Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013201.1 Corchorus capsularis cultivar CVL-1 contig13222, 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: 17432
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:753 original size:87 final size:87
Alignment explanation
Indices: 644--872 Score: 404
Period size: 87 Copynumber: 2.6 Consensus size: 87
634 TTCCTTTTCT
* * *
644 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATCCTCTTTATTAACTCAATCTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAACTCAATCTT
709 TATAATTTATTTATTTCTTAAA
66 TATAATTTATTTATTTCTTAAA
* *
731 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTAGCTCAATCTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAACTCAATCTT
796 TATAATTTATTTATTTCTTAAA
66 TATAATTTATTTATTTCTTAAA
*
818 ATATCTCCTAAATCTCCCACAAGTTGGCAAGATTTAGAAAATATTCTCATTATTA
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTA
873 TTTTAACAAT
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 135 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (87 bp):
ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAACTCAATCTT
TATAATTTATTTATTTCTTAAA
Found at i:3985 original size:11 final size:10
Alignment explanation
Indices: 3967--4000 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
3957 GATGTTCATG
3967 TTTTGAAGAT
1 TTTTGAAGAT
3977 TTCTTGAAGAT
1 TT-TTGAAGAT
3988 ATTTTGAAGAT
1 -TTTTGAAGAT
3999 TT
1 TT
4001 GAAGACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:5848 original size:26 final size:25
Alignment explanation
Indices: 5815--5863 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5805 GTCCCTCTAG
* *
5815 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
5840 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
5864 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Found at i:6851 original size:21 final size:21
Alignment explanation
Indices: 6806--6845 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6796 ACTAGACACC
6806 TGGGTGATCAGACAAACCACA
1 TGGGTGATCAGACAAACCACA
*
6827 TGGGTGTTCAGACAAACCA
1 TGGGTGATCAGACAAACCA
6846 TGTGGGCACC
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:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (21 bp):
TGGGTGATCAGACAAACCACA
Found at i:12345 original size:6 final size:6
Alignment explanation
Indices: 12334--12366 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
12324 AAAGCAAAAC
12334 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
12367 GCAGAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:15612 original size:21 final size:22
Alignment explanation
Indices: 15566--15612 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
15556 GTGACTCGGC
*
15566 ATGGCGCGGCATCGGCTCGTGG
1 ATGGCGCGGCATCGGCTCGCGG
15588 -TGGCGCGGCAT-GG-TGCGCGG
1 ATGGCGCGGCATCGGCT-CGCGG
15608 ATGGC
1 ATGGC
15613 TTGGCAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 1 0.05
20 6 0.27
21 15 0.68
ACGTcount: A:0.09, C:0.26, G:0.49, T:0.17
Consensus pattern (22 bp):
ATGGCGCGGCATCGGCTCGCGG
Done.