Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012575.1 Corchorus capsularis cultivar CVL-1 contig12596, 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: 9695
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2264 original size:27 final size:27
Alignment explanation
Indices: 2210--2279 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
2200 GCCTGAGCTG
*
2210 CCCCATCATAATAACCGAACCCAGCAC
1 CCCCATCATAATAACCGAACCCAACAC
** *
2237 CCCCATCATAATAACCGGGCTCAACAC
1 CCCCATCATAATAACCGAACCCAACAC
* *
2264 CCTCATCATAGTAACC
1 CCCCATCATAATAACC
2280 CGGTTGACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.34, C:0.41, G:0.09, T:0.16
Consensus pattern (27 bp):
CCCCATCATAATAACCGAACCCAACAC
Found at i:2541 original size:13 final size:14
Alignment explanation
Indices: 2478--2554 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 14
2468 ACATATTAAC
*
2478 AATTATAATTAATT
1 AATTAAAATTAATT
*
2492 AAATAGAAATATAATT
1 AATTA-AAAT-TAATT
2508 AATCGT-AAA-TAACTCT
1 AAT--TAAAATTAA-T-T
2524 AATTAAAATTAA-T
1 AATTAAAATTAATT
2537 AATTAAAATTAATT
1 AATTAAAATTAATT
2551 AATT
1 AATT
2555 TCAATATTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
13 13 0.25
14 13 0.25
15 7 0.14
16 17 0.33
18 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (14 bp):
AATTAAAATTAATT
Found at i:2625 original size:13 final size:12
Alignment explanation
Indices: 2602--2655 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
2592 TATTAAAACT
2602 AATAATTTAAAA
1 AATAATTTAAAA
2614 AATAATTTTAAAA
1 AATAA-TTTAAAA
* *
2627 AATAACCATAAAAA
1 AATAA--TTTAAAA
2641 AATAATTTAAGAA
1 AATAATTTAA-AA
2654 AA
1 AA
2656 AACAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 8 0.24
13 16 0.47
14 10 0.29
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (12 bp):
AATAATTTAAAA
Found at i:2640 original size:27 final size:24
Alignment explanation
Indices: 2610--2668 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 24
2600 CTAATAATTT
2610 AAAAAATAATTTTAA-AAAATAACCATA
1 AAAAAATAA-TTTAAGAAAA-AA-CA-A
2637 AAAAAATAATTTAAGAAAAAACAA
1 AAAAAATAATTTAAGAAAAAACAA
2661 AAAAAATA
1 AAAAAATA
2669 GCTGGCCGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 9 0.29
25 2 0.06
26 7 0.23
27 13 0.42
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAAATAATTTAAGAAAAAACAA
Found at i:2739 original size:32 final size:32
Alignment explanation
Indices: 2685--2811 Score: 89
Period size: 32 Copynumber: 4.0 Consensus size: 32
2675 CGCCCTAGTA
* *
2685 GGGCGGCTCAGCCATGGAAAGGCCGCACCCTAG
1 GGGCGGC-CTGCCATGGCAAGGCCGCACCCTAG
* *
2718 GGGCGGCCTGCCGTGGCAAGGCCG-ACCCCAG
1 GGGCGGCCTGCCATGGCAAGGCCGCACCCTAG
* * **
2749 GGTGCGGCCTACCCTGGCGCGGCCGC-CCCTAG
1 GG-GCGGCCTGCCATGGCAAGGCCGCACCCTAG
* * * * *
2781 AGTGCGGCTTG-CTTGCCAAGGCCGCCCCCTA
1 -GGGCGGCCTGCCATGGCAAGGCCGCACCCTA
2812 TGTGCGGTCT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
31 18 0.24
32 48 0.65
33 8 0.11
ACGTcount: A:0.13, C:0.39, G:0.36, T:0.12
Consensus pattern (32 bp):
GGGCGGCCTGCCATGGCAAGGCCGCACCCTAG
Found at i:3012 original size:20 final size:20
Alignment explanation
Indices: 2987--3026 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2977 CGGCTCAGCC
*
2987 CCTAGATCTATTTTTTTACA
1 CCTAGATCTAATTTTTTACA
3007 CCTAGATCTAATTTTTTACA
1 CCTAGATCTAATTTTTTACA
3027 TCCATTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
CCTAGATCTAATTTTTTACA
Found at i:4453 original size:17 final size:17
Alignment explanation
Indices: 4431--4463 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4421 GTTCAAATAT
*
4431 TTTCGGATTTGGTCTCA
1 TTTCGGATTTGATCTCA
4448 TTTCGGATTTGATCTC
1 TTTCGGATTTGATCTC
4464 GATACGATAT
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:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (17 bp):
TTTCGGATTTGATCTCA
Found at i:5558 original size:27 final size:27
Alignment explanation
Indices: 5504--5559 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
5494 AACCACTGGA
* * **
5504 CAGCCATGATTCCTGCTGTTGGTGTAC
1 CAGCCACGATTCCCGCTGTTGGCATAC
5531 CAGCCACGATTCCCGCTGTTGGCATAC
1 CAGCCACGATTCCCGCTGTTGGCATAC
5558 CA
1 CA
5560 ACTCTGTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.32, G:0.23, T:0.27
Consensus pattern (27 bp):
CAGCCACGATTCCCGCTGTTGGCATAC
Done.