Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004029.1 Corchorus capsularis cultivar CVL-1 contig04037, 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, 671

Length: 1119
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:64 original size:37 final size:37

Alignment explanation


    Indices: 5--118  Score: 124
    Period size: 37  Copynumber: 3.0  Consensus size: 37

          1 AGAC

                       *                          
          5 ACCTAAACAGGGACCTTAAACAAGGATTTGAT-AAGAA
          1 ACCTAAACAGGAACCTTAAACAAGGATTTGATGAA-AA

             *           *   *                   *
         42 ATCTAAACAGGAATCTTGAACAA-GATTTTGATGAAAC
          1 ACCTAAACAGGAACCTTAAACAAGGA-TTTGATGAAAA

                                *                  
         79 ACCTAAACAGGAACCTTAAATAAGGATTTGTCATGAAAA
          1 ACCTAAACAGGAACCTTAAACAAGGATTTG--ATGAAAA

             
        118 A
          1 A

        119 GGATTTTGAG


Statistics
Matches: 62,  Mismatches: 10, Indels: 8
        0.77            0.12        0.10

Matches are distributed among these distances:
  36    2  0.03
  37   49  0.79
  38    4  0.06
  39    7  0.11

ACGTcount: A:0.46, C:0.15, G:0.17, T:0.23


Consensus pattern (37 bp):   
ACCTAAACAGGAACCTTAAACAAGGATTTGATGAAAA

Found at i:971 original size:87 final size:87

Alignment explanation


    Indices: 825--992  Score: 246
    Period size: 87  Copynumber: 1.9  Consensus size: 87

        815 TGATTGATGC

                       *         *     *                        *            
        825 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGTTTCTGGATCAG
          1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG

                                  
        890 CTTCTCACCTCAAGAATCATTT
         66 CTTCTCACCTCAAGAATCATTT

                  *                                * *                       
        912 CCCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCTAGCTCAATTGATATTTCTGGATCAG
          1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG

            *      *  *     
        977 TTTCTCATCTTAAGAA
         66 CTTCTCACCTCAAGAA

        993 ATTTTCAAAC


Statistics
Matches: 71,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  87   71  1.00

ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38


Consensus pattern (87 bp):   
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATATTTCTGGATCAG
CTTCTCACCTCAAGAATCATTT
Done.