Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008006.1 Corchorus capsularis cultivar CVL-1 contig08027, 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: 41392
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5092 original size:22 final size:22
Alignment explanation
Indices: 5067--5108 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5057 CGCATTTTTT
5067 TCGATCTTTTCTT-TTTCTTTCA
1 TCGATCTTTT-TTCTTTCTTTCA
5089 TCGATCTTTTTTCTTTCTTT
1 TCGATCTTTTTTCTTTCTTT
5109 TTGAGGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.07, C:0.21, G:0.05, T:0.67
Consensus pattern (22 bp):
TCGATCTTTTTTCTTTCTTTCA
Found at i:6318 original size:189 final size:190
Alignment explanation
Indices: 6074--6427 Score: 638
Period size: 189 Copynumber: 1.9 Consensus size: 190
6064 GATTGATTTA
6074 AATATGCTGCAAAAAGACACAATGAGGGCATTCCTATTATACATCATGATATAATGGTGCATCCA
1 AATATGCTGCAAAAAGACACAATGAGGGCATTCCTATTATACATCATGATATAATGGTGCATCCA
** *
6139 TTAAAAGTTTATGATGGTAATTCTTATTATGTGGTAAAAAGTCACAATGGAAGCATTCCTATTAT
66 ACAAAAGTTTATGATGGTAATTCTTATTATGTGGTAAAAAGGCACAATGGAAGCATTCCTATTAT
6204 ACATGAAGGTATAATGGTGCATCCTAACAAAAGTTGGTAATGGTGCATATATGAAGGTAT
131 ACATGAAGGTATAATGGTGCATCCTAACAAAAGTTGGTAATGGTGCATATATGAAGGTAT
* * *
6264 AATATGCTGCAAAAAGGCACAATGA-TGCATTCCTATTATACATCATGGTATAATGGTGCATCCA
1 AATATGCTGCAAAAAGACACAATGAGGGCATTCCTATTATACATCATGATATAATGGTGCATCCA
*
6328 ACAAAAGTTTCTGATGGTAATTCTTATTATGTGGTAAAAAGGCACAATGGAAGCATTCCTATTAT
66 ACAAAAGTTTATGATGGTAATTCTTATTATGTGGTAAAAAGGCACAATGGAAGCATTCCTATTAT
6393 ACATGAAGGTATAATGGTGCATCCTAACAAAAGTT
131 ACATGAAGGTATAATGGTGCATCCTAACAAAAGTT
6428 AGCAAAGTTT
Statistics
Matches: 157, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
189 133 0.85
190 24 0.15
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (190 bp):
AATATGCTGCAAAAAGACACAATGAGGGCATTCCTATTATACATCATGATATAATGGTGCATCCA
ACAAAAGTTTATGATGGTAATTCTTATTATGTGGTAAAAAGGCACAATGGAAGCATTCCTATTAT
ACATGAAGGTATAATGGTGCATCCTAACAAAAGTTGGTAATGGTGCATATATGAAGGTAT
Found at i:7934 original size:20 final size:20
Alignment explanation
Indices: 7909--7951 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
7899 GACGTATAAC
7909 AAGCAAAATAGCGGGGGTAA
1 AAGCAAAATAGCGGGGGTAA
7929 AAGCAAAATAGCGGGGGTAA
1 AAGCAAAATAGCGGGGGTAA
7949 AAG
1 AAG
7952 TGACGCTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.35, T:0.09
Consensus pattern (20 bp):
AAGCAAAATAGCGGGGGTAA
Found at i:14052 original size:30 final size:31
Alignment explanation
Indices: 14018--14157 Score: 117
Period size: 30 Copynumber: 4.5 Consensus size: 31
14008 GGTGTCCGAC
* * *
14018 GTGGCACGCTACGTGTATCAAAAA-TGACAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
14048 GTGGCACGCCACATGTACCAAAAAGTCGTGCCACAT
1 GTGGCACGCCACATGTACCAAAAA---GTG--ACAT
* *
14084 GT--CACGCCACGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
* ** *
14113 GTGGCATGCCACATGTTTCAAAAA-TGGCAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
*
14143 GTGGCATGCCACATG
1 GTGGCACGCCACATG
14158 CACAAAAGGA
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
29 5 0.05
30 40 0.44
31 19 0.21
34 21 0.23
36 6 0.07
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.20
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTGACAT
Found at i:21060 original size:440 final size:434
Alignment explanation
Indices: 20132--21437 Score: 1694
Period size: 440 Copynumber: 3.0 Consensus size: 434
20122 TTTCAAAAGT
* * * * *
20132 AATTACCTCTTGAACCTT-CATGAAACTCATTAATTAAATTCAGCTTTCAGGCCCTTAAAGAAAG
1 AATTACCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCAGACCCTTAACGAAAG
* ** *
20196 TCGTAGATCACACAATAACCTTTTAACCGACACTTGAACAA-CTTCAATCGGACACGTAAACCGT
66 TCGTAGATCACACAATAACCTTTTAACCGACACTTGAACAATC-TCAATCGGACAAGTGGACCGA
* * * *
20260 AAATTATACATTATTAGATAAAACGGCAATCGAGACCACCAAATCTTGGAAGCATTTTTTAGAA-
130 AAATTATACAATATTAGAT-AGACGGCAATCGAGACCACAAAAT-TTGGAAGCAATTTTTAGAAT
* * * *
20324 CTGAAACCTCAAAATTGGCTTTTGAGAACTTAATGAAAGTTGTAGATCATTAAATTACCTTTTAA
193 CAG-AACATCAAAATTGGCTTTTGAG-TCTTAATGAAAGTTGTAGATCATGAAATTACCTTTTAA
** * *
20389 TGACACTTGAATCACCTTAATCGGACAAACATGACAAAAAATAAAAGAATTAAAGCCGAAACATT
256 TGACACTTGAATCACCTTAATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGGCGAAACGTT
*
20454 AAATCGTCCAACCCAGAATTTGTGAGGGATTAAATAGTATAAAGCATAAAAGTATGAGGATCATT
321 AAATCGTCCAACCCAAAATTTGTGAGGGATTAAATAGTATAAAGCAT-AAAGTATGAGGATCATT
* *
20519 TAATAAATAATCCAGCAAAAAAAAATTTTGTTTATGGAGACCAAACATAAA
385 TGATAAATAATCCAGCAAAAAAATA-TTTGTTTATGGAGACCAAACATAAA
* * *
20570 AATTTCCTCTCGAACCCTCCACAAAACTCATTAATCAAATTCAGCTTTCAGATCCC-TAACGAAA
1 AATTACCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCAGA-CCCTTAACGAAA
* * *
20634 GTCATAGATCACACAATAACCTTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGATCAA
65 GTCGTAGATCACACAATAACCTTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGA
** * *
20699 AAATTATACAATATTAGATAGACTGGCAATCGAGAAAAAAAAAATTTGGAAGCAATTTTTATAAT
130 AAATTATACAATATTAGATAGAC-GGCAATCGAG-ACCACAAAATTTGGAAGCAATTTTTAGAAT
* * * *
20764 CAGAACATGAAAATTGGCTTCTGAGCTCTTAATGAAAGTTATAGATCATGAAATTACCTTATAAT
193 CAGAACATCAAAATTGGCTTTTGAG-TCTTAATGAAAGTTGTAGATCATGAAATTACCTTTTAAT
* * *
20829 AGACACTTGAATCACCTTAATCGAACAAATAAAACAAAAAAATACAAA-AATAAAAGGC-AAAGC
257 -GACACTTGAATCACCTTAATCGGACAAACAAAAC-AAAAAATA-AAAGAATTAAAGGCGAAA-C
* * * * * *
20892 GTCAAATCATCCAACCCATAATTT-TAAAGGATTAAATAGTATAAAGCATAAATGTATGAGAATC
318 GTTAAATCGTCCAACCCAAAATTTGTGAGGGATTAAATAGTATAAAGCATAAA-GTATGAGGATC
*
20956 ATTTGATAAATAATCCAACAAAAAAAGTATTTGTTTATGGAGACCAAACATAAA
382 ATTTGATAAATAATCCAGCAAAAAAA-TATTTGTTTATGGAGACCAAACATAAA
* * *
21010 AATTCCCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAACTTTCAGACCCTTGACGAAAG
1 AATTACCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCAGACCCTTAACGAAAG
* * *
21075 TCGTATATCACACAATAACCTTTTAACTGACACTTGAACAATCTTAATCGGACAAGTGGACCGAA
66 TCGTAGATCACACAATAACCTTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAA
* *
21140 AATTATACGATATTAGATAGACCGGCAATCGAGACCACAAAATTTCAGAAGC-ATTGTTTAGAAT
131 AATTATACAATATTAGATAGA-CGGCAATCGAGACCACAAAATTT-GGAAGCAATT-TTTAGAAT
* * * * * *
21204 CAAAATATTAAAATTGGCTTTTGAGTCTTTCATGAAAGTTGTAGATTATGAAATTATCTTTTAAT
193 CAGAACATCAAAATTGGCTTTTGAGTC-TTAATGAAAGTTGTAGATCATGAAATTACCTTTTAAT
* * *
21269 GGACACTTGAATCACCTTGATCGGATAAGCAAAACAAAAAATAAAAGAATTAAAGGCGAAACGTT
257 -GACACTTGAATCACCTTAATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGGCGAAACGTT
* * * **
21334 TAATCGTCCAACCCAAAATTTGTGAGGGACTAAATAGCATAAATTATAAAGTAT-AGGGATCATT
321 AAATCGTCCAACCCAAAATTTGTGAGGGATTAAATAGTATAAAGCATAAAGTATGA-GGATCATT
*
21398 TGATAAATAATCCAGCAAAAAAATGATTTGTTTATTGAGA
385 TGATAAATAATCCAGCAAAAAAAT-ATTTGTTTATGGAGA
21438 GTGGGACTCA
Statistics
Matches: 752, Mismatches: 94, Indels: 43
0.85 0.11 0.05
Matches are distributed among these distances:
438 23 0.03
439 296 0.39
440 391 0.52
441 39 0.05
442 3 0.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (434 bp):
AATTACCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCAGACCCTTAACGAAAG
TCGTAGATCACACAATAACCTTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAA
AATTATACAATATTAGATAGACGGCAATCGAGACCACAAAATTTGGAAGCAATTTTTAGAATCAG
AACATCAAAATTGGCTTTTGAGTCTTAATGAAAGTTGTAGATCATGAAATTACCTTTTAATGACA
CTTGAATCACCTTAATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGGCGAAACGTTAAATC
GTCCAACCCAAAATTTGTGAGGGATTAAATAGTATAAAGCATAAAGTATGAGGATCATTTGATAA
ATAATCCAGCAAAAAAATATTTGTTTATGGAGACCAAACATAAA
Found at i:37290 original size:27 final size:27
Alignment explanation
Indices: 37237--37291 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
37227 ATATTGTTAA
37237 TCATGTAGAACCTGCTATTATTATATC
1 TCATGTAGAACCTGCTATTATTATATC
37264 TCATGTAGAACCTGCTATTATTATATC
1 TCATGTAGAACCTGCTATTATTATATC
37291 T
1 T
37292 TCAAATTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (27 bp):
TCATGTAGAACCTGCTATTATTATATC
Done.