Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016307.1 Corchorus olitorius cultivar O-4 contig16340, 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: 31273
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2348 original size:19 final size:19
Alignment explanation
Indices: 2326--2372 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2316 GCCCAAAAAA
2326 AATGCCTAAATGCAAACCC
1 AATGCCTAAATGCAAACCC
* * * *
2345 AATGCCCAAGTGCAAGCCT
1 AATGCCTAAATGCAAACCC
2364 AATG-CTAAA
1 AATGCCTAAA
2373 AACAAGTCCA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (19 bp):
AATGCCTAAATGCAAACCC
Found at i:2719 original size:26 final size:27
Alignment explanation
Indices: 2652--2730 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
2642 ATTTGAACTT
*
2652 AAAATGACCAAAATGCCCCCTGAATGTA
1 AAAATGACCAAAATG-CCCCTGAATGCA
2680 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
*
2707 AAAATGACC-AAATGCCCCTAAATG
1 AAAATGACCAAAATGCCCCTGAATG
2731 ACCTAAGTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.29
27 20 0.41
28 15 0.31
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:5461 original size:45 final size:45
Alignment explanation
Indices: 5410--5500 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
5400 TTGCAGTATG
5410 TACTATGAGGTTTAATTTTCTTATTATGGCATGAAATCTTTGTAC
1 TACTATGAGGTTTAATTTTCTTATTATGGCATGAAATCTTTGTAC
*
5455 TACTATGAGGTTTAATTTTCTTATTGTGGCATGAAATCTTTGTAC
1 TACTATGAGGTTTAATTTTCTTATTATGGCATGAAATCTTTGTAC
5500 T
1 T
5501 CTTCAACATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (45 bp):
TACTATGAGGTTTAATTTTCTTATTATGGCATGAAATCTTTGTAC
Found at i:10696 original size:21 final size:21
Alignment explanation
Indices: 10672--10719 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
10662 CTTTTTGTTA
*
10672 GTTAGCTAT-AACTAATCTATG
1 GTTAG-TATAAACTAACCTATG
10693 GTTAAGTATACAACTAACCTATG
1 GTT-AGTATA-AACTAACCTATG
10716 GTTA
1 GTTA
10720 AGTGTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 6 0.26
22 3 0.13
23 14 0.61
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTAGTATAAACTAACCTATG
Found at i:15629 original size:21 final size:22
Alignment explanation
Indices: 15605--15653 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
15595 CTTTCTGTTA
* *
15605 GTTAGT-TATAACTAATCTATG
1 GTTAGTATACAACTAACCTATG
15626 GTTAAGTATACAACTAACCTATG
1 GTT-AGTATACAACTAACCTATG
15649 GTTAG
1 GTTAG
15654 GTGTTAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 16 0.67
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTAGTATACAACTAACCTATG
Found at i:15683 original size:22 final size:22
Alignment explanation
Indices: 15643--15685 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
15633 ATACAACTAA
* **
15643 CCTATGGTTAGGTGTTAGTTAG
1 CCTATGGTTAGATACTAGTTAG
15665 CCTATGGTTAGATACTAGTTA
1 CCTATGGTTAGATACTAGTTA
15686 ATTAGCAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.40
Consensus pattern (22 bp):
CCTATGGTTAGATACTAGTTAG
Found at i:25859 original size:25 final size:26
Alignment explanation
Indices: 25811--25859 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
25801 GCCCATATTT
*
25811 ATTTTTTAAAATAAAATGATAATTAA
1 ATTTTTTAAAATAAAATGAAAATTAA
25837 ATTTTTTAATAA-AAAAT-AAAATT
1 ATTTTTTAA-AATAAAATGAAAATT
25860 TATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 14 0.67
27 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATGAAAATTAA
Found at i:30070 original size:22 final size:22
Alignment explanation
Indices: 30042--30087 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
30032 TCGTAAAGCC
30042 CAAGACTTTAACCTCATAAGAT
1 CAAGACTTTAACCTCATAAGAT
*
30064 CAAGACTTTAACCTTATAAGAT
1 CAAGACTTTAACCTCATAAGAT
30086 CA
1 CA
30088 CCTTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (22 bp):
CAAGACTTTAACCTCATAAGAT
Done.