Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01003236.1 Corchorus olitorius cultivar O-4 contig03242, 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: 2028
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2008 original size:331 final size:331
Alignment explanation
Indices: 1263--2028 Score: 859
Period size: 330 Copynumber: 2.3 Consensus size: 331
1253 CCGAAATATT
* * * ** * *
1263 TTTCCTCAATTTTTGGCA-AAAATACTCATAAAATATATATAATTC-A-ATGCCAAAAGGTTGGA
1 TTTCCTCAATTTCTAG-AGAAAATAATCATAAAA-ATATATAATTCAACAT-AAAAAAGATTGAA
* * * ** * * *
1325 GGACTTTTCACGTTTTTAATA-TCGTTTTCATATTTTCTATGAATTAATTTCTAATTAAATTGAA
63 AGCCTTTTCACGCTTTTAATATTATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAA
* *
1389 ACAAGATTCAGATTCACATAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGA
128 ACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAAATGA
* * *
1454 ATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAACCGTGGCCCTGAAACG
193 ATAAAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAACCGTGGCCCCGAAACA
* *
1519 CGTTTTTAGCCAAAAACCGTGATGGATTATACATGATTTCGGCTAAAATTTTGCAAAAATTGACC
258 CGTTTTTAGCCAAAAACCGTGATGGATTACACATGATTTCGGCTAAAATTTTACAAAAATTGACC
*
1584 TAAAAGATA
323 CAAAAGATA
* * * * ** * *
1593 TTTCCTCAATTTTTGGATAAAATAATCATAAAGATATATAATTTGACATAAAAAAGATTGAAGGG
1 TTTCCTCAATTTCTAGAGAAAATAATCATAAAAATATATAATTCAACATAAAAAAGATTGAAAGC
* * * *
1658 CTTTTAACGCTTCTAATATTATTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAATA
66 CTTTTCACGCTTTTAATATTATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * * * ** *
1723 AGATTCATATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGAGATTTGGTTAAATGAATA
131 AGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAAATGAATA
* * * * * *
1788 TAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCTG-GGCCCCGGAACACGT
196 AAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAACCGTGGCCCCGAAACACGT
* * * *
1852 TTTTAGCCGAAAACCGTGATGG-TTAGCACATGATTTCGGCTATAATTTTACAAAAATTTACCCG
261 TTTTAGCCAAAAACCGTGATGGATTA-CACATGATTTCGGCTAAAATTTTACAAAAATTGACCCA
1916 AAAGAT-
325 AAAGATA
** * * *
1922 TTATCCTTGATTTCTAGCGAAAATACTCATAAAAAAATATATAATTCAACGT-AAAAA-ATTGAA
1 TT-TCCTCAATTTCTAGAGAAAATAATCAT--AAAAATATATAATTCAACATAAAAAAGATTGAA
* *
1985 ATCCTTTGTCACGCTTTTAATATTGTTTTTCATA-TTTTTCTGAA
63 AGCCTTT-TCACGCTTTTAATATTATTTTTCATATTTTTTCTGAA
Statistics
Matches: 366, Mismatches: 61, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
329 16 0.04
330 167 0.46
331 167 0.46
332 16 0.04
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (331 bp):
TTTCCTCAATTTCTAGAGAAAATAATCATAAAAATATATAATTCAACATAAAAAAGATTGAAAGC
CTTTTCACGCTTTTAATATTATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAAATGAATA
AAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAACCGTGGCCCCGAAACACGT
TTTTAGCCAAAAACCGTGATGGATTACACATGATTTCGGCTAAAATTTTACAAAAATTGACCCAA
AAGATA
Done.