Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013392.1 Corchorus olitorius cultivar O-4 contig13425, 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: 35347
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5432 original size:3 final size:3
Alignment explanation
Indices: 5426--5461 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5416 CCACCATTGG
5426 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
5462 TATAACGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:5606 original size:6 final size:6
Alignment explanation
Indices: 5597--5652 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
5587 TAGCCACGGC
* * * *
5597 CACGAT CACGAT CGCGAT CGCGAT CACG-T CCACGAT CACGGT TACGAT
1 CACGAT CACGAT CACGAT CACGAT CACGAT -CACGAT CACGAT CACGAT
*
5645 CACCAT CA
1 CACGAT CA
5653 TAATCTCTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.18
Consensus pattern (6 bp):
CACGAT
Found at i:13542 original size:121 final size:120
Alignment explanation
Indices: 13280--13704 Score: 545
Period size: 121 Copynumber: 3.5 Consensus size: 120
13270 CTCAAACTTA
* * * * * *
13280 TCAAATTCGATTAAAGATTTACTTAAATCTTAAAAGAATTATGAAAGTTTCCAAAGAGTTTATTT
1 TCAAATTCCATTAAAGATTCACTTAAATCTTAAAAGAATTATGAAA-TTACC-AA-ATTTTACTA
* * *
13345 ACTAAAGGTCTTAATCACTTAATTAAACCTTAA-CTTTT-GGGTCACTTAACCTTAATT
63 ACTAAAGGT-TTAATCACTTAATTAAACCTAAAGTTTTTAAGGTCACTTAACCTTAATT
* * *
13402 TCAAATTCGATTAAAGATTCACTTAAATCTTAAGAGAATTATGAAATTACCAACTTTTACTAACT
1 TCAAATTCCATTAAAGATTCACTTAAATCTTAAAAGAATTATGAAATTACCAAATTTTACTAACT
* *
13467 AAAGGTTTCAATCACTTAATTAAATCTAAAGTTTTTAAGGTCACTTAACCTTGATT
66 AAAGGTTT-AATCACTTAATTAAACCTAAAGTTTTTAAGGTCACTTAACCTTAATT
* * *
13523 TCAAATTCCATTAAGGATTCACTTAAATCTTAAAAGAATTATGAAAATCCCAAATTTTA-TCAAC
1 TCAAATTCCATTAAAGATTCACTTAAATCTTAAAAGAATTATGAAATTACCAAATTTTACT-AAC
* *
13587 TAAAGGTTGTAATCACTTAATTAAAGCTAAAGTTTTAAAGGTCACTTAA-CTTCAATT
65 TAAAGGTT-TAATCACTTAATTAAACCTAAAGTTTTTAAGGTCACTTAACCTT-AATT
* *
13644 TCAAATTCCATTAAGGATTCACTTAAATCTTAAAAGAA-TATGAAAATTACCAACTTTTACT
1 TCAAATTCCATTAAAGATTCACTTAAATCTTAAAAGAATTATG-AAATTACCAAATTTTACT
13705 CTTTTCTTAA
Statistics
Matches: 271, Mismatches: 24, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
118 2 0.01
119 33 0.12
120 14 0.05
121 176 0.65
122 46 0.17
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (120 bp):
TCAAATTCCATTAAAGATTCACTTAAATCTTAAAAGAATTATGAAATTACCAAATTTTACTAACT
AAAGGTTTAATCACTTAATTAAACCTAAAGTTTTTAAGGTCACTTAACCTTAATT
Found at i:17664 original size:13 final size:14
Alignment explanation
Indices: 17646--17676 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
17636 TTGTTTCGTA
17646 TTTTGTTTTTGT-T
1 TTTTGTTTTTGTGT
17659 TTTTGTTTTTGTGT
1 TTTTGTTTTTGTGT
17673 TTTT
1 TTTT
17677 CTTGACTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (14 bp):
TTTTGTTTTTGTGT
Found at i:18838 original size:16 final size:19
Alignment explanation
Indices: 18812--18849 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
18802 ATCTCTTTAA
18812 TTTTCTTTAA-T-TTATTG
1 TTTTCTTTAATTGTTATTG
18829 TTTT-TTTAATTGTTATTG
1 TTTTCTTTAATTGTTATTG
18847 TTT
1 TTT
18850 CAATTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (19 bp):
TTTTCTTTAATTGTTATTG
Found at i:19734 original size:4 final size:4
Alignment explanation
Indices: 19727--19753 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19717 TGTCAAAAAA
19727 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
19754 AGAGTCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:19937 original size:10 final size:11
Alignment explanation
Indices: 19912--19938 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19902 TGAATTAAAA
19912 AAAAATTGAAC
1 AAAAATTGAAC
19923 AAAAATTGAAC
1 AAAAATTGAAC
19934 AAAAA
1 AAAAA
19939 AAGACACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAATTGAAC
Found at i:32382 original size:42 final size:42
Alignment explanation
Indices: 32331--32416 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
32321 TATATTGGGG
32331 TTTCCTTCTTGATTAAACTCAATTCATACACATAATCATCAT
1 TTTCCTTCTTGATTAAACTCAATTCATACACATAATCATCAT
32373 TTTCCTTCTTGATTAAACTCAATTCATACACATAATCATCAT
1 TTTCCTTCTTGATTAAACTCAATTCATACACATAATCATCAT
32415 TT
1 TT
32417 CATAAACCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (42 bp):
TTTCCTTCTTGATTAAACTCAATTCATACACATAATCATCAT
Done.