Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012053.1 Corchorus olitorius cultivar O-4 contig12086, 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: 1947
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:733 original size:322 final size:321
Alignment explanation
Indices: 4--1947 Score: 2878
Period size: 321 Copynumber: 6.0 Consensus size: 321
1 GTC
* ** * * * *
4 AACGCCAAAAAGATTGAAAGGCTTTTCA-AGCATCTAATATCGCTTTTCCTATTTTTTTCTGAAT
1 AACGCCTAAAAGATTGACGGGCTTTTCACA-CTTCTAATATC-ATTTTGC-ATTTTTTTCCGAAT
* * * * * * *
68 TAATTTCTGATTAAATCCAAACATGATTCAGATGCTCG-TAAAATCAAATCCTTAAATCCAATGT
63 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAA--AAATCGTTAAATCGAATTT
* ** ** * *
132 GGC-GGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGACGCTAAAAATCAAGCAAA
126 GGCTGGA-ATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAA
* * * * * * *
196 ACTGAGTC-GGTCCCCATAACGCGTTTTTAG-CCAAAAACCGTGATTGTTAGTACACGATTTCGG
190 ACTGAGGCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGG
* * *
259 CTAAAAACTGACCCAAAAATTTTTTTCTGAAATTTTCTACCACAATACACAGGAAAAATATATAA
255 CTAAAAACTGACCCAAAAATTTTTTTCT-TAATTTTCTACCACAATACTCAGAAAAAATATATAA
324 TTT
319 TTT
* * *
327 AACGCCTAAAAGATTGACGGGCTTTTCACAATTCTAATATCATTTTGCATCTTTTTCCGAAGTTA
1 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATTTTTTTCCGAATTTA
* *
392 TTTCTAATTAAATCGAAACAAGATACAGATTCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTG
66 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTG
457 GAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAG
131 GAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAG
*
522 GCAGGGCCACAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
196 GCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
* *
587 ACTGACCCAAAAATTTTTTTCTTTATTTTCTGCCACAATACTCAGAAAAAATATATAATTT
261 ACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATACTCAGAAAAAATATATAATTT
648 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATTTTTTTTCCGAATTT
1 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCA-TTTTTTTCCGAATTT
*
713 ATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCT
65 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCT
778 GGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGA
130 GGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGA
* * * *
843 GGCAGGGCCCCGGAACTCGTTTTTTGCCCACAAACTATGATGGTTAGTAGACGATTTCGGCTAAA
195 GGCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
908 AACTGACCCGAAAATTTTGTTCTGAATTTTCTACCACAATACTCATAAAAAATGTATAATTT
260 AACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATACTCAGAAAAAATATATAATTT
* * * * *
970 AACGCCCAAAAGATTGATGGG-TTTTAACACTTGTAATATAATTTTGCATTTTTTTTCCGAATTT
1 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCA-TTTTTTTCCGAATTT
* * * * *
1034 ATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTTTAAAAAATCGTAAAATCGAATTTGGTT
65 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCT
* *
1099 GGAATTTGGTTCGATGAATATAGGCATTTCAAGAAGTCTTCACGCAAAAAATCATGCAAAACTGA
130 GGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGA
* * * * * *
1164 GGCAGGGTCCCGGAACTCGTTTTTTGCCCAAAAACTTTGATGATTAGTATAAGATTTCGGCTAAA
195 GGCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * * *
1229 AACTGAACCGAAAATTTTGTTATGAATTTTCTACCACAATACTCATAAAAAATATATAATTT
260 AACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATACTCAGAAAAAATATATAATTT
* *
1291 AACGCCCAAAAGATTGACGGGCTTTTCACATTTCTAATATCATTTTGCATTTTTTTCCGAATTTA
1 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATTTTTTTCCGAATTTA
* *
1356 TTTCTAATTAAATCGAAACAAGATACAGATTCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTG
66 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTG
1421 GAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAG
131 GAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAG
* *
1486 GCAGGGCCACAGAACTCGTTTTCTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
196 GCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
* * *
1551 ACTGACCCAGAAATTTTTTTCTTTATTTTCTACCACAATACACAGAAAAAATATATAATTT
261 ACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATACTCAGAAAAAATATATAATTT
* * * *
1612 AACGCCTAAAAGATTGACGGGCTTTTCACAATTCTAATATCATTTTGCATCTTTTTCTGAAATTA
1 AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATTTTTTTCCGAATTTA
*
1677 TTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTTAAAAAATATCGTTAAATCGAATTTGGCT
66 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAA-ATCGTTAAATCGAATTTGGCT
* *
1742 GGAATTTGGTTCGATGAATATAGGCATTTTAAGGAGTCTTCACGCCAAAAATCATGCAAAACTAA
130 GGAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGA
* * *
1807 GGCGGGGCCCCGGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAA
195 GGCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
* * *
1872 AACTGACCCAAAAA-TTTTTTCTTTATTTTCTGCCACAATACACCA-AAAAAATATATAATTT
260 AACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATAC-TCAGAAAAAATATATAATTT
1933 AACGCCTAAAAGATT
1 AACGCCTAAAAGATT
Statistics
Matches: 1486, Mismatches: 126, Indels: 20
0.91 0.08 0.01
Matches are distributed among these distances:
320 76 0.05
321 850 0.57
322 525 0.35
323 34 0.02
324 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (321 bp):
AACGCCTAAAAGATTGACGGGCTTTTCACACTTCTAATATCATTTTGCATTTTTTTCCGAATTTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTTAAAAAAATCGTTAAATCGAATTTGGCTG
GAATTTGGTTCGATGAATATAGGCATTTCAAGGAGTCTTCACGCCAAAAATCATGCAAAACTGAG
GCAGGGCCCCAGAACTCGTTTTTTGCCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
ACTGACCCAAAAATTTTTTTCTTAATTTTCTACCACAATACTCAGAAAAAATATATAATTT
Done.