Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019959.1 Corchorus olitorius cultivar O-4 contig19992, 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: 10578
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:798 original size:15 final size:15
Alignment explanation
Indices: 778--812 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
768 TCTTGATTGC
778 TTTTCGGGGATATGG
1 TTTTCGGGGATATGG
793 TTTTCGGGGATATGG
1 TTTTCGGGGATATGG
808 TTTTC
1 TTTTC
813 CTTATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.34, T:0.46
Consensus pattern (15 bp):
TTTTCGGGGATATGG
Found at i:2736 original size:46 final size:46
Alignment explanation
Indices: 2669--2764 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
2659 CCATTGATCA
2669 GGTAGTTTGTCTTGGTATTTTGGTCATCCTAGCTAATGATTGGTAT
1 GGTAGTTTGTCTTGGTATTTTGGTCATCCTAGCTAATGATTGGTAT
2715 GGTAGTTTGTCTTGGTATTTTGGTCATCCTAGCTAATGATTGGTAT
1 GGTAGTTTGTCTTGGTATTTTGGTCATCCTAGCTAATGATTGGTAT
2761 GGTA
1 GGTA
2765 TCTTGCCAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (46 bp):
GGTAGTTTGTCTTGGTATTTTGGTCATCCTAGCTAATGATTGGTAT
Found at i:5036 original size:11 final size:11
Alignment explanation
Indices: 5020--5051 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5010 GTTTGTGGGC
5020 TCGTCGGAGGT
1 TCGTCGGAGGT
5031 TCGTCGGAGGT
1 TCGTCGGAGGT
*
5042 TCATCGGAGG
1 TCGTCGGAGG
5052 GAAGAAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.44, T:0.25
Consensus pattern (11 bp):
TCGTCGGAGGT
Found at i:5466 original size:49 final size:51
Alignment explanation
Indices: 5380--5494 Score: 121
Period size: 49 Copynumber: 2.3 Consensus size: 51
5370 CCTTTAATTT
* * * *
5380 AATCTTGGTAAGATAGGAATAAAAGTGAGATCTTTTAGCTT-AAA-TGATC
1 AATCTTGGTAAGTTAAGAATAAAAGTCAGATCTTTTAGCTTCAAAGAGATC
*
5429 AATCTTGGTAAGTTAAGAATAAAAGCTTCA-ATC-TTTAGGTTCAAAGAGATC
1 AATCTTGGTAAGTTAAGAATAAAAG--TCAGATCTTTTAGCTTCAAAGAGATC
*
5480 AAGTTTTGGTAAGTT
1 AA-TCTTGGTAAGTT
5495 TAAATTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
49 30 0.55
50 6 0.11
51 8 0.15
52 11 0.20
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (51 bp):
AATCTTGGTAAGTTAAGAATAAAAGTCAGATCTTTTAGCTTCAAAGAGATC
Found at i:6234 original size:33 final size:34
Alignment explanation
Indices: 6185--6277 Score: 118
Period size: 33 Copynumber: 2.7 Consensus size: 34
6175 AGTCTTCGAA
*
6185 GTTTTCAAATTGGGAAAGTTCCCACCAGGTTTTA-
1 GTTTT-AAATTGGGAAAGTTCCCACAAGGTTTTAG
*
6219 GTTCTT-AATTGGGAAAGTTCCCAACAAGTTTTTAG
1 GTT-TTAAATTGGGAAAGTTCCC-ACAAGGTTTTAG
6254 GTTTTAAAATTGGGAAAGTTCCCA
1 GTTTT-AAATTGGGAAAGTTCCCA
6278 TTCACTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
33 16 0.31
34 14 0.27
35 6 0.12
36 16 0.31
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (34 bp):
GTTTTAAATTGGGAAAGTTCCCACAAGGTTTTAG
Found at i:6272 original size:36 final size:34
Alignment explanation
Indices: 6184--6277 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 34
6174 CAGTCTTCGA
*
6184 AGTTTTCAAATTGGGAAAGTTCCC-ACCAGGTTTT
1 AGTTTT-AAATTGGGAAAGTTCCCAACAAGGTTTT
*
6218 AGTTCTT-AATTGGGAAAGTTCCCAACAAGTTTTT
1 AGTT-TTAAATTGGGAAAGTTCCCAACAAGGTTTT
6252 AGGTTTTAAAATTGGGAAAGTTCCCA
1 A-GTTTT-AAATTGGGAAAGTTCCCA
6278 TTCACTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
33 16 0.30
34 15 0.28
35 5 0.09
36 17 0.32
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (34 bp):
AGTTTTAAATTGGGAAAGTTCCCAACAAGGTTTT
Found at i:6335 original size:43 final size:42
Alignment explanation
Indices: 6254--6337 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
6244 AAGTTTTTAG
*
6254 GTTTTAAAATTGGGAAAGTTCCCATTCACTTTTTTTTTCAAA
1 GTTTTAAAATTGGGAAAGTTCCCATTCACTTTTGTTTTCAAA
* * *
6296 GTTTTTAAATTGGGAGAGTTCCCA-TCAGGTTTTAGTTTTCAA
1 GTTTTAAAATTGGGAAAGTTCCCATTCA-CTTTT-GTTTTCAA
6338 TTTGGGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.08
42 26 0.72
43 7 0.19
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (42 bp):
GTTTTAAAATTGGGAAAGTTCCCATTCACTTTTGTTTTCAAA
Found at i:8366 original size:23 final size:23
Alignment explanation
Indices: 8329--8382 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
8319 CAGGTAGGTG
* *
8329 TAGTAGTATATTGTAATGTAAAT
1 TAGTAATATTTTGTAATGTAAAT
*
8352 TGGTAATATTTTGTAATGTAAAT
1 TAGTAATATTTTGTAATGTAAAT
8375 TAGTAATA
1 TAGTAATA
8383 CTAGGGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (23 bp):
TAGTAATATTTTGTAATGTAAAT
Done.