Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023671.1 Corchorus olitorius cultivar O-4 contig23704, 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: 4472
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1355 original size:25 final size:25
Alignment explanation
Indices: 1319--1366 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1309 TTAGTTGATT
1319 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
1344 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
1367 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:1415 original size:39 final size:39
Alignment explanation
Indices: 1361--1444 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
1351 CTTTGAGCTA
*
1361 CATGAACGCAAAATACTAAATTTCTAAATGATGCTAAGC
1 CATGAACGCAAAATACTAAATTTCTAAATGAAGCTAAGC
1400 CATGAACGCAAAATACTAAATTTCTAAATGAAGCTAAGC
1 CATGAACGCAAAATACTAAATTTCTAAATGAAGCTAAGC
1439 CATGAA
1 CATGAA
1445 AACATGTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (39 bp):
CATGAACGCAAAATACTAAATTTCTAAATGAAGCTAAGC
Found at i:2196 original size:69 final size:68
Alignment explanation
Indices: 2101--2367 Score: 381
Period size: 69 Copynumber: 3.9 Consensus size: 68
2091 CTCTGCTGTA
* * * * * * * * *
2101 TGGATGGACCCAATGTTTAAAATGACTCGCATGCAAACGAGTTTGACTTATGGAAAAGTCCATAT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CCATGT
2166 GGCT
65 GGCT
*
2170 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-CCATGT
*
2235 TGCT
65 GGCT
* *
2239 TGGATGGAACCAAGGCTTAAATTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC-ATGT
2304 GGCT
65 GGCT
*
2308 TGGATGGAACCAAGGCTTAAACTTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
2368 CAAAACATTC
Statistics
Matches: 178, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
68 2 0.01
69 176 0.99
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (68 bp):
TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCATGTG
GCT
Found at i:3678 original size:17 final size:18
Alignment explanation
Indices: 3653--3694 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
3643 ATTCTTTCCT
3653 TTTTCTTTTTC-TTTTTCA
1 TTTT-TTTTTCATTTTTCA
3671 -TTTTTTTTCATTTTTCA
1 TTTTTTTTTCATTTTTCA
3688 TTCTTTT
1 TT-TTTT
3695 GTGCACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 1 0.05
19 4 0.19
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTCATTTTTCA
Found at i:4022 original size:8 final size:8
Alignment explanation
Indices: 4009--4038 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3999 TTTATACTGA
4009 TTTTTGAT
1 TTTTTGAT
4017 TTTTTGATT
1 TTTTTGA-T
4026 TTTTTGAT
1 TTTTTGAT
4034 TTTTT
1 TTTTT
4039 TTGGAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (8 bp):
TTTTTGAT
Found at i:4041 original size:10 final size:9
Alignment explanation
Indices: 4009--4039 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3999 TTTATACTGA
4009 TTTTTGA-T
1 TTTTTGATT
4017 TTTTTGATT
1 TTTTTGATT
4026 TTTTTGATT
1 TTTTTGATT
4035 TTTTT
1 TTTTT
4040 TGGAATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (9 bp):
TTTTTGATT
Found at i:4432 original size:8 final size:8
Alignment explanation
Indices: 4419--4459 Score: 75
Period size: 8 Copynumber: 5.2 Consensus size: 8
4409 AATGCCTTTA
4419 TTTTCATT
1 TTTTCATT
4427 TTTTCA-T
1 TTTTCATT
4434 TTTTCATT
1 TTTTCATT
4442 TTTTCATT
1 TTTTCATT
4450 TTTTCATT
1 TTTTCATT
4458 TT
1 TT
4460 ATGGGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:4437 original size:15 final size:16
Alignment explanation
Indices: 4419--4459 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
4409 AATGCCTTTA
4419 TTTTCATTTTTTCA-T
1 TTTTCATTTTTTCATT
4434 TTTTCATTTTTTCATT
1 TTTTCATTTTTTCATT
4450 TTTTCATTTT
1 TTTTCATTTT
4460 ATGGGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCATTTTTTCATT
Done.