Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019206.1 Corchorus olitorius cultivar O-4 contig19239, 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: 17824
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:116 original size:29 final size:28

Alignment explanation


    Indices: 77--132  Score: 94
    Period size: 29  Copynumber: 2.0  Consensus size: 28

         67 GTTATTGCAC

                  *                      
         77 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
          1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT

                                       
        106 GTTCTTGAGCGTTCTTGAAATTAGAAA
          1 GTTCTTGAGCGTTCTTGAAATTAGAAA

        133 GTTTGAAGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28    8  0.31
  29   18  0.69

ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39


Consensus pattern (28 bp):   
GTTCTTGAGCGTTCTTGAAATTAGAAAT

Found at i:10857 original size:16 final size:15

Alignment explanation


    Indices: 10836--10865  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

      10826 TAAGACTAGA

                            
      10836 CCCGGCCCGAATCCAG
          1 CCCGGCCCG-ATCCAG

                          
      10852 CCCGGCCCGATCCA
          1 CCCGGCCCGATCCA

      10866 TGAACAGGTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.17, C:0.53, G:0.23, T:0.07


Consensus pattern (15 bp):   
CCCGGCCCGATCCAG

Found at i:15632 original size:88 final size:88

Alignment explanation


    Indices: 15483--15660  Score: 311
    Period size: 88  Copynumber: 2.0  Consensus size: 88

      15473 GAATCCCGTC

                                                                             
      15483 CAAACCGATCTAACAACAGAAAATCAAGTTATACCATAAGGTCAAAGTACTCAATTAATAGATAA
          1 CAAACCGATCTAACAACAGAAAATCAAGTTATACCATAAGGTCAAAGTACTCAATTAATAGATAA

                           *       
      15548 GGGGACTAAAGAGTATAGACATA
         66 GGGGACTAAAGAGTAGAGACATA

                       *                     *      *                        
      15571 CAAACCGATCTGACAACAGAAAATCAAGTTATATCATAAGTTCAAAGTACTCAATTAATAGATAA
          1 CAAACCGATCTAACAACAGAAAATCAAGTTATACCATAAGGTCAAAGTACTCAATTAATAGATAA

                    *              
      15636 GGGGACTAGAGAGTAGAGACATA
         66 GGGGACTAAAGAGTAGAGACATA

              
      15659 CA
          1 CA

      15661 TATGCACTAG


Statistics
Matches: 85,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  88   85  1.00

ACGTcount: A:0.47, C:0.16, G:0.17, T:0.21


Consensus pattern (88 bp):   
CAAACCGATCTAACAACAGAAAATCAAGTTATACCATAAGGTCAAAGTACTCAATTAATAGATAA
GGGGACTAAAGAGTAGAGACATA
Done.