Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015233.1 Corchorus olitorius cultivar O-4 contig15266, 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: 2069
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Found at i:654 original size:36 final size:36
Alignment explanation
Indices: 607--676 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
597 TTCAATAACC
*
607 TTACATCTTTTG-AGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTA-ATTTTGATTATCATATTTCTTA
*
643 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
677 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1557 original size:202 final size:201
Alignment explanation
Indices: 1192--1599 Score: 694
Period size: 200 Copynumber: 2.0 Consensus size: 201
1182 GCTTAATAAC
* *
1192 TTTATCAATGGTGAATGTTATTAATTTTTTAAATCTAAGATCACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATAGTGAATGTTATTAATTTTTTAAATCTAAGATCACTAACAAAGTTGTACTGAATAA
*
1257 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
*
1322 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATT-TCAAA-ATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
*
1385 TGATTTA
195 CGATTTA
* *
1392 TTTATCAATAGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTACTGAATAA
1 TTTATCAATAGTGAATGTTATTAATTTTTTAAATCTAAGATCACTAACAAAGTTGTACTGAATAA
* *
1457 GATACAATACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
1522 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
1587 CCGATTTA
194 CCGATTTA
1595 TTTAT
1 TTTAT
1600 TATTAAGGAA
Statistics
Matches: 195, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
200 85 0.44
201 1 0.01
202 83 0.43
203 21 0.11
204 5 0.03
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (201 bp):
TTTATCAATAGTGAATGTTATTAATTTTTTAAATCTAAGATCACTAACAAAGTTGTACTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Done.