Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 24 of 25
Found at i:3607490 original size:27 final size:27
Alignment explanation
Indices: 3607441--3607499 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3607431 TTTTATAATA
* * **
3607441 AAAATATTTTAATTTAAATTTAATTAT
1 AAAATATATAAATTTAAATTTAAAAAT
3607468 AAAATATATAAATATTAAA-TTAAAAAT
1 AAAATATATAAAT-TTAAATTTAAAAAT
3607495 AAAAT
1 AAAAT
3607500 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATATATAAATTTAAATTTAAAAAT
Found at i:3607493 original size:22 final size:21
Alignment explanation
Indices: 3607455--3607495 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3607445 TATTTTAATT
3607455 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
3607476 TAAATATTAAATTA-AAAATA
1 TAAAT-TT-AATTATAAAATA
3607496 AAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:3609709 original size:20 final size:20
Alignment explanation
Indices: 3609660--3609701 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3609650 ATATATATAT
3609660 ATACATATATAAATATAGAC
1 ATACATATATAAATATAGAC
*
3609680 ATACATATATAAATATATAC
1 ATACATATATAAATATAGAC
3609700 AT
1 AT
3609702 TTATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (20 bp):
ATACATATATAAATATAGAC
Found at i:3609715 original size:20 final size:19
Alignment explanation
Indices: 3609692--3609783 Score: 72
Period size: 20 Copynumber: 5.1 Consensus size: 19
3609682 ACATATATAA
3609692 ATATATACATTTATATATGT
1 ATATATA-ATTTATATATGT
3609712 ATATAT-A--TATATATG-
1 ATATATAATTTATATATGT
3609727 -TATAT-ATTTATATATGT
1 ATATATAATTTATATATGT
* *
3609744 ATGTCTATATTTATATATGT
1 ATATATA-ATTTATATATGT
* * *
3609764 ATGTAT-ATATACATATGT
1 ATATATAATTTATATATGT
3609782 AT
1 AT
3609784 GTATTGTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
14 6 0.10
16 16 0.26
18 16 0.26
20 23 0.38
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (19 bp):
ATATATAATTTATATATGT
Found at i:3609723 original size:8 final size:8
Alignment explanation
Indices: 3609650--3609779 Score: 98
Period size: 8 Copynumber: 16.2 Consensus size: 8
3609640 CAGATCTTAC
3609650 ATATATAT
1 ATATATAT
*
3609658 ATATACAT
1 ATATATAT
*
3609666 ATATAAAT
1 ATATATAT
* *
3609674 ATAGACAT
1 ATATATAT
*
3609682 ACATATAT
1 ATATATAT
*
3609690 AAATATAT
1 ATATATAT
* *
3609698 ACATTTAT
1 ATATATAT
*
3609706 ATATGTAT
1 ATATATAT
3609714 ATATATAT
1 ATATATAT
*
3609722 ATATGTAT
1 ATATATAT
*
3609730 ATATTTAT
1 ATATATAT
*
3609738 ATATGTAT
1 ATATATAT
* *
3609746 GTCTATAT
1 ATATATAT
*
3609754 TTATATAT
1 ATATATAT
* *
3609762 GTATGTAT
1 ATATATAT
*
3609770 ATATACAT
1 ATATATAT
3609778 AT
1 AT
3609780 GTATGTATTG
Statistics
Matches: 96, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 96 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (8 bp):
ATATATAT
Found at i:3610647 original size:12 final size:12
Alignment explanation
Indices: 3610622--3610654 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3610612 AAAAAATAAT
3610622 TATAATAT--AA
1 TATAATATAAAA
3610632 TATAATATAAAA
1 TATAATATAAAA
3610644 TATAATATAAA
1 TATAATATAAA
3610655 TATGCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TATAATATAAAA
Found at i:3612721 original size:48 final size:48
Alignment explanation
Indices: 3612663--3612759 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
3612653 ATCAAAGTTA
*
3612663 ATATATATAATTGAATTAAAAATAAATTTAAAATATTTTTTGGTACAG
1 ATATACATAATTGAATTAAAAATAAATTTAAAATATTTTTTGGTACAG
* * * *
3612711 ATATACATAATTGAATTAACAATAAGTTTAGAATATTTTTTGGTGCAG
1 ATATACATAATTGAATTAAAAATAAATTTAAAATATTTTTTGGTACAG
3612759 A
1 A
3612760 AAAATTTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (48 bp):
ATATACATAATTGAATTAAAAATAAATTTAAAATATTTTTTGGTACAG
Found at i:3613979 original size:31 final size:31
Alignment explanation
Indices: 3613943--3614002 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
3613933 TCATATATTG
3613943 ACAACTTATAGTGTATCCTTCAAATAATGCA
1 ACAACTTATAGTGTATCCTTCAAATAATGCA
3613974 ACAACTTATAGTGTATCCTTCAAATAATG
1 ACAACTTATAGTGTATCCTTCAAATAATG
3614003 TTGCATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (31 bp):
ACAACTTATAGTGTATCCTTCAAATAATGCA
Found at i:3620062 original size:21 final size:21
Alignment explanation
Indices: 3620036--3620082 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3620026 TAATTTATAT
*
3620036 TAAATTTAATAT-TAAATTAAA
1 TAAATTTAAAATATAAA-TAAA
3620057 TAAA-TTAAAATATAAATAAA
1 TAAATTTAAAATATAAATAAA
3620077 -AAATTT
1 TAAATTT
3620083 TAACTACGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAAAATATAAATAAA
Found at i:3620484 original size:22 final size:22
Alignment explanation
Indices: 3620426--3620493 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 22
3620416 TTTTAAAAAT
*
3620426 AAAATATATTTATTAAATTTAATTA
1 AAAATAT-TTTATTATATTT--TTA
* **
3620451 ATAATAACTTATTATATTTTTA
1 AAAATATTTTATTATATTTTTA
*
3620473 AAAATATTTTATATTTATTTT
1 AAAATATTTTAT-TATATTTT
3620494 ATTTATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 12 0.35
23 7 0.21
24 10 0.29
25 5 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
AAAATATTTTATTATATTTTTA
Found at i:3620681 original size:31 final size:32
Alignment explanation
Indices: 3620601--3620690 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
3620591 ATATTTTATT
*
3620601 AAAAAATTAAAAATATGTTATAAATATATATA
1 AAAAAATTAAAAATATATTATAAATATATATA
* *
3620633 AAAAATATTTAAAATAT-TGATAAAT-T-TA-A
1 AAAAA-ATTAAAAATATATTATAAATATATATA
*
3620662 AAAAAATTAAAATATATATTTATACATAT
1 AAAAAATTAAAA-ATATA-TTATAAATAT
3620691 GAATATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
28 6 0.12
29 10 0.21
30 2 0.04
31 7 0.15
32 13 0.27
33 10 0.21
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (32 bp):
AAAAAATTAAAAATATATTATAAATATATATA
Found at i:3621427 original size:25 final size:25
Alignment explanation
Indices: 3621399--3621456 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3621389 TATTTACGTT
*
3621399 AATTAAACA-TATCAAATTTTAAATA
1 AATTAAA-AGTATCAAATTATAAATA
* *
3621424 AATTAAAAGTATTAAATTATATATA
1 AATTAAAAGTATCAAATTATAAATA
3621449 ACATTAAA
1 A-ATTAAA
3621457 TATGTCTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.75
26 6 0.21
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (25 bp):
AATTAAAAGTATCAAATTATAAATA
Found at i:3624100 original size:2 final size:2
Alignment explanation
Indices: 3624088--3624132 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
3624078 ATCTTTACAG
3624088 AT AT AT CAT 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 AT
3624131 AT
1 AT
3624133 GCAAGCAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3625082 original size:18 final size:18
Alignment explanation
Indices: 3625059--3625094 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3625049 TTGTAACATT
*
3625059 ATAAAAATTAAAAATTAA
1 ATAAAAAATAAAAATTAA
*
3625077 ATAAAAAATAAAATTTAA
1 ATAAAAAATAAAAATTAA
3625095 TTCTATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAAATAAAAATTAA
Found at i:3626496 original size:20 final size:21
Alignment explanation
Indices: 3626473--3626531 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
3626463 AGTTAAATTA
*
3626473 ATTATATTAATAA-TAAAAAT
1 ATTATAATAATAATTAAAAAT
3626493 ATTATAATAATAATTTAAAAAT
1 ATTATAATAATAA-TTAAAAAT
* *
3626515 ATAATAAATACTAATTA
1 ATTAT-AATAATAATTA
3626532 TATTTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 12 0.36
22 14 0.42
23 7 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTATAATAATAATTAAAAAT
Found at i:3626764 original size:18 final size:19
Alignment explanation
Indices: 3626729--3626767 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3626719 AATTATTTTT
*
3626729 TAAAAATATGATATTTAAA
1 TAAAAATATGATAATTAAA
*
3626748 TAAAAAT-TTATAATTAAA
1 TAAAAATATGATAATTAAA
3626766 TA
1 TA
3626768 TTTAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAAATATGATAATTAAA
Found at i:3626853 original size:14 final size:14
Alignment explanation
Indices: 3626836--3626877 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3626826 AAAAGTTTTT
3626836 AATTTTAAAAAATA
1 AATTTTAAAAAATA
*
3626850 AATTATAAAATAA-A
1 AATTTTAAAA-AATA
*
3626864 AATTTTTAAAAATA
1 AATTTTAAAAAATA
3626878 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATTTTAAAAAATA
Found at i:3627172 original size:39 final size:39
Alignment explanation
Indices: 3627106--3627182 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
3627096 TCCGAAAGAC
* *
3627106 AAAGTAAATGAATAGAACATTCGGAGAAAACTAAACTAG
1 AAAGTAAATGAATACAACATTCCGAGAAAACTAAACTAG
*
3627145 AAAGTAAATGAATACAATATTCCGAGAAAACTAAACTA
1 AAAGTAAATGAATACAACATTCCGAGAAAACTAAACTA
3627183 AACTAAGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (39 bp):
AAAGTAAATGAATACAACATTCCGAGAAAACTAAACTAG
Found at i:3627503 original size:2 final size:2
Alignment explanation
Indices: 3627496--3627525 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3627486 CATGAGTGTT
3627496 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
3627526 ATTAATTGAG
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):
TA
Found at i:3627817 original size:18 final size:19
Alignment explanation
Indices: 3627785--3627820 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3627775 TCATTTTGCT
3627785 TCTAAAAATAATTACTCAC
1 TCTAAAAATAATTACTCAC
*
3627804 TCTAAAAA-ATTTACTCA
1 TCTAAAAATAATTACTCA
3627821 TATTTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (19 bp):
TCTAAAAATAATTACTCAC
Found at i:3629079 original size:37 final size:36
Alignment explanation
Indices: 3629037--3629157 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 36
3629027 TACTTTTAAC
*
3629037 ATAAATATGATTTTAATAATTATAATTATTATTTAGT
1 ATAAATATAATTTTAATAATTATAATTATTATTTA-T
* *
3629074 ATAAATTTAATTTTGAT-A-TA-AATTATTCA---AT
1 ATAAATATAATTTTAATAATTATAATTATT-ATTTAT
* *
3629105 ATAAATATATTTTTAATAATTTTTAATTATTTATTATAT
1 ATAAATATAATTTTAATAA-TTATAATTA-TTATT-TAT
3629144 ATAAATATAATTTT
1 ATAAATATAATTTT
3629158 TTTAATCTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
31 15 0.23
32 2 0.03
34 8 0.12
35 9 0.14
36 3 0.05
37 14 0.21
39 15 0.23
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (36 bp):
ATAAATATAATTTTAATAATTATAATTATTATTTAT
Found at i:3629355 original size:22 final size:22
Alignment explanation
Indices: 3629330--3629372 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3629320 AAATTTTAGT
*
3629330 TAAAT-TTAATTATTAAAATATA
1 TAAATATTAA-TATAAAAATATA
3629352 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
3629373 TTATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:3630738 original size:14 final size:14
Alignment explanation
Indices: 3630721--3630750 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3630711 TTTATCTTAA
*
3630721 TTAATTTATTCAAT
1 TTAATTTAATCAAT
3630735 TTAATTTAATCAAT
1 TTAATTTAATCAAT
3630749 TT
1 TT
3630751 TAATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATTTAATCAAT
Found at i:3631544 original size:20 final size:19
Alignment explanation
Indices: 3631517--3631558 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3631507 ATAATATTAA
3631517 TTATTAAA-ATATTAAAATT
1 TTATTAAATATA-TAAAATT
*
3631536 TTATATAAATATATAATATT
1 TTAT-TAAATATATAAAATT
3631556 TTA
1 TTA
3631559 AATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTAAATATATAAAATT
Found at i:3631570 original size:20 final size:20
Alignment explanation
Indices: 3631523--3631574 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3631513 TTAATTATTA
* *
3631523 AAATAT-TAAAATTTTATAT
1 AAATATATAATATTTTAAAT
3631542 AAATATATAATATTTTAAAT
1 AAATATATAATATTTTAAAT
3631562 ATAAT-TATAATAT
1 A-AATATATAATAT
3631575 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.69
21 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATATAATATTTTAAAT
Found at i:3634886 original size:24 final size:24
Alignment explanation
Indices: 3634840--3634884 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3634830 TTCATAAATA
3634840 TTTCTTTTTTAAATTAATTTTTAT
1 TTTCTTTTTTAAATTAATTTTTAT
3634864 TTTCTTTTTTAAA-TAATTTTT
1 TTTCTTTTTTAAATTAATTTTT
3634885 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTCTTTTTTAAATTAATTTTTAT
Found at i:3635169 original size:21 final size:20
Alignment explanation
Indices: 3635126--3635170 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3635116 AATATTTGAC
* *
3635126 AATA-TATAAAAATAATTAA
1 AATATTATAAAAAAAATAAA
3635145 AATATTATAAAATAAAATAAA
1 AATATTATAAAA-AAAATAAA
3635166 AATAT
1 AATAT
3635171 GAACATGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
21 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATTATAAAAAAAATAAA
Found at i:3635330 original size:19 final size:18
Alignment explanation
Indices: 3635306--3635351 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
3635296 ATAATATTTT
3635306 TATAAATTTAATTATAAAA
1 TATAAATTTAATTA-AAAA
3635325 TATAAATATTAATTAAAAA
1 TATAAAT-TTAATTAAAAA
3635344 TA-AAATTT
1 TATAAATTT
3635352 TGAATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 4 0.15
19 13 0.50
20 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATTTAATTAAAAA
Found at i:3635501 original size:15 final size:15
Alignment explanation
Indices: 3635478--3635520 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3635468 AGAATATCTC
3635478 AAAATTTATATAATA
1 AAAATTTATATAATA
* *
3635493 AAAAATTATCAT-ATT
1 AAAATTTAT-ATAATA
3635508 AAAATTTATATAA
1 AAAATTTATATAA
3635521 ATATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTATATAATA
Found at i:3635536 original size:27 final size:26
Alignment explanation
Indices: 3635459--3635537 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
3635449 TGAGTAAGTT
* *
3635459 TATAATATAAGAATATCTCAAAATTTA
1 TATAATATAA-AATATTTTAAAATTTA
*
3635486 TATAATAAAAAATTATCATATTAAAATTTA
1 TATAATATAAAA-TAT--T-TTAAAATTTA
3635516 TATAAATATAAAATATTTTAAA
1 TAT-AATATAAAATATTTTAAA
3635538 TATAATTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 2 0.05
27 17 0.40
28 1 0.02
30 15 0.35
31 8 0.19
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (26 bp):
TATAATATAAAATATTTTAAAATTTA
Found at i:3639509 original size:2 final size:2
Alignment explanation
Indices: 3639502--3639543 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3639492 GACACCGGTG
3639502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3639543 A
1 A
3639544 ATTAGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3640427 original size:22 final size:24
Alignment explanation
Indices: 3640402--3640446 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3640392 GTGAAAAAAA
3640402 TTTAAATT-TAATTTTTT-TTATT
1 TTTAAATTATAATTTTTTATTATT
*
3640424 TTTATATTATAATTTTTTATTAT
1 TTTAAATTATAATTTTTTATTAT
3640447 AAAAACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTAAATTATAATTTTTTATTATT
Found at i:3640529 original size:12 final size:12
Alignment explanation
Indices: 3640512--3640536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3640502 TTATATTATG
3640512 TAAATTATAAAT
1 TAAATTATAAAT
3640524 TAAATTATAAAT
1 TAAATTATAAAT
3640536 T
1 T
3640537 TATTAATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATTATAAAT
Found at i:3641089 original size:29 final size:30
Alignment explanation
Indices: 3641052--3641115 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
3641042 CGATAAAGTG
*
3641052 AATATTTTAATTTTTATATTATTAAATT-T
1 AATAATTTAATTTTTATATTATTAAATTAT
* *
3641081 AATAATTTAATTTTTATGTTTTTAAATTAT
1 AATAATTTAATTTTTATATTATTAAATTAT
3641111 AATAA
1 AATAA
3641116 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
AATAATTTAATTTTTATATTATTAAATTAT
Found at i:3641174 original size:19 final size:18
Alignment explanation
Indices: 3641110--3641174 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
3641100 TTTTAAATTA
*
3641110 TAATAAATAAAAAATAATT
1 TAATATATAAAAAAT-ATT
3641129 TAGAGTAT-TAAAAAATATTT
1 TA-A-TATATAAAAAATA-TT
3641149 TAA-ATATAATAAAATATT
1 TAATATATAA-AAAATATT
3641167 TAATATAT
1 TAATATAT
3641175 CATATTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 14 0.36
20 13 0.33
21 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATATATAAAAAATATT
Found at i:3641313 original size:21 final size:22
Alignment explanation
Indices: 3641289--3641329 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3641279 ATACTTTATT
3641289 AATATT-TAAATAATTTTTTTA
1 AATATTATAAATAATTTTTTTA
* *
3641310 AATATTATTAATTATTTTTT
1 AATATTATAAATAATTTTTT
3641330 ATTTATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AATATTATAAATAATTTTTTTA
Found at i:3641336 original size:21 final size:20
Alignment explanation
Indices: 3641303--3641342 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3641293 TTTAAATAAT
3641303 TTTTTTAAATATTATTAATTA
1 TTTTTTAAATATTA-TAATTA
**
3641324 TTTTTTATTTATTATAATT
1 TTTTTTAAATATTATAATT
3641343 TAAAACTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTAAATATTATAATTA
Found at i:3641385 original size:29 final size:30
Alignment explanation
Indices: 3641333--3641393 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
3641323 ATTTTTTATT
*
3641333 TATTATAATTTAAAACTATGAAAATTAAAA
1 TATTATAATTTAAAACTATAAAAATTAAAA
* * *
3641363 TATTA-AATTTAATAGTATAAAAATTATAA
1 TATTATAATTTAAAACTATAAAAATTAAAA
3641392 TA
1 TA
3641394 CTTTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (30 bp):
TATTATAATTTAAAACTATAAAAATTAAAA
Found at i:3642032 original size:17 final size:17
Alignment explanation
Indices: 3641990--3642041 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
3641980 GAATAAATAA
3641990 AATATTAAAATTTATAT
1 AATATTAAAATTTATAT
3642007 AATA-T-AAA-TTATTAT
1 AATATTAAAATTTA-TAT
3642022 AATATTAAAATTTATAT
1 AATATTAAAATTTATAT
3642039 AAT
1 AAT
3642042 TTATAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.10
15 10 0.32
16 2 0.06
17 13 0.42
18 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATTAAAATTTATAT
Found at i:3642036 original size:15 final size:15
Alignment explanation
Indices: 3641990--3642037 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3641980 GAATAAATAA
3641990 AATATTAAAATTTAT
1 AATATTAAAATTTAT
*
3642005 -ATAATATAAATTATTAT
1 AAT-AT-TAAAAT-TTAT
3642022 AATATTAAAATTTAT
1 AATATTAAAATTTAT
3642037 A
1 A
3642038 TAATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 7 0.26
16 10 0.37
17 6 0.22
18 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTAAAATTTAT
Found at i:3652686 original size:2 final size:2
Alignment explanation
Indices: 3652679--3652720 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3652669 CTAGTAATTC
3652679 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3652721 GTGTTTTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3655494 original size:20 final size:18
Alignment explanation
Indices: 3655469--3655508 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
3655459 AGTTCAAAAA
3655469 TTTAATCAAAGTTTTTTATT
1 TTTAAT-AAA-TTTTTTATT
*
3655489 TTTAATATATTTTTTATT
1 TTTAATAAATTTTTTATT
3655507 TT
1 TT
3655509 AAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAATAAATTTTTTATT
Found at i:3655516 original size:17 final size:18
Alignment explanation
Indices: 3655480--3655516 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3655470 TTAATCAAAG
*
3655480 TTTTTTATTTTTAATATA
1 TTTTTTATTTTAAATATA
3655498 TTTTTTATTTTAAAT-TA
1 TTTTTTATTTTAAATATA
3655515 TT
1 TT
3655517 AAGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTATTTTAAATATA
Found at i:3658114 original size:2 final size:2
Alignment explanation
Indices: 3658107--3658143 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3658097 TTCCCCTTGA
3658107 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3658144 TATATTGACA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3661756 original size:2 final size:2
Alignment explanation
Indices: 3661749--3661787 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3661739 TTAAAGGGTC
*
3661749 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3661788 CTTAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3665861 original size:18 final size:18
Alignment explanation
Indices: 3665838--3665874 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3665828 GAAAATCCAT
3665838 TGGTCTAGGGTTAGTGTA
1 TGGTCTAGGGTTAGTGTA
3665856 TGGTCTAGGGTTAGTGTA
1 TGGTCTAGGGTTAGTGTA
3665874 T
1 T
3665875 AGATTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.38, T:0.41
Consensus pattern (18 bp):
TGGTCTAGGGTTAGTGTA
Found at i:3669246 original size:19 final size:18
Alignment explanation
Indices: 3669221--3669264 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3669211 TTAAATTTTA
3669221 ATATATTAATAATATATATT
1 ATATATTAAT-AT-TATATT
*
3669241 -TATATTTATATTATATT
1 ATATATTAATATTATATT
3669258 ATATATT
1 ATATATT
3669265 TTAATTATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATTAATATTATATT
Found at i:3669252 original size:12 final size:13
Alignment explanation
Indices: 3669221--3669265 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
3669211 TTAAATTTTA
* *
3669221 ATATATTAATAAT
1 ATATATTTATATT
3669234 ATATATTTATATT
1 ATATATTTATATT
3669247 -TATA-TTATATT
1 ATATATTTATATT
3669258 ATATATTT
1 ATATATTT
3669266 TAATTATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 8 0.29
13 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATATTTATATT
Found at i:3669271 original size:18 final size:16
Alignment explanation
Indices: 3669230--3669273 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
3669220 AATATATTAA
3669230 TAATATATATTTATATT
1 TAAT-TATATTTATATT
3669247 TATATTATATTATATATTT
1 TA-ATTATATT-TATA-TT
3669266 TAATTATA
1 TAATTATA
3669274 CTTTTATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTATATTTATATT
Found at i:3669568 original size:2 final size:2
Alignment explanation
Indices: 3669561--3669585 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3669551 TTATTTTTCT
3669561 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3669586 TTTAAATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3672884 original size:3 final size:3
Alignment explanation
Indices: 3672876--3672901 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3672866 AAAAATAAGT
3672876 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3672902 TACAATGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3675772 original size:2 final size:2
Alignment explanation
Indices: 3675767--3675812 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3675757 TTTTTTTATG
3675767 AT 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 AT
3675809 AT AT
1 AT AT
3675813 TGCTGTAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3679020 original size:15 final size:15
Alignment explanation
Indices: 3678991--3679046 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3678981 TTTTTAATTT
3678991 ATAAATAAAATTTAA
1 ATAAATAAAATTTAA
3679006 ATAAGATAAAA-TTAA
1 ATAA-ATAAAATTTAA
* ** *
3679021 ATATATTTAATTAAA
1 ATAAATAAAATTTAA
3679036 TATAAATAAAA
1 -ATAAATAAAA
3679047 ATAAGGTCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
14 4 0.13
15 14 0.45
16 13 0.42
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAAATAAAATTTAA
Found at i:3679228 original size:2 final size:2
Alignment explanation
Indices: 3679221--3679269 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3679211 CCACTTTGTT
*
3679221 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3679263 TC TC TC T
1 TC TC TC T
3679270 ACTTTTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3680801 original size:20 final size:22
Alignment explanation
Indices: 3680747--3680819 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 22
3680737 GATACTATTT
3680747 TTTA-TTATATTTTTATAAATTA
1 TTTATTTATA-TTTTATAAATTA
* *
3680769 TTTATATAAATTTTA-AAA-TA
1 TTTATTTATATTTTATAAATTA
*
3680789 TTTATTTATATTTT-TAATTTA
1 TTTATTTATATTTTATAAATTA
3680810 TTCT-TTTATA
1 TT-TATTTATA
3680820 ATTAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 16 0.38
21 13 0.31
22 10 0.24
23 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTATATTTTATAAATTA
Found at i:3681138 original size:17 final size:17
Alignment explanation
Indices: 3681112--3681160 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3681102 ATAAATAACA
*
3681112 AATAAAATTATTAATAT
1 AATAATATTATTAATAT
3681129 AATAATATTATT-ATA-
1 AATAATATTATTAATAT
3681144 AA-AATA-TATTAAT-T
1 AATAATATTATTAATAT
3681158 AAT
1 AAT
3681161 TTTAAAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 2 0.07
16 3 0.11
17 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATATTATTAATAT
Found at i:3681266 original size:27 final size:27
Alignment explanation
Indices: 3681235--3681315 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
3681225 AATATGACTA
*
3681235 ATAATGATATTTTTAAACT-TATTATAC
1 ATAATAATATTTTTAAA-TATATTATAC
*
3681262 ATAATAATATTTTTAAATATATTATAA
1 ATAATAATATTTTTAAATATATTATAC
* * *
3681289 ATATTATTATATTTAATATAATATTAT
1 ATAATAATATTTTTAA-AT-ATATTAT
3681316 TACTATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.02
27 36 0.78
28 2 0.04
29 7 0.15
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (27 bp):
ATAATAATATTTTTAAATATATTATAC
Found at i:3682058 original size:25 final size:26
Alignment explanation
Indices: 3682000--3682060 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
3681990 TTAAATTATT
* **
3682000 ATTTAATAATAAAATATTTTTATTTAA
1 ATTTAATTATAAAATAAATTTA-TTAA
3682027 ATTTAATTATAAAATAAATTTA-TAA
1 ATTTAATTATAAAATAAATTTATTAA
3682052 ATTTAATTA
1 ATTTAATTA
3682061 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 12 0.39
27 19 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATTATAAAATAAATTTATTAA
Found at i:3682062 original size:29 final size:30
Alignment explanation
Indices: 3682029--3682085 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
3682019 TTATTTAAAT
3682029 TTAATTATAAAAT-A-AATTTATAAATTTAA
1 TTAATTATAAAATAATAATTTA-AAATTTAA
* *
3682058 TTAATTTTTAAATAATAATTTAAAATTT
1 TTAATTATAAAATAATAATTTAAAATTT
3682086 TAAAATAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 7 0.29
31 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATTATAAAATAATAATTTAAAATTTAA
Found at i:3682072 original size:21 final size:19
Alignment explanation
Indices: 3682048--3682110 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 19
3682038 AAATAAATTT
3682048 ATAAATTTAATTAATTTTTAA
1 ATAAATTTAA--AATTTTTAA
*
3682069 ATAATAATTTAAAATTTTAAA
1 AT-A-AATTTAAAATTTTTAA
*
3682090 ATAGATCTTAAAAATTTTTAA
1 ATAAAT-TT-AAAATTTTTAA
3682111 GGATCATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 22 0.63
22 1 0.03
23 7 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAAATTTAAAATTTTTAA
Found at i:3682488 original size:20 final size:20
Alignment explanation
Indices: 3682443--3682488 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3682433 AAGACTTTTA
*
3682443 ATTTGTTATATGTTTAATTAT
1 ATTT-TTATATGTTTAACTAT
* *
3682464 TTTTTTATATTTTTAACTAT
1 ATTTTTATATGTTTAACTAT
3682484 ATTTT
1 ATTTT
3682489 AATTAATCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
ATTTTTATATGTTTAACTAT
Found at i:3686568 original size:12 final size:12
Alignment explanation
Indices: 3686551--3686735 Score: 69
Period size: 10 Copynumber: 15.9 Consensus size: 12
3686541 GTATATATTT
3686551 TATATATTTATA
1 TATATATTTATA
*
3686563 TATATATTT-GA
1 TATATATTTATA
3686574 TAT-TATTTA-A
1 TATATATTTATA
3686584 TAT-T-TTTAT-
1 TATATATTTATA
3686593 TAT-TATTTTATTAA
1 TATATA-TTTA-T-A
* *
3686607 AATTATATTTAAAA
1 TA-TATATTT-ATA
3686621 TATATATTT-TA
1 TATATATTTATA
*
3686632 -ATATATTAATA
1 TATATATTTATA
* *
3686643 -ATTTTAATTATA
1 TA-TATATTTATA
* *
3686655 TAAATTTTGATATA
1 TATATATT--TATA
3686669 TTAATATATTTAT-
1 -T-ATATATTTATA
*
3686682 TTTATATTTATA
1 TATATATTTATA
3686694 T-TA-ATTTATA
1 TATATATTTATA
3686704 TAT-TATTTATA
1 TATATATTTATA
*
3686715 -AT-TATTTTTA
1 TATATATTTATA
*
3686725 TATTTATTTAT
1 TATATATTTAT
3686736 TTTATGATAT
Statistics
Matches: 133, Mismatches: 18, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
9 8 0.06
10 34 0.26
11 33 0.25
12 27 0.20
13 8 0.06
14 10 0.08
15 5 0.04
16 8 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
TATATATTTATA
Found at i:3686568 original size:21 final size:21
Alignment explanation
Indices: 3686542--3686586 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3686532 ACATTAATTG
*
3686542 TATATATTTTATA-TATTTATA
1 TATATATTTGATATTATTTA-A
3686563 TATATATTTGATATTATTTAA
1 TATATATTTGATATTATTTAA
3686584 TAT
1 TAT
3686587 TTTTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATATATTTGATATTATTTAA
Found at i:3686637 original size:14 final size:14
Alignment explanation
Indices: 3686551--3686669 Score: 50
Period size: 14 Copynumber: 8.2 Consensus size: 14
3686541 GTATATATTT
3686551 TATATA-TTT-ATA
1 TATATATTTTAATA
*
3686563 TATATATTTGATATTA
1 TATATATTT--TAATA
* *
3686579 TTTAATATTTTTAT-
1 TAT-ATATTTTAATA
*
3686593 TAT-TATTTTATTA
1 TATATATTTTAATA
* *
3686606 -AAATTATATTTAAAA
1 TATA-TAT-TTTAATA
3686621 TATATATTTTAATA
1 TATATATTTTAATA
3686635 TATTAATAATTTTAATTA
1 TA-T-AT-ATTTTAA-TA
* *
3686653 TATAAATTTTGATA
1 TATATATTTTAATA
3686667 TAT
1 TAT
3686670 TAATATATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 26
0.66 0.12 0.22
Matches are distributed among these distances:
12 14 0.18
13 2 0.03
14 18 0.23
15 18 0.23
16 9 0.11
17 14 0.18
18 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATATATTTTAATA
Found at i:3686689 original size:11 final size:11
Alignment explanation
Indices: 3686673--3686733 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
3686663 GATATATTAA
3686673 TATATTTATTT
1 TATATTTATTT
*
3686684 TATATTTATAT
1 TATATTTATTT
3686695 TA-ATTTA---
1 TATATTTATTT
3686702 TATA-TTA-TT
1 TATATTTATTT
*
3686711 TATAATTATTTT
1 TATATTTA-TTT
3686723 TATATTTATTT
1 TATATTTATTT
3686734 ATTTTATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
9 4 0.10
10 8 0.19
11 15 0.36
12 9 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATTT
Found at i:3686691 original size:6 final size:6
Alignment explanation
Indices: 3686673--3686731 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
3686663 GATATATTAA
* *
3686673 TATATT TAT-TT TATATT TATA-T TA-ATT TATATA T-TATT TATAAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
*
3686717 TATTTT TATATT TAT
1 TATATT TATATT TAT
3686732 TTATTTTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 1 0.02
5 15 0.35
6 27 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:3686700 original size:39 final size:39
Alignment explanation
Indices: 3686624--3686745 Score: 110
Period size: 39 Copynumber: 3.1 Consensus size: 39
3686614 TTTAAAATAT
* *
3686624 ATATTTTAATATATTAATAATTTTA-A-TTATATAAATTTTG
1 ATATATTAATATATT--T-ATTTTATATTTATATTAATTTTG
3686664 ATATATTAATATATTTATTTTATATTTATATTAA-TTT-
1 ATATATTAATATATTTATTTTATATTTATATTAATTTTG
* * *
3686701 ATATATTATTTATAATTATTTTTATATTTAT-TTATTTTATG
1 ATATATTA-ATATATTTA-TTTTATATTTATATTAATTT-TG
3686742 ATAT
1 ATAT
3686746 TTACCTAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
37 14 0.20
38 15 0.21
39 22 0.31
40 15 0.21
41 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (39 bp):
ATATATTAATATATTTATTTTATATTTATATTAATTTTG
Found at i:3686703 original size:27 final size:27
Alignment explanation
Indices: 3686665--3686740 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
3686655 TAAATTTTGA
*
3686665 TATATTAA--TATATTTATTTTATATT
1 TATATTAATTTATATTTATTTTATAAT
3686690 TATATTAATTTATATATTA-TTTATAAT
1 TATATTAATTTATAT-TTATTTTATAAT
* *
3686717 TATTTTTATATT-TATTTATTTTAT
1 TATATTAAT-TTATATTTATTTTAT
3686741 GATATTTACC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 8 0.19
26 3 0.07
27 27 0.63
28 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATATTAATTTATATTTATTTTATAAT
Found at i:3686707 original size:25 final size:25
Alignment explanation
Indices: 3686665--3686740 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
3686655 TAAATTTTGA
* *
3686665 TATATTAATATATTTATTTTATATT
1 TATATTAATTTATTTATTTTATAAT
*
3686690 TATATTAATTTATATATTATTTATAAT
1 TATATTAATTTATTTA-T-TTTATAAT
*
3686717 TATTTTTATATTTATTTATTTTAT
1 TA-TATTA-ATTTATTTATTTTAT
3686741 GATATTTACC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
25 14 0.33
26 1 0.02
27 14 0.33
28 5 0.12
29 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATATTAATTTATTTATTTTATAAT
Found at i:3686740 original size:21 final size:23
Alignment explanation
Indices: 3686686--3686735 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
3686676 ATTTATTTTA
*
3686686 TATTTAT-ATTA-ATTTATATAT
1 TATTTATAATTATTTTTATATAT
3686707 TATTTATAATTATTTTTATAT-T
1 TATTTATAATTATTTTTATATAT
3686729 TATTTAT
1 TATTTAT
3686736 TTTATGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.27
22 12 0.46
23 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTATAATTATTTTTATATAT
Found at i:3690005 original size:3 final size:3
Alignment explanation
Indices: 3689997--3690026 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3689987 AGTTTATGGG
3689997 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3690027 TTGTTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3692864 original size:2 final size:2
Alignment explanation
Indices: 3692857--3692886 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3692847 AGAAAGCTAA
3692857 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3692887 ATAAGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3694791 original size:8 final size:8
Alignment explanation
Indices: 3694780--3694866 Score: 56
Period size: 8 Copynumber: 10.2 Consensus size: 8
3694770 TAAATACGAT
3694780 AATATATA
1 AATATATA
3694788 AATATATA
1 AATATATA
3694796 ATATATATA
1 A-ATATATA
3694805 TATATATATTA
1 -A-ATATA-TA
3694816 AATTTTATATA
1 AA---TATATA
3694827 AATATAT-
1 AATATATA
*
3694834 AATAATTTA
1 AAT-ATATA
3694843 AATA-ATA
1 AATATATA
3694850 TAAT-TAT-
1 -AATATATA
3694857 AATATATA
1 AATATATA
3694865 AA
1 AA
3694867 ATTAATATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
6 3 0.05
7 8 0.12
8 25 0.38
9 11 0.17
10 8 0.12
11 6 0.09
12 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AATATATA
Found at i:3694794 original size:2 final size:2
Alignment explanation
Indices: 3694781--3694834 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
3694771 AAATACGATA
* *
3694781 AT AT AT AA AT AT AT A- AT AT AT AT AT AT AT AT AT -T AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3694820 TT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT A
3694835 ATAATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3694854 original size:14 final size:16
Alignment explanation
Indices: 3694825--3694869 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
3694815 AAATTTTATA
3694825 TAAATATATAATAATT
1 TAAATATATAATAATT
3694841 TAAATA-AT-ATAA-T
1 TAAATATATAATAATT
3694854 TATAATATATAA-AATT
1 TA-AATATATAATAATT
3694870 AATATAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 6 0.24
16 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATATAATAATT
Found at i:3695732 original size:19 final size:17
Alignment explanation
Indices: 3695702--3695772 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
3695692 ACAACAAATA
3695702 AAATAT-AAATTTATAT
1 AAATATAAAATTTATAT
*
3695718 AATATATTAAAATTTTTAT
1 AA-ATA-TAAAATTTATAT
3695737 AAATATAAAATATTAT-T
1 AAATATAAAAT-TTATAT
*
3695754 AAA-ATAAAA-ATATAT
1 AAATATAAAATTTATAT
3695769 AAAT
1 AAAT
3695773 TTATGAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.07
15 4 0.09
16 8 0.17
17 13 0.28
18 7 0.15
19 11 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAAAATTTATAT
Found at i:3695964 original size:2 final size:2
Alignment explanation
Indices: 3695957--3695991 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3695947 TATGTGAAAC
*
3695957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3695992 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3696439 original size:11 final size:11
Alignment explanation
Indices: 3696423--3696454 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3696413 TTATAAATAT
3696423 ATTTTTTATTA
1 ATTTTTTATTA
*
3696434 ATTTTTTAATA
1 ATTTTTTATTA
3696445 ATTTTTTATT
1 ATTTTTTATT
3696455 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTATTA
Found at i:3696450 original size:12 final size:11
Alignment explanation
Indices: 3696418--3696452 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3696408 AAAAATTATA
3696418 AATATATTTTTT
1 AATA-ATTTTTT
*
3696430 ATTAATTTTTT
1 AATAATTTTTT
3696441 AATAATTTTTT
1 AATAATTTTTT
3696452 A
1 A
3696453 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AATAATTTTTT
Found at i:3696931 original size:17 final size:16
Alignment explanation
Indices: 3696906--3696945 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
3696896 AGAATTTAGA
*
3696906 AATAAATATTAAATAAT
1 AATATATATTAAAT-AT
3696923 AATATATATTAAATAT
1 AATATATATTAAATAT
3696939 AATATAT
1 AATATAT
3696946 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATATTAAATAT
Found at i:3702337 original size:26 final size:24
Alignment explanation
Indices: 3702295--3702346 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3702285 TATTGAGATA
*
3702295 AATTTAAATTTAAATTTTTATACATT
1 AATTTAAATATAAATTTTT-TA-ATT
3702321 AATTTAAA-ATAATATTTTTTAATT
1 AATTTAAATATAA-ATTTTTTAATT
3702345 AA
1 AA
3702347 AATAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 5 0.21
26 14 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTTAAATATAAATTTTTTAATT
Found at i:3702342 original size:20 final size:20
Alignment explanation
Indices: 3702319--3702366 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
3702309 TTTTTATACA
*
3702319 TTAATTTAAAATAATATTTT
1 TTAATTTAAAATAATATATT
3702339 TTAA-TTAAAATAATATATT
1 TTAATTTAAAATAATATATT
3702358 TT-ATTTAAA
1 TTAATTTAAA
3702367 TTTAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.81
20 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTTAAAATAATATATT
Found at i:3703967 original size:14 final size:14
Alignment explanation
Indices: 3703948--3703975 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3703938 CTTATTAAAA
3703948 AATATTTTTATATT
1 AATATTTTTATATT
3703962 AATATTTTTATATT
1 AATATTTTTATATT
3703976 TTATATAATT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:3704099 original size:21 final size:17
Alignment explanation
Indices: 3704082--3704153 Score: 65
Period size: 19 Copynumber: 4.1 Consensus size: 17
3704072 AAATTAAATC
3704082 AAAT-TATTTAATTTTT
1 AAATATATTTAATTTTT
3704098 AAATATATTTAATTTTT
1 AAATATATTTAATTTTT
* *
3704115 ATTAATTTATTTTATATTTT
1 A--AATATATTTAAT-TTTT
* *
3704135 ATATAATATTTAAATTTT
1 AAAT-ATATTTAATTTTT
3704153 A
1 A
3704154 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.09
17 13 0.29
18 7 0.16
19 16 0.36
20 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATATTTAATTTTT
Found at i:3704113 original size:16 final size:16
Alignment explanation
Indices: 3704082--3704115 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
3704072 AAATTAAATC
3704082 AAATTATTTAATTTTT
1 AAATTATTTAATTTTT
3704098 AAATATATTTAATTTTT
1 AAAT-TATTTAATTTTT
3704115 A
1 A
3704116 TTAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTATTTAATTTTT
Found at i:3704588 original size:24 final size:24
Alignment explanation
Indices: 3704561--3704630 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
3704551 AATAAAAATT
*
3704561 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
3704585 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
3704609 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
3704631 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:3704630 original size:27 final size:27
Alignment explanation
Indices: 3704563--3704659 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
3704553 TAAAAATTAG
* *
3704563 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
3704587 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
3704614 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
3704641 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
3704660 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:3704678 original size:24 final size:25
Alignment explanation
Indices: 3704647--3704704 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
3704637 GTAACCACCA
3704647 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAATGGTGGCTT
3704671 TTGTTGACAAACACAAATGGTGGCTT
1 TTGTTGACAAACAC-AATGGTGGCTT
3704697 TTGTTGAC
1 TTGTTGAC
3704705 TAGCCACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 14 0.44
26 18 0.56
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAATGGTGGCTT
Found at i:3709185 original size:24 final size:24
Alignment explanation
Indices: 3709158--3709227 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
3709148 AATAAAAATT
*
3709158 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
3709182 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
3709206 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
3709228 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:3709227 original size:27 final size:27
Alignment explanation
Indices: 3709160--3709256 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
3709150 TAAAAATTAG
* *
3709160 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
3709184 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
3709211 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
3709238 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
3709257 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:3709275 original size:24 final size:25
Alignment explanation
Indices: 3709244--3709301 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
3709234 GTAACCACCA
3709244 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAATGGTGGCTT
3709268 TTGTTGACAAACACAAATGGTGGCTT
1 TTGTTGACAAACAC-AATGGTGGCTT
3709294 TTGTTGAC
1 TTGTTGAC
3709302 TAGCCACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 14 0.44
26 18 0.56
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAATGGTGGCTT
Found at i:3709572 original size:23 final size:25
Alignment explanation
Indices: 3709527--3709573 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
3709517 TGACAACATT
*
3709527 ATTTTTTAAAATGATAATTTTATTA
1 ATTTTTTAAAATGATAATATTATTA
*
3709552 ATTTTTT-AAAT-ATTATATTATT
1 ATTTTTTAAAATGATAATATTATT
3709574 GACGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTTTTAAAATGATAATATTATTA
Found at i:3710761 original size:8 final size:8
Alignment explanation
Indices: 3710750--3710876 Score: 57
Period size: 8 Copynumber: 15.2 Consensus size: 8
3710740 TATTCATATA
3710750 ATATTTAT
1 ATATTTAT
*
3710758 ATATTTTT
1 ATATTTAT
3710766 ATATTATAAT
1 ATATT-T-AT
3710776 CATATTTA-
1 -ATATTTAT
3710784 ATATATTAT
1 ATAT-TTAT
*
3710793 ATGTTTAT
1 ATATTTAT
3710801 ATAAATATTATT
1 AT--AT-TTA-T
*
3710813 ATATTAAT
1 ATATTTAT
3710821 A-ATTTAT
1 ATATTTAT
* *
3710828 -TATATAA
1 ATATTTAT
3710835 AT-TTTAAT
1 ATATTT-AT
*
3710843 ATATTAAT
1 ATATTTAT
3710851 ATATTTATT
1 ATATTTA-T
*
3710860 TTATTTAT
1 ATATTTAT
*
3710868 -TTTTTAT
1 ATATTTAT
3710875 AT
1 AT
3710877 CATATAATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 30
0.67 0.10 0.22
Matches are distributed among these distances:
7 21 0.23
8 37 0.41
9 16 0.18
10 5 0.06
11 8 0.09
12 3 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:3710804 original size:30 final size:29
Alignment explanation
Indices: 3710729--3710858 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 29
3710719 ATGTAGATTA
* *
3710729 AATA-ATTCATATATTCATAT-AATATTT
1 AATATATTAATATATTTATATAAATATTT
** *
3710756 -ATATATTTTTATA-TTATA-ATCATATTT
1 AATATATTAATATATTTATATA-AATATTT
*
3710783 AATATATT-ATATGTTTATATAAATA-TT
1 AATATATTAATATATTTATATAAATATTT
* *
3710810 ATTATATTAATAATTTATTATATAAAT-TTT
1 AATATATTAAT-ATAT-TTATATAAATATTT
3710840 AATATATTAATATATTTAT
1 AATATATTAATATATTTAT
3710859 TTTATTTATT
Statistics
Matches: 82, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
26 7 0.09
27 25 0.30
28 21 0.26
29 7 0.09
30 22 0.27
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (29 bp):
AATATATTAATATATTTATATAAATATTT
Found at i:3710808 original size:14 final size:14
Alignment explanation
Indices: 3710797--3710852 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
3710787 TATTATATGT
3710797 TTATATAAATATTA
1 TTATATAAATATTA
*
3710811 TTATATTAATAATTTA
1 TTATATAAAT-A-TTA
*
3710827 TTATATAAATTTTA
1 TTATATAAATATTA
* *
3710841 ATATATTAATAT
1 TTATATAAATAT
3710853 ATTTATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 21 0.62
15 1 0.03
16 12 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATAAATATTA
Found at i:3710860 original size:22 final size:22
Alignment explanation
Indices: 3710748--3710862 Score: 62
Period size: 22 Copynumber: 5.1 Consensus size: 22
3710738 TATATTCATA
*
3710748 TAATAT-TTATATATTTTTATATT
1 TAATATATTA-ATATATTTAT-TT
3710771 ATAATCATATTTAATATATTATATGTT
1 -TAAT-ATA-TTAATATATT-TAT-TT
*
3710798 T-ATATA--AATAT-TATTATAT
1 TAATATATTAATATAT-TTATTT
* **
3710817 TAATA-ATTTATTATATAAATTT
1 TAATATA-TTAATATATTTATTT
3710839 TAATATATTAATATATTTATTT
1 TAATATATTAATATATTTATTT
3710861 TA
1 TA
3710863 TTTATTTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
19 3 0.04
20 7 0.10
21 6 0.09
22 26 0.37
23 2 0.03
24 7 0.10
25 4 0.06
26 7 0.10
27 8 0.11
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (22 bp):
TAATATATTAATATATTTATTT
Found at i:3710876 original size:30 final size:30
Alignment explanation
Indices: 3710797--3710876 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
3710787 TATTATATGT
*
3710797 TTATATAAATATTATTATATTAATAATTTA
1 TTATATAAATTTTATTATATTAATAATTTA
*
3710827 TTATATAAATTTTAATATATTAATATATTTA
1 TTATATAAATTTTATTATATTAATA-ATTTA
* **
3710858 TTTTATTTATTTT-TTATAT
1 TTATATAAATTTTATTATAT
3710877 CATATAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 28 0.65
31 15 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATAAATTTTATTATATTAATAATTTA
Found at i:3712024 original size:27 final size:27
Alignment explanation
Indices: 3712001--3712053 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
3711991 ATAATAATTA
*
3712001 GAAATATAATAAATATTATTATAATAAG
1 GAAAAATAATAAA-ATTATTATAATAAG
*
3712029 GAAAAATATTAAAATTATTA-AATAA
1 GAAAAATAATAAAATTATTATAATAA
3712054 TAATTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 7 0.30
28 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
GAAAAATAATAAAATTATTATAATAAG
Found at i:3712182 original size:17 final size:18
Alignment explanation
Indices: 3712159--3712197 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3712149 CTTTTTTAAA
3712159 ATTTTTTT-TAAT-TTTT
1 ATTTTTTTATAATATTTT
*
3712175 ATTTTTTTATCATATTTT
1 ATTTTTTTATAATATTTT
3712193 ATTTT
1 ATTTT
3712198 ATTCGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTTTATAATATTTT
Found at i:3712545 original size:11 final size:11
Alignment explanation
Indices: 3712515--3712577 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
3712505 TTACATGATT
*
3712515 ATATAATATAAA
1 ATATAA-ATATA
*
3712527 ATAAAAATATA
1 ATATAAATATA
3712538 ATATAAATATA
1 ATATAAATATA
*
3712549 TTATAAATAT-
1 ATATAAATATA
*
3712559 ATATATATATA
1 ATATAAATATA
3712570 TATATAAA
1 -ATATAAA
3712578 AGATTTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.19
11 23 0.55
12 11 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3712560 original size:2 final size:2
Alignment explanation
Indices: 3712533--3712575 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3712523 TAAAATAAAA
* *
3712533 AT AT A- AT AT AA AT AT AT -T AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3712573 AT A
1 AT A
3712576 AAAGATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3721696 original size:3 final size:3
Alignment explanation
Indices: 3721688--3721722 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3721678 TTGGTCGTAA
3721688 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
3721723 AGGTTTATTT
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:3722344 original size:3 final size:3
Alignment explanation
Indices: 3722336--3722379 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3722326 TTAATTTAAC
3722336 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3722380 CTCATTAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3722952 original size:19 final size:19
Alignment explanation
Indices: 3722905--3722952 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3722895 GGGGTGAATG
*
3722905 TATTTTAATTGATAAAATT
1 TATTTTATTTGATAAAATT
* * **
3722924 TAATTAATTTGATTCAATT
1 TATTTTATTTGATAAAATT
3722943 TATTTTATTT
1 TATTTTATTT
3722953 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TATTTTATTTGATAAAATT
Found at i:3723284 original size:14 final size:14
Alignment explanation
Indices: 3723256--3723288 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3723246 TTTTAAATTT
*
3723256 TTTAA-TTAATTAA
1 TTTAATTTAATCAA
3723269 TTTAATTTAATCAA
1 TTTAATTTAATCAA
3723283 TTTAAT
1 TTTAAT
3723289 ATTATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTTAATCAA
Found at i:3728696 original size:2 final size:2
Alignment explanation
Indices: 3728689--3728720 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3728679 ATATAATGGA
3728689 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
3728721 TTCTTTATAG
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:3733685 original size:2 final size:2
Alignment explanation
Indices: 3733678--3733713 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3733668 TTTACTTTCT
3733678 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3733714 GGTACCTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3733877 original size:24 final size:22
Alignment explanation
Indices: 3733843--3733887 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3733833 TAATTTATTT
3733843 TAAATTATTATTTATTAATTTAAA
1 TAAATTATTATTTA--AATTTAAA
*
3733867 TAAATTTTTATTTAAATTTAA
1 TAAATTATTATTTAAATTTAA
3733888 TTATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATTATTATTTAAATTTAAA
Found at i:3733881 original size:21 final size:21
Alignment explanation
Indices: 3733835--3733887 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
3733825 ATTTTAATTA
* *
3733835 ATTTATTTTAAATTATTATTT
1 ATTTAATTTAAATAATTATTT
3733856 A-TTAATTTAAATAAATT-TTT
1 ATTTAATTTAAAT-AATTATTT
3733876 ATTTAAATTTAA
1 ATTT-AATTTAA
3733888 TTATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 14 0.52
21 6 0.22
22 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTAATTTAAATAATTATTT
Found at i:3733929 original size:19 final size:20
Alignment explanation
Indices: 3733905--3733943 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3733895 ATTATAAATA
3733905 TTAATATATAAATA-ATTTT
1 TTAATATATAAATATATTTT
*
3733924 TTAATATTTAAATATATTTT
1 TTAATATATAAATATATTTT
3733944 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATATATAAATATATTTT
Found at i:3733948 original size:19 final size:19
Alignment explanation
Indices: 3733907--3733948 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3733897 TATAAATATT
*
3733907 AATATATAAATAATTTTTT
1 AATATATAAATAATTTTTA
*
3733926 AATATTTAAAT-ATATTTTA
1 AATATATAAATAAT-TTTTA
3733945 AATA
1 AATA
3733949 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATATAAATAATTTTTA
Found at i:3734309 original size:20 final size:20
Alignment explanation
Indices: 3734271--3734309 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3734261 ATTATATAAA
**
3734271 TATTAAAAATATTTTAATAT
1 TATTAAAAATATTAAAATAT
*
3734291 TATTATAAATATTAAAATA
1 TATTAAAAATATTAAAATA
3734310 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAAAAATATTAAAATAT
Found at i:3734316 original size:31 final size:28
Alignment explanation
Indices: 3734261--3734318 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
3734251 TTTAAATTTA
*
3734261 ATTATATAAATATTAAAAATATTTTAAT
1 ATTATATAAATATTAAAAAAATTTTAAT
3734289 ATTATTATAAATATTAAAATAAAATTTTAA
1 ATTA-TATAAATATT-AAA-AAAATTTTAA
3734319 ATCTATGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 3 0.12
31 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTATATAAATATTAAAAAAATTTTAAT
Found at i:3734470 original size:5 final size:5
Alignment explanation
Indices: 3734451--3734526 Score: 59
Period size: 5 Copynumber: 15.4 Consensus size: 5
3734441 AAATTTATTT
* * * *
3734451 ATATC ATATT ATATA ATATAA ATATA ATA-A AAATA ACTAAA ATATA ATATA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA A-TATA ATATA ATATA
* *
3734502 ATAAA AAAT- ATATA ATAT- ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
3734527 TTAAATTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 10 0.18
5 38 0.68
6 8 0.14
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:3734475 original size:11 final size:11
Alignment explanation
Indices: 3734461--3734525 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
3734451 ATATCATATT
3734461 ATATAATATAA
1 ATATAATATAA
3734472 ATATAATA-AA
1 ATATAATATAA
3734482 A-ATAACTA-AA
1 ATATAA-TATAA
3734492 ATATAATATAA
1 ATATAATATAA
* *
3734503 TAAAAAATATATA
1 -ATATAATATA-A
3734516 ATAT-ATATAA
1 ATATAATATAA
3734526 TTTAAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.09
10 11 0.24
11 19 0.42
12 10 0.22
13 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3734504 original size:19 final size:18
Alignment explanation
Indices: 3734470--3734525 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
3734460 TATATAATAT
* *
3734470 AAATATAATAAAAATAACTA
1 AAATATAAT-ATAATAA-AA
3734490 AAATATAATATAATAAAA
1 AAATATAATATAATAAAA
3734508 AATATATAATATATATAA
1 AA-ATATAATATA-ATAA
3734526 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.09
19 16 0.50
20 13 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATATAATATAATAAAA
Found at i:3734509 original size:26 final size:23
Alignment explanation
Indices: 3734460--3734526 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 23
3734450 TATATCATAT
*
3734460 TATATAATATAAATATAATAAAAA
1 TATAAAATAT-AATATAATAAAAA
3734484 TAACTAAAATATAATATAATAAAAAA
1 T-A-TAAAATATAATATAAT-AAAAA
*
3734510 TATATAATAT-ATATAAT
1 TATAAAATATAATATAAT
3734527 TTAAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.18
24 8 0.21
25 10 0.26
26 13 0.34
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (23 bp):
TATAAAATATAATATAATAAAAA
Found at i:3734584 original size:22 final size:22
Alignment explanation
Indices: 3734512--3734584 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
3734502 ATAAAAAATA
3734512 TATAATATATATAAT-TTA-AAT
1 TATAAT-TATATAATATTATAAT
*
3734533 TATTAATT-TATTAAAATT-T--T
1 TA-TAATTATA-TAATATTATAAT
*
3734553 TATAAATATATAATATTATAAT
1 TATAATTATATAATATTATAAT
3734575 TATAATTATA
1 TATAATTATA
3734585 ATATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
19 10 0.25
20 8 0.20
21 6 0.15
22 16 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAATTATATAATATTATAAT
Found at i:3738037 original size:2 final size:2
Alignment explanation
Indices: 3738024--3738053 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3738014 TGTAACTGTT
*
3738024 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3738054 CCTAAAACCA
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:3747894 original size:15 final size:15
Alignment explanation
Indices: 3747871--3747902 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3747861 ATTAGAAAAC
*
3747871 AAAATGAAAAAAAGA
1 AAAAAGAAAAAAAGA
3747886 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
3747901 AA
1 AA
3747903 GGATCTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Done.