Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021096.1 Corchorus olitorius cultivar O-4 contig21129, 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: 7890
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Found at i:3594 original size:204 final size:201
Alignment explanation
Indices: 3210--3614 Score: 740
Period size: 202 Copynumber: 2.0 Consensus size: 201
3200 GCTTAATAAC
3210 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
3275 GATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTTGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATACAAAAAAAAAGTTGTTGAACATTAGTGGTTG
3340 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
3405 CGATTTA
195 CGATTTA
3412 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
3477 GATACAACACATTACTATTATATATATAGAACTATAC-CAAAAAAATTTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTATATATAT--AACTATACAAAAAAAAAGTT-GTTGAACATTAGTGG
3541 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
3606 TCCGATTTA
193 TCCGATTTA
3615 AGGAAACAAT
Statistics
Matches: 197, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
202 91 0.46
203 22 0.11
204 84 0.43
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATACAAAAAAAAAGTTGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:3776 original size:39 final size:40
Alignment explanation
Indices: 3720--3800 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
3710 ATACCTAAGA
* *
3720 ATTTAATTAATGCAAGTATTTCGGTTATTATA-GTATTAC
1 ATTTAATTAATGCAAGTATTTCAGTTATTATATATATTAC
* *
3759 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGCAAGTATTTCAGTTATTATATATATTAC
3799 AT
1 AT
3801 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGCAAGTATTTCAGTTATTATATATATTAC
Done.