Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011052.1 Corchorus olitorius cultivar O-4 contig11085, 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, 808
Length: 1347
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Found at i:1318 original size:659 final size:658
Alignment explanation
Indices: 1--1347 Score: 2152
Period size: 659 Copynumber: 2.0 Consensus size: 658
1 TTTCAAGGAGTCTTTATGCCAAAAA-CATGTAAAATTGAGACGTCACTCCGGAACGCATTTTTAG
1 TTTCAAGGAGTCTTTATGCCAAAAATCATGTAAAATTGAGACGTCACTCCGGAACGCATTTTTAG
*
65 CCAAAAACAGTAATGATTATTACACGATTTCAGATAAAATTTTAGCCAAAAAAAAAATAGAATAC
66 CCAAAAACAGTAATGATTAGTACACGATTTCAGATAAAATTTTAGCC-AAAAAAAAATAGAATAC
* * * *
130 GAAACGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAA
130 AAAAAGTTATTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTAAACACCAAAAAA
*
195 ATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCCTTTTTTCTGAATTTATTTCTAATAAAA
195 ATTGAAGGGTTTTTCACGCTTCAAATATCATTTTTCCCTTTTTTCTGAATTTATTTCTAATAAAA
260 TCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGACTAAGATTTGATTA
260 TCAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGACTAAGATTTGATTA
*
325 CTTGAATATAAATATTTCAAGGAGTCGTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCG
325 CTTGAATATAAATATTTCAAGGAGTCGTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCG
* *
390 AAACGCGTTTTTCAGCCGAAAACCGTGATGGTTCACGATTTCGGCTAAAATCTGACCCGAAAAGT
390 AAACGCGTTTTTCAGCCGAAAACCGTGATGGTACACGATTTCGGCTAAAATCTAACCCGAAAAGT
* *
455 TTCTTCACATTTTTTTGTGAAATATTCAGAAAAAATATATAATTCAATGCAAAAAAGATTGGCGG
455 TTCTTCACATTTTTTTCTGAAATATTCAGAAAAAATATATAATTCAATGCAAAAAAGATTGACGG
* * *
520 GCTTTTCACGCTTCTCATATCGTTTTTCCAGTTTTTTTTTCGAACGAATTTCTAATTAAATTAAA
520 GCTTTTCACGCTTCTAATATCGTTTTTCCAGTTTTTTTTCCGAACGAATTTCTAATTAAATCAAA
* *
585 ACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGTTTCGATTA
585 ACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGA
650 ATATAGATA
650 ATATAGATA
* *
659 TTTCAAGGAGTCTTTACGCCAAAAATCATGTAAAATTGAGACGTGACTCCGGAACGCATTTTTAG
1 TTTCAAGGAGTCTTTATGCCAAAAATCATGTAAAATTGAGACGTCACTCCGGAACGCATTTTTAG
* * ** * * * *
724 CCAAAAACTGTGATGATTAGTACACGATTTTGGCTAAAATTTT-G-C-AAAAAAACT-TAA-CCA
66 CCAAAAACAGTAATGATTAGTACACGATTTCAGATAAAATTTTAGCCAAAAAAAAATAGAATACA
*
784 AAAAGTTATTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTAAACACCAAAAAAA
131 AAAAGTTATTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTAAACACCAAAAAAA
*
849 TTGGAGGGTTTTTCACGCTTCAAATATCATTTTTCCCTTTTTTCTGAATTTATTTCTAATAAAAT
196 TTGAAGGGTTTTTCACGCTTCAAATATCATTTTTCCCTTTTTTCTGAATTTATTTCTAATAAAAT
** *
914 CAAAACAAGATTTAGATGCTCATGAAAAACAAATCCTTTTATCCATTTTGGCTAAGATTTGATTA
261 CAAAACAAGATTTAGATGCTCAT-AAAAACAAATCCTTAAATCCATTTTGACTAAGATTTGATTA
* * * * *
979 CTTGAATATAGATATTTCAAGGATTTGTTCTGCCATAAATCATGCAAAACTGAGCCATGGCCCCG
325 CTTGAATATAAATATTTCAAGGAGTCGTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCG
* *
1044 AAACGTGTTTTTTAGCCGAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATCTAACCCGAA
390 AAACGCGTTTTTCAGCCGAAAACCGTGATG----GTACACGATTTCGGCTAAAATCTAACCCGAA
** * * *
1109 ATTTTTTTTCACAATTTTTTTCTGAAATATTCAGAAAAAATATATAATTCAATGCTAAAAATATT
451 AAGTTTCTTCAC-ATTTTTTTCTGAAATATTCAGAAAAAATATATAATTCAATGCAAAAAAGATT
1174 GACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTTACCGAACGAATTTCTAATTA
515 GACGGGCTTTTCACGCTTCTAATATCGTTTTTCC-AGTTTTTTTT-CCGAACGAATTTCTAATTA
*
1238 AATCAAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGT
578 AATCAAAACAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGT
1303 TCGATGAAT-TAGATA
643 TCGATGAATATAGATA
1318 TTTCAAGGAGTCTTTATGACCAAAAATCAT
1 TTTCAAGGAGTCTTTATG-CCAAAAATCAT
Statistics
Matches: 634, Mismatches: 45, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
653 148 0.23
654 127 0.20
655 8 0.01
657 1 0.00
658 63 0.10
659 187 0.29
660 100 0.16
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (658 bp):
TTTCAAGGAGTCTTTATGCCAAAAATCATGTAAAATTGAGACGTCACTCCGGAACGCATTTTTAG
CCAAAAACAGTAATGATTAGTACACGATTTCAGATAAAATTTTAGCCAAAAAAAAATAGAATACA
AAAAGTTATTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTAAACACCAAAAAAA
TTGAAGGGTTTTTCACGCTTCAAATATCATTTTTCCCTTTTTTCTGAATTTATTTCTAATAAAAT
CAAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCATTTTGACTAAGATTTGATTAC
TTGAATATAAATATTTCAAGGAGTCGTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGA
AACGCGTTTTTCAGCCGAAAACCGTGATGGTACACGATTTCGGCTAAAATCTAACCCGAAAAGTT
TCTTCACATTTTTTTCTGAAATATTCAGAAAAAATATATAATTCAATGCAAAAAAGATTGACGGG
CTTTTCACGCTTCTAATATCGTTTTTCCAGTTTTTTTTCCGAACGAATTTCTAATTAAATCAAAA
CAAGATTGAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAA
TATAGATA
Done.