Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 20 of 27
Found at i:2641078 original size:42 final size:42
Alignment explanation
Indices: 2640998--2641079 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2640988 TATATATATA
* * *
2640998 TATATCATATTTATATTTAAAATTTTAATATGATAAATAATT
1 TATATCATATTTATATTTAAAATTTTAAAATAAAAAATAATT
* *
2641040 TATATTATATTTATATTT-ATATTATTAAAATAAAAAATAA
1 TATATCATATTTATATTTAAAATT-TTAAAATAAAAAATAA
2641080 GATATATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (42 bp):
TATATCATATTTATATTTAAAATTTTAAAATAAAAAATAATT
Found at i:2641906 original size:14 final size:15
Alignment explanation
Indices: 2641878--2641920 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2641868 AATATAATCT
* *
2641878 TTTAAATATATAAAA
1 TTTAAACATAAAAAA
2641893 TTTAAA-ATAAAAAA
1 TTTAAACATAAAAAA
2641907 -TTAAACATAAAAAA
1 TTTAAACATAAAAAA
2641921 ATATATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 15 0.58
15 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TTTAAACATAAAAAA
Found at i:2642370 original size:2 final size:2
Alignment explanation
Indices: 2642363--2642435 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
2642353 TTGAGCATTT
2642363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2642405 TC TA TA TA TA TA TA TA TC TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2642436 TTGAACTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2646028 original size:14 final size:14
Alignment explanation
Indices: 2645997--2646036 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2645987 TTTCATAAGA
2645997 TATATAAATATT-T
1 TATATAAATATTAT
*
2646010 TATATTAATATTAT
1 TATATAAATATTAT
2646024 TATATAAATATTA
1 TATATAAATATTA
2646037 AAATAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAAATATTAT
Found at i:2647784 original size:2 final size:2
Alignment explanation
Indices: 2647777--2647808 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2647767 TGAATCTCTG
*
2647777 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2647809 TATGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2648739 original size:4 final size:4
Alignment explanation
Indices: 2648732--2648757 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2648722 TATATATATA
2648732 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
2648758 ATAATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2649084 original size:16 final size:16
Alignment explanation
Indices: 2649065--2649098 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2649055 TTTTTATTTA
* *
2649065 TTAATATTTATATATT
1 TTAATAATTAAATATT
2649081 TTAATAATTAAATATT
1 TTAATAATTAAATATT
2649097 TT
1 TT
2649099 TATTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATAATTAAATATT
Found at i:2649639 original size:18 final size:18
Alignment explanation
Indices: 2649609--2649647 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
2649599 ATATCATATA
2649609 ATTTTTTTAAAAAAAATT
1 ATTTTTTTAAAAAAAATT
2649627 ATTTTATTTAAAAAAAATT
1 ATTTT-TTTAAAAAAAATT
2649646 AT
1 AT
2649648 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTTTAAAAAAAATT
Found at i:2650697 original size:2 final size:2
Alignment explanation
Indices: 2650690--2650726 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2650680 ATACCTTGAA
* *
2650690 AT AT AT AT AC AT AT AT AT AT AC 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 A
2650727 CACTCATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2650707 original size:12 final size:12
Alignment explanation
Indices: 2650690--2650722 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2650680 ATACCTTGAA
2650690 ATATATATACAT
1 ATATATATACAT
2650702 ATATATATACAT
1 ATATATATACAT
2650714 ATATATATA
1 ATATATATA
2650723 TATACACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATACAT
Found at i:2656681 original size:17 final size:18
Alignment explanation
Indices: 2656644--2656682 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2656634 CAAATATTTG
**
2656644 ATTTAATACTTAATTGTC
1 ATTTAATACTTAATTAAC
2656662 ATTTAAT-CTTAATTAAC
1 ATTTAATACTTAATTAAC
2656679 ATTT
1 ATTT
2656683 TTGATTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTAATACTTAATTAAC
Found at i:2657615 original size:10 final size:9
Alignment explanation
Indices: 2657594--2657654 Score: 65
Period size: 8 Copynumber: 7.0 Consensus size: 9
2657584 AAACATTATT
*
2657594 ATATAAAAA
1 ATATATAAA
2657603 ATAATATAAA
1 AT-ATATAAA
2657613 ATATAT-AA
1 ATATATAAA
*
2657621 ATATATAAT
1 ATATATAAA
*
2657630 A-ATATAAT
1 ATATATAAA
2657638 ATATAT-AA
1 ATATATAAA
2657646 ATATATAAA
1 ATATATAAA
2657655 TTATTAACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
8 23 0.51
9 14 0.31
10 8 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATATAAA
Found at i:2657632 original size:25 final size:25
Alignment explanation
Indices: 2657602--2657653 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2657592 TTATATAAAA
2657602 AATAATATAAAATATATAAATATAT
1 AATAATATAAAATATATAAATATAT
*
2657627 AATAATATAATATATATAAATATAT
1 AATAATATAAAATATATAAATATAT
2657652 AA
1 AA
2657654 ATTATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATAATATAAAATATATAAATATAT
Found at i:2657820 original size:16 final size:17
Alignment explanation
Indices: 2657798--2657846 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
2657788 TCATTATAAT
2657798 TATATTTAAATTATTAA
1 TATATTTAAATTATTAA
2657815 -ATATTTATATATT-TTAA
1 TATATTTA-A-ATTATTAA
*
2657832 TATATTTATATTATT
1 TATATTTAAATTATT
2657847 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 10 0.37
17 7 0.26
18 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTTAAATTATTAA
Found at i:2657838 original size:18 final size:18
Alignment explanation
Indices: 2657798--2657848 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2657788 TCATTATAAT
2657798 TATATTTA-A-ATTATTAA
1 TATATTTATATATT-TTAA
2657815 -ATATTTATATATTTTAA
1 TATATTTATATATTTTAA
2657832 TATATTTATATTATTTT
1 TATATTTATA-TATTTT
2657849 TTATTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 12 0.40
19 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTATATATTTTAA
Found at i:2657905 original size:40 final size:39
Alignment explanation
Indices: 2657819--2657905 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
2657809 TATTAAATAT
* *
2657819 TTATATATTTTAATATATTTATATTATTTTTTATTTTATA
1 TTATAT-TTTTAATATATTTATATTATTTTTTATTTAAAA
*
2657859 TCATATTTTATAATATAATTTA-ATTA-TTTTTATTATAAAA
1 TTATATTTT-TAATAT-ATTTATATTATTTTTTATT-TAAAA
2657899 TTATATT
1 TTATATT
2657906 ATATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 11 0.28
40 24 0.60
41 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (39 bp):
TTATATTTTTAATATATTTATATTATTTTTTATTTAAAA
Found at i:2657906 original size:22 final size:22
Alignment explanation
Indices: 2657854--2657912 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
2657844 ATTTTTTATT
* *
2657854 TTATATCATATTTTATAATATAA
1 TTATATTAT-TTTTATAATAAAA
*
2657877 TT-TAATTATTTTTATTATAAAA
1 TTAT-ATTATTTTTATAATAAAA
*
2657899 TTATATTATATTTA
1 TTATATTATTTTTA
2657913 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATATTATTTTTATAATAAAA
Found at i:2660073 original size:2 final size:2
Alignment explanation
Indices: 2660066--2660091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2660056 TGTTTTTACA
2660066 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
2660092 TAGTTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2661368 original size:16 final size:17
Alignment explanation
Indices: 2661347--2661389 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2661337 TTAAATATAA
2661347 AAATTATTTT-AT-ATT
1 AAATTATTTTCATAATT
2661362 AATATTATATTTCATAATT
1 AA-ATTAT-TTTCATAATT
2661381 AAATTATTT
1 AAATTATTT
2661390 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.08
16 5 0.21
17 5 0.21
18 7 0.29
19 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATTTTCATAATT
Found at i:2661424 original size:30 final size:31
Alignment explanation
Indices: 2661379--2661447 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
2661369 TATTTCATAA
**
2661379 TTAAATTATTTAAAATAAAATTTAA-TTAAT
1 TTAAATTATAAAAAATAAAATTTAATTTAAT
* **
2661409 TTAAATTATAAAAAATTATTTTTAATTTAAT
1 TTAAATTATAAAAAATAAAATTTAATTTAAT
*
2661440 GTAAATTA
1 TTAAATTA
2661448 AATTTGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
TTAAATTATAAAAAATAAAATTTAATTTAAT
Found at i:2662043 original size:21 final size:19
Alignment explanation
Indices: 2662003--2662046 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
2661993 ATTTTTAAAA
2662003 TATTTGAATTTAATTAATT
1 TATTTGAATTTAATTAATT
*
2662022 TATTTGATATTTAAATTTATT
1 TATTTGA-ATTT-AATTAATT
2662043 TATT
1 TATT
2662047 ATTATCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTTGAATTTAATTAATT
Found at i:2662498 original size:16 final size:17
Alignment explanation
Indices: 2662477--2662519 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2662467 TAATATTATT
*
2662477 TAATTTAAAATTAA-AA
1 TAATTTAAAATAAATAA
2662493 TAATTT-AAATAAATAA
1 TAATTTAAAATAAATAA
2662509 T-ATTTAAAATA
1 TAATTTAAAATA
2662520 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATTTAAAATAAATAA
Found at i:2662535 original size:15 final size:15
Alignment explanation
Indices: 2662495--2662539 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
2662485 AATTAAAATA
* **
2662495 ATTTAAATAAATAAT
1 ATTTAAATATATTTT
2662510 ATTTAAA-ATATTTT
1 ATTTAAATATATTTT
2662524 ATTTAAATATATTTT
1 ATTTAAATATATTTT
2662539 A
1 A
2662540 ATATCATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTAAATATATTTT
Found at i:2662540 original size:25 final size:25
Alignment explanation
Indices: 2662487--2662537 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2662477 TAATTTAAAA
2662487 TTAAAATAATTTAAATAAATAATAT
1 TTAAAATAATTTAAATAAATAATAT
* **
2662512 TTAAAATATTTTATTTAAAT-ATAT
1 TTAAAATAATTTAAATAAATAATAT
2662536 TT
1 TT
2662538 TAATATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAAATAATTTAAATAAATAATAT
Found at i:2664403 original size:9 final size:9
Alignment explanation
Indices: 2664389--2664417 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2664379 TAACTTATAA
2664389 AATTAAATT
1 AATTAAATT
2664398 AATTAAATT
1 AATTAAATT
2664407 AATT-AATT
1 AATTAAATT
2664415 AAT
1 AAT
2664418 ATTTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTAAATT
Found at i:2664410 original size:13 final size:14
Alignment explanation
Indices: 2664388--2664416 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2664378 TTAACTTATA
2664388 AAATTAAATTAATT
1 AAATTAAATTAATT
2664402 AAATT-AATTAATT
1 AAATTAAATTAATT
2664415 AA
1 AA
2664417 TATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAAATTAATT
Found at i:2683918 original size:17 final size:16
Alignment explanation
Indices: 2683886--2683921 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2683876 ATATAATTGT
*
2683886 TAATTTAATTATTAAA
1 TAATTTAATAATTAAA
2683902 TAATTTGAATAATTAAA
1 TAATTT-AATAATTAAA
2683919 TAA
1 TAA
2683922 AGTCAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAATTTAATAATTAAA
Found at i:2684507 original size:16 final size:16
Alignment explanation
Indices: 2684486--2684624 Score: 77
Period size: 16 Copynumber: 9.4 Consensus size: 16
2684476 CTCAAACAAC
2684486 TAAATTTAAATTATTT
1 TAAATTTAAATTATTT
* *
2684502 TAAATTCAACTTATTT
1 TAAATTTAAATTATTT
*
2684518 TAAATTTAAAATA-TT
1 TAAATTTAAATTATTT
*
2684533 TAAATAT-AA-TA-TT
1 TAAATTTAAATTATTT
2684546 TAAA-TT-AATTAATTT
1 TAAATTTAAATT-ATTT
*
2684561 TAAA--TAAATTA-AT
1 TAAATTTAAATTATTT
* *
2684574 T--ACTTAAATTAATT
1 TAAATTTAAATTATTT
* *
2684588 AAAATTTAAA-CATTT
1 TAAATTTAAATTATTT
* *
2684603 CAAATTTAGATTATTT
1 TAAATTTAAATTATTT
*
2684619 TTAATT
1 TAAATT
2684625 CAACTCACGT
Statistics
Matches: 95, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
11 1 0.01
12 3 0.03
13 18 0.19
14 6 0.06
15 29 0.31
16 38 0.40
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.49
Consensus pattern (16 bp):
TAAATTTAAATTATTT
Found at i:2684564 original size:15 final size:15
Alignment explanation
Indices: 2684494--2684589 Score: 71
Period size: 15 Copynumber: 6.4 Consensus size: 15
2684484 ACTAAATTTA
2684494 AATT-ATTTTAAATT
1 AATTAATTTTAAATT
2684508 CAACTT-ATTTTAAATTT
1 -AA-TTAATTTTAAA-TT
2684525 AA--AATATTTAAA-T
1 AATTAAT-TTTAAATT
2684538 -A-TAATATTTAAATT
1 AATTAAT-TTTAAATT
*
2684552 AATTAATTTTAAATA
1 AATTAATTTTAAATT
2684567 AATTAATTACTTAAATT
1 AATTAATT--TTAAATT
2684584 AATTAA
1 AATTAA
2684590 AATTTAAACA
Statistics
Matches: 69, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.01
13 11 0.16
14 3 0.04
15 24 0.35
16 16 0.23
17 14 0.20
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATTTTAAATT
Found at i:2688291 original size:2 final size:2
Alignment explanation
Indices: 2688286--2688313 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2688276 AAACTCTCTC
2688286 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2688314 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2688318 original size:2 final size:2
Alignment explanation
Indices: 2688313--2688346 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2688303 ACACACACAC
2688313 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
2688347 GAAAAAACTC
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:2691180 original size:5 final size:5
Alignment explanation
Indices: 2691134--2691195 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
2691124 ATATCTAATG
* * * *
2691134 ATATT -TATT ACATT ATAATC ATATT -TATT A-AAT ATATC ATATT ATATT
1 ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT ATATT
2691182 -TATT ATATT ATATT
1 ATATT ATATT ATATT
2691196 CATGTTCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
4 15 0.34
5 25 0.57
6 4 0.09
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:2691181 original size:43 final size:43
Alignment explanation
Indices: 2691120--2691211 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
2691110 TACGTGTATG
*
2691120 AAATATATCTAATGATATTTATTACATTATAATCATATTTATT
1 AAATATATCTAATGATATTTATTACATTATAATCATATTCATT
* * * *
2691163 AAATATATC-ATATTATATTTATTATATTATATTCATGTTCATT
1 AAATATATCTA-ATGATATTTATTACATTATAATCATATTCATT
2691206 AAATAT
1 AAATAT
2691212 TTTATGTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (43 bp):
AAATATATCTAATGATATTTATTACATTATAATCATATTCATT
Found at i:2691187 original size:9 final size:10
Alignment explanation
Indices: 2691134--2691195 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
2691124 ATATCTAATG
2691134 ATATT-TATT
1 ATATTATATT
* *
2691143 ACATTATAATC
1 ATATTAT-ATT
2691154 ATATT-TATT
1 ATATTATATT
* *
2691163 A-AATATATC
1 ATATTATATT
2691172 ATATTATATT
1 ATATTATATT
2691182 -TATTATATT
1 ATATTATATT
2691191 ATATT
1 ATATT
2691196 CATGTTCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
8 2 0.05
9 20 0.50
10 12 0.30
11 6 0.15
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATTATATT
Found at i:2691189 original size:14 final size:14
Alignment explanation
Indices: 2691134--2691195 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2691124 ATATCTAATG
*
2691134 ATATTTATTACATT
1 ATATTTATTATATT
*
2691148 ATAATCATATT-TATT
1 AT-AT-TTATTATATT
* * *
2691163 AAATATATCATATT
1 ATATTTATTATATT
2691177 ATATTTATTATATT
1 ATATTTATTATATT
2691191 ATATT
1 ATATT
2691196 CATGTTCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 4 0.11
14 24 0.63
15 6 0.16
16 4 0.11
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTATTATATT
Found at i:2691619 original size:73 final size:73
Alignment explanation
Indices: 2691527--2691667 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 73
2691517 TGGGTCATCA
* * * *
2691527 AATAAAGTATTTAAGTTTGATTGATTCAAATCAATTAAAATATATGTTATTTTGTCTCATCATAA
1 AATAAAGTATTTAAATTTGATTAATTCAAATCAATTAAAATATAGGTTATTTTGACTCATCATAA
2691592 AAGCATAT
66 AAGCATAT
2691600 AATAAAGTATTTAAATTTGATTAATTCAAATCAATTAAAATATAGGTTATTTTGACTCATCATAA
1 AATAAAGTATTTAAATTTGATTAATTCAAATCAATTAAAATATAGGTTATTTTGACTCATCATAA
2691665 AAG
66 AAG
2691668 TATACGTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (73 bp):
AATAAAGTATTTAAATTTGATTAATTCAAATCAATTAAAATATAGGTTATTTTGACTCATCATAA
AAGCATAT
Found at i:2694773 original size:2 final size:2
Alignment explanation
Indices: 2694766--2694791 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2694756 GAATTTTCTG
2694766 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2694792 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2698187 original size:18 final size:17
Alignment explanation
Indices: 2698164--2698199 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2698154 AATTTTAAAT
2698164 TTAAATTTTAATATTTTA
1 TTAAATTTTAAT-TTTTA
*
2698182 TTAAATTTTTATTTTTA
1 TTAAATTTTAATTTTTA
2698199 T
1 T
2698200 ATTATGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAAATTTTAATTTTTA
Found at i:2702336 original size:22 final size:22
Alignment explanation
Indices: 2702308--2702350 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2702298 AGCTTGGGGA
2702308 CGAAGGAAAACAACGACGCTTG
1 CGAAGGAAAACAACGACGCTTG
2702330 CGAAGGAAAACAACGACGCTT
1 CGAAGGAAAACAACGACGCTT
2702351 AGGTTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (22 bp):
CGAAGGAAAACAACGACGCTTG
Found at i:2702714 original size:21 final size:20
Alignment explanation
Indices: 2702690--2702730 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2702680 TATATATCAT
*
2702690 TATTTTATATAATAATATAAA
1 TATTTTATAAAATAAT-TAAA
*
2702711 TATTTTTTAAAATAATTAAA
1 TATTTTATAAAATAATTAAA
2702731 CGATTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTTATAAAATAATTAAA
Found at i:2702778 original size:18 final size:18
Alignment explanation
Indices: 2702757--2702812 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
2702747 ATTTAAATTT
*
2702757 TTTAATTAATCAATTTAA
1 TTTAATTAATTAATTTAA
*
2702775 TTTAATTAATTATTTTAA
1 TTTAATTAATTAATTTAA
* *
2702793 GTAAATTCAATTAATTTAA
1 TTTAATT-AATTAATTTAA
2702812 T
1 T
2702813 AATTTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAATTAATTAATTTAA
Found at i:2703245 original size:15 final size:16
Alignment explanation
Indices: 2703222--2703258 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2703212 TCGAATCAGA
2703222 TTTAATTA-TAAAAAT
1 TTTAATTATTAAAAAT
*
2703237 TTTATTTATTAAAAA-
1 TTTAATTATTAAAAAT
2703252 TTTAATT
1 TTTAATT
2703259 CATTTTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAATTATTAAAAAT
Found at i:2703396 original size:31 final size:32
Alignment explanation
Indices: 2703360--2703419 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2703350 TTTATAATTA
2703360 AATTTAAATTAAAAAATATT-TA-TTAAATAAT
1 AATTTAAATT-AAAAATATTATATTTAAATAAT
*
2703391 AATTTAAATTTAAAATATTATATTTAAAT
1 AATTTAAATTAAAAATATTATATTTAAAT
2703420 TTACATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 12 0.46
32 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATTTAAATTAAAAATATTATATTTAAATAAT
Found at i:2704880 original size:3 final size:3
Alignment explanation
Indices: 2704874--2704906 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2704864 ATAATAATAA
2704874 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2704907 GAGTGATTGG
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):
TAT
Found at i:2705209 original size:52 final size:48
Alignment explanation
Indices: 2705149--2705259 Score: 116
Period size: 53 Copynumber: 2.2 Consensus size: 48
2705139 AACTTTTTTT
* *
2705149 AAATAATTTAATATTAAAATATTTTTTAATATTGAAAAATAAAATAT-TAAAA
1 AAATAATTTAAAATTAAAATAATTTTT-ATATT-AAAAATAAAAT-TGT--AA
** *
2705201 AAATAATTTTAAAATTTTAATAATTTTTATATTAATAATAAAATTGTAA
1 AAATAA-TTTAAAATTAAAATAATTTTTATATTAAAAATAAAATTGTAA
2705250 AAATAATTTA
1 AAATAATTTA
2705260 TATGTTATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
48 4 0.08
49 8 0.15
50 1 0.02
51 11 0.21
52 11 0.21
53 17 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (48 bp):
AAATAATTTAAAATTAAAATAATTTTTATATTAAAAATAAAATTGTAA
Found at i:2711550 original size:169 final size:157
Alignment explanation
Indices: 2711340--2711814 Score: 572
Period size: 169 Copynumber: 3.0 Consensus size: 157
2711330 TGGTGAAAAG
** *
2711340 AATAATTTTTCATGTGTATGTACTTTACATTTAAGTAAGATGGTTAGTTTTAACATCTAAAAAAA
1 AATAATTTTTTGTGTGTATGTAC-TTACATTTAAGTAAGATGATTAGTTTTAACATCTAAAAAAA
* * *
2711405 ACTTAATTATTGAAATTATTCTAGCTCAAACTTGTTATGACGAGGTGCATATATATATATATATA
65 ACTCAATTATTGAAATTATTCAAGCTCAAACTTGGTATGACGA-G-G--TATATATATATATATA
* *
2711470 TATATAATATGATTTTAGTATATAAATATATAAAAAT
126 TATATAATATGATTATAATATAT-AA-ATAT---AAT
2711507 ATATTAATTATTTTGTGTGTATGTACTTACATTTAAGTAAGATGATTAGTTTTAACATCTAAAAA
1 A-A-TAATT-TTTTGTGTGTATGTACTTACATTTAAGTAAGATGATTAGTTTTAACATCTAAAAA
* *
2711572 ACACTCAATTATTGAAATTATTCAAGCTCAAACTTGGTATGATGAGGTATATATATATATATATA
63 AAACTCAATTATTGAAATTATTCAAGCTCAAACTTGGTATGACGAGGTATATATATATATATATA
2711637 TATAATATGATTATAATATATAAATATAAT
128 TATAATATGATTATAATATATAAATATAAT
* * *
2711667 AATAATTTTTTGTGTGTATGTATTTACATTTTAAGTAAAATGATTAATTTTAACATCT-AAAAAA
1 AATAATTTTTTGTGTGTATGTACTTACA-TTTAAGTAAGATGATTAGTTTTAACATCTAAAAAAA
* * * * * *
2711731 ATTCAATTATT-AATGTTATTCAAACTCATA--T-G-AT-A--AAGTACATATATATATATATAT
65 ACTCAATTATTGAA-ATTATTCAAGCTCAAACTTGGTATGACGAGGTATATATATATATATATAT
*
2711788 ATAATATGATTATAATACATAAATATA
129 ATAATATGATTATAATATATAAATATA
2711815 TAAAAATATA
Statistics
Matches: 282, Mismatches: 21, Indels: 27
0.85 0.06 0.08
Matches are distributed among these distances:
150 46 0.16
152 1 0.00
153 2 0.01
154 1 0.00
155 1 0.00
156 2 0.01
157 48 0.17
158 32 0.11
159 1 0.00
160 4 0.01
163 4 0.01
164 2 0.01
165 37 0.13
167 2 0.01
168 2 0.01
169 83 0.29
170 14 0.05
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (157 bp):
AATAATTTTTTGTGTGTATGTACTTACATTTAAGTAAGATGATTAGTTTTAACATCTAAAAAAAA
CTCAATTATTGAAATTATTCAAGCTCAAACTTGGTATGACGAGGTATATATATATATATATATAT
AATATGATTATAATATATAAATATAAT
Found at i:2711626 original size:2 final size:2
Alignment explanation
Indices: 2711619--2711664 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
2711609 TATGATGAGG
2711619 TA TA TA TA TA TA TA TA TA TA TA -A TA TGA T- TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
2711659 AA TA TA
1 TA TA TA
2711665 ATAATAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2712060 original size:17 final size:18
Alignment explanation
Indices: 2712028--2712063 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2712018 TTTAAATTTA
*
2712028 AATTTATTAAATATTATT
1 AATTTATTAAAAATTATT
2712046 AATTT-TTAAAAATTATT
1 AATTTATTAAAAATTATT
2712063 A
1 A
2712064 TATAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTATTAAAAATTATT
Found at i:2712376 original size:21 final size:20
Alignment explanation
Indices: 2712352--2712451 Score: 78
Period size: 21 Copynumber: 4.8 Consensus size: 20
2712342 ATACAAACAC
2712352 AATATAATATTATAAATATAA
1 AATATAATA-TATAAATATAA
* *
2712373 AATATAGATTTAT-ATTATAA
1 AATATA-ATATATAAATATAA
*
2712393 TATATATAA-ATATAATTATAA
1 -A-ATATAATATATAAATATAA
* * *
2712414 TATAATAAAATATAAATATAT
1 AAT-ATAATATATAAATATAA
2712435 AATATAAGTATATAAAT
1 AATATAA-TATATAAAT
2712452 TATTATATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
19 2 0.03
20 17 0.27
21 38 0.59
22 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATAATATATAAATATAA
Found at i:2712395 original size:8 final size:7
Alignment explanation
Indices: 2712354--2712454 Score: 52
Period size: 7 Copynumber: 14.4 Consensus size: 7
2712344 ACAAACACAA
2712354 TATAATAT
1 TATAA-AT
2712362 TATAAA-
1 TATAAAT
*
2712368 TATAAAA
1 TATAAAT
*
2712375 TATAGAT
1 TATAAAT
*
2712382 T-TATAT
1 TATAAAT
2712388 TATAATAT
1 TATAA-AT
2712396 ATATAAA-
1 -TATAAAT
2712403 TAT-AAT
1 TATAAAT
2712409 TATAATAT
1 TATAA-AT
* *
2712417 AATAAAA
1 TATAAAT
2712424 TATAAA-
1 TATAAAT
2712430 TATATAA-
1 TATA-AAT
*
2712437 TATAAGT
1 TATAAAT
2712444 ATATAAAT
1 -TATAAAT
2712452 TAT
1 TAT
2712455 TATATTTAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
5 2 0.03
6 22 0.30
7 25 0.34
8 20 0.27
9 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (7 bp):
TATAAAT
Found at i:2712400 original size:29 final size:28
Alignment explanation
Indices: 2712365--2712450 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
2712355 ATAATATTAT
*
2712365 AAATATAAAATATAGATT-T-ATATTATA
1 AAATATAAAATATA-ATTATAATATAATA
*
2712392 ATATATATAAATATAATTATAATATAATA
1 AAATATA-AAATATAATTATAATATAATA
2712421 AAATATAAATATATAA-TATAAGTAT-ATA
1 AAATATAAA-ATATAATTATAA-TATAATA
2712449 AA
1 AA
2712451 TTATTATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.18
28 20 0.39
29 22 0.43
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATATAAAATATAATTATAATATAATA
Found at i:2713031 original size:26 final size:26
Alignment explanation
Indices: 2713002--2713068 Score: 64
Period size: 30 Copynumber: 2.4 Consensus size: 26
2712992 TATTTAATTT
2713002 AATAATAATTTTT-AAAATAAAATATA
1 AATAATAATTTTTAAAAATAAAA-ATA
*
2713028 AATATATAAATATATTTAAAAATTAAAATA
1 AATA-AT-AAT-T-TTTAAAAATAAAAATA
*
2713058 AATAAAAATTT
1 AATAATAATTT
2713069 AATTTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
26 5 0.15
27 3 0.09
28 6 0.18
29 2 0.06
30 10 0.29
31 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAATAATTTTTAAAAATAAAAATA
Found at i:2719140 original size:20 final size:19
Alignment explanation
Indices: 2719085--2719136 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2719075 AAAAAAAACC
* *
2719085 ATAATAAATTAAAATTTTTG
1 ATAA-AAATTAAAATATTTA
*
2719105 ATAAAATTTAAAATATTTA
1 ATAAAAATTAAAATATTTA
2719124 ATAAAAATTAAAA
1 ATAAAAATTAAAA
2719137 ATATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAAATTAAAATATTTA
Found at i:2727671 original size:18 final size:18
Alignment explanation
Indices: 2727650--2727684 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2727640 AATTTTAATA
*
2727650 AATTTAAATGTAATATAT
1 AATTTAAATATAATATAT
2727668 AATTTAAATATAATATA
1 AATTTAAATATAATATA
2727685 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTTAAATATAATATAT
Found at i:2729019 original size:28 final size:27
Alignment explanation
Indices: 2728988--2729044 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
2728978 AAAAATAAAA
2728988 TTTATCAAATTTTTAAATAAAATTTATT
1 TTTATCAAATTTTTAAATAAAA-TTATT
** * *
2729016 TTTATTTAATTTTTTATTAAAATTATT
1 TTTATCAAATTTTTAAATAAAATTATT
2729043 TT
1 TT
2729045 AAATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATCAAATTTTTAAATAAAATTATT
Found at i:2729124 original size:2 final size:2
Alignment explanation
Indices: 2729117--2729145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2729107 AAGTCACGAA
2729117 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 T
2729146 GACCGACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2735395 original size:3 final size:3
Alignment explanation
Indices: 2735387--2735418 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2735377 CTTTAAGATT
*
2735387 ATG ATG ATG ATG ATG ATG ATG ATG CTG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2735419 TAGCAAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2736344 original size:11 final size:10
Alignment explanation
Indices: 2736334--2736387 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 10
2736324 TTTAAATTAT
*
2736334 TATATATTTA
1 TATATTTTTA
2736344 TATATTTTTA
1 TATATTTTTA
2736354 T-TATTTTTA
1 TATATTTTTA
* *
2736363 TAT-TATAT-
1 TATATTTTTA
2736371 TATATTTTTA
1 TATATTTTTA
2736381 T-TATTTT
1 TATATTTT
2736388 CTAAATCGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
8 3 0.08
9 21 0.58
10 12 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTTA
Found at i:2736357 original size:35 final size:36
Alignment explanation
Indices: 2736318--2736387 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
2736308 TAATATTATA
2736318 ATTATATTTAAATTAT-TATATATTTATA-TATTTTT
1 ATTATATTTAAATTATAT-TATATTTATATTATTTTT
* * *
2736353 ATTATTTTTATATTATATTATATTTTTATTATTTT
1 ATTATATTTAAATTATATTATATTTATATTATTTT
2736388 CTAAATCGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 23 0.77
36 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (36 bp):
ATTATATTTAAATTATATTATATTTATATTATTTTT
Found at i:2736363 original size:27 final size:27
Alignment explanation
Indices: 2736304--2736387 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
2736294 TTTCCTCTCT
**
2736304 TTTTTAATATTATAATTATATTTAAATTA
1 TTTTT-ATATTAT-ATTATATTTTTATTA
*
2736333 -TTATATATT-TA-TATATTTTTATTA
1 TTTTTATATTATATTATATTTTTATTA
2736357 TTTTTATATTATATTATATTTTTATTA
1 TTTTTATATTATATTATATTTTTATTA
2736384 TTTT
1 TTTT
2736388 CTAAATCGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 11 0.23
25 9 0.19
26 3 0.06
27 22 0.46
28 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTATATTATATTATATTTTTATTA
Found at i:2736381 original size:8 final size:8
Alignment explanation
Indices: 2736336--2736387 Score: 59
Period size: 8 Copynumber: 6.0 Consensus size: 8
2736326 TAAATTATTA
*
2736336 TATATTTA
1 TATATTTT
2736344 TATATTTT
1 TATATTTT
2736352 TATTATTTT
1 TA-TATTTT
2736361 TATATTATAT
1 TATATT-T-T
2736371 TATATTTT
1 TATATTTT
2736379 TATTATTTT
1 TA-TATTTT
2736388 CTAAATCGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 16 0.41
9 16 0.41
10 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:2736756 original size:18 final size:19
Alignment explanation
Indices: 2736715--2736764 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2736705 ATAAACGTGA
*
2736715 TTAATAAAATGATAAATAATT
1 TTAA-AAAATAAT-AATAATT
*
2736736 TTAAAATATAATAATAA-T
1 TTAAAAAATAATAATAATT
2736754 TTAAAAAATAA
1 TTAAAAAATAA
2736765 AAAATTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 6 0.23
21 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TTAAAAAATAATAATAATT
Found at i:2737211 original size:4 final size:4
Alignment explanation
Indices: 2737202--2737226 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2737192 TTATGCATAA
2737202 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2737227 GTTTGTTTGT
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:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2737595 original size:29 final size:28
Alignment explanation
Indices: 2737558--2737616 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
2737548 TATTATAGTA
* * *
2737558 ATTATTTTATCTTAATCATATTTATTAT
1 ATTATTTTATATTAATAAAATTTATTAT
*
2737586 ATTATTTTTATATTTATAAAATTTATTAT
1 ATTA-TTTTATATTAATAAAATTTATTAT
2737615 AT
1 AT
2737617 ACTATCACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTATTTTATATTAATAAAATTTATTAT
Found at i:2738242 original size:21 final size:20
Alignment explanation
Indices: 2738218--2738257 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2738208 AAAATTTATT
*
2738218 TTAAATCTGATTTATTTAAAA
1 TTAAAT-TGATTTAATTAAAA
*
2738239 TTAAATTTATTTAATTAAA
1 TTAAATTGATTTAATTAAA
2738258 TAAATAGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAAATTGATTTAATTAAAA
Found at i:2738246 original size:16 final size:17
Alignment explanation
Indices: 2738209--2738252 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2738199 AAATTATTAA
*
2738209 AAATTTATTTTAAATCT
1 AAATTTATTTAAAATCT
*
2738226 -GATTTATTTAAAAT-T
1 AAATTTATTTAAAATCT
2738241 AAATTTATTTAA
1 AAATTTATTTAA
2738253 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATTTATTTAAAATCT
Found at i:2740473 original size:7 final size:8
Alignment explanation
Indices: 2740463--2740510 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
2740453 TTATATCATG
2740463 TATTTA-A
1 TATTTATA
2740470 TATTTATA
1 TATTTATA
*
2740478 TATATATA
1 TATTTATA
*
2740486 TATATATA
1 TATTTATA
*
2740494 TATATATA
1 TATTTATA
*
2740502 TATATATA
1 TATTTATA
2740510 T
1 T
2740511 GTGTGTGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
7 6 0.15
8 33 0.85
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TATTTATA
Found at i:2740481 original size:2 final size:2
Alignment explanation
Indices: 2740469--2740510 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2740459 CATGTATTTA
*
2740469 AT AT TT 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
2740511 GTGTGTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2741632 original size:262 final size:261
Alignment explanation
Indices: 2741151--2741670 Score: 724
Period size: 262 Copynumber: 2.0 Consensus size: 261
2741141 CTTCGCATTG
* * * *
2741151 ATACATAGTGGGTATCGGAAGGGACTGGGAGAATCAGGGTGGAGTTTTGGGTTTTGTTTTTCTTA
1 ATACATAGTGGGTATAGGAAGGGACTGGGAGAATCAGGATGGAGCTTTGCGTTTTGTTTTTCTTA
* * ** * * * * *
2741216 ATGATTGGAGATTGTTGCTTCTTTATGAAGCTCTGGGATATGTTCATGGGAGGATGAGGAGACCA
66 ATGATTGGAGATTATTGCTCCCATATGAAGCTCTGGAAAATGTTCATGGAAGAATGAAGAGACCA
* * * * *
2741281 AATTAGGTTTCAAATCTTGTTATGGCTTGTGGAGCATCTTTGGAGCGAATGAGCGATGGAGCTTG
131 AACTAAGTTTCAAATCTTGTTATAGCTTGTGGAGCATCTTTGGAGCAAATGAGCAATGGAGCTTG
* * *
2741346 TGGAGTATCTGTCTCTATTGGAGGAAATGCTCACTTGGTGTGCTTCATGGTTTTTGGTT-TGCAA
196 TGGAGCATCCGTCTCTACTGGAGGAAATGCTCACTTGGTGTGCTTCAT-GTTTTTGGTTATGCAA
2741410 TA
260 TA
* *
2741412 ATACATAG-GGGTTATAGGAAGGGAGTGGGAGAATCATGATGGAGCTTTGCGTTTTGTTTTGT-T
1 ATACATAGTGGG-TATAGGAAGGGACTGGGAGAATCAGGATGGAGCTTTGCGTTTTGTTTT-TCT
* *
2741475 TAATGATTGGAGATTATTGCTCCCATATGAAGCTCTGGCAAAATGTTCATGGAAGAATGAAGTGT
64 TAATGATTGGAGATTATTGCTCCCATATGAAGCTCTGG-AAAATGTTCATGGAAGAATGAAGAGA
2741540 CCAAACTAAGTTTCAAATCTTGTTATAGCTTGTGGAGCATCTTTGGAGCAAATGAGCAATGGAGC
128 CCAAACTAAGTTTCAAATCTTGTTATAGCTTGTGGAGCATCTTTGGAGCAAATGAGCAATGGAGC
* *
2741605 TTGTTGAGCA-CCGCTCTCTACTGGAGGAATTGCTCACTTGGTGTGCTTCATGTTTTTGGTTATG
193 TTGTGGAGCATCCG-TCTCTACTGGAGGAAATGCTCACTTGGTGTGCTTCATGTTTTTGGTTATG
2741669 CA
257 CA
2741671 GTAAGTTTTT
Statistics
Matches: 227, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
260 3 0.01
261 97 0.43
262 127 0.56
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (261 bp):
ATACATAGTGGGTATAGGAAGGGACTGGGAGAATCAGGATGGAGCTTTGCGTTTTGTTTTTCTTA
ATGATTGGAGATTATTGCTCCCATATGAAGCTCTGGAAAATGTTCATGGAAGAATGAAGAGACCA
AACTAAGTTTCAAATCTTGTTATAGCTTGTGGAGCATCTTTGGAGCAAATGAGCAATGGAGCTTG
TGGAGCATCCGTCTCTACTGGAGGAAATGCTCACTTGGTGTGCTTCATGTTTTTGGTTATGCAAT
A
Found at i:2752848 original size:20 final size:21
Alignment explanation
Indices: 2752820--2752858 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2752810 AACTCGAAAA
2752820 AAATATAAAAAT-TTAAATTT
1 AAATATAAAAATGTTAAATTT
* *
2752840 AAATTTAAATATGTTAAAT
1 AAATATAAAAATGTTAAAT
2752859 GACACTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAATATAAAAATGTTAAATTT
Found at i:2754499 original size:23 final size:22
Alignment explanation
Indices: 2754473--2754516 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2754463 AAATCTCAAG
2754473 TTTTCAATATT-TATATTTTTTTA
1 TTTTCAA-ATTATA-ATTTTTTTA
*
2754496 TTTTGAAATTATAATTTTTTT
1 TTTTCAAATTATAATTTTTTT
2754517 TATGATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTCAAATTATAATTTTTTTA
Found at i:2754931 original size:17 final size:15
Alignment explanation
Indices: 2754898--2754937 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2754888 CTTTTGTTAG
2754898 ATATAATA-ATTTAT
1 ATATAATATATTTAT
*
2754912 ATATAATATATATAT
1 ATATAATATATTTAT
*
2754927 ATATATTATAT
1 ATATAATATAT
2754938 GTCGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATATATTTAT
Found at i:2754991 original size:18 final size:18
Alignment explanation
Indices: 2754968--2755009 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2754958 ATCATATAAA
2754968 ATTAAAATA-ATAAAAATT
1 ATTAAAATATATAAAAA-T
*
2754986 ATTAAAATATATTAAAAT
1 ATTAAAATATATAAAAAT
2755004 ATTAAA
1 ATTAAA
2755010 TAAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAATATATAAAAAT
Found at i:2754998 original size:10 final size:10
Alignment explanation
Indices: 2754968--2755005 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
2754958 ATCATATAAA
2754968 ATTAAAATA-
1 ATTAAAATAT
*
2754977 ATAAAAAT-T
1 ATTAAAATAT
2754986 ATTAAAATAT
1 ATTAAAATAT
2754996 ATTAAAATAT
1 ATTAAAATAT
2755006 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:2755052 original size:24 final size:25
Alignment explanation
Indices: 2755015--2755076 Score: 92
Period size: 23 Copynumber: 2.6 Consensus size: 25
2755005 TTAAATAAAA
* *
2755015 ATATGATATATATTTTAAATATATC
1 ATATTATATTTATTTTAAATATATC
2755040 ATATTA-ATTTA-TTTAAATATATC
1 ATATTATATTTATTTTAAATATATC
2755063 ATATTATATTTATT
1 ATATTATATTTATT
2755077 AAAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 18 0.55
24 9 0.27
25 6 0.18
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATTATATTTATTTTAAATATATC
Found at i:2755058 original size:23 final size:24
Alignment explanation
Indices: 2755028--2755103 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 24
2755018 TGATATATAT
2755028 TTTAAATATATCATATTA-ATTTA
1 TTTAAATATATCATATTATATTTA
2755051 TTTAAATATATCATATTATATTTA
1 TTTAAATATATCATATTATATTTA
*
2755075 -TTAAA-AT-T--TTTTATATTTA
1 TTTAAATATATCATATTATATTTA
2755094 -TTAAATATAT
1 TTTAAATATAT
2755104 TATGTAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
19 15 0.31
20 2 0.04
21 2 0.04
22 2 0.04
23 23 0.47
24 5 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAATATATCATATTATATTTA
Found at i:2755074 original size:20 final size:20
Alignment explanation
Indices: 2755010--2755074 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
2755000 AAATATTAAA
* *
2755010 TAAAAATATGATA-TATATTT
1 TAAATATATCATATTATA-TT
2755030 TAAATATATCATATTAATTTATT
1 TAAATATATCATATT-A--TATT
2755053 TAAATATATCATATTATATT
1 TAAATATATCATATTATATT
2755073 TA
1 TA
2755075 TTAAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 17 0.44
21 1 0.03
22 2 0.05
23 17 0.44
24 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (20 bp):
TAAATATATCATATTATATT
Found at i:2755167 original size:3 final size:3
Alignment explanation
Indices: 2755159--2755185 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2755149 TGGTTACTAT
2755159 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2755186 TTTCATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2755730 original size:26 final size:25
Alignment explanation
Indices: 2755675--2755730 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
2755665 AATATAATTA
*
2755675 AATAATTTTTATTATATTAATTTTT
1 AATAAATTTTATTATATTAATTTTT
2755700 -A-AAATTTTATTATA-TAATACTTTT
1 AATAAATTTTATTATATTAAT--TTTT
2755724 AATAAAT
1 AATAAAT
2755731 ATAAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
23 12 0.46
24 5 0.19
25 1 0.04
26 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATAAATTTTATTATATTAATTTTT
Found at i:2755757 original size:20 final size:19
Alignment explanation
Indices: 2755732--2755773 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2755722 TTAATAAATA
2755732 TAAATATAATATAAAATATT
1 TAAATATAAT-TAAAATATT
*
2755752 TAAATATAATTAATATATT
1 TAAATATAATTAAAATATT
2755771 TAA
1 TAA
2755774 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATATAATTAAAATATT
Found at i:2755826 original size:23 final size:23
Alignment explanation
Indices: 2755800--2755844 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2755790 TTTTTATATT
2755800 ATAAT-TATAATAATATTTAAAAA
1 ATAATATATAAT-ATATTTAAAAA
*
2755823 ATAATATATAATTTATTTAAAA
1 ATAATATATAATATATTTAAAA
2755845 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAATATATAATATATTTAAAAA
Found at i:2755847 original size:7 final size:7
Alignment explanation
Indices: 2755837--2755862 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2755827 TATATAATTT
2755837 ATTTAAA
1 ATTTAAA
2755844 ATTTAAA
1 ATTTAAA
2755851 ATTTAAA
1 ATTTAAA
2755858 ATTTA
1 ATTTA
2755863 TTATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAA
Found at i:2756292 original size:5 final size:5
Alignment explanation
Indices: 2756282--2756312 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2756272 ATAAATTGCC
*
2756282 ATTAT ATTAT ATTAC ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
2756313 CGTAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:2756301 original size:15 final size:15
Alignment explanation
Indices: 2756281--2756310 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2756271 CATAAATTGC
2756281 CATTATATTATATTA
1 CATTATATTATATTA
2756296 CATTATATTATATTA
1 CATTATATTATATTA
2756311 TACGTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
CATTATATTATATTA
Found at i:2756478 original size:18 final size:16
Alignment explanation
Indices: 2756423--2756481 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
2756413 ACTTTTCATC
*
2756423 ATTTTATTTTTATTTA
1 ATTTTATTTTTATTAA
*
2756439 ATTATATTTTATTATTAA
1 ATTTTA-TTT-TTATTAA
2756457 ATTTTAATTTTTGATTAA
1 ATTTT-ATTTTT-ATTAA
2756475 ATTTTAT
1 ATTTTAT
2756482 CACTTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.14
17 7 0.19
18 23 0.64
19 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTTTATTTTTATTAA
Found at i:2756719 original size:19 final size:19
Alignment explanation
Indices: 2756697--2756734 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2756687 ATGTTAAGTG
2756697 TTAAAATTTAATTAAAAAA
1 TTAAAATTTAATTAAAAAA
*
2756716 TTAAAATTTAGTTAAAAAA
1 TTAAAATTTAATTAAAAAA
2756735 CTCAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAAATTTAATTAAAAAA
Found at i:2756950 original size:16 final size:16
Alignment explanation
Indices: 2756921--2756971 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2756911 ATAAAAATTT
*
2756921 TAAAATTTATATAATA
1 TAAATTTTATATAATA
2756937 TAAATTATTA-ATAA-A
1 TAAATT-TTATATAATA
2756952 TTAAATTTTATATAAATA
1 -TAAATTTTATAT-AATA
2756970 TA
1 TA
2756972 TAATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
15 4 0.14
16 17 0.59
17 7 0.24
18 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:2756982 original size:27 final size:27
Alignment explanation
Indices: 2756901--2756984 Score: 69
Period size: 32 Copynumber: 2.9 Consensus size: 27
2756891 TAAAGATATG
* * *
2756901 ATATAAAGATATAAAAATTTTAAAATTT
1 ATATAAATATAT-AATATTTTAAATTTT
**
2756929 ATATAATATAAATTATTAATAAATTAAATTTT
1 ATATAA-AT--A-TA-TAATATTTTAAATTTT
2756961 ATATAAATATATAATATTTTAAAT
1 ATATAAATATATAATATTTTAAAT
2756985 AAAATTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
27 11 0.25
28 8 0.18
29 2 0.05
31 3 0.07
32 19 0.43
33 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATAAATATATAATATTTTAAATTTT
Found at i:2756990 original size:32 final size:32
Alignment explanation
Indices: 2756921--2756990 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
2756911 ATAAAAATTT
2756921 TAAAA-TTTATATAATATAAATTATTAATAAA
1 TAAAATTTTATATAATATAAATTATTAATAAA
* *
2756952 TTAAATTTTATATAAATATATAA-TATT-TTAAA
1 TAAAATTTTATAT-AATATA-AATTATTAATAAA
2756984 TAAAATT
1 TAAAATT
2756991 AAAATACGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 4 0.12
32 17 0.52
33 10 0.30
34 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAAATTTTATATAATATAAATTATTAATAAA
Found at i:2759197 original size:18 final size:18
Alignment explanation
Indices: 2759151--2759200 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
2759141 TTTAAATTAT
* *
2759151 TTTATATT-TAATAAAAA
1 TTTATATTATATTAATAA
*
2759168 TTT-TAATATATTAATAA
1 TTTATATTATATTAATAA
2759185 TTTATATTATATTAAT
1 TTTATATTATATTAAT
2759201 TTTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 13 0.48
18 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATATTATATTAATAA
Found at i:2759205 original size:44 final size:41
Alignment explanation
Indices: 2759123--2759207 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 41
2759113 ATTATTTTTT
*
2759123 AAAATTATAATAATTATATTTAAATTATTTTATATTTAATA
1 AAAATTATAATAATTATATTTAAATTATTTAATATTTAATA
* *
2759164 AAAATTTTAATATATTAATAATTTATATTATATTAAT-TTTAATA
1 AAAATTATAATA-ATT-AT-ATTTAAATTAT-TTAATATTTAATA
2759208 TATTTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 11 0.30
42 3 0.08
43 2 0.05
44 17 0.46
45 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
AAAATTATAATAATTATATTTAAATTATTTAATATTTAATA
Found at i:2759223 original size:20 final size:19
Alignment explanation
Indices: 2759187--2759224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2759177 ATTAATAATT
2759187 TATATTATATTAATTTTAA
1 TATATTATATTAATTTTAA
*
2759206 TATATTTATATTATTTTTA
1 TATA-TTATATTAATTTTA
2759225 TGTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTATATTAATTTTAA
Found at i:2760195 original size:17 final size:18
Alignment explanation
Indices: 2760173--2760206 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2760163 AGTTATATTT
2760173 ATTTTAAATTT-TTTATA
1 ATTTTAAATTTATTTATA
*
2760190 ATTTTATATTTATTTAT
1 ATTTTAAATTTATTTAT
2760207 TAATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTAAATTTATTTATA
Found at i:2763035 original size:29 final size:29
Alignment explanation
Indices: 2763003--2763060 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2762993 TAACGAGTCA
2763003 CATGATGGGATAGATAAAACAGAGTTATT
1 CATGATGGGATAGATAAAACAGAGTTATT
2763032 CATGATGGGATAGATAAAACAGAGTTATT
1 CATGATGGGATAGATAAAACAGAGTTATT
2763061 AATTTCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (29 bp):
CATGATGGGATAGATAAAACAGAGTTATT
Found at i:2767153 original size:18 final size:18
Alignment explanation
Indices: 2767132--2767173 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2767122 AAGAAGATGC
2767132 TGATGACGACGACGAGGA
1 TGATGACGACGACGAGGA
* * *
2767150 TGATGAGGATGACGATGA
1 TGATGACGACGACGAGGA
2767168 TGATGA
1 TGATGA
2767174 TAAAGAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.38, T:0.19
Consensus pattern (18 bp):
TGATGACGACGACGAGGA
Found at i:2769420 original size:2 final size:2
Alignment explanation
Indices: 2769413--2769446 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2769403 TTTAACCAAT
2769413 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
2769447 CGTCTTTGGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2772870 original size:32 final size:33
Alignment explanation
Indices: 2772834--2772895 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
2772824 GGTAGGTTGA
2772834 TTTTAATTATTATTT-AATAAATAAA-ATATTAT
1 TTTTAATTA-TATTTAAATAAATAAATATATTAT
* *
2772866 TTTTATTTATATTTAAATATATAAATATAT
1 TTTTAATTATATTTAAATAAATAAATATAT
2772896 AAATATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 17 0.65
33 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTTAATTATATTTAAATAAATAAATATATTAT
Found at i:2772908 original size:14 final size:13
Alignment explanation
Indices: 2772891--2772931 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2772881 AATATATAAA
*
2772891 TATATAAATATTAT
1 TATAAAAATATT-T
2772905 TATAAAAATATTT
1 TATAAAAATATTT
*
2772918 TTTAAAAATATTT
1 TATAAAAATATTT
2772931 T
1 T
2772932 TTATCTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAAAAATATTT
Found at i:2772925 original size:13 final size:13
Alignment explanation
Indices: 2772896--2772934 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2772886 ATAAATATAT
*
2772896 AAATATTATTATAA
1 AAATATT-TTTTAA
2772910 AAATATTTTTTAA
1 AAATATTTTTTAA
2772923 AAATATTTTTTA
1 AAATATTTTTTA
2772935 TCTCATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:2773992 original size:8 final size:8
Alignment explanation
Indices: 2773979--2774015 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2773969 TATTAATTTT
2773979 TTTATTAA
1 TTTATTAA
2773987 TTTATTAGA
1 TTTATTA-A
*
2773996 TTGATTAA
1 TTTATTAA
2774004 TTTATTAA
1 TTTATTAA
2774012 TTTA
1 TTTA
2774016 AATATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (8 bp):
TTTATTAA
Found at i:2774044 original size:17 final size:16
Alignment explanation
Indices: 2774018--2774065 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2774008 TTAATTTAAA
2774018 TATT-AAATAAATAATT
1 TATTAAAATAAA-AATT
2774034 TATTAAAAT-AAAATT
1 TATTAAAATAAAAATT
*
2774049 AATATAAAATAAAAATT
1 TAT-TAAAATAAAAATT
2774066 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.21
16 12 0.43
17 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTAAAATAAAAATT
Found at i:2774045 original size:28 final size:28
Alignment explanation
Indices: 2774001--2774056 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2773991 TTAGATTGAT
**
2774001 TAATTTATTAATTTAAATATTAA-ATAAA
1 TAATTTATTAAAATAAA-ATTAATATAAA
2774029 TAATTTATTAAAATAAAATTAATATAAA
1 TAATTTATTAAAATAAAATTAATATAAA
2774057 ATAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATTTATTAAAATAAAATTAATATAAA
Found at i:2774066 original size:17 final size:17
Alignment explanation
Indices: 2774016--2774067 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2774006 TATTAATTTA
*
2774016 AATATTAAATAAATAATT
1 AATATAAAATAAA-AATT
*
2774034 TAT-TAAAAT-AAAATT
1 AATATAAAATAAAAATT
2774049 AATATAAAATAAAAATT
1 AATATAAAATAAAAATT
2774066 AA
1 AA
2774068 AATTTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 8 0.28
17 13 0.45
18 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATAAAATAAAAATT
Found at i:2774150 original size:20 final size:21
Alignment explanation
Indices: 2774116--2774160 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
2774106 ATAACTTAAG
2774116 TTAATTTTCTTAAAAAATCAA
1 TTAATTTTCTTAAAAAATCAA
*
2774137 TTAATTTT-TTAAAAAATTAA
1 TTAATTTTCTTAAAAAATCAA
2774157 TTAA
1 TTAA
2774161 AATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTTTCTTAAAAAATCAA
Found at i:2774176 original size:30 final size:31
Alignment explanation
Indices: 2774129--2774188 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
2774119 ATTTTCTTAA
2774129 AAAATCAATTAATTTTTTAA-AAAATTAATT
1 AAAATCAATTAATTTTTTAAGAAAATTAATT
* *
2774159 AAAATTAATTTAA-TTTTTAAGTAAATTAAT
1 AAAATCAA-TTAATTTTTTAAGAAAATTAAT
2774189 AATATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
AAAATCAATTAATTTTTTAAGAAAATTAATT
Found at i:2782349 original size:16 final size:17
Alignment explanation
Indices: 2782310--2782351 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2782300 ATTTGTAAAT
*
2782310 ATAATAAATATGATCAA
1 ATAATAATTATGATCAA
*
2782327 A-ATTAATTATGAT-AA
1 ATAATAATTATGATCAA
2782342 ATAATAATTA
1 ATAATAATTA
2782352 AATCTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 17 0.81
17 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
ATAATAATTATGATCAA
Found at i:2783581 original size:2 final size:2
Alignment explanation
Indices: 2783574--2783602 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2783564 CGCAACCGCC
2783574 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2783603 AGAATCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2787796 original size:12 final size:11
Alignment explanation
Indices: 2787779--2787835 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
2787769 GAAATTTATT
2787779 ATTTAATATTAA
1 ATTTAA-ATTAA
*
2787791 ATTTAAATTTA
1 ATTTAAATTAA
*
2787802 ATTTAAATTTTA
1 ATTTAAA-TTAA
* *
2787814 TTTTAAATAAA
1 ATTTAAATTAA
*
2787825 AATTAAATTAA
1 ATTTAAATTAA
2787836 TTAATTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
11 21 0.57
12 16 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:2787806 original size:11 final size:11
Alignment explanation
Indices: 2787779--2787821 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2787769 GAAATTTATT
*
2787779 ATTTAATATTAA
1 ATTTAA-ATTTA
2787791 ATTTAAATTTA
1 ATTTAAATTTA
2787802 ATTTAAATTTTA
1 ATTTAAA-TTTA
*
2787814 TTTTAAAT
1 ATTTAAAT
2787822 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:2787979 original size:4 final size:4
Alignment explanation
Indices: 2787972--2788014 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
2787962 ATATTAAAAT
*
2787972 TTAA TTAA ATAA TT-A TTAA TTAA -TAA -TAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
2788015 TTATGAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 9 0.26
4 26 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:2787998 original size:14 final size:14
Alignment explanation
Indices: 2787972--2788014 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2787962 ATATTAAAAT
2787972 TTAATTAAATAATTA
1 TTAATT-AATAATTA
*
2787987 TTAATTAATAATAA
1 TTAATTAATAATTA
2788001 TTAATTAATTAATT
1 TTAATTAA-TAATT
2788015 TTATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTAATAATTA
Found at i:2788009 original size:18 final size:17
Alignment explanation
Indices: 2787979--2788013 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2787969 AATTTAATTA
2787979 AATAATTATTAATTAAT
1 AATAATTATTAATTAAT
2787996 AATAATTAATTAATTAAT
1 AATAATT-ATTAATTAAT
2788014 TTTATGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAATTATTAATTAAT
Found at i:2789612 original size:17 final size:18
Alignment explanation
Indices: 2789590--2789623 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2789580 TTAAAGATGC
2789590 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
2789607 AATTATATTATTTATTT
1 AATTATATTATTTATTT
2789624 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:2789624 original size:17 final size:17
Alignment explanation
Indices: 2789590--2789641 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2789580 TTAAAGATGC
2789590 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
2789607 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
2789624 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
2789638 AATT
1 AATT
2789642 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:2791106 original size:17 final size:17
Alignment explanation
Indices: 2791086--2791120 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2791076 CAATTGAGAT
2791086 AAAGTTCACTTCAGGAC
1 AAAGTTCACTTCAGGAC
*
2791103 AAAGTTCATTTCAGGAC
1 AAAGTTCACTTCAGGAC
2791120 A
1 A
2791121 GAAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (17 bp):
AAAGTTCACTTCAGGAC
Found at i:2796672 original size:17 final size:17
Alignment explanation
Indices: 2796650--2796714 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
2796640 GTTAGACATG
2796650 AATATATATTTAATAAA
1 AATATATATTTAATAAA
**
2796667 AATATATTAATTTTTTAAA
1 AATATA-T-ATTTAATAAA
*
2796686 ATTTATATATTTAA-AAA
1 A-ATATATATTTAATAAA
* *
2796703 ATTATATTTTTA
1 AATATATATTTA
2796715 TATATATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 5 0.13
19 10 0.26
20 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATATATTTAATAAA
Found at i:2797369 original size:33 final size:33
Alignment explanation
Indices: 2797327--2797392 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2797317 CCGGTCGCAA
2797327 GAGAAAAAGGTTTCTCTTTTTCTCTAATTTAAT
1 GAGAAAAAGGTTTCTCTTTTTCTCTAATTTAAT
*
2797360 GAGAAAAAGGTTTTTCTTTTTCTCTAATTTAAT
1 GAGAAAAAGGTTTCTCTTTTTCTCTAATTTAAT
2797393 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (33 bp):
GAGAAAAAGGTTTCTCTTTTTCTCTAATTTAAT
Found at i:2797401 original size:33 final size:33
Alignment explanation
Indices: 2797328--2797400 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
2797318 CGGTCGCAAG
*
2797328 AGAAAAAGGTTTCTCTTTTTCTCTAATTTAATG
1 AGAAAAAGGTTTCTCTTTTTCTCTAATTTAATA
*
2797361 AGAAAAAGGTTTTTCTTTTTCTCTAATTTAATAA
1 AGAAAAAGGTTTCTCTTTTTCTCTAATTTAAT-A
2797395 AGAAAA
1 AGAAAA
2797401 GTAGGGGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 31 0.84
34 6 0.16
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (33 bp):
AGAAAAAGGTTTCTCTTTTTCTCTAATTTAATA
Found at i:2800960 original size:21 final size:21
Alignment explanation
Indices: 2800930--2800969 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2800920 ACAAAATGAA
* *
2800930 ATGAATGGAACAAAGAAAGTG
1 ATGAAAGGAAAAAAGAAAGTG
2800951 ATGAAAGGAAAAAAGAAAG
1 ATGAAAGGAAAAAAGAAAG
2800970 CGGAACTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.28, T:0.10
Consensus pattern (21 bp):
ATGAAAGGAAAAAAGAAAGTG
Found at i:2801630 original size:2 final size:2
Alignment explanation
Indices: 2801623--2801651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2801613 TAAAAAGAAG
2801623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2801652 AAACTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.