Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 1 of 17
Found at i:2671 original size:21 final size:24
Alignment explanation
Indices: 2647--2712 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
2637 ATAATATTTT
*
2647 ATATTTAAAT-TTAAT-T-ATATA
1 ATATTTAAATATTAATATAAAATA
*
2668 ATATATAAATATTAATATAAAATA
1 ATATTTAAATATTAATATAAAATA
*
2692 ATATTT-AATATTATTATAAAA
1 ATATTTAAATATTAATATAAAA
2713 ATAAAACAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.24
22 5 0.13
23 15 0.39
24 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATTTAAATATTAATATAAAATA
Found at i:3283 original size:10 final size:10
Alignment explanation
Indices: 3270--3302 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3260 ATTAATAAAA
3270 AATATTTTTT
1 AATATTTTTT
3280 AATA-TTTTT
1 AATATTTTTT
*
3289 AATATTTTTA
1 AATATTTTTT
3299 AATA
1 AATA
3303 ATAATAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AATATTTTTT
Found at i:3289 original size:49 final size:51
Alignment explanation
Indices: 3210--3325 Score: 127
Period size: 52 Copynumber: 2.3 Consensus size: 51
3200 TATTATTATT
*
3210 TATTAATAAAAATATATTTTATTTTATTTT-A-A-TTATAAA-AATATATAAA
1 TATTAATAAAAA-ATATTTTATTATATTTTAATATTTATAAATAATA-ATAAA
*
3259 TATTAATAAAAAATATTTT-TTAATATTTTTAATATTTTTAAATAATAATAAA
1 TATTAATAAAAAATATTTTATT-ATA-TTTTAATATTTATAAATAATAATAAA
3311 -AGTTAATAAAAAATA
1 TA-TTAATAAAAAATA
3326 AAAAAAATCT
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
47 2 0.03
48 9 0.16
49 16 0.28
50 1 0.02
51 2 0.03
52 24 0.41
53 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.47
Consensus pattern (51 bp):
TATTAATAAAAAATATTTTATTATATTTTAATATTTATAAATAATAATAAA
Found at i:3296 original size:8 final size:9
Alignment explanation
Indices: 3270--3299 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3260 ATTAATAAAA
3270 AATATTTTTT
1 AATA-TTTTT
3280 AATATTTTT
1 AATATTTTT
3289 AATATTTTT
1 AATATTTTT
3298 AA
1 AA
3300 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:3575 original size:26 final size:28
Alignment explanation
Indices: 3545--3596 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
3535 CTCTTAATGA
*
3545 ATTATTTTAT-TAAAT-AATTTAATTTT
1 ATTATTTTATAAAAATAAATTTAATTTT
3571 ATTATTTTATAAAAATAAATTTAATT
1 ATTATTTTATAAAAATAAATTTAATT
3597 GAATACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 4 0.17
28 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTATTTTATAAAAATAAATTTAATTTT
Found at i:3609 original size:82 final size:82
Alignment explanation
Indices: 3523--3764 Score: 186
Period size: 82 Copynumber: 3.1 Consensus size: 82
3513 AGAATTTAAA
*
3523 AAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATTTAATTTTATTATTTTATAAAAATA
1 AAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATTAAATTTTATTATTTTATAAAAATA
3588 AATTTAATTGAATACAT
66 AATTTAATTGAATACAT
*** ** ** * * * * *
3605 AAAA--T-A-AAAT-TTAA--AAAAATTAAAGTACAATGATGAAATTTTA--A-ATTACCAAAAA
1 AAAATTTCATTCCTCTTAATGAATTATTTTATTA-AATAATTAAATTTTATTATTTTA-TAAAAA
* ** *
3660 -GAA-TTAACAGAATTTA-AA
64 TAAATTTAATTGAA--TACAT
*
3678 AAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATTCAATTTTATTATTTTATAAAAATA
1 AAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATTAAATTTTATTATTTTATAAAAATA
*
3743 AATTAAATTGAATACAT
66 AATTTAATTGAATACAT
3760 AAAAT
1 AAAAT
3765 AAAATTTTAA
Statistics
Matches: 108, Mismatches: 35, Indels: 34
0.61 0.20 0.19
Matches are distributed among these distances:
72 7 0.06
73 10 0.09
74 8 0.07
75 9 0.08
76 13 0.12
77 5 0.05
78 5 0.05
79 13 0.12
80 9 0.08
81 8 0.07
82 15 0.14
83 6 0.06
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (82 bp):
AAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATTAAATTTTATTATTTTATAAAAATA
AATTTAATTGAATACAT
Found at i:3679 original size:155 final size:155
Alignment explanation
Indices: 3499--3807 Score: 591
Period size: 155 Copynumber: 2.0 Consensus size: 155
3489 TTCATTTTAA
3499 CAAAAAGAATTAACAGAATTTAAAAAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATT
1 CAAAAAGAATTAACAGAATTTAAAAAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATT
* *
3564 TAATTTTATTATTTTATAAAAATAAATTTAATTGAATACATAAAATAAAATTTAAAAAAATTAAA
66 CAATTTTATTATTTTATAAAAATAAATTAAATTGAATACATAAAATAAAATTTAAAAAAATTAAA
3629 GTACAATGATGAAATTTTAAATTAC
131 GTACAATGATGAAATTTTAAATTAC
3654 CAAAAAGAATTAACAGAATTTAAAAAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATT
1 CAAAAAGAATTAACAGAATTTAAAAAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATT
*
3719 CAATTTTATTATTTTATAAAAATAAATTAAATTGAATACATAAAATAAAATTTTAAAAAATTAAA
66 CAATTTTATTATTTTATAAAAATAAATTAAATTGAATACATAAAATAAAATTTAAAAAAATTAAA
3784 GTACAATGATGAAATTTTAAATTA
131 GTACAATGATGAAATTTTAAATTA
3808 AATTATAATA
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (155 bp):
CAAAAAGAATTAACAGAATTTAAAAAAATTTCATTCCTCTTAATGAATTATTTTATTAAATAATT
CAATTTTATTATTTTATAAAAATAAATTAAATTGAATACATAAAATAAAATTTAAAAAAATTAAA
GTACAATGATGAAATTTTAAATTAC
Found at i:4053 original size:25 final size:23
Alignment explanation
Indices: 4019--4067 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
4009 TATTTTTAGT
*
4019 TTTAAAATTAATTTTATTTTAAAAA
1 TTTAAAATT-ATTTT-TTTAAAAAA
*
4044 TTTATAATTATTTTTTTAAAAAA
1 TTTAAAATTATTTTTTTAAAAAA
4067 T
1 T
4068 ATTTACACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 5 0.23
25 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAAATTATTTTTTTAAAAAA
Found at i:5157 original size:15 final size:16
Alignment explanation
Indices: 5137--5172 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5127 ATAATCATTT
5137 ATTTTAC-AAATAATA
1 ATTTTACAAAATAATA
*
5152 ATTTTACAAAATCATA
1 ATTTTACAAAATAATA
5168 ATTTT
1 ATTTT
5173 TATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTACAAAATAATA
Found at i:6061 original size:24 final size:23
Alignment explanation
Indices: 5992--6062 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 23
5982 TTATAAAATT
*
5992 AAAATATTAAAAA-TTTTATTT-
1 AAAATAATAAAAATTTTTATTTA
* ** *
6013 AATATAATAAAAATTTAAATATA
1 AAAATAATAAAAATTTTTATTTA
6036 AAAATAATAAAATATTTTTATTTA
1 AAAATAATAAAA-ATTTTTATTTA
6060 AAA
1 AAA
6063 TTTAACTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 11 0.29
22 5 0.13
23 11 0.29
24 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATAATAAAAATTTTTATTTA
Found at i:6418 original size:20 final size:19
Alignment explanation
Indices: 6395--6450 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 19
6385 TAATTATATT
6395 TAAAATATTTTATATTT-A
1 TAAAATATTTTATATTTAA
*
6413 TATAAAT-TTTAATATATTAA
1 TA-AAATATTTTATAT-TTAA
6433 TAAATTATATTTTATATT
1 TAAA--ATATTTTATATT
6451 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 9 0.30
19 8 0.27
20 3 0.10
21 3 0.10
22 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAAAATATTTTATATTTAA
Found at i:6435 original size:18 final size:17
Alignment explanation
Indices: 6388--6457 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 17
6378 TATATTATAA
6388 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
6404 TTATATTTATATAAATT
1 TTATATTTATATAAATT
6421 TTAATATATTA-ATAAATT
1 TT-ATAT-TTATATAAATT
* *
6439 ATAT-TTTATATTAATT
1 TTATATTTATATAAATT
6455 TTA
1 TTA
6458 AAATATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 3 0.07
16 18 0.39
17 8 0.17
18 14 0.30
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:6451 original size:20 final size:20
Alignment explanation
Indices: 6399--6453 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
6389 TATATTTAAA
6399 ATATTTTATATTTATATAAATT
1 ATATTTTATA-TTA-ATAAATT
**
6421 -T-TAATATATTAATAAATT
1 ATATTTTATATTAATAAATT
6439 ATATTTTATATTAAT
1 ATATTTTATATTAAT
6454 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 15 0.56
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTTATATTAATAAATT
Found at i:6455 original size:34 final size:36
Alignment explanation
Indices: 6404--6481 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 36
6394 TTAAAATATT
*
6404 TTATA-TTTATATAAATTTTAATATAT-TA-ATAAA
1 TTATATTTTATATAAATTTTAAAATATATATATAAA
* * *
6437 TTATATTTTATATTAATTTTAAAATATATATTTATA
1 TTATATTTTATATAAATTTTAAAATATATATATAAA
6473 TTATATTTT
1 TTATATTTT
6482 TAATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 5 0.13
34 19 0.50
35 2 0.05
36 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TTATATTTTATATAAATTTTAAAATATATATATAAA
Found at i:6470 original size:24 final size:25
Alignment explanation
Indices: 6433--6504 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
6423 AATATATTAA
*
6433 TAAATTATAT-TTTATATTA-ATTT
1 TAAAATATATATTTATATTATATTT
6456 TAAAATATATATTTATATTATATTT
1 TAAAATATATATTTATATTATATTT
* * *
6481 T-TAATTTTTATTTATATTATATTT
1 TAAAATATATATTTATATTATATTT
6505 ATATAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 9 0.21
24 29 0.67
25 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TAAAATATATATTTATATTATATTT
Found at i:6472 original size:6 final size:6
Alignment explanation
Indices: 6463--6508 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
6453 TTTTAAAATA
* *
6463 TATATT TATA-T TATATT TTTAATT TTTATT TATA-T TATATT TATAT
1 TATATT TATATT TATATT TAT-ATT TATATT TATATT TATATT TATAT
6509 AATTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 10 0.29
6 19 0.54
7 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:6873 original size:20 final size:21
Alignment explanation
Indices: 6848--6887 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6838 AATTATTGGT
6848 TATAAA-ATAACTTTTAAAAA
1 TATAAATATAACTTTTAAAAA
* *
6868 TATAAATATTATTTTTAAAA
1 TATAAATATAACTTTTAAAA
6888 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TATAAATATAACTTTTAAAAA
Found at i:7606 original size:22 final size:19
Alignment explanation
Indices: 7575--7616 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
7565 TATTTTTATT
7575 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
7596 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
7616 T
1 T
7617 TTTTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:7793 original size:2 final size:2
Alignment explanation
Indices: 7747--7782 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7737 TTTTCCAAAT
7747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7783 AATCAATATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9764 original size:22 final size:22
Alignment explanation
Indices: 9725--9767 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9715 TAATTAATAA
*
9725 AAATTTTATGATAATTAAATTT
1 AAATTTGATGATAATTAAATTT
9747 AAATTTGATG-TAATTTAAATT
1 AAATTTGATGATAA-TTAAATT
9768 AATAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
AAATTTGATGATAATTAAATTT
Found at i:9998 original size:13 final size:13
Alignment explanation
Indices: 9975--10033 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
9965 ACGTTATATT
9975 TAAATATATTA-A
1 TAAATATATTATA
9987 TAAATAATATTATA
1 TAAAT-ATATTATA
10001 T-AA-AT-TTA-A
1 TAAATATATTATA
10010 T--ATAT-TTATA
1 TAAATATATTATA
10020 TAAATATATTATA
1 TAAATATATTATA
10033 T
1 T
10034 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 1 0.03
9 7 0.17
10 5 0.12
11 2 0.05
12 9 0.22
13 14 0.35
14 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATATTATA
Found at i:10009 original size:32 final size:32
Alignment explanation
Indices: 9972--10033 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
9962 TATACGTTAT
9972 ATTTAA-ATATATTA-ATAAATAATATTATATAA
1 ATTTAATATAT-TTATATAAAT-ATATTATATAA
10004 ATTTAATATATTTATATAAATATATTATAT
1 ATTTAATATATTTATATAAATATATTATAT
10034 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTTAATATATTTATATAAATATATTATATAA
Found at i:10018 original size:19 final size:19
Alignment explanation
Indices: 9979--10036 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
9969 TATATTTAAA
*
9979 TATATTAATA-AATA-ATAT
1 TATATAAATATAATATAT-T
*
9997 TATATAAATTTAATATATT
1 TATATAAATATAATATATT
*
10016 TATATAAATATATTATATT
1 TATATAAATATAATATATT
10035 TA
1 TA
10037 AAATTTTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.24
19 24 0.71
20 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATAAATATAATATATT
Found at i:17338 original size:2 final size:2
Alignment explanation
Indices: 17333--17364 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17323 AAAAAATAAC
17333 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
17365 CGGAGTAATT
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:17971 original size:13 final size:14
Alignment explanation
Indices: 17934--17973 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
17924 ACAAGTATCG
*
17934 ATTTTTAAATTTTA
1 ATTTTTAAATATTA
17948 ATTTATTAAATATT-
1 ATTT-TTAAATATTA
17962 ATTTTTAAATAT
1 ATTTTTAAATAT
17974 AAAGTATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTAAATATTA
Found at i:21046 original size:18 final size:19
Alignment explanation
Indices: 21025--21071 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
21015 TTTACATTTA
21025 TATAATATTTATAT-ACTT
1 TATAATATTTATATCACTT
21043 TATAA-ATTT-TATCACTT
1 TATAATATTTATATCACTT
21060 T-TATATATTTAT
1 TATA-ATATTTAT
21072 TTTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 9 0.36
19 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAATATTTATATCACTT
Found at i:22266 original size:24 final size:24
Alignment explanation
Indices: 22225--22279 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
22215 ACATAAATAC
*
22225 ATATATTAAATATGTTATATTAATT
1 ATAT-TTAAATATATTATATTAATT
* *
22250 ATATTTAAATTTATTATATTTATT
1 ATATTTAAATATATTATATTAATT
22274 AT-TTTA
1 ATATTTA
22280 TTTTTGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 19 0.70
25 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATATTTAAATATATTATATTAATT
Found at i:25685 original size:34 final size:34
Alignment explanation
Indices: 25639--25823 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
25629 GTAAAAACCA
*
25639 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
25673 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
25707 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
25741 CCATTTAATCAACAATAGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
25775 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
25808 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
25824 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:25781 original size:102 final size:101
Alignment explanation
Indices: 25639--25823 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 101
25629 GTAAAAACCA
*
25639 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
25704 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
25741 CCATTTAATCAACAATAGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
25806 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
25824 TCTCCCACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 16 0.21
102 62 0.79
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:29916 original size:19 final size:19
Alignment explanation
Indices: 29889--29951 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
29879 TCACGTGTAC
* *
29889 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
29908 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
29927 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
29946 AGTACC
1 AGTACC
29952 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:30302 original size:34 final size:34
Alignment explanation
Indices: 30256--30439 Score: 255
Period size: 34 Copynumber: 5.4 Consensus size: 34
30246 GTAAAAACCA
*
30256 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
30290 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
30324 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
30358 CCATTTAATCAACAATAGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
30392 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
30425 CCATTTAATCAACAA
1 CCATTTAATCAACAA
30440 AACATACTCG
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:30398 original size:102 final size:101
Alignment explanation
Indices: 30256--30439 Score: 314
Period size: 102 Copynumber: 1.8 Consensus size: 101
30246 GTAAAAACCA
*
30256 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
30321 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
30358 CCATTTAATCAACAATAGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
30423 CACCATTTAATCAACAA
66 CACCATTTAATCAACAA
30440 AACATACTCG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 15 0.19
102 62 0.81
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATAGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:32165 original size:24 final size:26
Alignment explanation
Indices: 32128--32179 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
32118 GATTTAAAAT
*
32128 AATCATAAACATAA-AAAA-ATTTAA
1 AATCAAAAACATAATAAAATATTTAA
*
32152 AATCAAAAAGATAATAAAATATTTAA
1 AATCAAAAACATAATAAAATATTTAA
32178 AA
1 AA
32180 AATGAAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 4 0.17
26 8 0.33
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (26 bp):
AATCAAAAACATAATAAAATATTTAA
Found at i:32180 original size:27 final size:25
Alignment explanation
Indices: 32119--32180 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
32109 TATATTGATG
*
32119 ATTTAAAATAATCATAAACATAAAAAA
1 ATTT-AAA-AATCAAAAACATAAAAAA
*
32146 ATTT-AAAATCAAAAAGATAATAAAA
1 ATTTAAAAATCAAAAACATAA-AAAA
32171 TATTTAAAAA
1 -ATTTAAAAA
32181 ATGAAAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 12 0.40
25 6 0.20
26 4 0.13
27 8 0.27
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (25 bp):
ATTTAAAAATCAAAAACATAAAAAA
Found at i:34527 original size:33 final size:34
Alignment explanation
Indices: 34489--34552 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
34479 TTTTGAGATA
*
34489 ATATTTATCTCTAATATAATT-AAATTAAAAATG
1 ATATTTATCTCCAATATAATTAAAATTAAAAATG
* *
34522 ATATTTGTCTCCCATATAATTAAAATTAAAA
1 ATATTTATCTCCAATATAATTAAAATTAAAA
34553 TAGAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (34 bp):
ATATTTATCTCCAATATAATTAAAATTAAAAATG
Found at i:34723 original size:21 final size:22
Alignment explanation
Indices: 34698--34759 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
34688 ACTCAGCCCG
34698 ATTAAAATTATTATTTAT-TTT
1 ATTAAAATTATTATTTATATTT
*
34719 ATTAAAAATATT-TTTAAATATTT
1 ATTAAAATTATTATTT--ATATTT
34742 -TT-AAATTATTATTTATAT
1 ATTAAAATTATTATTTATAT
34760 ATTTTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 7 0.20
21 18 0.51
22 7 0.20
23 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAAAATTATTATTTATATTT
Found at i:34751 original size:11 final size:10
Alignment explanation
Indices: 34724--34764 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
34714 ATTTTATTAA
34724 AAATATTTTT
1 AAATATTTTT
34734 AAATATTTTT
1 AAATATTTTT
34744 AAATTATTATTT
1 AAA-TATT-TTT
*
34756 ATATATTTT
1 AAATATTTT
34765 ATAATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 15 0.54
11 8 0.29
12 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AAATATTTTT
Found at i:34770 original size:22 final size:22
Alignment explanation
Indices: 34703--34771 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
34693 GCCCGATTAA
*
34703 AATTATTATTTAT-T-TTATTAA
1 AATTATTATTTATATATT-TTAT
* *
34724 AAATATT-TTTAAATATTTT-T
1 AATTATTATTTATATATTTTAT
34744 AAATTATTATTTATATATTTTAT
1 -AATTATTATTTATATATTTTAT
34767 AATTA
1 AATTA
34772 AATTTAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.11
21 15 0.39
22 18 0.47
23 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTATTATTTATATATTTTAT
Found at i:34803 original size:20 final size:20
Alignment explanation
Indices: 34774--34821 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
34764 TATAATTAAA
* *
34774 TTTAAATAAACATATATTAT
1 TTTAAATAAAAAAATATTAT
*
34794 TTTAATTAAAAAAATATTAT
1 TTTAAATAAAAAAATATTAT
34814 TTTAAATA
1 TTTAAATA
34822 CGTCAAGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAATAAAAAAATATTAT
Found at i:37214 original size:18 final size:18
Alignment explanation
Indices: 37190--37241 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
37180 TACAATTCGC
37190 TATGTATCGATACAAG-A
1 TATGTATCGATACAAGAA
37207 TCATGTATCGATACAAAGCAA
1 T-ATGTATCGATAC-AAG-AA
37228 TATGTATCGATACA
1 TATGTATCGATACA
37242 TCTGGGTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 4 0.13
20 12 0.39
21 2 0.06
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (18 bp):
TATGTATCGATACAAGAA
Found at i:37234 original size:20 final size:19
Alignment explanation
Indices: 37170--37241 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
37160 CGGCCAGTTT
*
37170 TATGTATCGATACAATTCGC-
1 TATGTATCGATACAA--AGCA
37190 TATGTATCGATAC-AAG-A
1 TATGTATCGATACAAAGCA
37207 TCATGTATCGATACAAAGCAA
1 T-ATGTATCGATACAAAGC-A
37228 TATGTATCGATACA
1 TATGTATCGATACA
37242 TCTGGGTCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
19 4 0.09
20 26 0.57
21 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (19 bp):
TATGTATCGATACAAAGCA
Found at i:38439 original size:10 final size:10
Alignment explanation
Indices: 38426--38450 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38416 TTAATTAATA
38426 CATTTTCTAT
1 CATTTTCTAT
38436 CATTTTCTAT
1 CATTTTCTAT
38446 CATTT
1 CATTT
38451 ATTATAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
CATTTTCTAT
Found at i:38908 original size:85 final size:85
Alignment explanation
Indices: 38761--38987 Score: 373
Period size: 85 Copynumber: 2.7 Consensus size: 85
38751 GCGGGAACGG
* * * * *
38761 TGCAGCAACGATGGCCACAACTTCCGCAGGTGTCCAACGCGCGGTGGTGGTGGAAAAGGTGGAGT
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGGTGGAGT
*
38826 TGACTAGGCGATGCTCGCAT
66 TGACCAGGCGATGCTCGCAT
* *
38846 TGCGGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGATGGTGGCGGAAACGGTGGAGT
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGGTGGAGT
*
38911 TGACCCGGCGATGCTCGCAT
66 TGACCAGGCGATGCTCGCAT
38931 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAAC
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAAC
38988 CGAGCAGCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 131 1.00
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.17
Consensus pattern (85 bp):
TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGGTGGAGT
TGACCAGGCGATGCTCGCAT
Found at i:39106 original size:59 final size:59
Alignment explanation
Indices: 38931--39109 Score: 322
Period size: 59 Copynumber: 3.0 Consensus size: 59
38921 ATGCTCGCAT
*
38931 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACCG
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGG
*
38990 AGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGG
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGG
* *
39049 TGCAGCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGGTGGTGGCGGAAACGG
1 TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGG
39108 TG
1 TG
39110 GAGTTGACTC
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 115 1.00
ACGTcount: A:0.23, C:0.30, G:0.34, T:0.13
Consensus pattern (59 bp):
TGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAAACGG
Found at i:39139 original size:144 final size:144
Alignment explanation
Indices: 38682--39477 Score: 887
Period size: 144 Copynumber: 5.6 Consensus size: 144
38672 AGACTAGATA
* * *
38682 TGACTCGGCGATGTTCGCATTGCGGCAACAATGGCCACAACTTCCGCACGTGTCCGACGAGTC-G
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCG-CGG
* *
38746 TGGTGGCGGGAACGGTGCAGCAACGATGGCCACAACTTCCGCAGGTGTCC-AACGCGCGGTGGTG
65 TGGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGAA-GCGCGGTGGTG
* *
38810 GTGGAAAAGGTGGAGT
129 GAGGAAACGGTGGAGT
* * *
38826 TGACTAGGCGATGCTCGCATTGCGGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGAT
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
* ** ** * ** * ** * * *
38891 GGTGGCGGAAACGGTGGAGTTGAC-CCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTC
66 GGTGGCGGAAACGGTGCAG-CAACAATGGCCA--C-AAC-TT-CCGC-A-GGTGTCC-GAA---G
* * * **
38955 CGCACGT-GTCCGACG-CGCGGT-G-G-
119 CGC-GGTGGT-GGAGGAAACGGTGGAGT
* **
38978 TG--GC-G-GAAAC-CG-A--GCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
* *
39035 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGGTGGTGGC
66 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGAAGCGCGGTGGTGGA
39100 GGAAACGGTGGAGT
131 GGAAACGGTGGAGT
* * *
39114 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGTGGGGT
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
*
39179 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGGA
66 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGAAGCGCGGTGGTGGA
* *
39244 AGAAACGATGGAGT
131 GGAAACGGTGGAGT
* *
39258 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGTGCGGT
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
*
39323 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCG-A-CGC-GCGGTGGA
66 GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGAAGCGCGGTGGTGGA
39385 GG--ACGGTGGAGT
131 GGAAACGGTGGAGT
* *
39397 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGTGTT
1 TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
*
39462 GGTGGTGGAAACGGTG
66 GGTGGCGGAAACGGTG
39478 GAGTTGGCCG
Statistics
Matches: 551, Mismatches: 72, Indels: 63
0.80 0.10 0.09
Matches are distributed among these distances:
132 4 0.01
133 9 0.02
134 1 0.00
135 1 0.00
136 4 0.01
137 5 0.01
138 2 0.00
139 89 0.16
140 5 0.01
141 11 0.02
142 5 0.01
143 3 0.01
144 373 0.68
145 2 0.00
146 2 0.00
147 3 0.01
148 5 0.01
149 4 0.01
150 1 0.00
151 4 0.01
152 2 0.00
153 3 0.01
154 1 0.00
155 8 0.01
156 4 0.01
ACGTcount: A:0.22, C:0.27, G:0.34, T:0.17
Consensus pattern (144 bp):
TGACTCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGT
GGTGGCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGAAGCGCGGTGGTGGA
GGAAACGGTGGAGT
Found at i:39200 original size:203 final size:203
Alignment explanation
Indices: 38850--39242 Score: 696
Period size: 203 Copynumber: 1.9 Consensus size: 203
38840 TCGCATTGCG
* *
38850 GCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGATGGTGGCGGAAACGGTGGAGTTGAC
1 GCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGATGGTGGCGGAAACGGTGGAGTTGAC
38915 CCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTG
66 CCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTG
38980 GCGGAAACCGAGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAA
131 GCGGAAACCGAGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAA
39045 ACGGTGCA
196 ACGGTGCA
*
39053 GCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGGTGGTGGCGGAAACGGTGGAGTTGAC
1 GCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGATGGTGGCGGAAACGGTGGAGTTGAC
* * * *
39118 TCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGTGGGGTGGTG
66 CCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTG
* * *
39183 GCGGAAACGGTGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGG
131 GCGGAAACCGAGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGG
39243 AAGAAACGAT
Statistics
Matches: 180, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 180 1.00
ACGTcount: A:0.22, C:0.29, G:0.34, T:0.15
Consensus pattern (203 bp):
GCAACAATGGCCACAACTTCCGCAAGTGTCCGAAGCGCGATGGTGGCGGAAACGGTGGAGTTGAC
CCGGCGATGCTCGCATTGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTG
GCGGAAACCGAGCAGCAACAATGGCCACAACTTCCGCACGTGTCCGACGCGCGGTGGTGGCGGAA
ACGGTGCA
Found at i:39249 original size:59 final size:59
Alignment explanation
Indices: 39134--39250 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
39124 ATGCTCGCAT
* * **
39134 TGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGTGGGGTGGTGGCGGAAACGG
1 TGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGGAAGAAACGG
39193 TGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGGAAGAAACG
1 TGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGGAAGAAACG
39251 ATGGAGTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (59 bp):
TGCAGCAACAATGGCCACAACTTCCGCAGGTGTCCGACGCGCGGTGGTGGAAGAAACGG
Found at i:44199 original size:29 final size:26
Alignment explanation
Indices: 44144--44199 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 26
44134 AAAATTTATA
* *
44144 ATTAATAAAAAAATTAGGATTTTTAC
1 ATTAATAAAAAAACTAAGATTTTTAC
44170 ATTATATAAAAGAAACTAAGATATTTTAC
1 ATTA-ATAAAA-AAACTAAGAT-TTTTAC
44199 A
1 A
44200 ACAGTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 6 0.24
28 8 0.32
29 7 0.28
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (26 bp):
ATTAATAAAAAAACTAAGATTTTTAC
Found at i:45795 original size:56 final size:56
Alignment explanation
Indices: 45698--45825 Score: 229
Period size: 57 Copynumber: 2.3 Consensus size: 56
45688 ATAATATTTA
45698 ATAAATTTATATACAAAATTTTATATTTATAATTTATTTTTTAATTAAATTACGAT
1 ATAAATTTATATACAAAATTTTATATTTATAATTTATTTTTTAATTAAATTACGAT
45754 ATAAATTTATATACAAAATTTTTATATTTATAATTTATTTTTTAATTAAATTACGAT
1 ATAAATTTATATACAAAA-TTTTATATTTATAATTTATTTTTTAATTAAATTACGAT
* *
45811 ATATATATATATACA
1 ATAAATTTATATACA
45826 TATATGTATA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
56 18 0.26
57 51 0.74
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (56 bp):
ATAAATTTATATACAAAATTTTATATTTATAATTTATTTTTTAATTAAATTACGAT
Found at i:46060 original size:3 final size:3
Alignment explanation
Indices: 46052--46084 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
46042 CACTTTCAAT
46052 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46085 AAATAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47599 original size:46 final size:47
Alignment explanation
Indices: 47543--47632 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
47533 TTTATTAAAT
* * * * *
47543 TTATAGTTTTTATAAGGATAAATTTATAAA-TTTTTTTATAAATAAC
1 TTATAATTTTTATAAGAATAAAATTATAAACTTTATTCATAAATAAC
*
47589 TTATAATTTTTATACGAATAAAATTATAAACTTTATTCATAAAT
1 TTATAATTTTTATAAGAATAAAATTATAAACTTTATTCATAAAT
47633 TTTTATACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 26 0.70
47 11 0.30
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (47 bp):
TTATAATTTTTATAAGAATAAAATTATAAACTTTATTCATAAATAAC
Found at i:47615 original size:23 final size:23
Alignment explanation
Indices: 47538--47617 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
47528 CTTTATTTAT
* *
47538 TAAATTTATAGTTTTTATAAGGA
1 TAAATTTATAATTTTTATAAGAA
*
47561 TAAATTTATAAATTTTTTTATA-AA
1 TAAATTTAT-AATTTTTATA-AGAA
* *
47585 T-AACTTATAATTTTTATACGAA
1 TAAATTTATAATTTTTATAAGAA
*
47607 TAAAATTATAA
1 TAAATTTATAA
47618 ACTTTATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
22 12 0.26
23 23 0.50
24 10 0.22
25 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (23 bp):
TAAATTTATAATTTTTATAAGAA
Found at i:47809 original size:14 final size:13
Alignment explanation
Indices: 47775--47816 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
47765 TTTGATCATC
47775 AAATTATTTATTA
1 AAATTATTTATTA
*
47788 AAAATATTTATTA
1 AAATTATTTATTA
47801 AAATTTATTTATTA
1 AAA-TTATTTATTA
47815 AA
1 AA
47817 TAAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTATTTATTA
Found at i:48260 original size:36 final size:37
Alignment explanation
Indices: 48220--48304 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
48210 ATAAAACGTT
* *
48220 TTTTATATTTAAATTTTAAATTTATT-AA-AAATTATA
1 TTTTA-ATTTAAATTTTAAATTAATTGAATAAATTAAA
* *
48256 TTTTAAAATAAAATTTTAAATTAATTGAATTAAATTAAA
1 TTTT-AATTTAAATTTTAAATTAATTGAA-TAAATTAAA
48295 TTTTAATTTA
1 TTTTAATTTA
48305 TTTATTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
36 21 0.54
37 3 0.08
38 4 0.10
39 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTAATTTAAATTTTAAATTAATTGAATAAATTAAA
Found at i:50535 original size:15 final size:14
Alignment explanation
Indices: 50513--50582 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 14
50503 TTAGATAAAT
50513 ATTT-TTTAATTTAA
1 ATTTATTTAATTT-A
50527 ATTTATTTAATTTA
1 ATTTATTTAATTTA
*
50541 ATTTA---AATTATT
1 ATTTATTTAATT-TA
50553 ATTTATTATAATTT-
1 ATTTATT-TAATTTA
*
50567 -TTTATTTAAATTA
1 ATTTATTTAATTTA
50580 ATT
1 ATT
50583 ATAAAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
11 4 0.09
12 11 0.24
13 6 0.13
14 12 0.26
15 9 0.20
16 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATTTAATTTA
Found at i:50536 original size:10 final size:11
Alignment explanation
Indices: 50517--50549 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
50507 ATAAATATTT
50517 TTTAATTTAAA
1 TTTAATTTAAA
50528 TTT-ATTT-AA
1 TTTAATTTAAA
50537 TTTAATTTAAA
1 TTTAATTTAAA
50548 TT
1 TT
50550 ATTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.25
10 8 0.40
11 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:50540 original size:20 final size:20
Alignment explanation
Indices: 50517--50587 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
50507 ATAAATATTT
50517 TTTAATTTAAATTTATTTAA
1 TTTAATTTAAATTTATTTAA
50537 TTTAATTTAAATTATTATTT-A
1 TTTAATTTAAA-T-TTATTTAA
50558 TTATAATTT---TTTATTTAA
1 TT-TAATTTAAATTTATTTAA
*
50576 ATTAATTATAAA
1 TTTAATT-TAAA
50588 AATATATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
17 11 0.26
18 4 0.10
20 11 0.26
21 4 0.10
22 12 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATTTAAATTTATTTAA
Found at i:50556 original size:40 final size:39
Alignment explanation
Indices: 50490--50587 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
50480 GTTCAGTTTA
* *
50490 TATTTAATTGAATTTAGATAAATATTT-TT-TAATTTAAATT
1 TATTTAATTTAATTTAAATAAATATTTATTATAATTT---TT
* *
50530 TATTTAATTTAATTTAAATTATTATTTATTATAATTTTT
1 TATTTAATTTAATTTAAATAAATATTTATTATAATTTTT
*
50569 TATTTAAATTAATTATAAA
1 TATTTAATTTAATT-TAAA
50588 AATATATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 15 0.30
40 27 0.54
41 2 0.04
42 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (39 bp):
TATTTAATTTAATTTAAATAAATATTTATTATAATTTTT
Found at i:51739 original size:4 final size:4
Alignment explanation
Indices: 51730--51754 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
51720 TCTGTAAATT
51730 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
51755 TTTTGAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:52530 original size:48 final size:47
Alignment explanation
Indices: 52429--52548 Score: 208
Period size: 48 Copynumber: 2.6 Consensus size: 47
52419 CTTTCTACAC
*
52429 ATATAAACTATAACAATGAAAAA-T-TACACGCACACACACACATAT
1 ATATAAACTATAACAATGAAAAATTATACACACACACACACACATAT
52474 ATATAAACTATAACAATGAAAAATTATCACACACACACACACACATAT
1 ATATAAACTATAACAATGAAAAATTAT-ACACACACACACACACATAT
52522 ATATAAACTATAACAATGAAAAATTAT
1 ATATAAACTATAACAATGAAAAATTAT
52549 TAGAGCCTCC
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
45 23 0.32
46 1 0.01
47 1 0.01
48 46 0.65
ACGTcount: A:0.55, C:0.19, G:0.03, T:0.23
Consensus pattern (47 bp):
ATATAAACTATAACAATGAAAAATTATACACACACACACACACATAT
Found at i:63592 original size:20 final size:20
Alignment explanation
Indices: 63559--63636 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
63549 TAAAAATAAA
*
63559 TTAATTTTTATATTTAA-T-T
1 TTAA-TTTTAAATTTAATTAT
*
63578 TTAAATTTAATTATTT-AT-AT
1 TTAATTTTAA--ATTTAATTAT
63598 TTAATTTTAAATTTAATTAT
1 TTAATTTTAAATTTAATTAT
*
63618 TT-ATATTTAAATTAAATTA
1 TTAAT-TTTAAATTTAATTA
63637 AATTTTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.17
19 9 0.19
20 31 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATTTTAAATTTAATTAT
Found at i:63598 original size:26 final size:25
Alignment explanation
Indices: 63555--63644 Score: 130
Period size: 26 Copynumber: 3.6 Consensus size: 25
63545 TTAATAAAAA
63555 TAAA-TTAATTTTTATATTTAATTT
1 TAAATTTAATTTTTATATTTAATTT
63579 TAAATTTAATTATTTATATTTAATTT
1 TAAATTTAATT-TTTATATTTAATTT
*
63605 TAAATTTAATTATTTATATTTAA-AT
1 TAAATTTAATT-TTTATATTTAATTT
*
63630 TAAATTAAATTTTTA
1 TAAATTTAATTTTTA
63645 AATAATAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
24 8 0.13
25 17 0.27
26 37 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TAAATTTAATTTTTATATTTAATTT
Found at i:64022 original size:2 final size:2
Alignment explanation
Indices: 64015--64048 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
64005 TGCTATTGTC
64015 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
64049 CAGTAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65062 original size:29 final size:29
Alignment explanation
Indices: 65001--65062 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
64991 TACTCTCTCT
* * *
65001 CTCTCTCTCTCTCTTTACAACCTAAAATC
1 CTCTCTCCCTCTCTTTACAACATAAAATA
* * *
65030 CTCTCTCCCTCTCTTTATAATATATAATA
1 CTCTCTCCCTCTCTTTACAACATAAAATA
65059 CTCT
1 CTCT
65063 TAATATATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (29 bp):
CTCTCTCCCTCTCTTTACAACATAAAATA
Found at i:66559 original size:16 final size:16
Alignment explanation
Indices: 66490--66574 Score: 68
Period size: 16 Copynumber: 5.4 Consensus size: 16
66480 TTAAAAAGTC
66490 AAAAACCCAAACTCGA
1 AAAAACCCAAACTCGA
* *
66506 AATAACTCAAACT-GA
1 AAAAACCCAAACTCGA
* * *
66521 AATAGCTCAAACTC-A
1 AAAAACCCAAACTCGA
*
66536 AAAGAACCCGAACTCGA
1 AAA-AACCCAAACTCGA
*
66553 AAAAACCCGAA-TCCGA
1 AAAAACCCAAACT-CGA
66569 AAAAAC
1 AAAAAC
66575 TTGAACTCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
15 18 0.31
16 36 0.62
17 4 0.07
ACGTcount: A:0.53, C:0.27, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAACCCAAACTCGA
Found at i:70540 original size:27 final size:25
Alignment explanation
Indices: 70491--70541 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
70481 TTATGTTTTT
*
70491 AATTAAATAATGATATTTTTATTAA
1 AATTAAATAATGATAATTTTATTAA
*
70516 AATTAAAATATTGAGTAATTTTATTA
1 AATT-AAATAATGA-TAATTTTATTA
70542 TTAATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
AATTAAATAATGATAATTTTATTAA
Found at i:70643 original size:99 final size:100
Alignment explanation
Indices: 70480--70667 Score: 254
Period size: 99 Copynumber: 1.9 Consensus size: 100
70470 AGTATTGATT
* * *
70480 ATTATGTTTTTAATTAAATAATGATATTTTTATTAAAATTAAAATATTGAGTAATTTTATTATTA
1 ATTATGTTCTTAATTAAATAATGATATTTTTATTAAAATTAAAACATTGAATAATTTTATTATTA
*** *
70545 ATTTTGAATTCTTTGTTAACGTAATAATATGGACC
66 AACCTGAATTCTTTATTAACGTAATAATATGGACC
* * *
70580 ATTATGTTCTTAATTAATTAATGAT-TTTTTATTTAAATTAAAACA-TGAAATAATTTTCTTATT
1 ATTATGTTCTTAATTAAATAATGATATTTTTATTAAAATTAAAACATTG-AATAATTTTATTATT
*
70643 AAACCTGAATTCTTTATTCACGTAA
65 AAACCTGAATTCTTTATTAACGTAA
70668 ATATTTCATA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
98 2 0.03
99 51 0.67
100 23 0.30
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.48
Consensus pattern (100 bp):
ATTATGTTCTTAATTAAATAATGATATTTTTATTAAAATTAAAACATTGAATAATTTTATTATTA
AACCTGAATTCTTTATTAACGTAATAATATGGACC
Found at i:71102 original size:16 final size:16
Alignment explanation
Indices: 71059--71106 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
71049 TGAACTTGAA
* **
71059 CCCGAACCAGAAAAAG
1 CCCGAACCCGAACGAG
71075 CCCGAACCCGAACGAG
1 CCCGAACCCGAACGAG
*
71091 CCCGAACTCGAACGAG
1 CCCGAACCCGAACGAG
71107 TACGAATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.38, C:0.38, G:0.23, T:0.02
Consensus pattern (16 bp):
CCCGAACCCGAACGAG
Found at i:76091 original size:21 final size:19
Alignment explanation
Indices: 76067--76120 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
76057 TTCAACAAAT
76067 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* *
76088 TGTATCGATACATAAGTAT
1 TGTATCGATACAAAAGTAA
76107 TGTATCGATACAAA
1 TGTATCGATACAAA
76121 GTTGCCCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:76112 original size:19 final size:19
Alignment explanation
Indices: 76064--76122 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 19
76054 AATTTCAACA
76064 AATTGTATCGATACAAACAGT
1 AATTGTATCGATAC-AA-AGT
*
76085 AAATGTATCGATACATAAGT
1 AATTGTATCGATACA-AAGT
76105 -ATTGTATCGATACAAAGT
1 AATTGTATCGATACAAAGT
76123 TGCCCTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.11
19 13 0.37
20 4 0.11
21 14 0.40
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (19 bp):
AATTGTATCGATACAAAGT
Found at i:78502 original size:90 final size:88
Alignment explanation
Indices: 78383--78568 Score: 284
Period size: 90 Copynumber: 2.1 Consensus size: 88
78373 GGGATACTCT
* *
78383 AACCCCATGTCTCCAAGAGGATACTCCAACCCCACTTTTAAACTTTTCAAGATTTTTTTTTACAT
1 AACCCCATATCTCCAAGAGGATACTCCAACCCCACTTTTAAACTTGTCAAGA--TTTTTTTACAT
78448 AAATTATCATTGTCGGGGACA-TTCC
64 AAATTATCATTGTCGGGGACACTT-C
* * * *
78473 AACCCCATATCTCCGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGATTTTTTTACATAG
1 AACCCCATATCTCCAAGAGGATACTCCAACCCCACTTTTAAACTTGTCAAGATTTTTTTACATAA
78538 ATTATCATTGTCGGGGACACTTC
66 ATTATCATTGTCGGGGACACTTC
78561 AACCCCAT
1 AACCCCAT
78569 TCCTTCGAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
88 40 0.45
89 2 0.02
90 47 0.53
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (88 bp):
AACCCCATATCTCCAAGAGGATACTCCAACCCCACTTTTAAACTTGTCAAGATTTTTTTACATAA
ATTATCATTGTCGGGGACACTTC
Found at i:78599 original size:88 final size:89
Alignment explanation
Indices: 78383--78583 Score: 273
Period size: 88 Copynumber: 2.3 Consensus size: 89
78373 GGGATACTCT
* * * * *
78383 AACCCCATGTCTCCAAGAGGATACTCCAACCCCACTTTTAAACTTTTCAAGATTTTTTTTTACAT
1 AACCCCATATCTCCGAGAGAATACTCCAACCCCATTTTTAAACTTGTCAAGA-TTTTTTTTACAT
78448 AAATTATCATTGTCGGGGACATTCC
65 AAATTATCATTGTCGGGGACATTCC
* *
78473 AACCCCATATCTCCGAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGA-TTTTTTTACATA
1 AACCCCATATCTCCGAGAGAATACTCCAACCCCATTTTTAAACTTGTCAAGATTTTTTTTACATA
*
78537 GATTATCATTGTCGGGGACACTT-C
66 AATTATCATTGTCGGGGACA-TTCC
*
78561 AACCCCAT-TCCTTCGAGAGAATA
1 AACCCCATAT-CTCCGAGAGAATA
78584 TTCCCATCCC
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
87 1 0.01
88 50 0.50
89 2 0.02
90 47 0.47
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (89 bp):
AACCCCATATCTCCGAGAGAATACTCCAACCCCATTTTTAAACTTGTCAAGATTTTTTTTACATA
AATTATCATTGTCGGGGACATTCC
Found at i:80029 original size:28 final size:28
Alignment explanation
Indices: 79983--80070 Score: 83
Period size: 35 Copynumber: 3.0 Consensus size: 28
79973 TATTTTTACA
*
79983 TTTATT-TTTAATATGAATATAATTTTT
1 TTTATTATTTAATATAAATATAATTTTT
80010 TTTATTATTTAATATAAATATAGCTTTATTTATAT
1 TTTATTATTTAATATAAATATA-----ATTT-T-T
80045 TTTATTATTTAATATAAAT-T-ATTTTT
1 TTTATTATTTAATATAAATATAATTTTT
80071 AATTATTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 17
0.74 0.01 0.24
Matches are distributed among these distances:
26 1 0.02
27 7 0.13
28 18 0.35
33 4 0.08
34 2 0.04
35 20 0.38
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTATTATTTAATATAAATATAATTTTT
Found at i:80075 original size:24 final size:24
Alignment explanation
Indices: 80039--80084 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
80029 ATAGCTTTAT
80039 TTATATTTTATTATTTAATATAAA
1 TTATATTTTATTATTTAATATAAA
*
80063 TTAT-TTTTAATTATTTATTATA
1 TTATATTTT-ATTATTTAATATA
80085 TTACACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATTTTATTATTTAATATAAA
Found at i:80856 original size:16 final size:16
Alignment explanation
Indices: 80835--80880 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
80825 ACTTAAACAG
**
80835 ATTTAATTTAATTTAA
1 ATTTAATTTAAAATAA
*
80851 ATTTAATATAAAATAA
1 ATTTAATTTAAAATAA
80867 ATTTAATTATAAAA
1 ATTTAATT-TAAAA
80881 ATAATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAATTTAAAATAA
Found at i:80893 original size:20 final size:19
Alignment explanation
Indices: 80851--80909 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 19
80841 TTTAATTTAA
80851 ATTTAA-TAT-AAAATAA-
1 ATTTAATTATAAAAATAAT
80867 ATTTAATTATAAAAATAAT
1 ATTTAATTATAAAAATAAT
80886 ATTTTAATAATATAATAAATAAT
1 A-TTTAAT--TATAA-AAATAAT
80909 A
1 A
80910 AAATAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.17
17 3 0.08
18 7 0.19
19 1 0.03
20 6 0.17
22 5 0.14
23 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAATTATAAAAATAAT
Found at i:95324 original size:28 final size:26
Alignment explanation
Indices: 95291--95366 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 26
95281 TTTTAATTTA
*
95291 AATTAATTTTTATTAATAAAAATATTAT
1 AATTAATTTTAATT-ATAAAAATA-TAT
*
95319 AATTAAAATTTAATTATAAAAATATAT
1 AATT-AATTTTAATTATAAAAATATAT
*
95346 -ATTAATATTAA-TATAAAAATA
1 AATTAATTTTAATTATAAAAATA
95367 AAAATAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.23
25 6 0.14
26 3 0.07
27 3 0.07
28 13 0.30
29 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTAATTTTAATTATAAAAATATAT
Found at i:95370 original size:30 final size:29
Alignment explanation
Indices: 95334--95390 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
95324 AAATTTAATT
95334 ATAAAAAT-ATATATTAATATTAATATAAAA
1 ATAAAAATAAT-TATTAATA-TAATATAAAA
*
95364 ATAAAAATAATTTTTAATATAATATAA
1 ATAAAAATAATTATTAATATAATATAA
95391 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 15 0.60
31 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAAAATAATTATTAATATAATATAAAA
Found at i:95372 original size:14 final size:14
Alignment explanation
Indices: 95304--95372 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
95294 TAATTTTTAT
*
95304 TAATAAAAATATTA
1 TAATAAAAATATAA
* *
95318 TAATTAAAATTTAA
1 TAATAAAAATATAA
*
95332 TTATAAAAATATATA
1 TAATAAAAATATA-A
**
95347 TTAATATTAATATAA
1 -TAATAAAAATATAA
*
95362 AAATAAAAATA
1 TAATAAAAATA
95373 ATTTTTAATA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
14 29 0.71
15 2 0.05
16 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAAAAATATAA
Found at i:95380 original size:24 final size:24
Alignment explanation
Indices: 95327--95385 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
95317 ATAATTAAAA
* *
95327 TTTAATTATAAAAATATATATTAAT
1 TTTAA-TATAAAAATATAAAATAAT
*
95352 ATTAATATAAAAATA-AAAATAATT
1 TTTAATATAAAAATATAAAATAA-T
95376 TTTAATATAA
1 TTTAATATAA
95386 TATAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 20 0.69
25 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTAATATAAAAATATAAAATAAT
Found at i:95422 original size:18 final size:17
Alignment explanation
Indices: 95389--95423 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
95379 AATATAATAT
*
95389 AATTTAAATTTTAAAAA
1 AATTTAAATATTAAAAA
95406 AATTTAAATAATTAAAAA
1 AATTTAAAT-ATTAAAAA
95424 TAATAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTTAAATATTAAAAA
Found at i:95541 original size:19 final size:19
Alignment explanation
Indices: 95512--95562 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
95502 CGTAAAAAAA
95512 TAATATGATATAAAAATTAT
1 TAATAT-ATATAAAAATTAT
*
95532 TAATATATATATAAATTAT
1 TAATATATATAAAAATTAT
95551 TAATATAT-TAAA
1 TAATATATATAAA
95563 TTTATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 3 0.10
19 20 0.69
20 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATATATATAAAAATTAT
Found at i:95568 original size:26 final size:27
Alignment explanation
Indices: 95529--95593 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
95519 ATATAAAAAT
95529 TATTAATATATATATAAAT-TATTAATA
1 TATTAATATATATATAAATATATT-ATA
*
95556 TATTAA-ATTTATATAAATATATTATA
1 TATTAATATATATATAAATATATTATA
* *
95582 TTTTAACATATA
1 TATTAATATATA
95594 AATTTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTAATATATATATAAATATATTATA
Found at i:95574 original size:19 final size:17
Alignment explanation
Indices: 95528--95584 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
95518 GATATAAAAA
*
95528 TTATTAATATATATATAAA
1 TTATTAATATAT-TA-AAT
95547 TTATTAATATATTAAAT
1 TTATTAATATATTAAAT
*
95564 TTATATAAATATATTATAT
1 TTAT-T-AATATATTAAAT
95583 TT
1 TT
95585 TAACATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 25 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTAATATATTAAAT
Found at i:95576 original size:34 final size:31
Alignment explanation
Indices: 95538--95613 Score: 80
Period size: 34 Copynumber: 2.3 Consensus size: 31
95528 TTATTAATAT
*
95538 ATATATAAATTATTAATATATTAAATTTATATAA
1 ATATATAAATT-TTAACATA-TAAATTT-TATAA
*
95572 ATATATTATATTTTAACATATAAATTTTATAA
1 ATATA-TAAATTTTAACATATAAATTTTATAA
*
95604 AAATTATAAA
1 ATA-TATAAA
95614 ATCTACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
32 10 0.28
33 9 0.25
34 12 0.33
35 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATATAAATTTTAACATATAAATTTTATAA
Found at i:95581 original size:11 final size:10
Alignment explanation
Indices: 95513--95577 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
95503 GTAAAAAAAT
95513 AATATGATATA
1 AATAT-ATATA
*
95524 AAAAT-TATTA
1 AATATATA-TA
95534 ATATATATATA
1 A-ATATATATA
95545 AAT-TAT-T-
1 AATATATATA
95552 AATATAT-TA
1 AATATATATA
*
95561 AATTTATATA
1 AATATATATA
95571 AATATAT
1 AATATAT
95578 TATATTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
7 3 0.07
8 5 0.11
9 11 0.25
10 13 0.30
11 10 0.23
12 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (10 bp):
AATATATATA
Found at i:96231 original size:23 final size:23
Alignment explanation
Indices: 96204--96253 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
96194 ATTTTATTTT
96204 ATATTATTA-TTTAATTAATAAAA
1 ATATTATTATTTTAATT-ATAAAA
* *
96227 ATATTTTTATTTTAATTATAAAC
1 ATATTATTATTTTAATTATAAAA
96250 ATAT
1 ATAT
96254 AAATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTATTATTTTAATTATAAAA
Found at i:96614 original size:20 final size:21
Alignment explanation
Indices: 96572--96619 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
96562 TATATATTTT
*
96572 ATAATTAAT-TTTAAATAAAA
1 ATAATTTATATTTAAATAAAA
* *
96592 AT-ATTTATATTTAATTAATA
1 ATAATTTATATTTAAATAAAA
96612 ATAATTTA
1 ATAATTTA
96620 AATTAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTTATATTTAAATAAAA
Found at i:97841 original size:9 final size:9
Alignment explanation
Indices: 97827--97894 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
97817 ATAATATTTG
97827 ATTAATTAA
1 ATTAATTAA
97836 ATTAATTAA
1 ATTAATTAA
97845 ATTAA--AA
1 ATTAATTAA
*
97852 ATTGA-TAA
1 ATTAATTAA
* *
97860 TTTATTTAA
1 ATTAATTAA
*
97869 TTTAA-TAA
1 ATTAATTAA
*
97877 AATATATTAA
1 ATTA-ATTAA
97887 ATTAATTA
1 ATTAATTA
97895 TTTAAAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
7 6 0.13
8 9 0.19
9 26 0.55
10 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
ATTAATTAA
Found at i:98761 original size:19 final size:19
Alignment explanation
Indices: 98733--98776 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
98723 AAAAAATTTT
98733 AAAAAT-TAAATTTA-AATA
1 AAAAATATAAA-TTAGAATA
*
98751 AAAAATATAAATTAGATTA
1 AAAAATATAAATTAGAATA
98770 AAAAATA
1 AAAAATA
98777 AGTCATGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATAAATTAGAATA
Found at i:98772 original size:18 final size:19
Alignment explanation
Indices: 98731--98777 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
98721 TGAAAAAATT
98731 TTAAAAAT-TAAATTTAAA
1 TTAAAAATATAAATTTAAA
* *
98749 TAAAAAATATAAA-TTAGA
1 TTAAAAATATAAATTTAAA
98767 TTAAAAA-ATAA
1 TTAAAAATATAA
98778 GTCATGCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TTAAAAATATAAATTTAAA
Found at i:99394 original size:22 final size:22
Alignment explanation
Indices: 99351--99398 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
99341 AAATGTCTGG
* * **
99351 GAAAAAACAAAAGAAATTGGAA
1 GAAAAAAAAAAAAAAAAAGGAA
99373 GAAAAAAAAAAAAAAAAAGGAA
1 GAAAAAAAAAAAAAAAAAGGAA
99395 -AAAA
1 GAAAA
99399 GAAGACAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (22 bp):
GAAAAAAAAAAAAAAAAAGGAA
Found at i:101495 original size:11 final size:12
Alignment explanation
Indices: 101478--101509 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
101468 ATATTTCTAA
101478 ATTTTTATTTAT
1 ATTTTTATTTAT
101490 -TTTTTA-TTAT
1 ATTTTTATTTAT
101500 ATTTTTATTT
1 ATTTTTATTT
101510 TTTATCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTTTATTTAT
Found at i:101589 original size:18 final size:21
Alignment explanation
Indices: 101534--101610 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 21
101524 CAATAAACAC
* *
101534 AAAATATAAATAGTTATTATTTT
1 AAAATATAAATAATT-TTA-TTA
* *
101557 ATAATTTAAATTAATTTTA-TA
1 AAAATATAAA-TAATTTTATTA
101578 AAAAT-T-AATAA-TTTATTA
1 AAAATATAAATAATTTTATTA
101596 AAAATATAAATAATT
1 AAAATATAAATAATT
101611 ATTTTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
17 4 0.09
18 10 0.23
19 3 0.07
20 6 0.14
21 6 0.14
23 11 0.25
24 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
AAAATATAAATAATTTTATTA
Found at i:101609 original size:20 final size:19
Alignment explanation
Indices: 101562--101610 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
101552 ATTTTATAAT
101562 TTAAATTAATTTTATAAAAA
1 TTAAA-TAATTTTATAAAAA
101582 TT-AATAA-TTTATTAAAAA
1 TTAAATAATTTTA-TAAAAA
101600 TATAAATAATT
1 T-TAAATAATT
101611 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 3 0.12
20 7 0.28
21 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAATTTTATAAAAA
Found at i:101613 original size:19 final size:18
Alignment explanation
Indices: 101564--101610 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 18
101554 TTTATAATTT
101564 AAATTAAT--TTTA-TAA
1 AAATTAATAATTTATTAA
101579 AAATTAATAATTTATTAA
1 AAATTAATAATTTATTAA
101597 AAATATAAATAATT
1 AAAT-T-AATAATT
101611 ATTTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.30
17 4 0.15
18 7 0.26
19 1 0.04
20 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTAATAATTTATTAA
Found at i:101961 original size:12 final size:13
Alignment explanation
Indices: 101944--101972 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
101934 ACTTATAAAC
101944 AAAATAAAAGG-G
1 AAAATAAAAGGAG
101956 AAAATAAAAGGAG
1 AAAATAAAAGGAG
101969 AAAA
1 AAAA
101973 CAAGTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (13 bp):
AAAATAAAAGGAG
Found at i:102382 original size:19 final size:19
Alignment explanation
Indices: 102346--102384 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
102336 TTATGTGTTT
*
102346 ATTTATAAAAATATATAAA
1 ATTTATAAAAATAAATAAA
102365 ATTTA-AAAAATAAAATAAA
1 ATTTATAAAAAT-AAATAAA
102384 A
1 A
102385 GAGTAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTATAAAAATAAATAAA
Found at i:103111 original size:17 final size:19
Alignment explanation
Indices: 103074--103111 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
103064 GATTAATTTA
103074 AAAAATTTATTTTATTATT
1 AAAAATTTATTTTATTATT
103093 AAAAA-TTATTTTA-TATT
1 AAAAATTTATTTTATTATT
103110 AA
1 AA
103112 TATTTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAAATTTATTTTATTATT
Found at i:104255 original size:11 final size:11
Alignment explanation
Indices: 104213--104262 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
104203 TATTAGATAT
104213 AATATATATAAA
1 AATA-ATATAAA
104225 AA-AAT-TAAA
1 AATAATATAAA
104234 ATATAATATAAA
1 A-ATAATATAAA
*
104246 AATGATATAAA
1 AATAATATAAA
*
104257 TATAAT
1 AATAAT
104263 TTGATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.16
10 3 0.09
11 17 0.53
12 7 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAATATAAA
Found at i:104257 original size:22 final size:21
Alignment explanation
Indices: 104207--104262 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
104197 TGACAGTATT
104207 AGATAT-AATAT-ATATAAAA
1 AGATATAAATATAATATAAAA
*
104226 AAAT-TAAAATATAATATAAAA
1 AGATAT-AAATATAATATAAAA
104247 ATGATATAAATATAAT
1 A-GATATAAATATAAT
104263 TTGATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 5 0.17
21 9 0.30
22 11 0.37
23 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
AGATATAAATATAATATAAAA
Found at i:104304 original size:16 final size:17
Alignment explanation
Indices: 104234--104307 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 17
104224 AAAAATTAAA
* *
104234 ATAT-AATATAAAAATG
1 ATATAAATATAAAATTT
104250 ATATAAATAT--AATTT
1 ATATAAATATAAAATTT
104265 GATAT---TATAAAATTT
1 -ATATAAATATAAAATTT
104280 ATATAAATATAAAATATT
1 ATATAAATATAAAAT-TT
104298 -T-TAAATATAA
1 ATATAAATATAA
104308 TTATAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.06
14 4 0.08
15 8 0.17
16 17 0.35
17 14 0.29
18 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:106574 original size:22 final size:22
Alignment explanation
Indices: 106531--106575 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
106521 GAGAGATTAA
* *
106531 ATGGTAAAGGAGAAGAATTTTG
1 ATGGTAAAGAACAAGAATTTTG
106553 ATGGTAAAGAACAA-AATCTTTG
1 ATGGTAAAGAACAAGAAT-TTTG
106575 A
1 A
106576 ATTGCACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.27
Consensus pattern (22 bp):
ATGGTAAAGAACAAGAATTTTG
Found at i:107080 original size:15 final size:15
Alignment explanation
Indices: 107057--107099 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
107047 CAAAATCTTG
107057 TATATATTATATAAA
1 TATATATTATATAAA
*
107072 TATA-AAT-TATAAA
1 TATATATTATATAAA
*
107085 TATATTTTATATAAA
1 TATATATTATATAAA
107100 ATAGAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATTATATAAA
Found at i:107365 original size:15 final size:15
Alignment explanation
Indices: 107317--107367 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
107307 CGTTATAACG
*
107317 AAAAT-AAAAGTTCA
1 AAAATAAAAATTTCA
107331 AAAATAGAAAAATTAT-A
1 AAAAT--AAAAATT-TCA
107348 AAAATAAAAATTTCA
1 AAAATAAAAATTTCA
107363 AAAAT
1 AAAAT
107368 TTCTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 6 0.19
15 13 0.42
17 11 0.35
18 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (15 bp):
AAAATAAAAATTTCA
Found at i:107560 original size:17 final size:17
Alignment explanation
Indices: 107540--107581 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
107530 TTTTTTATAT
107540 ATTAAAT-TAAAAATTAA
1 ATTAAATATAAAAA-TAA
*
107557 ATTAAGTATAAAAATAA
1 ATTAAATATAAAAATAA
107574 A-TAAATAT
1 ATTAAATAT
107582 TTAATCCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTAAATATAAAAATAA
Found at i:108763 original size:29 final size:30
Alignment explanation
Indices: 108713--108769 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
108703 TAATAAAATA
**
108713 TTAAAAATATTTTTATTTTTATA-ATTACT
1 TTAAAAATATTTTTATAATTATATATTACT
108742 TTAAATAAT-TTTTTATAATTATATATTA
1 TTAAA-AATATTTTTATAATTATATATTA
108770 ATTCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAAAATATTTTTATAATTATATATTACT
Found at i:109820 original size:22 final size:22
Alignment explanation
Indices: 109772--109865 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 22
109762 ATTTCAGTAT
* *
109772 TAATATATAAATTTAATATAAA
1 TAATAAATAAATTTAAAATAAA
109794 TAATAAATAAATTTAAAATTTAAAA
1 TAATAAATAAATTTAAAA--T-AAA
** *
109819 TAATTTTATAAATTTAAATTTAAA
1 TAA-TAAATAAATTTAAA-ATAAA
* *
109843 TATTAAA-AAAATTATAAATAAA
1 TAATAAATAAATTTA-AAATAAA
109865 T
1 T
109866 GATTCCTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
22 27 0.48
23 4 0.07
24 6 0.11
25 7 0.12
26 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAAATAAATTTAAAATAAA
Found at i:109833 original size:19 final size:18
Alignment explanation
Indices: 109798--109850 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
109788 TATAAATAAT
109798 AAATAAATTTAAAATTTA
1 AAATAAATTTAAAATTTA
*
109816 AAATAATTTTATAAATTTA
1 AAATAAATTTA-AAATTTA
*
109835 AATTTAAATATTAAAA
1 AA-ATAAAT-TTAAAA
109851 AAATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 9 0.31
20 7 0.24
21 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATAAATTTAAAATTTA
Found at i:110273 original size:2 final size:2
Alignment explanation
Indices: 110266--110293 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
110256 TTCAAAAAGA
110266 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
110294 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110659 original size:38 final size:36
Alignment explanation
Indices: 110616--110702 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 36
110606 TCTCAATTAA
*
110616 AATTATTATTTAAATAATAAAAACTTTTAT-TTAAATTT
1 AATTATTATTT-AAT-ATAAAAAATTTTATATT-AATTT
* *
110654 AATTATAAATATTAATATAAAAAATTTTATATTATTTT
1 AATTAT-TAT-TTAATATAAAAAATTTTATATTAATTT
*
110692 AAATATTATTT
1 AATTATTATTT
110703 GAACCTTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
36 2 0.05
37 2 0.05
38 28 0.68
39 7 0.17
40 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
AATTATTATTTAATATAAAAAATTTTATATTAATTT
Found at i:112323 original size:24 final size:24
Alignment explanation
Indices: 112280--112328 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
112270 ATATAATAAA
** *
112280 ATTTTAAAAAATAATGTTAATATT
1 ATTTTAAAAAATAAAATTAAAATT
*
112304 ATTTTAAAAATTAAAATTAAAATT
1 ATTTTAAAAAATAAAATTAAAATT
112328 A
1 A
112329 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTTAAAAAATAAAATTAAAATT
Found at i:112357 original size:19 final size:18
Alignment explanation
Indices: 112330--112370 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
112320 TTAAAATTAA
*
112330 TTAATTTTAAATAAAAAAT
1 TTAAATTTAAAT-AAAAAT
*
112349 TTAAATTTAAATTAAAAT
1 TTAAATTTAAATAAAAAT
112367 TTAA
1 TTAA
112371 TTCAATCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATTTAAATAAAAAT
Found at i:113943 original size:23 final size:25
Alignment explanation
Indices: 113893--113944 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
113883 TAAAATAATA
* *
113893 AATAAAATTATTAATTATTCTATTT
1 AATAAAATTATTAATTATTATATAT
113918 AATAAAA-TATT-ATTATTATATAT
1 AATAAAATTATTAATTATTATATAT
113941 AATA
1 AATA
113945 CATTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.56
24 4 0.16
25 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AATAAAATTATTAATTATTATATAT
Found at i:114283 original size:30 final size:28
Alignment explanation
Indices: 114235--114311 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 28
114225 ATATTAAAAA
* *
114235 TTATATT-ATTAA-ATTTAATATTTGTT
1 TTATATTAAATAATATTTAATATTTATT
114261 ATTAATTATTAAAT-ATATTTAATATTTATT
1 -TT-A-TATTAAATAATATTTAATATTTATT
114291 TTATATTAAATAATATTTAAT
1 TTATATTAAATAATATTTAAT
114312 TATAAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
27 10 0.23
28 11 0.26
29 7 0.16
30 15 0.35
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTATATTAAATAATATTTAATATTTATT
Found at i:114366 original size:14 final size:13
Alignment explanation
Indices: 114330--114369 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
114320 ATATATATTA
**
114330 AATTAATTAATCT
1 AATTAATTAAAAT
114343 AATTAATTAAAAT
1 AATTAATTAAAAT
114356 AATTAAATTAAAAT
1 AATT-AATTAAAAT
114370 TAAGATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAATTAAAAT
Found at i:114457 original size:20 final size:20
Alignment explanation
Indices: 114434--114505 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
114424 TTAAATTAAT
*
114434 TAATATAATATTTATAATAA
1 TAATATAATATTTATAATTA
114454 TAATAATAATA-TTAT-ATTA
1 TAAT-ATAATATTTATAATTA
*
114473 -AATATAATAATTAATAATTA
1 TAATATAAT-ATTTATAATTA
* *
114493 TATTAAAATATTT
1 TAATATAATATTT
114506 TAAAATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 5 0.12
18 4 0.10
19 6 0.14
20 15 0.36
21 12 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATAATATTTATAATTA
Found at i:114514 original size:43 final size:42
Alignment explanation
Indices: 114467--114563 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 42
114457 TAATAATATT
* *
114467 ATATTAAATATAATAATTAATA-ATTATATTAAAATATTTTAAA
1 ATATTAAATATAA-AATTAATATATTA-AATAAAATAATTTAAA
* *
114510 ATATTAAATAATAAAATTATTATATTAAATATAATAATTTAAA
1 ATATTAAAT-ATAAAATTAATATATTAAATAAAATAATTTAAA
* *
114553 ATTTTATATAT
1 ATATTAAATAT
114564 TATTTTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 2 0.04
43 36 0.78
44 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
ATATTAAATATAAAATTAATATATTAAATAAAATAATTTAAA
Found at i:115025 original size:16 final size:15
Alignment explanation
Indices: 115002--115039 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
114992 ATATAATATT
115002 AATA-AAATAATTAAA
1 AATATAAATAATT-AA
*
115017 AATATAAATTATTAA
1 AATATAAATAATTAA
115032 AATATAAA
1 AATATAAA
115040 ACTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:115039 original size:32 final size:33
Alignment explanation
Indices: 115003--115071 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
114993 TATAATATTA
*
115003 ATAAAA-TAATTAAAAATATAAATTA-TTAAAAT
1 ATAAAACTAA-TAAAAATATAAAATATTTAAAAT
* * *
115035 ATAAAACTTATATAAATATAAAATATTTTAAAT
1 ATAAAACTAATAAAAATATAAAATATTTAAAAT
115068 ATAA
1 ATAA
115072 TTATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (33 bp):
ATAAAACTAATAAAAATATAAAATATTTAAAAT
Done.