Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014560.1 Corchorus olitorius cultivar O-4 contig14593, 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: 1783
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Found at i:686 original size:120 final size:121
Alignment explanation
Indices: 463--702 Score: 401
Period size: 120 Copynumber: 2.0 Consensus size: 121
453 AAGAGAAATT
*
463 TGCTTTATAATTCATAGAATGTATCGAACAAAGTCACCATACATGAGAATAACAAAGATTCTTAA
1 TGCTTTATAATTCATAGAATGTATCGAACAAAGTCACCATACATGAGAATAACAAAGACTCTTAA
* *
528 CCAGAAAATCAAGCATCATTTATTTCCATGGTGGTAATCAGAAG-ATTGGAGTGGA
66 CCAGAAAATCAAGCATCATTTATTTCCATGATGATAATCAGAAGAATTGGAGTGGA
* * *
583 TGCTTTATAATTCATAGAATGTATCGAACAAAGTTACCTTACATGAGAATCACAAAGACTCTTAA
1 TGCTTTATAATTCATAGAATGTATCGAACAAAGTCACCATACATGAGAATAACAAAGACTCTTAA
* *
648 CCATAAAATCAAGCATCATTTATTTTCATGATGATAATCAGAAGAATTGGAGTGG
66 CCAGAAAATCAAGCATCATTTATTTCCATGATGATAATCAGAAGAATTGGAGTGG
703 TATAGGGGGC
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
120 101 0.91
121 10 0.09
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (121 bp):
TGCTTTATAATTCATAGAATGTATCGAACAAAGTCACCATACATGAGAATAACAAAGACTCTTAA
CCAGAAAATCAAGCATCATTTATTTCCATGATGATAATCAGAAGAATTGGAGTGGA
Found at i:1367 original size:381 final size:382
Alignment explanation
Indices: 664--1429 Score: 1462
Period size: 381 Copynumber: 2.0 Consensus size: 382
654 AATCAAGCAT
664 CATTTATTTTCATGATGATAATCAGAAGAATTGGAGTGGTATAGGGGGCATGAGCCTTTACAGTG
1 CATTTATTTTCATGATGATAATCAGAAGAATTGGAGTGGTATAGGGGGCATGAGCCTTTACAGTG
*
729 GTCCATGTTTCATTACACGATAAGAGTGCCATAAAAAAGGTAATTTACTTGAACTGGCACCACTA
66 GTCCATGTTTCATTACACAATAAGAGTGCCATAAAAAAGGTAATTTACTTGAACTGGCACCACTA
794 TACCTTTATGTATAATAGGAATGCCACCACTTTGCCCTTTACTGCATGTTAAGAATTCCCATTAC
131 TACCTTTATGTATAATAGGAATGCCACCACTTTGCCCTTTACTGCATGTTAAGAATTCCCATTAC
859 CAACTTTTTTTGGATACACCATCATACCTTGTTGCATGATAGGAATGTCTCCATTGTGCCTTTCA
196 CAACTTTTTTTGGATACACCATCATACCTTGTTGCATGATAGGAATGTCTCCATTGTGCCTTTCA
*
924 CCCATAATAAGAAGAATTACCAGCACCATTATACCATGATGTATAACGGGAATGCCATCATTGTG
261 CCCATAATAAGAAGAATTACCAGCACCATTATACCATGATGTATAACAGGAATGCCATCATTGTG
989 CTTTTTACAGCATATTAAGATCAATCCAA-AACTATATTCAAGACAAAGTAATAAAA
326 CTTTTTACAGCATATTAAGATCAATCCAACAACTATATTCAAGACAAAGTAATAAAA
*
1045 CATTTATTTTCATGATGGTAATCAGAAGAATTGGAGTGGTATAGGGGGCATGAGCCTTTACAGTG
1 CATTTATTTTCATGATGATAATCAGAAGAATTGGAGTGGTATAGGGGGCATGAGCCTTTACAGTG
*
1110 GTCCATGTTTCATTACACAATAAGAGTGCCATAAAAAGGGTAATTTACTTGAACTGGCACCACTA
66 GTCCATGTTTCATTACACAATAAGAGTGCCATAAAAAAGGTAATTTACTTGAACTGGCACCACTA
1175 TACCTTTATGTATAATAGGAATGCCACCACTTTGCCCTTTACTGCATGTTAAGAATTCCCATTAC
131 TACCTTTATGTATAATAGGAATGCCACCACTTTGCCCTTTACTGCATGTTAAGAATTCCCATTAC
*
1240 CAACTTTTTTTGGATACACCATCATACCTTGTTGTATGATAGGAATGTCTCCATTGTGCCTTTCA
196 CAACTTTTTTTGGATACACCATCATACCTTGTTGCATGATAGGAATGTCTCCATTGTGCCTTTCA
*
1305 CCCATAATAAGAAGAATTACCAGCACCATTATACCATGATGTATAATAGGAATGCCATCATTGTG
261 CCCATAATAAGAAGAATTACCAGCACCATTATACCATGATGTATAACAGGAATGCCATCATTGTG
1370 CTTTTTACAGCATATTAAGATCAATCCAAGCAACTATATTCAAGACAAAGTAATAAAA
326 CTTTTTACAGCATATTAAGATCAATCCAA-CAACTATATTCAAGACAAAGTAATAAAA
1428 CA
1 CA
1430 AACCGAAAAA
Statistics
Matches: 377, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
381 348 0.92
383 29 0.08
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (382 bp):
CATTTATTTTCATGATGATAATCAGAAGAATTGGAGTGGTATAGGGGGCATGAGCCTTTACAGTG
GTCCATGTTTCATTACACAATAAGAGTGCCATAAAAAAGGTAATTTACTTGAACTGGCACCACTA
TACCTTTATGTATAATAGGAATGCCACCACTTTGCCCTTTACTGCATGTTAAGAATTCCCATTAC
CAACTTTTTTTGGATACACCATCATACCTTGTTGCATGATAGGAATGTCTCCATTGTGCCTTTCA
CCCATAATAAGAAGAATTACCAGCACCATTATACCATGATGTATAACAGGAATGCCATCATTGTG
CTTTTTACAGCATATTAAGATCAATCCAACAACTATATTCAAGACAAAGTAATAAAA
Done.