Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020098.1 Corchorus olitorius cultivar O-4 contig20131, 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: 32487
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4992 original size:57 final size:59
Alignment explanation
Indices: 4920--5038 Score: 170
Period size: 57 Copynumber: 2.0 Consensus size: 59
4910 GTGAATCTAC
* *
4920 TTAATATTGACGAAAACAAAATTACCACCATATTTC-AAACATAAA-ATTAATGTGATT
1 TTAATATTGACGAAAACAAAATTACCACCATATTTCAAAAAAAAAATATTAATGTGATT
* * *
4977 TTAATATTGATGAAAACAAGATTACCACCATGTTTCAAAAAAAAAAATATTAATGTGATT
1 TTAATATTGACGAAAACAAAATTACCACCATATTTC-AAAAAAAAAATATTAATGTGATT
5037 TT
1 TT
5039 GGATTAGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 33 0.61
59 7 0.13
60 14 0.26
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (59 bp):
TTAATATTGACGAAAACAAAATTACCACCATATTTCAAAAAAAAAATATTAATGTGATT
Found at i:5767 original size:7 final size:7
Alignment explanation
Indices: 5755--5808 Score: 101
Period size: 7 Copynumber: 7.9 Consensus size: 7
5745 GTGGAAGACC
5755 CAATAGG
1 CAATAGG
5762 CAATAGG
1 CAATAGG
5769 CAATAGG
1 CAATAGG
5776 CAATAGG
1 CAATAGG
5783 C-ATAGG
1 CAATAGG
5789 CAATAGG
1 CAATAGG
5796 CAATAGG
1 CAATAGG
5803 CAATAG
1 CAATAG
5809 CCAACAAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.13
7 40 0.87
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.15
Consensus pattern (7 bp):
CAATAGG
Found at i:5789 original size:27 final size:27
Alignment explanation
Indices: 5757--5808 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5747 GGAAGACCCA
5757 ATAGGCAATAGGCAATAGGCAATAGGC
1 ATAGGCAATAGGCAATAGGCAATAGGC
5784 ATAGGCAATAGGCAATAGGCAATAG
1 ATAGGCAATAGGCAATAGGCAATAG
5809 CCAACAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.29, T:0.15
Consensus pattern (27 bp):
ATAGGCAATAGGCAATAGGCAATAGGC
Found at i:11220 original size:2 final size:2
Alignment explanation
Indices: 11213--11241 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11203 CGACGCGAGC
11213 GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11242 AGGGAGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12230 original size:21 final size:21
Alignment explanation
Indices: 12189--12232 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12179 AAATTTTGTT
**
12189 TTTATTTATTTATTTTTAATA
1 TTTATTTATTTATTTACAATA
12210 TTTA-TTATTTAATTTACAATA
1 TTTATTTATTT-ATTTACAATA
12231 TT
1 TT
12233 ATCCTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTTATTTATTTACAATA
Found at i:14490 original size:3 final size:3
Alignment explanation
Indices: 14482--14509 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14472 TATATATAAT
14482 GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG G
14510 TAAAGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:30519 original size:15 final size:15
Alignment explanation
Indices: 30499--30529 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30489 TTTTGGAGAC
30499 TGTAAAATTACAACT
1 TGTAAAATTACAACT
30514 TGTAAAATTACAACT
1 TGTAAAATTACAACT
30529 T
1 T
30530 CCTTTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TGTAAAATTACAACT
Found at i:31423 original size:5 final size:5
Alignment explanation
Indices: 31413--31442 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
31403 CTTGATTTTC
31413 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
31443 GTTATTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Done.