Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006826.1 Corchorus olitorius cultivar O-4 contig06851, 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, 661

Length: 1102
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34


Found at i:684 original size:17 final size:17

Alignment explanation


    Indices: 664--697  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        654 AATAAAATCC

                             
        664 ATATTATTATAATTTTT
          1 ATATTATTATAATTTTT

                 *           
        681 ATATTGTTATAATTTTT
          1 ATATTATTATAATTTTT

        698 TAACTAGGAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65


Consensus pattern (17 bp):   
ATATTATTATAATTTTT

Found at i:896 original size:131 final size:131

Alignment explanation


    Indices: 723--975  Score: 386
    Period size: 131  Copynumber: 1.9  Consensus size: 131

        713 TCATTTATCC

                 *        *                 *                                
        723 AAATTTTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAA-TAAATTAGGTAT-A
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAA-TAGGTATAA

                            *                                                
        786 AGGATATAAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATAAT
         65 AGG-TATAAGATTTAAGTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATAAT

                
        851 CAAA
        128 CAAA

                                                       *              *      
        855 AAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAA
          1 AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAATAGGTATAAA

                 *           *                                       
        919 GGTATTAGATTTAAGTACATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGT
         66 GGTATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGT

        976 TTAAACAACG


Statistics
Matches: 111,  Mismatches: 8, Indels: 6
        0.89            0.06        0.05

Matches are distributed among these distances:
 130   37  0.33
 131   49  0.44
 132   25  0.23

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (131 bp):   
AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAATAGGTATAAA
GGTATAAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTATAATCAA
A
Done.