Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006928.1 Corchorus capsularis cultivar CVL-1 contig06949, 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: 25752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:67 original size:18 final size:18
Alignment explanation
Indices: 23--68 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
13 AAAAAAGCGG
*
23 AGAGCACA-GACGCCATA
1 AGAGCACACGAAGCCATA
*
40 A-AGGCGCACGAAGCCATA
1 AGA-GCACACGAAGCCATA
58 AGAGCACACGA
1 AGAGCACACGA
69 TATGCCACGC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 1 0.04
17 5 0.22
18 16 0.70
19 1 0.04
ACGTcount: A:0.41, C:0.28, G:0.26, T:0.04
Consensus pattern (18 bp):
AGAGCACACGAAGCCATA
Found at i:930 original size:32 final size:31
Alignment explanation
Indices: 887--978 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 31
877 GATGCACACG
*
887 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT
1 ACTCAG-TAGATCGAGCATCCCTCGATCGAAT
* *
919 ACTCAGCTAGATCGGGCATCCCTCTATCGAAT
1 ACTCAG-TAGATCGAGCATCCCTCGATCGAAT
951 ACT---TAGATCGAGCATCCCTCGATCGAAT
1 ACTCAGTAGATCGAGCATCCCTCGATCGAAT
979 GACATTCGTC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.43
32 31 0.57
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (31 bp):
ACTCAGTAGATCGAGCATCCCTCGATCGAAT
Found at i:3155 original size:12 final size:12
Alignment explanation
Indices: 3124--3157 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
3114 TGTATATAAT
3124 ATAATTTCATAC
1 ATAATTTCATAC
3136 AT-ATTTCATAC
1 ATAATTTCATAC
3147 ATAATTTCATA
1 ATAATTTCATA
3158 TAATATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAATTTCATAC
Found at i:5133 original size:21 final size:21
Alignment explanation
Indices: 5086--5136 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
5076 AAAATTCAAA
*
5086 ATAAAATAAAAACTACCCATT
1 ATAAGATAAAAACTACCCATT
* *
5107 -TTAGATAAAAACTATCCATT
1 ATAAGATAAAAACTACCCATT
5127 ATAAGATAAA
1 ATAAGATAAA
5137 TATAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAGATAAAAACTACCCATT
Found at i:5342 original size:20 final size:21
Alignment explanation
Indices: 5314--5353 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5304 AAATTCAAAA
5314 TAAATTAAAAAATACCTATTT
1 TAAATTAAAAAATACCTATTT
*
5335 TAAA-TAAAAACTACCTATT
1 TAAATTAAAAAATACCTATT
5354 AGAAGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATTAAAAAATACCTATTT
Found at i:8616 original size:30 final size:30
Alignment explanation
Indices: 8580--8641 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
8570 TTCCTCCAAT
*
8580 ATCTAAAATAGAC-TCAAAATTTTAAAATGC
1 ATCTAAAATAGACTTAAAAATTTT-AAATGC
8610 ATCTAAAATAGACTTAAAAATTTTAAATGC
1 ATCTAAAATAGACTTAAAAATTTTAAATGC
8640 AT
1 AT
8642 AATTAGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.32
Consensus pattern (30 bp):
ATCTAAAATAGACTTAAAAATTTTAAATGC
Found at i:9541 original size:12 final size:13
Alignment explanation
Indices: 9519--9557 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
9509 TTTTTTTTGC
9519 TATATATTATAAT
1 TATATATTATAAT
9532 TATA-ATTATAAT
1 TATATATTATAAT
*
9544 TATTATATTCTAAT
1 TA-TATATTATAAT
9558 ATTCTAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTATAAT
Found at i:11310 original size:30 final size:30
Alignment explanation
Indices: 11270--11327 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11260 ACTTGGTAAA
* *
11270 TCTCTTTACTTACAACAAAAG-TCAATTTGG
1 TCTCTCTACTTA-AAAAAAAGATCAATTTGG
11300 TCTCTCTACTTAAAAAAAAGATCAATTT
1 TCTCTCTACTTAAAAAAAAGATCAATTT
11328 AGTTCTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (30 bp):
TCTCTCTACTTAAAAAAAAGATCAATTTGG
Found at i:11340 original size:30 final size:28
Alignment explanation
Indices: 11272--11342 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
11262 TTGGTAAATC
*
11272 TCTTTACTTACAACAAAAGTCAATTTGG
1 TCTTTACTTACAAAAAAAGTCAATTTGG
*
11300 TCTCTCTACTTA-AAAAAAAGATCAATTTAGT
1 TCT-T-TACTTACAAAAAAAG-TCAATTT-GG
11331 TCTTGTACTTAC
1 TCTT-TACTTAC
11343 GGGTTCGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 3 0.09
29 8 0.23
30 20 0.57
31 4 0.11
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (28 bp):
TCTTTACTTACAAAAAAAGTCAATTTGG
Found at i:16859 original size:2 final size:2
Alignment explanation
Indices: 16852--16881 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16842 ATTTATTAAC
16852 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16882 TAATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18002 original size:214 final size:214
Alignment explanation
Indices: 17632--18058 Score: 775
Period size: 214 Copynumber: 2.0 Consensus size: 214
17622 TCGTACATTG
17632 TGTAAGAGATAATGAACAAATCAAATTTTAATTTTTGAAATTCATGCTGTAAATTTAAAATTGTA
1 TGTAAGAGATAATGAACAAATCAAATTTTAATTTTTGAAATTCATGCTGTAAATTTAAAATTGTA
* *
17697 ATTTGTTGTAACTTCTAGCTGTAGTGAACAGGAAGGTTATATCTAGAGTAGTTGGTTGAGAACCA
66 ATTTGTTGTAACTTCTAACTGTAGTGAACAGGAAGGTTATATCTAGAGTAGTTGGTTAAGAACCA
* *
17762 AACTCTAAGCTGTATAAAGCTTTGTAACAGATCATTCATCGATATACCTTTCTCTCGTCTTCCTC
131 AACTCTAAGCTGTATAAAGCTTTGTAACAGATCATTCATCAATATACATTTCTCTCGTCTTCCTC
17827 ACACTTTCTACATGGTATT
196 ACACTTTCTACATGGTATT
17846 TGTAAGAGATAATGAACAAATCAAATTTTAATTTTTGAAATTCATGCTGTAAATTTAAAATTGTA
1 TGTAAGAGATAATGAACAAATCAAATTTTAATTTTTGAAATTCATGCTGTAAATTTAAAATTGTA
* *
17911 ATTTGTTGTAAGC-TCTAACTGTAGTGATCAGGTAGGTTATATCTAGAGTAGTTGGTTAAGAACC
66 ATTTGTTGTAA-CTTCTAACTGTAGTGAACAGGAAGGTTATATCTAGAGTAGTTGGTTAAGAACC
*
17975 AAACTCTAAGCTGTATAAAGTTTTGTAACAGATCATTCATCAATATACATTTCTCTCGTCTTCCT
130 AAACTCTAAGCTGTATAAAGCTTTGTAACAGATCATTCATCAATATACATTTCTCTCGTCTTCCT
18040 CACACTTTCTACATGGTAT
195 CACACTTTCTACATGGTAT
18059 CAGATTTTTT
Statistics
Matches: 205, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
214 204 1.00
215 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (214 bp):
TGTAAGAGATAATGAACAAATCAAATTTTAATTTTTGAAATTCATGCTGTAAATTTAAAATTGTA
ATTTGTTGTAACTTCTAACTGTAGTGAACAGGAAGGTTATATCTAGAGTAGTTGGTTAAGAACCA
AACTCTAAGCTGTATAAAGCTTTGTAACAGATCATTCATCAATATACATTTCTCTCGTCTTCCTC
ACACTTTCTACATGGTATT
Done.