Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008287.1 Corchorus olitorius cultivar O-4 contig08314, 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, 720
Length: 1200
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Found at i:562 original size:203 final size:202
Alignment explanation
Indices: 200--609 Score: 734
Period size: 203 Copynumber: 2.0 Consensus size: 202
190 GCTTAATAAC
200 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATA
1 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATA
* *
265 AGATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
66 AGATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAATAGTTGAACATTAGTGGTT
330 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGAT
395 CCGATTT-
195 CCGATTTA
*
402 TTTATCAATGGTGAATGTTATT-AATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATA
*
466 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATAGTTTAACATTAGTGG
66 AGATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAATAGTTGAACATTAGTGG
*
531 TTGGTTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
129 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
596 TCCGATTTA
194 TCCGATTTA
605 TTTAT
1 TTTAT
610 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
201 67 0.34
202 35 0.17
203 98 0.49
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAAATTTTTTAAGTCTAAGATTACTAACAAAGTTATAGTGAATA
AGATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAATAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CGATTTA
Found at i:781 original size:39 final size:40
Alignment explanation
Indices: 722--802 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
712 ATACCTTAGA
* *
722 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
*
761 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
801 AT
1 AT
803 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Done.