Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020472.1 Corchorus olitorius cultivar O-4 contig20505, 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: 30893
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:20734 original size:28 final size:27

Alignment explanation


    Indices: 20680--20751  Score: 94
    Period size: 27  Copynumber: 2.7  Consensus size: 27

      20670 TTAGAAAAAA

                                    *  
      20680 TTTGCG-TT-AAAAAAATCTCTTATTT
          1 TTTGCGTTTAAAAAAAATCTCTTAATT

                                        
      20705 TTTGCGTTTAAAAAAAATCTCTCTAATT
          1 TTTGCGTTTAAAAAAAATCTCT-TAATT

                          *    
      20733 TTTGCGTTTTAAAAGAAAT
          1 TTTGCG-TTTAAAAAAAAT

      20752 TTTCTCTTAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  25    6  0.15
  26    2  0.05
  27   12  0.29
  28   10  0.24
  29   11  0.27

ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44


Consensus pattern (27 bp):   
TTTGCGTTTAAAAAAAATCTCTTAATT

Found at i:26633 original size:18 final size:18

Alignment explanation


    Indices: 26607--26646  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      26597 TATTGACTTA

                *             
      26607 CTTTAATAAATATGATTG
          1 CTTTGATAAATATGATTG

                     *        
      26625 CTTTGATAACTATGATTG
          1 CTTTGATAAATATGATTG

                 
      26643 -TTTG
          1 CTTTG

      26647 TGATGATTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17    4  0.20
  18   16  0.80

ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47


Consensus pattern (18 bp):   
CTTTGATAAATATGATTG
Done.