Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013116.1 Corchorus olitorius cultivar O-4 contig13149, 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: 40730
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:15233 original size:40 final size:40
Alignment explanation
Indices: 15178--15257 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
15168 TGAGCAGTAA
15178 CCTTTCCATATTAAGAACAAAAAGAAAGAAAAGGGGATTT
1 CCTTTCCATATTAAGAACAAAAAGAAAGAAAAGGGGATTT
*
15218 CCTTTCCATATTAAGAACAAAAAGAAAGATAAGGGGATTT
1 CCTTTCCATATTAAGAACAAAAAGAAAGAAAAGGGGATTT
15258 TCAAGCCTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.24
Consensus pattern (40 bp):
CCTTTCCATATTAAGAACAAAAAGAAAGAAAAGGGGATTT
Found at i:17137 original size:48 final size:48
Alignment explanation
Indices: 17066--17163 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
17056 GTCTGAATTC
17066 CTCTAAATGTAAATTACTTATATGAAATTCTATGATCAATCTTAGCTA
1 CTCTAAATGTAAATTACTTATATGAAATTCTATGATCAATCTTAGCTA
*
17114 CTCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTA
1 CTCTAAATGTAAATTACTTATATGAAATTCTATGATCAATCTTAGCTA
17162 CT
1 CT
17164 TATTATAGCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (48 bp):
CTCTAAATGTAAATTACTTATATGAAATTCTATGATCAATCTTAGCTA
Found at i:17228 original size:70 final size:70
Alignment explanation
Indices: 17115--17256 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
17105 TCTTAGCTAC
* *
17115 TCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTACTTATTATAGCTTCTCTT
1 TCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTACTTATTACAACTTCTCTT
17180 TCTGA
66 TCTGA
17185 TCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTACTTATTACAACTTCTCTT
1 TCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTACTTATTACAACTTCTCTT
17250 TCTGA
66 TCTGA
17255 TC
1 TC
17257 AATTTTCCTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (70 bp):
TCTAAATGTAAATTCCTTATATGAAATTCTATGATCAATCTTAGCTACTTATTACAACTTCTCTT
TCTGA
Found at i:17486 original size:54 final size:54
Alignment explanation
Indices: 17404--17510 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
17394 TAGAGACCTC
*
17404 CTAGCTTCTTCTTATATACTACAGAAAACTTAATACACCTTGAGAAAAATAAAT
1 CTAGCTTCTTCTTATATACTACAAAAAACTTAATACACCTTGAGAAAAATAAAT
17458 CTAGCTTCTTCTTATATACTACAAAAAACTTAATACACCTTGAGAAAAATAAA
1 CTAGCTTCTTCTTATATACTACAAAAAACTTAATACACCTTGAGAAAAATAAA
17511 AAGGCAAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.31
Consensus pattern (54 bp):
CTAGCTTCTTCTTATATACTACAAAAAACTTAATACACCTTGAGAAAAATAAAT
Found at i:35644 original size:12 final size:12
Alignment explanation
Indices: 35622--35655 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35612 GAAGAAAACA
35622 TATATTATATAT
1 TATATTATATAT
* *
35634 TTTATTTTATAT
1 TATATTATATAT
35646 TATATTATAT
1 TATATTATAT
35656 TAAAGATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATATAT
Found at i:36123 original size:21 final size:22
Alignment explanation
Indices: 36081--36135 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
36071 CGGAATTACT
36081 AAGTTGTGTTTGCTGAAAAAAA
1 AAGTTGTGTTTGCTGAAAAAAA
36103 AAGTTGTGTTTGCTG-AAAAAA
1 AAGTTGTGTTTGCTGAAAAAAA
36124 AAGTTGTGTTTG
1 AAGTTGTGTTTG
36136 ATTTGAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (22 bp):
AAGTTGTGTTTGCTGAAAAAAA
Found at i:38257 original size:41 final size:44
Alignment explanation
Indices: 38212--38307 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
38202 AAAGTGCATT
*
38212 AGCTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAA
1 AGCTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAA
* *
38253 AGCTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAG
1 AGCTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAA
*
38298 AGTTAATATT
1 AGCTAATATT
38308 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 6 0.13
42 8 0.17
44 1 0.02
45 32 0.68
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (44 bp):
AGCTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAA
Found at i:39605 original size:21 final size:24
Alignment explanation
Indices: 39560--39611 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
39550 CTATCTTAGA
39560 AATAATATATATTATTAAATAAAT
1 AATAATATATATTATTAAATAAAT
*
39584 AATAA-ATATATT-TTCAAT-AAT
1 AATAATATATATTATTAAATAAAT
39605 AAGTAAT
1 AA-TAAT
39612 GAGTTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 7 0.28
24 5 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATAATATATATTATTAAATAAAT
Done.