Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021578.1 Corchorus olitorius cultivar O-4 contig21611, 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: 3034
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Found at i:1334 original size:57 final size:58
Alignment explanation
Indices: 1266--1379 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
1256 ATTAATCAAA
*
1266 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
* * * *
1323 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC
1380 ATGATGTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 13 0.25
58 38 0.75
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:2943 original size:203 final size:202
Alignment explanation
Indices: 2568--3034 Score: 864
Period size: 203 Copynumber: 2.3 Consensus size: 202
2558 TTAATAACTT
2568 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
* *
2633 ACATTATTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTA
66 ACATTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTAGTTGATTTATTA
2698 AATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTAT
131 AATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTAT
2763 TTATCAA
196 TTATCAA
*
2770 TGGTAAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
* *
2835 ACATTACTATTATATATATAGAACTATAC-CAAAAAAATTAGTTGAACATTAGTAGTTGATTTAT
66 ACATTACTATTATATATA-A-AACTATACAAAAAAAAAGTAGTTGAACATTAGTAGTTGATTTAT
2899 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
129 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
2964 ATTTATCAA
194 ATTTATCAA
2973 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATAC
Statistics
Matches: 257, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
202 81 0.32
203 168 0.65
204 8 0.03
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (202 bp):
TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
ACATTACTATTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTAGTTGATTTATTA
AATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTAT
TTATCAA
Done.