Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005266.1 Corchorus capsularis cultivar CVL-1 contig05284, 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: 6880
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:810 original size:13 final size:13
Alignment explanation
Indices: 792--818 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
782 TTCACAGCAA
792 TACCAAACCTTAT
1 TACCAAACCTTAT
805 TACCAAACCTTAT
1 TACCAAACCTTAT
818 T
1 T
819 TACATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
TACCAAACCTTAT
Found at i:944 original size:40 final size:40
Alignment explanation
Indices: 900--981 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
890 TTTTTCGAAC
900 CCCAACTTCAATACCAAACTAAGCCTTAGAATGCTACAAT
1 CCCAACTTCAATACCAAACTAAGCCTTAGAATGCTACAAT
* *
940 CCCAACTTCAATACTACACTAAGCCTTAGAATGCTACAAT
1 CCCAACTTCAATACCAAACTAAGCCTTAGAATGCTACAAT
980 CC
1 CC
982 GTCATGTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (40 bp):
CCCAACTTCAATACCAAACTAAGCCTTAGAATGCTACAAT
Found at i:5050 original size:3 final size:3
Alignment explanation
Indices: 5042--5071 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5032 AACCACACAA
5042 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5072 GAAGAAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6710 original size:440 final size:440
Alignment explanation
Indices: 5889--6761 Score: 1069
Period size: 440 Copynumber: 2.0 Consensus size: 440
5879 TCCGTTCTCA
* * * *
5889 ATAAACAAATCATTTTTTTTGCTGGTTTATTTATCAAATGATCACTATACTTTTATGCTTTATGC
1 ATAAACAAATCATTTTATTTGCTGGATTATTTATCAAATGATCACCATACTTTTATCCTTTATGC
* * * * *
5954 TATTTAGTCCCTCGCAATTTTGGGTTGGACGATTCAACGTTTCGGCTTTGGTTCTTTTATTTTTT
66 TATTTAATCCCTCACAATTATGGGTCGGACGATTCAACGTTTCGGCTTTGATTCTTTTATTTTTT
* * *
6019 GTTTTGTTTGTCCGATTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGATTTACAACTT
131 GTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTAATGATTTACAACTT
* * * * **
6084 TCGTGAAGGACTCGAAATCCAATTTTAATGTTTTGATTCAAAGAAATGCTTCTGAAATTTTGTGG
196 TCATGAAGAACTCGAAAGCCAATTTTAATGTTTCGATTCAAAGAAATGCTTCCAAAATTTTGTGG
* * * * * * * *
6149 TCTCGATTGCCGGTCTATCTGATATTGTGTAATTTTCGATTCGCTTGTCCGATTGAGGTTGTTCA
261 TCTAGATTGCCGGTCTATCTAATATCGTATAATTTTCGATTCACATGTCCGATTGAAGTTATTCA
*** ** *
6214 AGTGTCAGTTAAAAGGTTATTGTGTGATCTACGACTTTCATGAAGGGCCTGAAAGCTGAATTTCA
326 AGTGTCAGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGAACCCGAAAGCTGAATTTCA
** * * * * * *
6279 TTATTGAGTTTCGTGGAGGGTTCGAGAGGGAATTTTTATGTTTGGTCTTC
391 TTAACGAGTTTCATGAAGAGCTCGAGAGGCAATGTTTATGTTTGGTCTTC
*
6329 ATAAACAAAT-ATTTTATTTGCTGGATTATTTATCAAATGATCCCCATACTTTT-TCCCCTTTAT
1 ATAAACAAATCATTTTATTTGCTGGATTATTTATCAAATGATCACCATACTTTTAT--CCTTTAT
* * * * *
6392 GCTATTTAATCCTTTACAATTATGGGTCGGACGATTTAATGCG-TT-GTCTTTTATT-TTTGTAT
64 GCTATTTAATCCCTCACAATTATGGGTCGGACGATTCAA--CGTTTCGGCTTTGATTCTTT-TAT
* * *
6454 TTTCTT-TTCTATTTGTCGGATTAAGGTGATTCGAGTGTCTATTGAAAGGTCATTTAATGATTTA
126 TTT-TTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTAATGATTTA
* *
6518 CAACTTTCATGAAGAACTCGAAAGCCAATTTTGATGTTTCGATTCTAAA-AAGTGCTTCCAAAAT
190 CAACTTTCATGAAGAACTCGAAAGCCAATTTTAATGTTTCGATTC-AAAGAAATGCTTCCAAAAT
* * * * *
6582 TTTGTGGTTTAGGTTGCCGGTCTCTTTAATATCGTATAATTTTTTG-TTCACATGTCCGATTGAA
254 TTTGTGGTCTAGATTGCCGGTCTATCTAATATCGTATAA-TTTTCGATTCACATGTCCGATTGAA
* * * *
6646 GTTATTTAAGTGTCGGTTAAAAGGTTATTACATGATCTATGACTTTCATGAATAACCCGAAAGCT
318 GTTATTCAAGTGTCAGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGAACCCGAAAGCT
*
6711 GAATTTGATTAACGAGTTTCATGAAGAGCTCGAGAGGCAATGTTTATGTTT
383 GAATTTCATTAACGAGTTTCATGAAGAGCTCGAGAGGCAATGTTTATGTTT
6762 CATCTCCATC
Statistics
Matches: 364, Mismatches: 61, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
438 1 0.00
439 42 0.12
440 307 0.84
441 12 0.03
442 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (440 bp):
ATAAACAAATCATTTTATTTGCTGGATTATTTATCAAATGATCACCATACTTTTATCCTTTATGC
TATTTAATCCCTCACAATTATGGGTCGGACGATTCAACGTTTCGGCTTTGATTCTTTTATTTTTT
GTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTAATGATTTACAACTT
TCATGAAGAACTCGAAAGCCAATTTTAATGTTTCGATTCAAAGAAATGCTTCCAAAATTTTGTGG
TCTAGATTGCCGGTCTATCTAATATCGTATAATTTTCGATTCACATGTCCGATTGAAGTTATTCA
AGTGTCAGTTAAAAGGTTATTACATGATCTACGACTTTCATGAAGAACCCGAAAGCTGAATTTCA
TTAACGAGTTTCATGAAGAGCTCGAGAGGCAATGTTTATGTTTGGTCTTC
Done.