Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011686.1 Corchorus olitorius cultivar O-4 contig11719, 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, 898
Length: 1497
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.22
Found at i:1388 original size:599 final size:599
Alignment explanation
Indices: 244--1390 Score: 1948
Period size: 599 Copynumber: 1.9 Consensus size: 599
234 TTTGCTTTTA
244 CTGGCCGGATGCGACCAGCCCGTAAAAACGGAGCCAGCCCCGCCCGGCGGGGGCGGAACCATTGA
1 CTGGCCGGATGCGACCAGCCCGTAAAAACGGAGCCAGCCCCGCCCGGCGGGGGCGGAACCATTGA
* *
309 AGCCATTAACCATACAAGCTGGGCCATCAACCGCTTCAGCGTTAACGGGCAGTCCGGCCTCGATA
66 AGCCATTAACCACACAAGCTGGGCCATCAACCGCTTCAGCGTGAACGGGCAGTCCGGCCTCGATA
*
374 TTATCGGCCCTTATTCGGGTGGCGGCGGAGGCTGCTGCTTTGGCGTGAGCGGGCCGTGGACGCCC
131 TTATCGGCCCTTATTCGGGTGACGGCGGAGGCTGCTGCTTTGGCGTGAGCGGGCCGTGGACGCCC
*
439 GGAATGACGGTGCAGGTTGACTGGGAAACGGGCGTCGCGTTTGCCAGCGATGTGCCTGAGATCCC
196 GGAATGACGGTACAGGTTGACTGGGAAACGGGCGTCGCGTTTGCCAGCGATGTGCCTGAGATCCC
*** * * *
504 ACTACCTGTACGACCTAATCTGGAGGGATTGAACGAAGAGGAAGGATACAAGGTAGCTCAGGCTT
261 ACTACCTGTACGACCTAATCCACAGGGATTGAACGAAGAGGAACGATACAAGGCAGCGCAGGCTT
569 ATTCAGATAAATATCACGAATGGTATGGCAAAATTAAAGCCATCAGTAAAACATATTCCCGAACA
326 ATTCAGATAAATATCACGAATGGTATGGCAAAATTAAAGCCATCAGTAAAACATATTCCCGAACA
634 GTGCCTGTCCCCGATTACAGCGGCCAGAAAACCTGCGGCATTACCGTTCACTTCCTGCCCTGTGA
391 GTGCCTGTCCCCGATTACAGCGGCCAGAAAACCTGCGGCATTACCGTTCACTTCCTGCCCTGTGA
*
699 CCAGGTGAAGGTCACCACCAGCTGTGCCGACTACGGTAGCCCTGATTACCCCATCAAAGACCCCG
456 CCAGGTGAAGGTCACCACCAGCTGTGCCGACTACGGCAGCCCTGATTACCCCATCAAAGACCCCG
* *
764 TGCATATGGAGAAGCCGACAGTATGTCCCAAGTGATTGCAGTATGGCATTCCCGCATTTTGCTGG
521 TGCATATGGAGAAGCCCAAAGTATGTCCCAAGTGATTGCAGTATGGCATTCCCGCATTTTGCTGG
829 CTGCAGCCCTGCTG
586 CTGCAGCCCTGCTG
*
843 CTGGCCGGGTGCGACCAGCCCGTAAAAACGGAGCCAGCCCCGCCCGGCGGGGGCGGAACCATTGA
1 CTGGCCGGATGCGACCAGCCCGTAAAAACGGAGCCAGCCCCGCCCGGCGGGGGCGGAACCATTGA
* *
908 AGCCATTAACCACACCAGTTGGGCCATCAACCGCTTCAGCGTGAACGGGCAGTCCGGCCTCGATA
66 AGCCATTAACCACACAAGCTGGGCCATCAACCGCTTCAGCGTGAACGGGCAGTCCGGCCTCGATA
973 TTATCGGCCCTTATTCGGGTGACGGCGGAGGCTGCTGCTTTGGCGTGAGCGGGCCGTGGACGCCC
131 TTATCGGCCCTTATTCGGGTGACGGCGGAGGCTGCTGCTTTGGCGTGAGCGGGCCGTGGACGCCC
1038 GGAATGACGGTACAGGTTGACTGGGAAACGGGCGTCGCGTTTGCCAGCGATGTGCCTGAGATCCC
196 GGAATGACGGTACAGGTTGACTGGGAAACGGGCGTCGCGTTTGCCAGCGATGTGCCTGAGATCCC
* * * * * * * * *
1103 GC-AGCCTG-ATGAACC-AGATACCACCGGGA-TGAACCG-GGATGACCGTTATAGGGCATG-GC
261 ACTA-CCTGTACG-ACCTA-AT-CCACAGGGATTGAA-CGAAGAGGAACGATACAAGGCA-GCGC
1162 AGGCTTATTCAGATAAATATCACGAATGGTATGGCAAAATTAAAGCCATCAGTAAAACATATTCC
320 AGGCTTATTCAGATAAATATCACGAATGGTATGGCAAAATTAAAGCCATCAGTAAAACATATTCC
1227 CGAACAGTGCCTGTCCCCGATTAC-GACGGCCAGAAAACCTGCGGCATTACCGTTCACTTCCTGC
385 CGAACAGTGCCTGTCCCCGATTACAG-CGGCCAGAAAACCTGCGGCATTACCGTTCACTTCCTGC
*
1291 CCTGTGACCAGGTGAAGGTCACCACCAGCTGTGCCGACTACGGCAGCCCTGATTATCCCATCAAA
449 CCTGTGACCAGGTGAAGGTCACCACCAGCTGTGCCGACTACGGCAGCCCTGATTACCCCATCAAA
1356 GACCCCGTGCATATGGAGAAGCCCAAAGTATGTCC
514 GACCCCGTGCATATGGAGAAGCCCAAAGTATGTCC
1391 AAACTGAACC
Statistics
Matches: 515, Mismatches: 26, Indels: 14
0.93 0.05 0.03
Matches are distributed among these distances:
598 5 0.01
599 502 0.97
600 8 0.02
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.19
Consensus pattern (599 bp):
CTGGCCGGATGCGACCAGCCCGTAAAAACGGAGCCAGCCCCGCCCGGCGGGGGCGGAACCATTGA
AGCCATTAACCACACAAGCTGGGCCATCAACCGCTTCAGCGTGAACGGGCAGTCCGGCCTCGATA
TTATCGGCCCTTATTCGGGTGACGGCGGAGGCTGCTGCTTTGGCGTGAGCGGGCCGTGGACGCCC
GGAATGACGGTACAGGTTGACTGGGAAACGGGCGTCGCGTTTGCCAGCGATGTGCCTGAGATCCC
ACTACCTGTACGACCTAATCCACAGGGATTGAACGAAGAGGAACGATACAAGGCAGCGCAGGCTT
ATTCAGATAAATATCACGAATGGTATGGCAAAATTAAAGCCATCAGTAAAACATATTCCCGAACA
GTGCCTGTCCCCGATTACAGCGGCCAGAAAACCTGCGGCATTACCGTTCACTTCCTGCCCTGTGA
CCAGGTGAAGGTCACCACCAGCTGTGCCGACTACGGCAGCCCTGATTACCCCATCAAAGACCCCG
TGCATATGGAGAAGCCCAAAGTATGTCCCAAGTGATTGCAGTATGGCATTCCCGCATTTTGCTGG
CTGCAGCCCTGCTG
Done.