Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010920.1 Corchorus capsularis cultivar CVL-1 contig10941, 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: 18515
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:3629 original size:29 final size:30

Alignment explanation


    Indices: 3580--3636  Score: 89
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       3570 CATACATGAA

                                 *        
       3580 CAAACTTGGACATTACCTAGTCTTACATTG
          1 CAAACTTGGACATTACCTAGTATTACATTG

                    *                   
       3610 CAAACTTGTACA-TACCTAGTATTACAT
          1 CAAACTTGGACATTACCTAGTATTACAT

       3637 CTCATGTCGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   14  0.56
  30   11  0.44

ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33


Consensus pattern (30 bp):   
CAAACTTGGACATTACCTAGTATTACATTG

Found at i:8898 original size:23 final size:23

Alignment explanation


    Indices: 8869--8953  Score: 73
    Period size: 23  Copynumber: 3.6  Consensus size: 23

       8859 GTTTTTCCGT

                   *               
       8869 TTTTTCTTTTAAAAAAAATTGCG
          1 TTTTTCTATTAAAAAAAATTGCG

                    **              
       8892 TTTTTCTAAAAAAAAAAATTAG-G
          1 TTTTTCTATTAAAAAAAATT-GCG

            *   * *                  
       8915 GTTTGCGATTAAAAAAAATTTTGCG
          1 TTTTTCTATTAAAAAAAA--TTGCG

                   *      
       8940 TTTTTCTCTTAAAA
          1 TTTTTCTATTAAAA

       8954 TTTTTTTTAT


Statistics
Matches: 46,  Mismatches: 12, Indels: 6
        0.72            0.19        0.09

Matches are distributed among these distances:
  23   31  0.67
  24    2  0.04
  25   13  0.28

ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42


Consensus pattern (23 bp):   
TTTTTCTATTAAAAAAAATTGCG

Found at i:15793 original size:33 final size:33

Alignment explanation


    Indices: 15710--15833  Score: 135
    Period size: 33  Copynumber: 3.7  Consensus size: 33

      15700 CCGCGCAACA

                                *              
      15710 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACACGACATGGACATGT

                       *                      
      15745 CCGGCCATC-ATCGGCCACACGACATGGACATGT
          1 CCGGCCA-CAACCGGCCACACGACATGGACATGT

                 *           *          *    *
      15778 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACACGACAT-GGACATGT

                              *    
      15811 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACACGAC

      15834 CCTTTGTCTA


Statistics
Matches: 76,  Mismatches: 10, Indels: 8
        0.81            0.11        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   66  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.24, C:0.41, G:0.26, T:0.09


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACACGACATGGACATGT
Done.