Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000463.1 Corchorus olitorius cultivar O-4 contig00463, 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, 624

Length: 1041
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34


Found at i:880 original size:19 final size:19

Alignment explanation


    Indices: 856--927  Score: 51
    Period size: 19  Copynumber: 3.7  Consensus size: 19

        846 AATCCTAAAG

                               
        856 CCCAAAGCAAAAATCTAGA
          1 CCCAAAGCAAAAATCTAGA

                       * *      
        875 CCCAAATG-AATAGTCTAGA
          1 CCCAAA-GCAAAAATCTAGA

                                   
        894 GCCC-AAGTCAAAGAAT-TAGAA
          1 -CCCAAAG-CAAA-AATCTAG-A

                  *      
        915 CCCAAATCAAAAA
          1 CCCAAAGCAAAAA

        928 ACCCAAGCAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 14
        0.68            0.08        0.23

Matches are distributed among these distances:
  18    1  0.02
  19   19  0.46
  20   16  0.39
  21    5  0.12

ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14


Consensus pattern (19 bp):   
CCCAAAGCAAAAATCTAGA

Found at i:880 original size:39 final size:40

Alignment explanation


    Indices: 836--921  Score: 99
    Period size: 39  Copynumber: 2.2  Consensus size: 40

        826 AATCCAAAAG

                                                       
        836 CCCAAAT-AATAATCCTAAAGCCCAAAG-CAAA-AATCTAG-A
          1 CCCAAATGAATAAT-CTAAAGCCC-AAGTCAAAGAAT-TAGAA

                        *    *                      
        875 CCCAAATGAATAGTCTAGAGCCCAAGTCAAAGAATTAGAA
          1 CCCAAATGAATAATCTAAAGCCCAAGTCAAAGAATTAGAA

                   
        915 CCCAAAT
          1 CCCAAAT

        922 CAAAAAACCC


Statistics
Matches: 41,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  38    3  0.07
  39   22  0.54
  40   16  0.39

ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16


Consensus pattern (40 bp):   
CCCAAATGAATAATCTAAAGCCCAAGTCAAAGAATTAGAA

Done.