Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013934.1 Corchorus olitorius cultivar O-4 contig13967, 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: 49179
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2014 original size:31 final size:31
Alignment explanation
Indices: 1979--2040 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1969 ATATTCGAAA
* *
1979 AATAAGGGTATGATAGACGATTCAAAAGTTT
1 AATAAGGATATAATAGACGATTCAAAAGTTT
*
2010 AATAAGGATATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGACGATTCAAAAGTTT
2041 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGATATAATAGACGATTCAAAAGTTT
Found at i:7846 original size:109 final size:109
Alignment explanation
Indices: 7655--7872 Score: 355
Period size: 109 Copynumber: 2.0 Consensus size: 109
7645 TAGTCATTTT
* * *
7655 GGTGCTTGTATTTTTCTTTAAATTCAATAGTTCATTGCACTTTGTATTGTATGATATTTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTATGACATGTGTGCTT
*
7720 ATTTAATAGCTTTAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
* * *
7764 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGCATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTATGACATGTGTGCTT
* *
7829 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
7873 ATATATATAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTATGACATGTGTGCTT
ATTTAATAGCTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:8945 original size:22 final size:21
Alignment explanation
Indices: 8898--8945 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
8888 TTGCCCTTCT
*
8898 TCTCT-CTCCCCCACTAACTC
1 TCTCTCCTCCCCCACTAACTA
* *
8918 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCC-CCCACTAACTA
8940 TCTCTC
1 TCTCTC
8946 TTCATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.35
Consensus pattern (21 bp):
TCTCTCCTCCCCCACTAACTA
Found at i:13083 original size:14 final size:14
Alignment explanation
Indices: 13066--13092 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13056 AACGTTTTTC
13066 ACGTTTTGTTTAAA
1 ACGTTTTGTTTAAA
13080 ACGTTTTGTTTAA
1 ACGTTTTGTTTAA
13093 GTAAAGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ACGTTTTGTTTAAA
Found at i:16188 original size:18 final size:18
Alignment explanation
Indices: 16165--16200 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16155 GAGGGAGAAA
16165 CTTCTGGTGAAGTTGCAC
1 CTTCTGGTGAAGTTGCAC
16183 CTTCTGGTGAAGTTGCAC
1 CTTCTGGTGAAGTTGCAC
16201 ATGATACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (18 bp):
CTTCTGGTGAAGTTGCAC
Found at i:19928 original size:27 final size:26
Alignment explanation
Indices: 19878--19932 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
19868 AGAATGAAAG
19878 AAAAAGACAAAAGGAAGGGAAATTGA
1 AAAAAGACAAAAGGAAGGGAAATTGA
19904 AAAAAGA-AAAGAGTGAATGGG-AATTGA
1 AAAAAGACAAA-AG-GAA-GGGAAATTGA
19931 AA
1 AA
19933 TTTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 3 0.12
26 9 0.35
27 11 0.42
28 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.27, T:0.11
Consensus pattern (26 bp):
AAAAAGACAAAAGGAAGGGAAATTGA
Found at i:23731 original size:87 final size:87
Alignment explanation
Indices: 23622--23794 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 87
23612 TCATTGGAGA
*
23622 TTTGAGCTTATAATGAATGTAATGAGATTTGAATATTGTATCACTTCCTAAAAACTACACAAAGC
1 TTTGAGCTTATAATAAATGTAATGAGATTTGAATATTGTATCACTTCCTAAAAACTACACAAAGC
*
23687 TTCTATGACTTCTTTCTTATTG
66 TTCTACGACTTCTTTCTTATTG
*
23709 TTTGAGCTTATAATAAATGTAATGAGATTTGAATATTGTATCACTTCCTAAAAACTGCACAAAGC
1 TTTGAGCTTATAATAAATGTAATGAGATTTGAATATTGTATCACTTCCTAAAAACTACACAAAGC
23774 TTCTACGACTTCTTTCTTATT
66 TTCTACGACTTCTTTCTTATT
23795 ATTTATGTGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (87 bp):
TTTGAGCTTATAATAAATGTAATGAGATTTGAATATTGTATCACTTCCTAAAAACTACACAAAGC
TTCTACGACTTCTTTCTTATTG
Found at i:29909 original size:538 final size:539
Alignment explanation
Indices: 28882--29969 Score: 2106
Period size: 538 Copynumber: 2.0 Consensus size: 539
28872 AAGTGTCTCC
*
28882 AGTTCTTGCTTCAACTCTTTCAAATCTCTCCCTTCTACAATACTTCTTTGTCAATTGGTTGGCCA
1 AGTTC-TGATTCAACTCTTTCAAATCTCTCCCTTCTACAATACTTCTTTGTCAATTGGTTGGCCA
*
28947 CCAGACTCGATGGTTCAGTCATAATCCTCCATGCTTGTTTGCATAAAAGGGCTTTGTTCATCTCT
65 CCAGACTCGATGGTTCAGTCATAATCCTCCATGCTTGTTTGCATAAAAGGGCTCTGTTCATCTCT
29012 TCTGTTTTTCTCAATCCTAATCCTCCTGCTATTTTTGGTTTGCAAAGATGATCCCATCCTTTTAA
130 TCTGTTTTTCTCAATCCTAATCCTCCTGCTATTTTTGGTTTGCAAAGATGATCCCATCCTTTTAA
29077 GTGCAGTTTTCGATTCTCTTCTCCATGACCCCACCAGAAGTTCCTTGTTGCTCTATCAATTTTCT
195 GTGCAGTTTTCGATTCTCTTCTCCATGACCCCACCAGAAGTTCCTTGTTGCTCTATCAATTTTCT
29142 CACACACATTGATAGGAGCCTTAAACACTGACATTGTGTAAATAGGAATGGATGCAATGGTTGAT
260 CACACACATTGATAGGAGCCTTAAACACTGACATTGTGTAAATAGGAATGGATGCAATGGTTGAT
29207 TTGATAAGAGTGAGTCTTCCTCCTGGTGACAGTAACTGGGATGTCCACCCTTGAAGTCTGGATTG
325 TTGATAAGAGTGAGTCTTCCTCCTGGTGACAGTAACTGGGATGTCCACCCTTGAAGTCTGGATTG
29272 TATTTTGTCAATTACTGGCTGATAGAAATCCTTCTTTCTTCTGAGTGATCCCATTTCCATAGGTA
390 TATTTTGTCAATTACTGGCTGATAGAAATCCTTCTTTCTTCTGAGTGATCCCATTTCCATAGGTA
*
29337 TTTCCCAGGCTTTTCAACTAGTTTGTATCCAAGGATCCCCTTAAACCACCTCTTCTTCCTGTGTG
455 TTTCCCAGGCTTTTCAACTAGTTTGTATCCAAGGATCCCCTTAAACCACCTCTTCTTCCTGCGTG
29402 GACAATTTGGACTTAGGAGA
520 GACAATTTGGACTTAGGAGA
29422 AGTTCTGATTCAACTCTTTCAAATCTCTCCCTTCTACAATACTTCTTTGTCAATTGGTTGGCCAC
1 AGTTCTGATTCAACTCTTTCAAATCTCTCCCTTCTACAATACTTCTTTGTCAATTGGTTGGCCAC
29487 CAGACTCGATGGTTCAGTCATAATCCTCCATGCTTGTTTGCATAAAAGGGC-CTGTTCATCTCTT
66 CAGACTCGATGGTTCAGTCATAATCCTCCATGCTTGTTTGCATAAAAGGGCTCTGTTCATCTCTT
29551 CTGTTTTTCTCAATCCTAATCCTCCTGCTATTTTTGGTTTGCAAAGATGATCCCATCCTTTTAAG
131 CTGTTTTTCTCAATCCTAATCCTCCTGCTATTTTTGGTTTGCAAAGATGATCCCATCCTTTTAAG
29616 TGCAGTTTTCGATTCTCTTCTCCATGACCCCACCAGAAGTTCCTTGTTGCTCTATCAATTTTCTC
196 TGCAGTTTTCGATTCTCTTCTCCATGACCCCACCAGAAGTTCCTTGTTGCTCTATCAATTTTCTC
* *
29681 ACACACATTGATAGGAGCCTTAAACATTGACATTGTGTAAATAGGAATGGATGTAATGGTTGATT
261 ACACACATTGATAGGAGCCTTAAACACTGACATTGTGTAAATAGGAATGGATGCAATGGTTGATT
*
29746 TGATAAGAGTGAGTCTTCCTCCTGGTGACAGTAACTGGGATTTCCACCCTTGAAGTCTGGATTGT
326 TGATAAGAGTGAGTCTTCCTCCTGGTGACAGTAACTGGGATGTCCACCCTTGAAGTCTGGATTGT
29811 ATTTTGTCAATTACTGGCTGATAGAAATCCTTCTTTCTTCTGAGTGATCCCATTTCCATAGGTAT
391 ATTTTGTCAATTACTGGCTGATAGAAATCCTTCTTTCTTCTGAGTGATCCCATTTCCATAGGTAT
29876 TTCCCAGGCTTTTCAACTAGTTTGTATCCAAGGATCCCCTTAAACCACCTCTTCTTCCTGCGTGG
456 TTCCCAGGCTTTTCAACTAGTTTGTATCCAAGGATCCCCTTAAACCACCTCTTCTTCCTGCGTGG
29941 ACAATTTGGACTTAGGAGA
521 ACAATTTGGACTTAGGAGA
29960 AGTTCTGATT
1 AGTTCTGATT
29970 TGTCTACATT
Statistics
Matches: 542, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
538 427 0.79
539 110 0.20
540 5 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (539 bp):
AGTTCTGATTCAACTCTTTCAAATCTCTCCCTTCTACAATACTTCTTTGTCAATTGGTTGGCCAC
CAGACTCGATGGTTCAGTCATAATCCTCCATGCTTGTTTGCATAAAAGGGCTCTGTTCATCTCTT
CTGTTTTTCTCAATCCTAATCCTCCTGCTATTTTTGGTTTGCAAAGATGATCCCATCCTTTTAAG
TGCAGTTTTCGATTCTCTTCTCCATGACCCCACCAGAAGTTCCTTGTTGCTCTATCAATTTTCTC
ACACACATTGATAGGAGCCTTAAACACTGACATTGTGTAAATAGGAATGGATGCAATGGTTGATT
TGATAAGAGTGAGTCTTCCTCCTGGTGACAGTAACTGGGATGTCCACCCTTGAAGTCTGGATTGT
ATTTTGTCAATTACTGGCTGATAGAAATCCTTCTTTCTTCTGAGTGATCCCATTTCCATAGGTAT
TTCCCAGGCTTTTCAACTAGTTTGTATCCAAGGATCCCCTTAAACCACCTCTTCTTCCTGCGTGG
ACAATTTGGACTTAGGAGA
Found at i:39163 original size:40 final size:40
Alignment explanation
Indices: 39115--39194 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
39105 TGATTCTAAA
39115 TTCTAACTTCTAACTTATAACTTGGTTTCTGATTTCTGAT
1 TTCTAACTTCTAACTTATAACTTGGTTTCTGATTTCTGAT
39155 TTCTAACTTCTAACTTATAACTTGGTTTCTGATTTCTGAT
1 TTCTAACTTCTAACTTATAACTTGGTTTCTGATTTCTGAT
39195 ATGGTGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (40 bp):
TTCTAACTTCTAACTTATAACTTGGTTTCTGATTTCTGAT
Found at i:39244 original size:26 final size:26
Alignment explanation
Indices: 39213--39271 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
39203 TTCTGATGTA
* *
39213 ATTTCTTGATTGGATTGTGATTTCTG
1 ATTTCTGGATTGGATTGTGATTTATG
39239 ATTTCTGGATTGGATTGTGATTTATG
1 ATTTCTGGATTGGATTGTGATTTATG
39265 ATTTCTG
1 ATTTCTG
39272 ATCTGTCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.53
Consensus pattern (26 bp):
ATTTCTGGATTGGATTGTGATTTATG
Found at i:41230 original size:6 final size:6
Alignment explanation
Indices: 41147--41286 Score: 118
Period size: 6 Copynumber: 23.3 Consensus size: 6
41137 TGGGCTTTTT
* * * * * * * *
41147 GAAGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAG
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
* * * * *
41195 GAAGAA GAAGAG GAAGAA GAAGAG GAAGAA GAAGAA GATGAA GACGAT
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
* * * * *
41243 GAAGAA TATGAA GAAGAA GAAGAC GAGGAA GATGAA GAAGAA GA
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GA
41287 TGATGAGTCT
Statistics
Matches: 112, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 112 1.00
ACGTcount: A:0.54, C:0.01, G:0.41, T:0.04
Consensus pattern (6 bp):
GAAGAA
Found at i:45633 original size:6 final size:6
Alignment explanation
Indices: 45622--45646 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45612 ATTTTCTGTT
45622 CCCAAA CCCAAA CCCAAA CCCAAA C
1 CCCAAA CCCAAA CCCAAA CCCAAA C
45647 AAACATATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:46121 original size:12 final size:13
Alignment explanation
Indices: 46100--46132 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
46090 TTAACCATAC
46100 ATAC-ATATCTAT
1 ATACTATATCTAT
46112 AT-CTATATCTAT
1 ATACTATATCTAT
46124 ATACTATAT
1 ATACTATAT
46133 AAGTCTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 12 0.63
13 6 0.32
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (13 bp):
ATACTATATCTAT
Found at i:46489 original size:21 final size:21
Alignment explanation
Indices: 46448--46491 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46438 TTATTAGTGG
* *
46448 TATTATAATTATTAAACTTAT
1 TATTATAATTAATAAAATTAT
46469 TATTATAA-TAATAATAATTAT
1 TATTATAATTAATAA-AATTAT
46490 TA
1 TA
46492 GTGGTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATAATTAATAAAATTAT
Found at i:46491 original size:30 final size:27
Alignment explanation
Indices: 46406--46488 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
46396 GTTAATTTAG
46406 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
46433 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* *
46463 ACTTATTATTATAATAATAATAATTA
1 ACTTATTATTATTATAATAATTATTA
46489 TTAGTGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.