Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006615.1 Corchorus olitorius cultivar O-4 contig06640, 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, 601
Length: 1002
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Found at i:132 original size:6 final size:6
Alignment explanation
Indices: 121--172 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
111 TTTCTTCATT
121 TTTTCA TTTTCA TTTTTCA -TTTCA -TTT-- TTTTCA TTTTCA TTTTCA
1 TTTTCA TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
166 TTTTCA T
1 TTTTCA T
173 CATTTTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.07
5 8 0.19
6 25 0.60
7 6 0.14
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:140 original size:21 final size:21
Alignment explanation
Indices: 115--172 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
105 GCTTCTTTTC
115 TTCATTTTTTCATTTTCATTT
1 TTCATTTTTTCATTTTCATTT
136 TTCATTTCATTT--TTTTCA-TT
1 TTCATTT--TTTCATTTTCATTT
156 TTCA--TTTTCATTTTCAT
1 TTCATTTTTTCATTTTCAT
173 CATTTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
16 3 0.09
18 7 0.22
20 6 0.19
21 13 0.41
23 3 0.09
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
TTCATTTTTTCATTTTCATTT
Found at i:149 original size:26 final size:26
Alignment explanation
Indices: 115--168 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
105 GCTTCTTTTC
115 TTCA-TTTTTTCATTTTCATTTTTCAT
1 TTCATTTTTTTCATTTTCA-TTTTCAT
141 TTCATTTTTTTCATTTTCATTTTCAT
1 TTCATTTTTTTCATTTTCATTTTCAT
167 TT
1 TT
169 TCATCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (26 bp):
TTCATTTTTTTCATTTTCATTTTCAT
Found at i:178 original size:27 final size:27
Alignment explanation
Indices: 121--178 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
111 TTTCTTCATT
**
121 TTTTCATTTTCATTTTTCATTTCATTT
1 TTTTCATTTTCATTTTTCATTTCATCA
148 TTTTCATTTTCA-TTTTCATTTTCATCA
1 TTTTCATTTTCATTTTTCA-TTTCATCA
175 TTTT
1 TTTT
179 TTTGATGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTCATTTTCATTTTTCATTTCATCA
Found at i:544 original size:10 final size:10
Alignment explanation
Indices: 531--569 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
521 TTTTCACTTC
531 TTTTTGTTTT
1 TTTTTGTTTT
541 TTTTTGTTTTTGT
1 TTTTTG--TTT-T
554 TTTTTGTTTT
1 TTTTTGTTTT
564 TTTTTG
1 TTTTTG
570 CATCTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 13 0.50
11 3 0.12
12 3 0.12
13 7 0.27
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:558 original size:13 final size:12
Alignment explanation
Indices: 537--568 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
527 CTTCTTTTTG
537 TTTTTTTTTGTT
1 TTTTTTTTTGTT
549 TTTGTTTTTTGTT
1 TTT-TTTTTTGTT
562 TTTTTTT
1 TTTTTTT
569 GCATCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTGTT
Done.