Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015213.1 Corchorus capsularis cultivar CVL-1 contig15234, 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: 28507
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:11326 original size:14 final size:14
Alignment explanation
Indices: 11307--11337 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11297 GCCAATTAAC
11307 AATAAAAAAAAACA
1 AATAAAAAAAAACA
*
11321 AATAAAAAAACACA
1 AATAAAAAAAAACA
11335 AAT
1 AAT
11338 TGACTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (14 bp):
AATAAAAAAAAACA
Found at i:11729 original size:16 final size:15
Alignment explanation
Indices: 11703--11735 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
11693 AAATGGGAGT
11703 AAGAAAAGAAGAATG
1 AAGAAAAGAAGAATG
11718 AAGAAGAAGAAGAATG
1 AAGAA-AAGAAGAATG
11734 AA
1 AA
11736 AGGAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (15 bp):
AAGAAAAGAAGAATG
Found at i:13700 original size:16 final size:16
Alignment explanation
Indices: 13666--13769 Score: 158
Period size: 16 Copynumber: 6.6 Consensus size: 16
13656 CGGGTTCGGG
*
13666 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
13681 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
13697 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* * *
13713 CAGGTTCGAGTTTTTT
1 CGGGTTCGGGTATTTT
13729 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
13744 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
13760 CGGGTTCGGG
1 CGGGTTCGGG
13770 CTCGGATCGG
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
15 27 0.34
16 53 0.66
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:13701 original size:31 final size:31
Alignment explanation
Indices: 13666--13769 Score: 163
Period size: 31 Copynumber: 3.3 Consensus size: 31
13656 CGGGTTCGGG
*
13666 CGGGTTCGGGTACTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTCGGGTTCGGGTATTTT
* * *
13697 CGGGTTCGGGTATTTTCAGGTTCGAGTTTTTT
1 CGGGTTCGGGTA-TTTCGGGTTCGGGTATTTT
13729 CGGGTTCGGGTATTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTCGGGTTCGGGTATTTT
13760 CGGGTTCGGG
1 CGGGTTCGGG
13770 CTCGGATCGG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 38 0.58
32 27 0.42
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.40
Consensus pattern (31 bp):
CGGGTTCGGGTATTTCGGGTTCGGGTATTTT
Found at i:13738 original size:6 final size:6
Alignment explanation
Indices: 13727--13812 Score: 59
Period size: 6 Copynumber: 13.5 Consensus size: 6
13717 TTCGAGTTTT
*
13727 TTCGGG TTCGGG TATTTCGGG TTCGGG TATTTTCGGG TTCGGG CTC-GG
1 TTCGGG TTCGGG ---TTCGGG TTCGGG ---T-TCGGG TTCGGG TTCGGG
* **
13775 ATCGGG TTCGGG TTCGGG CCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
13813 ATTTTCGATA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
5 8 0.12
6 44 0.68
7 1 0.02
9 7 0.11
10 5 0.08
ACGTcount: A:0.03, C:0.20, G:0.44, T:0.33
Consensus pattern (6 bp):
TTCGGG
Found at i:13780 original size:48 final size:48
Alignment explanation
Indices: 13680--13787 Score: 146
Period size: 47 Copynumber: 2.2 Consensus size: 48
13670 TTCGGGTACT
****
13680 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCGAGTTTTT
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCGAGTCGGA
* *
13728 TCGGGTTCGGGTA-TTTCGGGTTCGGGTATTTTCGGGTTCGGGCTCGGA
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCGAG-TCGGA
13776 TCGGGTTCGGGT
1 TCGGGTTCGGGT
13788 TCGGGCCCGG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 27 0.51
48 26 0.49
ACGTcount: A:0.06, C:0.15, G:0.39, T:0.40
Consensus pattern (48 bp):
TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCGAGTCGGA
Found at i:13781 original size:17 final size:17
Alignment explanation
Indices: 13759--13791 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13749 TCGGGTATTT
13759 TCGGGTTCGGGCTCGGA
1 TCGGGTTCGGGCTCGGA
*
13776 TCGGGTTCGGGTTCGG
1 TCGGGTTCGGGCTCGG
13792 GCCCGGGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.21, G:0.48, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGA
Found at i:13788 original size:23 final size:23
Alignment explanation
Indices: 13758--13812 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
13748 TTCGGGTATT
*
13758 TTCGGGTTCGGGCTCGGATCGGG
1 TTCGGGTTCGGGCCCGGATCGGG
*
13781 TTCGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGCCCGGATCGGG
13804 TTCGGGTTC
1 TTCGGGTTC
13813 ATTTTCGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.02, C:0.24, G:0.47, T:0.27
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCGGATCGGG
Found at i:14610 original size:16 final size:16
Alignment explanation
Indices: 14591--14631 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
14581 TCGGGTTGTC
* *
14591 TCGGGTTTGGGTATTT
1 TCGGGTTCGGGTAATT
14607 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
14623 TCGGGTTCG
1 TCGGGTTCG
14632 TGCGGGTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.12, G:0.39, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:15833 original size:35 final size:33
Alignment explanation
Indices: 15782--16620 Score: 801
Period size: 35 Copynumber: 24.7 Consensus size: 33
15772 TGCTTACTAA
*
15782 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACT
* * *
15817 ACTTAATTACCATGAATTAAGTT-TCTCATTAACT
1 ACTTAATTACCCTGAATTAAGTTAT-T-ACTGACT
*
15851 CACTTAATTACCCTGAATTAAAGTTGATTACTGATT
1 -ACTTAATTACCCTGAATT-AAGTT-ATTACTGACT
*
15887 CACTTAATTACCCTGAATTAAGCTACTTACTG---
1 -ACTTAATTACCCTGAATTAAGTTA-TTACTGACT
*
15919 ACTTAATTACCCTGAATTAAGTCATTAACTGACT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACT
*
15953 CACTTAATTACCCTGAATTAAGCTATT--T-ACT
1 -ACTTAATTACCCTGAATTAAGTTATTACTGACT
15984 GACTTAATTACCCTGAATTAAGTTATTCACTGACTT
1 -ACTTAATTACCCTGAATTAAGTTATT-ACTGAC-T
*
16020 ACTTAATTACCCTGAATTAAG---TTACTGCCTT
1 ACTTAATTACCCTGAATTAAGTTATTACTGAC-T
* * *
16051 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAC--T
* *
16087 ACTTAATTACCCTGAATTAAGCTACTTATTG---
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACT
*
16118 ACTTAATTACCCTGAATTAAGTTATCTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTAT-TACTGAC-T
*
16152 ACTTAATTACCCTGAATTAAG---TTGCTGACTT
1 ACTTAATTACCCTGAATTAAGTTATTACTGAC-T
* *
16183 ACTTAATTACCCTTAATTAAGCTATTCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGAC-T
* *
16218 ACTTAATTGCCCTGAATTAAGTTACTTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACT
*
16253 ACTTAATTACCCTGAATTAAGTTGATTACTAACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACT
*
16287 CACTTAATTACCCTGAATTAAGTTGAGTACTGACTT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACTGAC-T
16323 ACTTAATTACCCTGAATTAAGTTA--A-T---T
1 ACTTAATTACCCTGAATTAAGTTATTACTGACT
*
16350 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTG-ACT
*
16385 ACTTAATTACCCTGAATTAAGTTTATTA-TTACTT
1 ACTTAATTACCCTGAATTAAG-TTATTACTGAC-T
* *
16419 ACTTAATTACCCTGAATTAAGTTGATTACTAAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACT-GACT
16454 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGAC-T
*
16489 ACTTAATTACCCTGAATTAAGTTTATTA-TTACTT
1 ACTTAATTACCCTGAATTAAG-TTATTACTGAC-T
* *
16523 ACTTAATTACCCTGAATTAAGTTACTGACTTACTAAATT
1 ACTTAATTACCCTGAATTAAG-T--T-A-TTACT-GACT
*
16562 ACTTAATTACCCTGAATTAATTTATTCACTGACCT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGA-CT
16597 ACTTAATTACCCTGAATTAAGTTA
1 ACTTAATTACCCTGAATTAAGTTA
16621 CTTATTACTG
Statistics
Matches: 693, Mismatches: 51, Indels: 120
0.80 0.06 0.14
Matches are distributed among these distances:
27 24 0.03
28 1 0.00
30 6 0.01
31 133 0.19
32 4 0.01
33 4 0.01
34 91 0.13
35 331 0.48
36 69 0.10
37 2 0.00
38 5 0.01
39 22 0.03
40 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (33 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACT
Found at i:15966 original size:66 final size:65
Alignment explanation
Indices: 15782--16620 Score: 824
Period size: 66 Copynumber: 12.4 Consensus size: 65
15772 TGCTTACTAA
* * *
15782 ACTTAATTACCCTGAATTAAGTTACTTATTGAAC-TACTTAATTACCATGAATTAAGTTTCTCAT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACTTACTTAATTACCCTGAATTAAG-TT-AC-T
*
15846 TAACTC
61 T-ACTG
*
15852 ACTTAATTACCCTGAATTAAAGTTGATTACTGA-TTCACTTAATTACCCTGAATTAAGCTACTTA
1 ACTTAATTACCCTGAATT-AAGTT-ATTACTGACTT-ACTTAATTACCCTGAATTAAGTTACTTA
15916 CTG
63 CTG
* * * *
15919 ACTTAATTACCCTGAATTAAGTCATTAACTGACTCACTTAATTACCCTGAATTAAGCTATTTACT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
15984 G
65 G
**
15985 ACTTAATTACCCTGAATTAAGTTATTCACTGACTTACTTAATTACCCTGAATTAAGTTACTGCCT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
*
16050 T
65 G
* * * * *
16051 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTTACTTAATTACCCTGAATTAAGCTACTTAT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAC-TTACTTAATTACCCTGAATTAAGTTACTTAC
16116 TG
64 TG
* * *
16118 ACTTAATTACCCTGAATTAAGTTATCTA-TTACTTACTTAATTACCCTGAATTAAGTTGCTGACT
1 ACTTAATTACCCTGAATTAAGTTAT-TACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
*
16182 T
65 G
* * *
16183 ACTTAATTACCCTTAATTAAGCTATTCACTGACTTACTTAATTGCCCTGAATTAAGTTACTTACT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
16248 G
65 G
* *
16249 AATTACTTAATTACCCTGAATTAAGTTGATTACTAACTCACTTAATTACCCTGAATTAAGTTGAG
1 ----ACTTAATTACCCTGAATTAAGTT-ATTACTGACTTACTTAATTACCCTGAATTAAG-T---
* *
16314 TACTGACTT
57 TACTTACTG
16323 ACTTAATTACCCTGAATTAAG---TTA---A-TTACTTAATTACCCTGAATTAAGTTGA-TTACT
1 ACTTAATTACCCTGAATTAAGTTATTACTGACTTACTTAATTACCCTGAATTAAGTT-ACTTACT
16380 G
65 G
*
16381 AATTACTTAATTACCCTGAATTAAGTTTATTA-TTACTTACTTAATTACCCTGAATTAAGTTGA-
1 ----ACTTAATTACCCTGAATTAAG-TTATTACTGACTTACTTAATTACCCTGAATTAAGTT-AC
*
16444 TTACTAAATT
60 TTAC----TG
*
16454 ACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTATTATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTTACTTAATTACCCTGAATTAAG-TTA--CTT
*
16519 ACTT
62 ACTG
* * *
16523 ACTTAATTACCCTGAATTAAGTTACTGACTTACTAAATTACTTAATTACCCTGAATTAATTTA-T
1 ACTTAATTACCCTGAATTAAG-T--T-A-TTACTGACTTACTTAATTACCCTGAATTAAGTTACT
16587 TCACTG
61 T-ACTG
16593 ACCTACTTAATTACCCTGAATTAAGTTA
1 ----ACTTAATTACCCTGAATTAAGTTA
16621 CTTATTACTG
Statistics
Matches: 662, Mismatches: 56, Indels: 102
0.81 0.07 0.12
Matches are distributed among these distances:
58 5 0.01
59 1 0.00
61 1 0.00
62 43 0.06
63 1 0.00
64 1 0.00
65 55 0.08
66 167 0.25
67 74 0.11
68 5 0.01
69 82 0.12
70 121 0.18
71 37 0.06
72 7 0.01
73 34 0.05
74 28 0.04
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (65 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTTACTTAATTACCCTGAATTAAGTTACTTACTG
Found at i:16352 original size:27 final size:27
Alignment explanation
Indices: 16321--16386 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
16311 GAGTACTGAC
16321 TTACTTAATTACCCTGAATTAAGTTAA
1 TTACTTAATTACCCTGAATTAAGTTAA
*
16348 TTACTTAATTACCCTGAATTAAGTTGA
1 TTACTTAATTACCCTGAATTAAGTTAA
*
16375 TTACTGAATTAC
1 TTACTTAATTAC
16387 TTAATTACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (27 bp):
TTACTTAATTACCCTGAATTAAGTTAA
Found at i:16430 original size:69 final size:71
Alignment explanation
Indices: 16348--16629 Score: 380
Period size: 69 Copynumber: 4.0 Consensus size: 71
16338 ATTAAGTTAA
16348 TTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTTA-TT
1 TTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTTACTT
16412 A-TTAC
66 ACTTAC
* *
16417 TTACTTAATTACCCTGAATTAAGTTGATTACTAAATTACTTAATTACCCTGAATTAAGTTGA-TT
1 TTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTTACTT
*
16481 ACTGAC
66 ACTTAC
* * *
16487 TTACTTAATTACCCTGAATTAAGTTTATTA-TTACTTACTTAATTACCCTGAATTAAGTTACTGA
1 TTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTT--T-A
* *
16551 CTTACTAAA
63 CTTACTTAC
* **
16560 TTACTTAATTACCCTGAATTAA-TTTATTCACTGACCTACTTAATTACCCTGAATTAAG-TTACT
1 TTACTTAATTACCCTGAATTAAGTTGATT-ACTGAATTACTTAATTACCCTGAATTAAGTTTACT
16623 TA-TTAC
65 TACTTAC
16629 T
1 T
16630 GATTCACCTT
Statistics
Matches: 193, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
69 93 0.48
70 37 0.19
71 1 0.01
72 7 0.04
73 30 0.16
74 25 0.13
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (71 bp):
TTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTTACTT
ACTTAC
Found at i:16476 original size:104 final size:107
Alignment explanation
Indices: 16346--16629 Score: 479
Period size: 104 Copynumber: 2.7 Consensus size: 107
16336 GAATTAAGTT
*
16346 AATTACTTAATTACCCTGAATTAAGTTGATTACTGAATTACTTAATTACCCTGAATTAAGTTTAT
1 AATTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTAT
16411 TATTACTTACTTAATTACCCTGAATTAAG-T-TGA-TTACTA
66 TATTACTTACTTAATTACCCTGAATTAAGTTATGACTTACTA
16450 AATTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTAT
1 AATTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTAT
16515 TATTACTTACTTAATTACCCTGAATTAAGTTACTGACTTACTA
66 TATTACTTACTTAATTACCCTGAATTAAGTTA-TGACTTACTA
* *
16558 AATTACTTAATTACCCTGAATTAA-TTTATTCACTGACCTACTTAATTACCCTGAATTAAG-TTA
1 AATTACTTAATTACCCTGAATTAAGTTGATT-ACTGACTTACTTAATTACCCTGAATTAAGTTTA
16621 CTTATTACT
65 -TTATTACT
16630 GATTCACCTT
Statistics
Matches: 171, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
104 93 0.54
105 1 0.01
107 11 0.06
108 66 0.39
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (107 bp):
AATTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTAT
TATTACTTACTTAATTACCCTGAATTAAGTTATGACTTACTA
Found at i:18364 original size:20 final size:20
Alignment explanation
Indices: 18319--18357 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18309 ACTTGCACTC
*
18319 ACTTAACTGTTCTGCGATTA
1 ACTTGACTGTTCTGCGATTA
18339 ACTTGACTGTTCTGCGATT
1 ACTTGACTGTTCTGCGATT
18358 GAATTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
ACTTGACTGTTCTGCGATTA
Found at i:23950 original size:30 final size:30
Alignment explanation
Indices: 23894--23950 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
23884 GACAAAAGGA
* *
23894 AATAAATTAACTACTTTAGGTTGATTGGGT
1 AATAAATTAACTACTTTAGATCGATTGGGT
* *
23924 AATATATTAATTACTTTAGATCGATTG
1 AATAAATTAACTACTTTAGATCGATTG
23951 ATTAATTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (30 bp):
AATAAATTAACTACTTTAGATCGATTGGGT
Found at i:25961 original size:15 final size:15
Alignment explanation
Indices: 25943--25973 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25933 TTACTTTTGC
*
25943 TACTTTTATCATTTT
1 TACTTTTACCATTTT
25958 TACTTTTACCATTTT
1 TACTTTTACCATTTT
25973 T
1 T
25974 CTTACGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:25973 original size:24 final size:24
Alignment explanation
Indices: 25901--25973 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
25891 TATTAACTAC
* * *
25901 CATTTTTACTAATTATCCTCTTCTTAC
1 CATTTTTACT-TTTA-CCACTT-TTAT
* *
25928 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCACTTTTAT
*
25952 CATTTTTACTTTTACCATTTTT
1 CATTTTTACTTTTACCACTTTT
25974 CTTACGCTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 22 0.58
25 4 0.11
26 2 0.05
27 10 0.26
ACGTcount: A:0.19, C:0.21, G:0.01, T:0.59
Consensus pattern (24 bp):
CATTTTTACTTTTACCACTTTTAT
Found at i:26252 original size:15 final size:16
Alignment explanation
Indices: 26232--26271 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
26222 TCACTACTTC
26232 TTTTACTTTTACC-AT
1 TTTTACTTTTACCTAT
*
26247 TTTTACTATTTACCTTT
1 TTTTACT-TTTACCTAT
26264 TTTTACTT
1 TTTTACTT
26272 ACTATCTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTACTTTTACCTAT
Found at i:26260 original size:16 final size:14
Alignment explanation
Indices: 26232--26265 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
26222 TCACTACTTC
26232 TTTTACTTTTACCAT
1 TTTTACTTTTACC-T
26247 TTTTACTATTTACCT
1 TTTTACT-TTTACCT
26262 TTTT
1 TTTT
26266 TTACTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTACTTTTACCT
Found at i:26591 original size:37 final size:37
Alignment explanation
Indices: 26536--26672 Score: 134
Period size: 37 Copynumber: 3.6 Consensus size: 37
26526 TAATCACTCA
* * * *
26536 ACTCTTAATTA-CTAATTTACTGATTACCATCACTTTG
1 ACTCTTAATTATC-GATTTACTGATTACTATTACCTTG
*
26573 ACTCTTCATTATCGATTTACTGATTACTATTTTTACCTTG
1 ACTCTTAATTATCGATTTACTGATTACTA---TTACCTTG
* *
26613 ACTCTTGATTA-CTGACTTTACTGATCACTATTACCTTG
1 ACTCTTAATTATC-GA-TTTACTGATTACTATTACCTTG
*
26651 ACTCTTAATTATCAATTTACTG
1 ACTCTTAATTATCGATTTACTG
26673 GTTAATCTCT
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
37 31 0.37
38 20 0.24
39 2 0.02
40 18 0.21
41 13 0.15
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (37 bp):
ACTCTTAATTATCGATTTACTGATTACTATTACCTTG
Done.