Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012218.1 Corchorus capsularis cultivar CVL-1 contig12239, 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: 23926
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--81 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1 TCTTCT
7 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
82 TCTTATGCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7286 original size:21 final size:20
Alignment explanation
Indices: 7248--7288 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
7238 ACCCAGAACT
7248 TTTCTTTCCAATTCTTTTGA
1 TTTCTTTCCAATTCTTTTGA
* *
7268 TTTCTTATTCAATTTTTTTGA
1 TTTCTT-TCCAATTCTTTTGA
7289 AACCTCGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTCTTTCCAATTCTTTTGA
Found at i:8823 original size:168 final size:167
Alignment explanation
Indices: 8526--9308 Score: 869
Period size: 168 Copynumber: 4.7 Consensus size: 167
8516 TTGCTGTTGT
* * * * ** **
8526 AACTGTCCTGTAACTAGTATGCACACGGTGTTGATCCAAATCTGCTTGCTTACATTGGTGTATTC
1 AACTGTCCTCTAACTAGTGTGCACACGGTGTTGGTCCAAATTTGCTTGCTTACGCTGGCATATTC
* * * * * * *
8591 ATTTTGCTGTCATTTTCTAGGTTTTTCCATAAATAGCTTACAAATCCGCAGCATTTGGAGTTAAA
66 ATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGTATTAGGAGTTAAA
* ** *
8656 GTATTCCAGCTGAGTATGTTTCATATGATAATGCTTGG
131 GTAGTCCAGCTGAGTATCATT-ATATAATAATGCTTGG
* * * *
8694 AACTGTCCTGTAACTAGTGTGCACAGGGTGCTGGTCCAAATTTGCTTGCTTACGCTGGCATATTA
1 AACTGTCCTCTAACTAGTGTGCACACGGTGTTGGTCCAAATTTGCTTGCTTACGCTGGCATATTC
* * *
8759 ATTTTCCTGTCGTTTTCTAGGTTTTCCCATAAATAGCTTACGAATCAGCTGTATTAGTAGTTAAA
66 ATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGTATTAGGAGTTAAA
*
8824 ATAGTCCAGCTGAGTATCATTATATAATAATGCTTGG
131 GTAGTCCAGCTGAGTATCATTATATAATAATGCTTGG
* * * * * *
8861 AACTGTCCTCCAACTATTGTGCACACAGTGTTGGTCCAAATTTGCTTGCTTATGATGGCGTATTC
1 AACTGTCCTCTAACTAGTGTGCACACGGTGTTGGTCCAAATTTGCTTGCTTACGCTGGCATATTC
* * * * * * *
8926 ATTTTGCTGTCGTTTTCTAGGATTTTCCATAAAAAGCTTACGTATCAGCTGTGTTCGGGGTTAAA
66 ATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGTATTAGGAGTT-AA
* *
8991 AGTAGTCCAGCTGAGCATCATTATATAATAACGCTTGG
130 AGTAGTCCAGCTGAGTATCATTATATAATAATGCTTGG
* *
9029 AACTGT-CT-T--C-AGTGTGCACACGGTGTTGGAT-CAAACTTT-CTTGCGTATGCTGGCATAT
1 AACTGTCCTCTAACTAGTGTGCACACGGTGTTGG-TCCAAA-TTTGCTTGCTTACGCTGGCATAT
* * * *
9087 TTATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGGATTAGCTGTATAAGGAGTTA
64 TCATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGTATTAGGAGTTA
* * * ** *
9152 AAGTATTGCAACTGACAATCATTATATAATATTGCTTGG
129 AAGTAGTCCAGCTGAGTATCATTATATAATAATGCTTGG
* * * * * * * *
9191 AACTGTCCTCCAACTAGTTTGTACACGGTGGTGTTCCAAATTGGGCCTGCTTACGCTGGCATACT
1 AACTGTCCTCTAACTAGTGTGCACACGGTGTTGGTCCAAATT-TGCTTGCTTACGCTGGCATATT
* * * **
9256 CATTTTACTGTCGTTTTCTAGGTTTTGCCATAAATGGATTGTGAATCAGCTGT
65 CATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGT
9309 TTTTGGAATT
Statistics
Matches: 517, Mismatches: 87, Indels: 22
0.83 0.14 0.04
Matches are distributed among these distances:
162 39 0.08
163 93 0.18
164 5 0.01
166 4 0.01
167 144 0.28
168 232 0.45
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (167 bp):
AACTGTCCTCTAACTAGTGTGCACACGGTGTTGGTCCAAATTTGCTTGCTTACGCTGGCATATTC
ATTTTACTGTCGTTTTCTAGGTTTTTCCATAAATAGCTTACGAATCAGCTGTATTAGGAGTTAAA
GTAGTCCAGCTGAGTATCATTATATAATAATGCTTGG
Found at i:9190 original size:330 final size:331
Alignment explanation
Indices: 8526--9289 Score: 894
Period size: 330 Copynumber: 2.3 Consensus size: 331
8516 TTGCTGTTGT
** * * * *
8526 AACTGTCCTGTAACTAGTATGCACACGGTGTTGATCCAAATCTGCTTGCTTACATTGGTGTATTC
1 AACTGTCCTCCAACTA-TTTGCACACGGTGTTGATCCAAATTTGCTTGCTTAGA-TGGCGTATTC
* * * *
8591 ATTTTGCTGTCATTTTCTAGGTTTTTCCATAAATAGCTTACAAATCCGCAGCATTTGGAGTTAAA
64 ATTTTGCTGTCGTTTTCTAGG-TTTTCCATAAAAAGCTTACAAATCAGCAGCATTCGGAGTTAAA
* * ** * * *
8656 GTATTCCAGCTGAGTATGTTTCATATGATAATGCTTGGAACTGTCCTGTAACTAGTGTGCACAGG
128 GTAGTCCAGCTGAGCATCATTCATATAATAACGCTTGGAACTGTCCTGT-ACTAGTGTGCACACG
* *
8721 GTGCTGGTCCAAATTTGCTTGCTTACGCTGGCATATTAATTTTCCTGTCGTTTTCTAGGTTTTCC
192 GTGCTGGTCCAAATTTGCTTGCGTACGCTGGCATATTAATTTTACTGTCGTTTTCTAGGTTTTCC
* * * **
8786 CATAAATAGCTTACGAATCAGCTGTATTAGTAGTTAAAATAGTCCAGCTGAGTATCATTATATAA
257 CATAAATAGCTTACGAATCAGCTGTATAAGGAGTTAAAATAGTCCAACTGACAATCATTATATAA
8851 TAATGCTTGG
322 TAATGCTTGG
* *
8861 AACTGTCCTCCAACTATTGTGCACACAGTGTTGGTCCAAATTTGCTTGCTTATGATGGCGTATTC
1 AACTGTCCTCCAACTATT-TGCACACGGTGTTGATCCAAATTTGCTTGCTTA-GATGGCGTATTC
** * ** *
8926 ATTTTGCTGTCGTTTTCTAGGATTTTCCATAAAAAGCTTACGTATCAGCTGTGTTCGGGGTTAAA
64 ATTTTGCTGTCGTTTTCTAGG-TTTTCCATAAAAAGCTTACAAATCAGCAGCATTCGGAGTT-AA
8991 AGTAGTCCAGCTGAGCATCATT-ATATAATAACGCTTGGAACTGT-CT-T-C-AGTGTGCACACG
127 AGTAGTCCAGCTGAGCATCATTCATATAATAACGCTTGGAACTGTCCTGTACTAGTGTGCACACG
* * *
9051 GTGTTGGAT-CAAACTTT-CTTGCGTATGCTGGCATATTTATTTTACTGTCGTTTTCTAGGTTTT
192 GTGCTGG-TCCAAA-TTTGCTTGCGTACGCTGGCATATTAATTTTACTGTCGTTTTCTAGGTTTT
* * * * * *
9114 TCCATAAATAGCTTACGGATTAGCTGTATAAGGAGTTAAAGTATTGCAACTGACAATCATTATAT
255 CCCATAAATAGCTTACGAATCAGCTGTATAAGGAGTTAAAATAGTCCAACTGACAATCATTATAT
*
9179 AATATTGCTTGG
320 AATAATGCTTGG
* * * * * * * *
9191 AACTGTCCTCCAACTAGTTTGTACACGGTGGTGTTCCAAATTGGGCCTGCTTACGCTGGCATACT
1 AACTGTCCTCCAACTA-TTTGCACACGGTGTTGATCCAAATT-TGCTTGCTTA-GATGGCGTATT
*
9256 CATTTTACTGTCGTTTTCTAGGTTTTGCCATAAA
63 CATTTTGCTGTCGTTTTCTAGGTTTT-CCATAAA
9290 TGGATTGTGA
Statistics
Matches: 367, Mismatches: 54, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
330 167 0.46
331 51 0.14
333 1 0.00
334 3 0.01
335 124 0.34
336 21 0.06
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (331 bp):
AACTGTCCTCCAACTATTTGCACACGGTGTTGATCCAAATTTGCTTGCTTAGATGGCGTATTCAT
TTTGCTGTCGTTTTCTAGGTTTTCCATAAAAAGCTTACAAATCAGCAGCATTCGGAGTTAAAGTA
GTCCAGCTGAGCATCATTCATATAATAACGCTTGGAACTGTCCTGTACTAGTGTGCACACGGTGC
TGGTCCAAATTTGCTTGCGTACGCTGGCATATTAATTTTACTGTCGTTTTCTAGGTTTTCCCATA
AATAGCTTACGAATCAGCTGTATAAGGAGTTAAAATAGTCCAACTGACAATCATTATATAATAAT
GCTTGG
Found at i:9980 original size:66 final size:66
Alignment explanation
Indices: 9874--10126 Score: 461
Period size: 66 Copynumber: 3.8 Consensus size: 66
9864 TCGTTTATAG
9874 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTCCTACTGTATT
1 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTCCTACTGTATT
9939 C
66 C
* *
9940 GTCCTACTGGATGGGGGGATACCGAAGAGGGTGCAGTGAAGGAGAATAACATGACCTACTGTATT
1 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTCCTACTGTATT
10005 C
66 C
*
10006 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTTAAGGAGAATAACATGTCCTACTGTATT
1 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTCCTACTGTATT
10071 C
66 C
* *
10072 ATCCTACTGGATGGGGGGATGTCGAAGAGGGTGCAGTGAAGGAGAATAACATGTC
1 GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTC
10127 TTCCAATTGG
Statistics
Matches: 179, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 179 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (66 bp):
GTCCTACTGGATGGGGGGATGCCGAAGAGGGTGCAGTGAAGGAGAATAACATGTCCTACTGTATT
C
Found at i:15983 original size:16 final size:17
Alignment explanation
Indices: 15962--16009 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
15952 GTTTTCGAGT
*
15962 TCGGGTTAAATTT-TGA
1 TCGGGTTAAATTTGGGA
* *
15978 TCGGGTT-GATTTGGGT
1 TCGGGTTAAATTTGGGA
15994 TCGGGTTAAATTTGGG
1 TCGGGTTAAATTTGGG
16010 TCAGGTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.17, C:0.06, G:0.35, T:0.42
Consensus pattern (17 bp):
TCGGGTTAAATTTGGGA
Found at i:16001 original size:32 final size:32
Alignment explanation
Indices: 15955--16062 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
15945 TCATGCTGTT
* *
15955 TTCGAGTTCGGGTTAAATTTTGATCGGGTTGA
1 TTCGGGTTCGGGTTAAATTTTGATCAGGTTGA
* * *
15987 TTTGGGTTCGGGTTAAATTTGGGTCAGGTTGA
1 TTCGGGTTCGGGTTAAATTTTGATCAGGTTGA
* *
16019 TTCGGGTTCGGG-TCAATTTTGTGTCAGGTT-A
1 TTCGGGTTCGGGTTAAATTTTG-ATCAGGTTGA
16050 GTTCGGGTTCGGG
1 -TTCGGGTTCGGG
16063 CTCGGATTGG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
31 8 0.12
32 58 0.88
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (32 bp):
TTCGGGTTCGGGTTAAATTTTGATCAGGTTGA
Found at i:16284 original size:16 final size:16
Alignment explanation
Indices: 16265--16355 Score: 96
Period size: 16 Copynumber: 5.7 Consensus size: 16
16255 TTTCAGATTT
*
16265 GGGTTCGGGTTTTTTC
1 GGGTTCGAGTTTTTTC
*
16281 GGGTTTC-AGATTTTTC
1 GGG-TTCGAGTTTTTTC
16297 GGGTTCTGA-TTTTTTC
1 GGGTTC-GAGTTTTTTC
*
16313 GGGTTTGAGTTTTTTC
1 GGGTTCGAGTTTTTTC
* *
16329 GGGTTCGTGTTTTTTT
1 GGGTTCGAGTTTTTTC
*
16345 GAGTTCGAGTT
1 GGGTTCGAGTT
16356 CGGGCGGGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
15 5 0.08
16 53 0.85
17 4 0.06
ACGTcount: A:0.07, C:0.10, G:0.31, T:0.53
Consensus pattern (16 bp):
GGGTTCGAGTTTTTTC
Found at i:16301 original size:32 final size:32
Alignment explanation
Indices: 16265--16343 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
16255 TTTCAGATTT
16265 GGGTTCGGGTTTTTTCGGGTTTCAGATTTTTC
1 GGGTTCGGGTTTTTTCGGGTTTCAGATTTTTC
* * * *
16297 GGGTTCTGATTTTTTCGGGTTTGAGTTTTTTC
1 GGGTTCGGGTTTTTTCGGGTTTCAGATTTTTC
*
16329 GGGTTCGTGTTTTTT
1 GGGTTCGGGTTTTTT
16344 TGAGTTCGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.05, C:0.10, G:0.30, T:0.54
Consensus pattern (32 bp):
GGGTTCGGGTTTTTTCGGGTTTCAGATTTTTC
Found at i:23214 original size:30 final size:30
Alignment explanation
Indices: 23145--23219 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
23135 ATATTGTGTC
* *
23145 AAGGACCCAATTACTCAGTTAACTCCATTT
1 AAGGACCCAATTGCTCAGCTAACTCCATTT
* *
23175 AATGGACCCAATTGCTCA-CTAAGTTCACTTT
1 AA-GGACCCAATTGCTCAGCTAACTCCA-TTT
*
23206 AAGGACCCATTTGC
1 AAGGACCCAATTGC
23220 ACATCCGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (30 bp):
AAGGACCCAATTGCTCAGCTAACTCCATTT
Done.