Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004934.1 Corchorus capsularis cultivar CVL-1 contig04952, 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: 14174
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 TA TA TA 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 TA TA TA T
42 TGTTGTTGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1911 original size:2 final size:2
Alignment explanation
Indices: 1904--1928 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1894 AGTTATGAGA
1904 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 A
1929 CCATGTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2792 original size:18 final size:19
Alignment explanation
Indices: 2769--2806 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
2759 CAAAAGAAGG
2769 AAAAAAAAAA-GGAGGGAA
1 AAAAAAAAAAGGGAGGGAA
2787 AAAAAAAAAAGGGAGGGAA
1 AAAAAAAAAAGGGAGGGAA
2806 A
1 A
2807 GAAATCGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGGGAGGGAA
Found at i:2793 original size:19 final size:19
Alignment explanation
Indices: 2769--2806 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2759 CAAAAGAAGG
2769 AAAAAAAAAAGGAGGGAAA
1 AAAAAAAAAAGGAGGGAAA
*
2788 AAAAAAAAAGGGAGGGAAA
1 AAAAAAAAAAGGAGGGAAA
2807 GAAATCGGTC
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGGAGGGAAA
Found at i:2799 original size:15 final size:16
Alignment explanation
Indices: 2760--2800 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2750 AATCATTCAC
2760 AAAAGAA-GGAAAAAA
1 AAAAGAAGGGAAAAAA
*
2775 AAAAGGAGGGAAAAAA
1 AAAAGAAGGGAAAAAA
2791 AAAA-AAGGGA
1 AAAAGAAGGGA
2801 GGGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAAGAAGGGAAAAAA
Found at i:5995 original size:22 final size:22
Alignment explanation
Indices: 5970--6014 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5960 TCAGCAGTTG
5970 GGGAAGAAAATGGCAGGAGCGT
1 GGGAAGAAAATGGCAGGAGCGT
5992 GGGAAGAAAATGGCAGGAGCGT
1 GGGAAGAAAATGGCAGGAGCGT
6014 G
1 G
6015 CTTAGCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.47, T:0.09
Consensus pattern (22 bp):
GGGAAGAAAATGGCAGGAGCGT
Found at i:11548 original size:23 final size:22
Alignment explanation
Indices: 11522--11587 Score: 91
Period size: 21 Copynumber: 3.0 Consensus size: 22
11512 GAGTTGGTAT
11522 ATAATGACATGGATTGTTATTGG
1 ATAATGACATGGATTGTTATT-G
*
11545 ATAATGACATGGATTGAGTA-T-
1 ATAATGACATGGATTG-TTATTG
11566 ATAATGACATGGATTGTTATTG
1 ATAATGACATGGATTGTTATTG
11588 TCATCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.05
21 17 0.45
23 17 0.45
24 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (22 bp):
ATAATGACATGGATTGTTATTG
Found at i:11571 original size:21 final size:20
Alignment explanation
Indices: 11515--11581 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 20
11505 ATTAGTTGAG
11515 TTGGTATATAATGACATGGA
1 TTGGTATATAATGACATGGA
*
11535 TTGTTATTGGATAATGACATGGA
1 TTGGTA-T--ATAATGACATGGA
11558 TTGAGTATATAATGACATGGA
1 TTG-GTATATAATGACATGGA
11579 TTG
1 TTG
11582 TTATTGTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.12
21 17 0.41
23 17 0.41
24 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGGTATATAATGACATGGA
Found at i:12630 original size:30 final size:29
Alignment explanation
Indices: 12563--12634 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
12553 ACACCGAACC
****
12563 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
12592 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
12621 TGTCAAATAAGCCC
1 -GTCAAATAAGCCC
12635 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Done.