Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007317.1 Corchorus capsularis cultivar CVL-1 contig07338, 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: 21445
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Found at i:789 original size:32 final size:33
Alignment explanation
Indices: 753--815 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
743 AAAAAAGCCA
*
753 AAATAGCGGCG-TTTCTTTAAGGAAACGCCACT
1 AAATAGCGGCGTTTTATTTAAGGAAACGCCACT
* *
785 AAATAGTGGTGTTTTATTTAAGGAAACGCCA
1 AAATAGCGGCGTTTTATTTAAGGAAACGCCA
816 ATATTTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (33 bp):
AAATAGCGGCGTTTTATTTAAGGAAACGCCACT
Found at i:881 original size:13 final size:13
Alignment explanation
Indices: 863--887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
853 TCCTAAATAA
863 AAAATTAATTCTT
1 AAAATTAATTCTT
876 AAAATTAATTCT
1 AAAATTAATTCT
888 ACGGCGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTAATTCTT
Found at i:2076 original size:71 final size:70
Alignment explanation
Indices: 2001--2135 Score: 184
Period size: 71 Copynumber: 1.9 Consensus size: 70
1991 CATACATATA
* * *
2001 TTTTTTTC-TATATTTCCCATTTGCACTTATGTTGACAACTTTGTG-TGTCAAGTGGCAAAAGTT
1 TTTTTCTCATATATTT--CATTTGCACTTATGTTGACAACTTTG-GATGTCAAATGGAAAAAGTT
2064 TATCTTCC
63 TATCTTCC
*
2072 TTTTTCTCAGTATATTTCATTTGCACTTATGTTGGCAACTTTGGATGTCAAATGGAAAAAGTTT
1 TTTTTCTCA-TATATTTCATTTGCACTTATGTTGACAACTTTGGATGTCAAATGGAAAAAGTTT
2136 GTCAAGTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 1 0.02
71 49 0.86
73 7 0.12
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (70 bp):
TTTTTCTCATATATTTCATTTGCACTTATGTTGACAACTTTGGATGTCAAATGGAAAAAGTTTAT
CTTCC
Found at i:4954 original size:48 final size:49
Alignment explanation
Indices: 4863--4956 Score: 154
Period size: 48 Copynumber: 1.9 Consensus size: 49
4853 CCAAAGATTG
4863 CCAATTTTGCTCCACCTCAATAGATATTGCAGAGTCATCCAACTCCGAA
1 CCAATTTTGCTCCACCTCAATAGATATTGCAGAGTCATCCAACTCCGAA
* * *
4912 CCAATTTTGCTCCAGCTCGAT-GATATTGCCGAGTCATCCAACTCC
1 CCAATTTTGCTCCACCTCAATAGATATTGCAGAGTCATCCAACTCC
4957 ACACTGCCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 23 0.55
49 19 0.45
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.28
Consensus pattern (49 bp):
CCAATTTTGCTCCACCTCAATAGATATTGCAGAGTCATCCAACTCCGAA
Found at i:13371 original size:21 final size:20
Alignment explanation
Indices: 13338--13376 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13328 AGCAACATTG
13338 ATATGATCGTAGTCTAAATCT
1 ATATGATCGTAGTC-AAATCT
* *
13359 ATATGTTCTTAGTCAAAT
1 ATATGATCGTAGTCAAAT
13377 AATGTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATATGATCGTAGTCAAATCT
Found at i:14441 original size:14 final size:14
Alignment explanation
Indices: 14422--14450 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14412 TTGTCGCCTG
14422 GGTTTGTTTTAACT
1 GGTTTGTTTTAACT
14436 GGTTTGTTTTAACT
1 GGTTTGTTTTAACT
14450 G
1 G
14451 TTGTTGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (14 bp):
GGTTTGTTTTAACT
Found at i:18360 original size:2 final size:2
Alignment explanation
Indices: 18353--18382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18343 CTCAGCACAT
18353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18383 ACAGTGGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19444 original size:29 final size:29
Alignment explanation
Indices: 19369--19460 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
19359 CAGCAACTCC
**
19369 AAATTGCCAAAACCCTGCCGC-AGTAACCCA
1 AAATT-CCAAAAAACTGCCGCAAGT-ACCCA
* *
19399 AAGATTGC--AAAATTGCCGCAAGTACCCA
1 AA-ATTCCAAAAAACTGCCGCAAGTACCCA
* *
19427 AAATTCCAAAAAACTGCCGCAACTAGCCA
1 AAATTCCAAAAAACTGCCGCAAGTACCCA
19456 AAATT
1 AAATT
19461 ATAAAAACCC
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.08
28 15 0.30
29 25 0.50
30 3 0.06
31 3 0.06
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.16
Consensus pattern (29 bp):
AAATTCCAAAAAACTGCCGCAAGTACCCA
Found at i:19466 original size:29 final size:29
Alignment explanation
Indices: 19407--19467 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
19397 CAAAGATTGC
* * *
19407 AAAATTGCCGCAAGTACCCAAAATTCCAA
1 AAAACTGCCGCAACTACCCAAAATTACAA
* *
19436 AAAACTGCCGCAACTAGCCAAAATTATAA
1 AAAACTGCCGCAACTACCCAAAATTACAA
19465 AAA
1 AAA
19468 CCCCATAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.25, G:0.10, T:0.16
Consensus pattern (29 bp):
AAAACTGCCGCAACTACCCAAAATTACAA
Found at i:19571 original size:1 final size:1
Alignment explanation
Indices: 19565--19597 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
19555 CAACCAAAGC
19565 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19598 CCTACTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.