Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009785.1 Corchorus capsularis cultivar CVL-1 contig09806, 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: 17212
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1867 original size:21 final size:21
Alignment explanation
Indices: 1841--1885 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1831 CGAGTTCAAG
*
1841 AAATTTATAGACCTAAACTCC
1 AAATTTATAGACCCAAACTCC
1862 AAATTTATAGACCCAAACTCC
1 AAATTTATAGACCCAAACTCC
1883 AAA
1 AAA
1886 CGTGCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATTTATAGACCCAAACTCC
Found at i:2049 original size:22 final size:21
Alignment explanation
Indices: 2024--2085 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2014 TAAGATTTAA
*
2024 TGTGGTTTGACTATTAAGTTTT
1 TGTGGTTTGACTATTAA-ATTT
*
2046 TGTGGTTTGTCTATTAAATTT
1 TGTGGTTTGACTATTAAATTT
* * *
2067 AGGGGTTTGACTATCAAAT
1 TGTGGTTTGACTATTAAAT
2086 CGAGCATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (21 bp):
TGTGGTTTGACTATTAAATTT
Found at i:2303 original size:22 final size:21
Alignment explanation
Indices: 2277--2333 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2267 GGTTTAACAT
*
2277 GTTTTGACTATCAAATTTTGG
1 GTTTTGACTATCAAACTTTGG
*
2298 AGTTTT-ACTATTAAACTTTGG
1 -GTTTTGACTATCAAACTTTGG
*
2319 GATTTGACTATCAAA
1 GTTTTGACTATCAAA
2334 ATGAAATGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 21 0.70
22 5 0.17
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (21 bp):
GTTTTGACTATCAAACTTTGG
Found at i:2669 original size:21 final size:21
Alignment explanation
Indices: 2645--2684 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2635 TGGTTTAAAT
*
2645 ATTAAACTTTGGGGTTTGATA
1 ATTAAACTTTGGGGATTGATA
2666 ATTAAACTTTGGGGATTGA
1 ATTAAACTTTGGGGATTGA
2685 CTATCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (21 bp):
ATTAAACTTTGGGGATTGATA
Found at i:4714 original size:21 final size:21
Alignment explanation
Indices: 4685--4724 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4675 ATGAAAAATT
*
4685 TTTGTTTTTTTTGAATTTTGA
1 TTTGATTTTTTTGAATTTTGA
*
4706 TTTGATTTTTTTGGATTTT
1 TTTGATTTTTTTGAATTTT
4725 TGGAAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.72
Consensus pattern (21 bp):
TTTGATTTTTTTGAATTTTGA
Found at i:4717 original size:22 final size:21
Alignment explanation
Indices: 4685--4726 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4675 ATGAAAAATT
*
4685 TTTGTTTTTTTTGAATTTTGA
1 TTTGTTTTTTTGGAATTTTGA
*
4706 TTTGATTTTTTTGGATTTTTG
1 TTTG-TTTTTTTGGAATTTTG
4727 GAAAACCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (21 bp):
TTTGTTTTTTTGGAATTTTGA
Found at i:7770 original size:19 final size:19
Alignment explanation
Indices: 7748--7817 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 19
7738 AGTGAGGCCC
7748 AAAAGCACAAGGGATTGGG
1 AAAAGCACAAGGGATTGGG
* *
7767 AAAAGCCCAAAAGGAATGTGAGG
1 AAAAG--CACAAGGGAT-TG-GG
7790 CCCAAAAGCACAAGGGATTGGG
1 ---AAAAGCACAAGGGATTGGG
7812 AAAAGC
1 AAAAGC
7818 CCAAAAGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
19 11 0.28
21 8 0.20
22 4 0.10
23 4 0.10
24 8 0.20
26 5 0.12
ACGTcount: A:0.44, C:0.16, G:0.31, T:0.09
Consensus pattern (19 bp):
AAAAGCACAAGGGATTGGG
Found at i:7774 original size:27 final size:27
Alignment explanation
Indices: 7744--7824 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
7734 AGGTAGTGAG
7744 GCCCAAAAGCACAAGGGATTGGGAAAA
1 GCCCAAAAGCACAAGGGATTGGGAAAA
* * *
7771 GCCCAAAAGGA-ATGTGA---GG----
1 GCCCAAAAGCACAAGGGATTGGGAAAA
7790 -CCCAAAAGCACAAGGGATTGGGAAAA
1 GCCCAAAAGCACAAGGGATTGGGAAAA
7816 GCCCAAAAG
1 GCCCAAAAG
7825 GAATGGGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 18
0.62 0.10 0.29
Matches are distributed among these distances:
18 9 0.23
19 4 0.10
22 2 0.05
23 2 0.05
26 4 0.10
27 18 0.46
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (27 bp):
GCCCAAAAGCACAAGGGATTGGGAAAA
Found at i:7789 original size:45 final size:45
Alignment explanation
Indices: 7731--7829 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
7721 ACAAAGTTAA
*
7731 AAAAGGTA-GTGAGGCCCAAAAGCACAAGGGATTGGGAAAAGCCC
1 AAAAGGAATGTGAGGCCCAAAAGCACAAGGGATTGGGAAAAGCCC
7775 AAAAGGAATGTGAGGCCCAAAAGCACAAGGGATTGGGAAAAGCCC
1 AAAAGGAATGTGAGGCCCAAAAGCACAAGGGATTGGGAAAAGCCC
7820 AAAAGGAATG
1 AAAAGGAATG
7830 GGTAATATCC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 7 0.13
45 46 0.87
ACGTcount: A:0.43, C:0.16, G:0.31, T:0.09
Consensus pattern (45 bp):
AAAAGGAATGTGAGGCCCAAAAGCACAAGGGATTGGGAAAAGCCC
Done.