Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018140.1 Corchorus olitorius cultivar O-4 contig18173, 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, 869
Length: 1449
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Found at i:727 original size:322 final size:322
Alignment explanation
Indices: 145--1449 Score: 2150
Period size: 322 Copynumber: 4.1 Consensus size: 322
135 AAACGTGTTT
* *
145 TTAGTACATGATTTCGGCCAAAAACTGACCCGAAAAGTTTTTTCTCAA-TTTTTACCACAATACT
1 TTAGTACATGATTTCGGCCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
* * *
209 CAGAAAAAATATATAATTTAACGCCAAGAAAATAGAAGGGTTTTTCATGCTTCAAATATCG-TTT
66 CAGAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTTT
*
273 TCC-TTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAA
131 TCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* *
337 TCCTTTAATCCATTGTGGCTGAGATTTAGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGC
196 TCCTTTAATCCATTATGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGC
* *
402 CAAAAATCATCCAAAACCGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
261 CAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
*
464 TTAGTACATGATTTCGGCCAAAAACTAACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
1 TTAGTACATGATTTCGGCCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
* * * ** **
529 CACAAGAAATATATAATTCAACGCCAAAAACACCGAAGGGTTTTTCACGCTTCAAATATCAATTT
66 CAGAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTTT
*
594 TCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTACAAACAAA
131 TCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * *
659 TCCTTTAATCCATTATGACTGAGATTTGGTTCGATGGATATAGATGTTTCAAAGAGTCTTTCTGC
196 TCCTTTAATCCATTATGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGC
724 CAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
261 CAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
* * *
786 TTAGTACATGATTTCGCCCAAAAACTTACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATTCT
1 TTAGTACATGATTTCGGCCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
* * * * *
851 CAGAAAAATTATATAATTCAATGCCAAAAAAATTGAAGGTTTTTTCACGCTTCCAATATCGTTTT
66 CAGAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTTT
*
916 TCCTTTTTATTTTCTGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
131 TCC-TTTT-TTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* *
981 AATCCTTTAATCCATTGTGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAATAGTCTTTCT
194 AATCCTTTAATCCATTATGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCT
* * *
1046 GCCAAAAATCATTCAAAACTGAGTCGATGCCCTGAAACGCGTTTTTAGCAAAAAAACCGTGATGG
259 GCCAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGC-CAAAAACCGTGATGG
* *
1111 TTAATACATGATTTC-GCCAAAAAACTGACCCGAAAAGTTTTTCCTCAATTTATTGCCACAATAC
1 TTAGTACATGATTTCGGCC-AAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATAC
*
1175 TCAGAAAAAATATATAATTTAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTT
65 TCAGAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTT
*
1240 TTCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTACAAACAA
130 TTCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* *
1305 ATCCTTTAATCCATTATGGCTGAGATTTGGTTCGATGGATATAGATATTTAAAAGAGTCTTTCTG
195 ATCCTTTAATCCATTATGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTG
* *
1370 CCAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACAGTGATGT
260 CCAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
1433 TTAGTACATGATTTCGG
1 TTAGTACATGATTTCGG
Statistics
Matches: 910, Mismatches: 68, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
319 46 0.05
320 67 0.07
321 6 0.01
322 324 0.36
323 167 0.18
324 167 0.18
325 133 0.15
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (322 bp):
TTAGTACATGATTTCGGCCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT
CAGAAAAAATATATAATTCAACGCCAAAAAAATAGAAGGGTTTTTCACGCTTCAAATATCGTTTT
TCCTTTTTTTTCCGAATTTATTTCGAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
TCCTTTAATCCATTATGGCTGAGATTTGGTTAGATGGATATAGATATTTCAAAGAGTCTTTCTGC
CAAAAATCATTCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
Done.