATATTTTT
111944 AAAATAATAATATTTT
1 AAAATAATAATATTTT
111960 AATAATTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
12 8 0.17
13 10 0.21
14 6 0.12
15 6 0.12
16 6 0.12
17 12 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATAATAATATTTTT
Found at i:111963 original size:14 final size:14
Alignment explanation
Indices: 111888--111965 Score: 74
Period size: 14 Copynumber: 5.4 Consensus size: 14
111878 TAAGGATAAA
111888 AATAATAATATTTT
1 AATAATAATATTTT
111902 AAT-A-AATATTTTT
1 AATAATAATA-TTTT
111915 AAAATAATAATATTTT
1 --AATAATAATATTTT
111931 AAT-A-AATATTTTT
1 AATAATAATA-TTTT
111944 AAAATAATAATATTTT
1 --AATAATAATATTTT
111960 AATAAT
1 AATAAT
111966 TAAATTAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
12 8 0.15
13 10 0.19
14 12 0.22
15 6 0.11
16 10 0.19
17 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:112871 original size:15 final size:15
Alignment explanation
Indices: 112851--112913 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
112841 ACAATTGTAG
112851 TAAAATATATAAATA
1 TAAAATATATAAATA
* *
112866 TAAAATTTTTAAATA
1 TAAAATATATAAATA
*
112881 T--AAT-TATAATATT
1 TAAAATATATAA-ATA
112894 TAAAAATAATATAAATA
1 T-AAAAT-ATATAAATA
112911 TAA
1 TAA
112914 TATAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.11
13 6 0.16
15 14 0.38
16 5 0.14
17 3 0.08
18 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATATATAAATA
Found at i:112900 original size:21 final size:21
Alignment explanation
Indices: 112851--112901 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
112841 ACAATTGTAG
112851 TAAAATATATAAATATAAAATT
1 TAAAA-ATATAAATATAAAATT
** * *
112873 TTTAAATATAATTATAATATT
1 TAAAAATATAAATATAAAATT
112894 TAAAAATA
1 TAAAAATA
112902 ATATAAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATATAAATATAAAATT
Found at i:112910 original size:19 final size:19
Alignment explanation
Indices: 112862--112911 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
112852 AAAATATATA
* *
112862 AATATAAAATTTTTAAATAT
1 AATAT-AAATATTTAAAAAT
112882 AAT-TATAATATTTAAAAAT
1 AATATA-AATATTTAAAAAT
112901 AATATAAATAT
1 AATATAAATAT
112912 AATATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 20 0.77
20 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATAAATATTTAAAAAT
Done.