Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010086.1 Corchorus olitorius cultivar O-4 contig10118, 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: 2963
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:481 original size:56 final size:57

Alignment explanation


    Indices: 391--505  Score: 187
    Period size: 56  Copynumber: 2.0  Consensus size: 57

        381 TATCCGTTTC

                            *                     *           *      
        391 CTTTCACACAATAAATGTTATAATAAATCATATCCC-CCTATCTCTACTTCATTATT
          1 CTTTCACACAATAAATATTATAATAAATCATATCCCTCATATCTCTACTTAATTATT

                                         *                           
        447 CTTTCACACAATAAATATTATAATAAATCCTATCCCTCATATCTCTACTTAATTATT
          1 CTTTCACACAATAAATATTATAATAAATCATATCCCTCATATCTCTACTTAATTATT

              
        504 CT
          1 CT

        506 ACAAAATAAA


Statistics
Matches: 54,  Mismatches: 4, Indels: 1
        0.92            0.07        0.02

Matches are distributed among these distances:
  56   34  0.63
  57   20  0.37

ACGTcount: A:0.35, C:0.24, G:0.01, T:0.40


Consensus pattern (57 bp):   
CTTTCACACAATAAATATTATAATAAATCATATCCCTCATATCTCTACTTAATTATT

Found at i:630 original size:42 final size:43

Alignment explanation


    Indices: 571--652  Score: 130
    Period size: 43  Copynumber: 1.9  Consensus size: 43

        561 TAAGGATCAG

                                                       
        571 GATTTGAGTTAAGTA-TTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTTAAGTATTTTCTTAATTTACAAAGAATTTTCTAT

                      *        *          *         
        613 GATTTGAGTTGAGTATTTTTTTAATTTACAGAGAATTTTC
          1 GATTTGAGTTAAGTATTTTCTTAATTTACAAAGAATTTTC

        653 AAGACTTGGC


Statistics
Matches: 36,  Mismatches: 3, Indels: 1
        0.90            0.08        0.03

Matches are distributed among these distances:
  42   14  0.39
  43   22  0.61

ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49


Consensus pattern (43 bp):   
GATTTGAGTTAAGTATTTTCTTAATTTACAAAGAATTTTCTAT

Done.