Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006048.1 Corchorus olitorius cultivar O-4 contig06073, 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, 732
Length: 1220
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Found at i:683 original size:208 final size:201
Alignment explanation
Indices: 296--709 Score: 693
Period size: 208 Copynumber: 2.0 Consensus size: 201
286 GCTTAATAAC
*
296 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATAA
*
361 GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTAGTTG
66 GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAATAGTTG
426 ATTTATTAAATCAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATCAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
491 CGACTTA
195 CGACTTA
498 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATAA
* *
563 GATACAACACATTACTATTATATATATATATATAACTATACCAAAAAAAATTAGTTGAACATTAA
66 GATACAACACA-T--TATTAT-TATATATA-A-AACTATACAAAAAAAAAGTAGTTGAACATTAA
* * *
628 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
125 TAGTTGATTTATTAAATCAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTA
*
693 AGATCCGATTTA
190 AGATCCGACTTA
705 TTTAT
1 TTTAT
710 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
202 75 0.38
203 1 0.01
205 6 0.03
206 8 0.04
207 18 0.09
208 90 0.45
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATAA
GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAATAGTTG
ATTTATTAAATCAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GACTTA
Done.