Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008043.1 Hibiscus syriacus cultivar Beakdansim tig00110530_pilon, whole genome shotgun sequence
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: 108012
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:380 original size:7 final size:7
Alignment explanation
Indices: 368--404 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
358 GTCAAAGAAA
368 GTCAACG
1 GTCAACG
375 GTCAACG
1 GTCAACG
382 GTC-ACG
1 GTCAACG
388 GTCAACG
1 GTCAACG
395 GTCAACG
1 GTCAACG
402 GTC
1 GTC
405 GGTCGGGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:390 original size:13 final size:14
Alignment explanation
Indices: 368--404 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
358 GTCAAAGAAA
368 GTCAACGGTCAACG
1 GTCAACGGTCAACG
382 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
395 GTCAACGGTC
1 GTCAACGGTC
405 GGTCGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:415 original size:16 final size:16
Alignment explanation
Indices: 394--432 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
384 CACGGTCAAC
*
394 GGTCAACGGTCGGTCG
1 GGTCAACAGTCGGTCG
410 GGTCAACAGTCGGTCG
1 GGTCAACAGTCGGTCG
426 GGTCAAC
1 GGTCAAC
433 CCGGTTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (16 bp):
GGTCAACAGTCGGTCG
Found at i:450 original size:19 final size:19
Alignment explanation
Indices: 426--514 Score: 126
Period size: 19 Copynumber: 4.7 Consensus size: 19
416 CAGTCGGTCG
*
426 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
445 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
464 GGTCAAACC-GTTCAGACC
1 GGTCAAACCGGTTCAGACC
* * *
482 GGTCAAACCTGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
502 GGTCAAACCGGTT
1 GGTCAAACCGGTT
515 TTCTAGCAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
18 18 0.28
19 31 0.48
20 15 0.23
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:456 original size:9 final size:9
Alignment explanation
Indices: 426--513 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
416 CAGTCGGTCG
*
426 GGTCAACCC
1 GGTCAAACC
*
435 GGTTCAGACC
1 GG-TCAAACC
445 GGTCAAACC
1 GGTCAAACC
*
454 GGTTCAGACC
1 GG-TCAAACC
464 GGTCAAACC
1 GGTCAAACC
* *
473 GTTCAGACC
1 GGTCAAACC
482 GGTCAAACC
1 GGTCAAACC
* *
491 TGTTCAAAACT
1 -GGTC-AAACC
502 GGTCAAACC
1 GGTCAAACC
511 GGT
1 GGT
514 TTTCTAGCAG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
9 37 0.60
10 21 0.34
11 4 0.06
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:7676 original size:6 final size:7
Alignment explanation
Indices: 7654--7683 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
7644 GTCAAAGAAA
7654 GTCAACG
1 GTCAACG
7661 GTCAACG
1 GTCAACG
7668 GTC-ACG
1 GTCAACG
7674 GTCAACG
1 GTCAACG
7681 GTC
1 GTC
7684 GGGTCGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:7676 original size:13 final size:13
Alignment explanation
Indices: 7658--7683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7648 AAGAAAGTCA
7658 ACGGTCAACGGTC
1 ACGGTCAACGGTC
7671 ACGGTCAACGGTC
1 ACGGTCAACGGTC
7684 GGGTCGGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:7728 original size:17 final size:16
Alignment explanation
Indices: 7672--7730 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 16
7662 TCAACGGTCA
*
7672 CGGTCAACGGTCGGGT
1 CGGTCAACAGTCGGGT
7688 CGGATCAACAGTCGGGT
1 CGG-TCAACAGTCGGGT
7705 CGGGTCAACAGTCGGGT
1 C-GGTCAACAGTCGGGT
7722 CGAGTCAAC
1 CG-GTCAAC
7731 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 4 0.10
17 33 0.85
18 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.37, T:0.17
Consensus pattern (16 bp):
CGGTCAACAGTCGGGT
Found at i:7744 original size:10 final size:10
Alignment explanation
Indices: 7726--7775 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
7716 TCGGGTCGAG
*
7726 TCAACCCGGT
1 TCAAACCGGT
*
7736 TCAGACCGG-
1 TCAAACCGGT
7745 TCAAACCGGT
1 TCAAACCGGT
7755 TCAAAACCGG-
1 TC-AAACCGGT
*
7765 TCAAACTGGT
1 TCAAACCGGT
7775 T
1 T
7776 TTCCAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 14 0.42
10 12 0.36
11 7 0.21
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:7763 original size:20 final size:19
Alignment explanation
Indices: 7725--7775 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
7715 GTCGGGTCGA
* *
7725 GTCAACCCGGTTCAGACCG
1 GTCAAACCGGTTCAAACCG
7744 GTCAAACCGGTTCAAAACCG
1 GTCAAACCGGTTC-AAACCG
*
7764 GTCAAACTGGTT
1 GTCAAACCGGTT
7776 TTCCAGCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (19 bp):
GTCAAACCGGTTCAAACCG
Found at i:19782 original size:21 final size:20
Alignment explanation
Indices: 19756--19797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
19746 TATTTTATTG
19756 TTTTTAATTAA-TTAATTTAAT
1 TTTTTAA-TAATTTAA-TTAAT
19777 TTTTTAATAATTTAATTAAT
1 TTTTTAATAATTTAATTAAT
19797 T
1 T
19798 AATTTGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATAATTTAATTAAT
Found at i:19819 original size:29 final size:30
Alignment explanation
Indices: 19757--19834 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
19747 ATTTTATTGT
* * *
19757 TTTTAATTAATTAATTTAATTTTTTAATAA
1 TTTTAATTAATTAATTTGAGTTTATAATAA
19787 -TTTAATTAATTAATTTGAGTTTATAA-AA
1 TTTTAATTAATTAATTTGAGTTTATAATAA
* *
19815 TTTTAACTTATTTAAATTGA
1 TTTTAA-TTAATTAATTTGA
19835 ATATATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 28 0.68
30 11 0.27
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTTAATTAATTAATTTGAGTTTATAATAA
Found at i:19930 original size:2 final size:2
Alignment explanation
Indices: 19923--19948 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19913 ATTTCTAATA
19923 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
19949 TCATGTTTAA
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:20602 original size:25 final size:26
Alignment explanation
Indices: 20540--20602 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 26
20530 TTTTTAATTT
*
20540 TCATTTATTTAAAATTTACATATTTAA
1 TCATTTATTT-AAATTTACAAATTTAA
**
20567 TC-TTTCCTTAAATTTA-AAATTTAAA
1 TCATTTATTTAAATTTACAAATTT-AA
20592 TCATTT-TTTAA
1 TCATTTATTTAA
20603 TATAAAGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 5 0.17
25 15 0.50
26 8 0.27
27 2 0.07
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (26 bp):
TCATTTATTTAAATTTACAAATTTAA
Found at i:26255 original size:34 final size:36
Alignment explanation
Indices: 26201--26270 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
26191 TGAAGACCGG
*
26201 TCAATAATGTAAAAAAAGGTGT-GATTGATATGCTA
1 TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
26236 TCAATAATGT-AAAAAAGGTGTCGATTAATATGCTA
1 TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
26271 CATCAACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 11 0.33
35 22 0.67
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (36 bp):
TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
Found at i:28232 original size:23 final size:23
Alignment explanation
Indices: 28196--28259 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
28186 CAACTCATAT
*
28196 AAATGCACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * *
28219 AATTACACCTAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
28242 AAATGCACCGAAGTGCCA
1 AAATACACCGAAGTGCCA
28260 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:28727 original size:30 final size:30
Alignment explanation
Indices: 28668--28727 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
28658 TCAAATTTAT
* *
28668 CATTTATTCACATAAATCAATTACTCATAG
1 CATTTAATCACATAAATCAATTACGCATAG
28698 CATTTAATCACATAGAA-C-ATATACGCATAG
1 CATTTAATCACATA-AATCAAT-TACGCATAG
28728 TGCTTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.08
30 22 0.85
31 2 0.08
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (30 bp):
CATTTAATCACATAAATCAATTACGCATAG
Found at i:36307 original size:31 final size:31
Alignment explanation
Indices: 36266--36325 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
36256 TCACTTCAAC
*
36266 CTCATATCATTTCAAGTTGTTTAAGATGTAG
1 CTCATATCATTTCAAGTTATTTAAGATGTAG
* *
36297 CTCATGTCATTTTAAGTTATTTAAGATGT
1 CTCATATCATTTCAAGTTATTTAAGATGT
36326 GGGTCATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (31 bp):
CTCATATCATTTCAAGTTATTTAAGATGTAG
Found at i:38367 original size:31 final size:31
Alignment explanation
Indices: 38280--38367 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
38270 ATTTTTAAAA
* *
38280 ATTATAAAATGATTATTAAATTTATTAAATT
1 ATTATAAAATGATCATTAAATTTATCAAATT
* * *
38311 ATTATAAAACGATCATTAATTTTATCGAATT
1 ATTATAAAATGATCATTAAATTTATCAAATT
*
38342 ATTATAAAATGGTCATTAAATTTATC
1 ATTATAAAATGATCATTAAATTTATC
38368 CAACTTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATTATAAAATGATCATTAAATTTATCAAATT
Found at i:39611 original size:20 final size:19
Alignment explanation
Indices: 39570--39612 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
39560 AATTTTTATT
*
39570 TTATTTTAATATTCAAAGA
1 TTATTTTAATATTCAAAAA
* *
39589 TTATTTTTATAATTGAAAAA
1 TTATTTTAAT-ATTCAAAAA
39609 TTAT
1 TTAT
39613 AGATGATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATTTTAATATTCAAAAA
Found at i:40585 original size:30 final size:30
Alignment explanation
Indices: 40549--40608 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40539 AAGAACACTC
40549 GAATATCAAATAGTATACTAATTTAAAGAA
1 GAATATCAAATAGTATACTAATTTAAAGAA
40579 GAATATCAAATAGTATACTAATTTAAAGAA
1 GAATATCAAATAGTATACTAATTTAAAGAA
40609 AGCTGCAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (30 bp):
GAATATCAAATAGTATACTAATTTAAAGAA
Found at i:42891 original size:27 final size:28
Alignment explanation
Indices: 42846--42898 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
42836 TTCTTCTAAA
**
42846 ATATTTATATATTTTAAATATATTTTTT
1 ATATTTATATATTAAAAATATATTTTTT
*
42874 ATATTT-TATATTAAAAATCTATTTT
1 ATATTTATATATTAAAAATATATTTT
42899 CGTAGTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTTATATATTAAAAATATATTTTTT
Found at i:46038 original size:6 final size:6
Alignment explanation
Indices: 46027--46055 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46017 TGTTTCCATC
46027 TGAACT TGAACT TGAACT TGAACT TGAAC
1 TGAACT TGAACT TGAACT TGAACT TGAAC
46056 CATGGATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (6 bp):
TGAACT
Found at i:49849 original size:29 final size:30
Alignment explanation
Indices: 49816--49888 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
49806 AAAAGGAATA
49816 AAATTATTGAA-AGA-CCATTGACATATCGT
1 AAATTATT-AATAGAGCCATTGACATATCGT
* *
49845 AAATTA-TAATCGAGCTATTGACATATCGT
1 AAATTATTAATAGAGCCATTGACATATCGT
*
49874 AAATTA-TAATCGAGC
1 AAATTATTAATAGAGC
49889 TATGTGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 2 0.05
28 3 0.08
29 35 0.88
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (30 bp):
AAATTATTAATAGAGCCATTGACATATCGT
Found at i:49889 original size:29 final size:29
Alignment explanation
Indices: 49832--49891 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
49822 TTGAAAGACC
49832 ATTGACATATCGTAAATTATAATCGAGCT
1 ATTGACATATCGTAAATTATAATCGAGCT
49861 ATTGACATATCGTAAATTATAATCGAGCT
1 ATTGACATATCGTAAATTATAATCGAGCT
49890 AT
1 AT
49892 GTGAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (29 bp):
ATTGACATATCGTAAATTATAATCGAGCT
Found at i:50821 original size:75 final size:75
Alignment explanation
Indices: 50670--50877 Score: 283
Period size: 75 Copynumber: 2.8 Consensus size: 75
50660 GAAAGCCAAA
* * * **
50670 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
50735 TTGGCTCCGAG
65 TTGGCTCCGAG
*
50746 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
50811 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
50821 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
50878 GTTCAACGGT
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 86 0.73
76 32 0.27
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:56663 original size:21 final size:21
Alignment explanation
Indices: 56637--56719 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
56627 TTTTGGTGCA
* *
56637 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCACT
* **
56658 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCACT
*
56679 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGA-TCCCCCCACT
* *
56703 G-GGGAATCGATACCCCC
1 GAGGGAACCGATCCCCCC
56720 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.12
21 26 0.53
22 1 0.02
23 9 0.18
24 7 0.14
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.14
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCACT
Found at i:58703 original size:17 final size:17
Alignment explanation
Indices: 58681--58714 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58671 TTCAATATTT
*
58681 TGGATTGTTTGATTTTA
1 TGGATTGTTGGATTTTA
58698 TGGATTGTTGGATTTTA
1 TGGATTGTTGGATTTTA
58715 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTA
Found at i:59452 original size:75 final size:75
Alignment explanation
Indices: 59302--59487 Score: 255
Period size: 75 Copynumber: 2.5 Consensus size: 75
59292 GAAAGCCAAA
* * * * **
59302 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACTGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
59367 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
59379 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
59444 TTGTTCCGAG
66 TGGCTCCGAG
* *
59454 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
59488 CAAGGGGGTA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 71 0.73
77 26 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:59503 original size:75 final size:74
Alignment explanation
Indices: 59302--59508 Score: 247
Period size: 75 Copynumber: 2.7 Consensus size: 74
59292 GAAAGCCAAA
* * **
59302 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACTGATTCCCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAAC-GATTCCCCCCTAAACAG
59367 TTTGGCTCCGAG
63 TTTGGCTCCGAG
* *
59379 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAA-CGATTCCCCCCTAAACAGT
* *
59443 TTTGTTCCGAG
64 TTGGCTCCGAG
* *
59454 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTATCGATTCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCCATAGGAGG-AACGATTCCCCC
59509 TGTTCAACGG
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
75 80 0.71
76 9 0.08
77 23 0.20
78 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:61467 original size:24 final size:24
Alignment explanation
Indices: 61431--61480 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
61421 TCCTCAGTCA
61431 TTGTACTCCTTTTAAAATTGAAAT
1 TTGTACTCCTTTTAAAATTGAAAT
* *
61455 TTGTAGTCTTTTTAAAATTGAAAT
1 TTGTACTCCTTTTAAAATTGAAAT
61479 TT
1 TT
61481 AGTCCTCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (24 bp):
TTGTACTCCTTTTAAAATTGAAAT
Found at i:62098 original size:2 final size:2
Alignment explanation
Indices: 62091--62125 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
62081 TCATAACTTT
62091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62126 CGTTTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62633 original size:21 final size:21
Alignment explanation
Indices: 62582--62634 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
62572 ATTCTAACTA
62582 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* ** *
62603 TAGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
62624 TCGCAATGCGA
1 TCGCATTGCGA
62635 ATACGTAAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:62654 original size:20 final size:20
Alignment explanation
Indices: 62624--62796 Score: 220
Period size: 20 Copynumber: 8.6 Consensus size: 20
62614 TTTTCCTAAT
62624 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
62644 TTGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* ** *
62665 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
62686 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
62706 TCGCAATGCTATTACGTAAA
1 TCGCAATGCGAATACGTAAA
62726 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
62746 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
62766 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
62786 TCGCAATGCGA
1 TCGCAATGCGA
62797 TTTACATAGA
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
20 103 0.75
21 35 0.25
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:62999 original size:22 final size:22
Alignment explanation
Indices: 62974--63039 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
62964 GGCGACATCC
62974 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
62996 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
63018 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
63040 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:63434 original size:34 final size:33
Alignment explanation
Indices: 63365--63437 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
63355 ACTATCGCAA
** *
63365 TGCGATTCTGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAATCAATTCGCGT
63398 TGCGATTCT-TACGTTGCGATAATCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAATC-AATTCGCGT
63432 TGCGAT
1 TGCGAT
63438 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (33 bp):
TGCGATTCTGTCGTTGCGATAATCAATTCGCGT
Found at i:63478 original size:20 final size:20
Alignment explanation
Indices: 63425--63479 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
63415 GATAATCAAA
* **
63425 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
63445 TTCATGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
63465 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
63480 AAAGTTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:63487 original size:20 final size:20
Alignment explanation
Indices: 63444--63488 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
63434 CGATAGTCAT
** *
63444 TTTCATGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTAAAG
*
63464 TTTCGTGTTGCGATTTAAAG
1 TTTCATGTTGCGATTTAAAG
63484 TTTCA
1 TTTCA
63489 GAAACTATTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTAAAG
Found at i:65372 original size:20 final size:20
Alignment explanation
Indices: 65347--65489 Score: 147
Period size: 20 Copynumber: 7.5 Consensus size: 20
65337 AATAGTTTAT
*
65347 TATCGCAATGTGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
65367 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
65387 TATCGCAA--CG-AGA-GA-
1 TATCGCAATGCGAAAATGAC
*
65402 -ATCGCAATGCG-AAATGAA
1 TATCGCAATGCGAAAATGAC
* *
65420 AATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* *
65440 TATCGTAATGAGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* *
65460 TATCGCAATGTGAAAATGAT
1 TATCGCAATGCGAAAATGAC
65480 TATCGCAATG
1 TATCGCAATG
65490 AAAGAATTGC
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 4 0.04
18 2 0.02
19 10 0.10
20 75 0.72
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:65506 original size:93 final size:93
Alignment explanation
Indices: 65347--65519 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
65337 AATAGTTTAT
* *
65347 TATCGCAATGTGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGC
1 TATCGCAATGAGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGC
65412 GAAATGAAAATCGCAACGCGAAAATGAC
66 GAAATGAAAATCGCAACGCGAAAATGAC
* * * * * *
65440 TATCGTAATGAGAAAATGACTATCGCAATGTGAAAATGATTATCGCAATGAAAGAATTGCAATGC
1 TATCGCAATGAGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGC
65505 GAAATGAAAATCGCA
66 GAAATGAAAATCGCA
65520 TTGCGATTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.20
Consensus pattern (93 bp):
TATCGCAATGAGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGC
GAAATGAAAATCGCAACGCGAAAATGAC
Found at i:65591 original size:20 final size:20
Alignment explanation
Indices: 65533--65585 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
65523 CGATTCTCTC
*
65533 ATTGCGATAGTTAAATTCGT
1 ATTGCGATAGTCAAATTCGT
*
65553 ATTGCAATAGTCAAATTCGT
1 ATTGCGATAGTCAAATTCGT
65573 ATTGCGATAGTCA
1 ATTGCGATAGTCA
65586 TTTTCGCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTGCGATAGTCAAATTCGT
Found at i:66125 original size:18 final size:19
Alignment explanation
Indices: 66086--66127 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
66076 CTCACCTGTC
66086 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
66107 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
66125 ATC
1 ATC
66128 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:67587 original size:14 final size:14
Alignment explanation
Indices: 67568--67603 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
67558 ATTGTTTAAT
67568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
67582 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
67596 TGATTTGT
1 TGATTTGT
67604 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:67797 original size:34 final size:33
Alignment explanation
Indices: 67733--67804 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
67723 ATGACTATTG
*
67733 CAACGAGAGAATCGTAATGCGAAATGAAAATCA
1 CAACGAGAGAATCGCAATGCGAAATGAAAATCA
* *
67766 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCG-AAATGAAAATCA
67800 CAACG
1 CAACG
67805 CGAAACTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
CAACGAGAGAATCGCAATGCGAAATGAAAATCA
Found at i:67885 original size:20 final size:20
Alignment explanation
Indices: 67858--67946 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
67848 TCACTCGTGT
67858 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
67878 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
67898 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
67918 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
67938 CGTTGCGAT
1 CGTTGCGAT
67947 TTCCGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:70801 original size:12 final size:13
Alignment explanation
Indices: 70784--70812 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70774 ATTTGTTTAA
70784 GAAATT-ATTTTT
1 GAAATTGATTTTT
70796 GAAATTGATTTTT
1 GAAATTGATTTTT
70809 GAAA
1 GAAA
70813 AACTTACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
GAAATTGATTTTT
Found at i:70848 original size:31 final size:32
Alignment explanation
Indices: 70810--70890 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 32
70800 TTGATTTTTG
70810 AAAAACTTACTCCCCCTTACTATAGCACATC-
1 AAAAACTTACTCCCCCTTACTATAGCACATCT
70841 AAAAACTTACTCCCCCTTACTATAGCACATCT
1 AAAAACTTACTCCCCCTTACTATAGCACATCT
* * *
70873 ATAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
70891 TTTGTTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 31 0.67
32 15 0.33
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.31
Consensus pattern (32 bp):
AAAAACTTACTCCCCCTTACTATAGCACATCT
Found at i:79942 original size:24 final size:24
Alignment explanation
Indices: 79908--79961 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
79898 CTGAAAAATC
79908 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
79932 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
79956 ATCAAA
1 ATCAAA
79962 TTTCGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:79972 original size:24 final size:24
Alignment explanation
Indices: 79908--79975 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
79898 CTGAAAAATC
* * *
79908 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAGTCCGAATATTGACCAAG
**
79932 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATATTGACCAAG
* *
79956 ATCAAATTTCGAATATTGAC
1 ATCAAAGTCCGAATATTGAC
79976 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATATTGACCAAG
Found at i:80828 original size:20 final size:20
Alignment explanation
Indices: 80803--80849 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
80793 AAATTCAGTA
* *
80803 TTGCGATGGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
80823 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
80843 TTGCGAT
1 TTGCGAT
80850 TTATGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:80859 original size:20 final size:20
Alignment explanation
Indices: 80836--80924 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
80826 CGATAGTCAG
* *
80836 ATTCGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
80856 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
80876 A-GCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
80896 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
80916 ATTCACATT
1 ATTCGCATT
80925 ACGAATTAGG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.19
20 35 0.65
21 9 0.17
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:80883 original size:19 final size:20
Alignment explanation
Indices: 80843--80890 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
80833 CAGATTCGCG
* *
80843 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATGCGCA
80863 TTGCGATTTACGTA-GCGCA
1 TTGCGATTTACGTATGCGCA
80882 TTGCGATTT
1 TTGCGATTT
80891 TTCAAATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATGCGCA
Found at i:83781 original size:20 final size:20
Alignment explanation
Indices: 83756--83795 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
83746 AAGTGTTAGA
83756 CCTAAGACTACAGATATTAT
1 CCTAAGACTACAGATATTAT
83776 CCTAAGACTACAGATATTAT
1 CCTAAGACTACAGATATTAT
83796 GGAGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
CCTAAGACTACAGATATTAT
Found at i:84376 original size:32 final size:31
Alignment explanation
Indices: 84306--84369 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
84296 AGTAAATTAT
** *
84306 CATAAAAGATGAGGGGACAAAGTGTAATTAA
1 CATAAAAGATGAGGGGACAAAGTCAAAATAA
84337 CCATAAAAGATGAAGGGGACAAAGTCAAAATAA
1 -CATAAAAGATG-AGGGGACAAAGTCAAAATAA
84370 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (31 bp):
CATAAAAGATGAGGGGACAAAGTCAAAATAA
Found at i:92258 original size:15 final size:15
Alignment explanation
Indices: 92238--92267 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
92228 TTATGGGTTA
*
92238 AACAATAATTCTAAC
1 AACAATAAGTCTAAC
92253 AACAATAAGTCTAAC
1 AACAATAAGTCTAAC
92268 CATCAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.23
Consensus pattern (15 bp):
AACAATAAGTCTAAC
Found at i:98836 original size:23 final size:23
Alignment explanation
Indices: 98800--98872 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
98790 GGAATCGATA
98800 CCCC-TTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
* *
98822 CCCCTTTGAAAGGGAATCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
98845 CCCCTTTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
98868 CCCCT
1 CCCCT
98873 AGGGGAATCG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 4 0.09
23 42 0.91
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTC
Found at i:98892 original size:20 final size:19
Alignment explanation
Indices: 98854--98896 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
98844 CCCCCTTTGA
*
98854 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
98873 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
98893 -GGGG
1 AGGGG
98897 TTCAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:103461 original size:3 final size:3
Alignment explanation
Indices: 103453--103485 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
103443 ATTTGTAATG
103453 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
103486 TTTTTGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:105725 original size:41 final size:42
Alignment explanation
Indices: 105637--105751 Score: 115
Period size: 41 Copynumber: 2.7 Consensus size: 42
105627 ATGATACTGG
* *
105637 AGCCGATGGCAAGGAGCCTAAACCTAATACAGAAAATACCATCGA
1 AGCCAATGGCAAGGAGCCT-AACCTAAT--AGAAAATACCACCGA
** * *
105682 AGCCTTTGGCAAGGAGCCTAACCTAAT-GAAAATGCCGCCGA
1 AGCCAATGGCAAGGAGCCTAACCTAATAGAAAATACCACCGA
* *
105723 AGCCAAAGGCAACGAGCCTAACCCTAATA
1 AGCCAATGGCAAGGAGCCTAA-CCTAATA
105752 CAAAGAAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 28 0.47
42 6 0.10
44 8 0.14
45 17 0.29
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (42 bp):
AGCCAATGGCAAGGAGCCTAACCTAATAGAAAATACCACCGA
Done.