Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007152.1 Corchorus olitorius cultivar O-4 contig07177, 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, 745
Length: 1242
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Found at i:144 original size:36 final size:36
Alignment explanation
Indices: 97--166 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
87 TTCAATAACC
*
97 TTACATATTTTGTGATTTTGATTATCATATTTCTTA
1 TTACATATTTTGTAATTTTGATTATCATATTTCTTA
*
133 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATATTTTGTAATTTTGATTATCATATTTCT
167 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATATTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1063 original size:204 final size:199
Alignment explanation
Indices: 686--1095 Score: 703
Period size: 204 Copynumber: 2.0 Consensus size: 199
676 GCTTAATAAC
* *
686 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAT
1 TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
751 GATACAACACATTATTATTATATATAATACTTACCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
66 GATACAACACATTACTATTATATATAAAACTTACCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
* *
816 TTATTAAGTTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCG
881 ATTTA
195 ATTTA
886 TTTATTAATGGTGTAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATTAATGGTG-AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
951 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAATTAGTTGAACATTAGTGGT
65 AGATACAACACATTACTATTATATATA-A-AACT-TACCAAAAAAAGTAGTTGAACATTAGTGGT
*
1016 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTGTAAAAGATATTAAGAT
127 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
1081 CCGATTTA
192 CCGATTTA
1089 TTTATTA
1 TTTATTA
1096 TTAAGGAGAC
Statistics
Matches: 198, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
200 12 0.06
201 76 0.38
202 1 0.01
203 22 0.11
204 87 0.44
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (199 bp):
TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTTACCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGA
TTTA
Done.