Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007491.1 Corchorus capsularis cultivar CVL-1 contig07512, 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: 11602
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32


Found at i:460 original size:113 final size:112

Alignment explanation


    Indices: 242--456  Score: 290
    Period size: 113  Copynumber: 1.9  Consensus size: 112

        232 GATAAGCTGT

                                     **                      *               
        242 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGTTAGAGAAGTAATCTTTTTCGTCT
          1 GTGGAATTACTAAAAGATCCCTACCAAGGATTAATGATGAGTTAGAGAACTAATCTTTTTCGTCT

                                                           
        307 TTACCTACCTGGCAGATTACTTAAATGTCCTAAACTTTAATAGAGTA
         66 TTACCTACCTGGCAGATTACTTAAATGTCCTAAACTTTAATAGAGTA

                                         *  ** **          *    *            
        354 GTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAACTTAT-TTTTCTCGT
          1 GTGGAATTACTAAAAGATCCCTACCAAGGATTAATGAT-GAGTTAGAGAACTAATCTTTT-TCGT

                *     *                             
        418 CTTTTCCTACTTGGCAGATTACTTAAATGTCCT-AACTTT
         64 CTTTACCTACCTGGCAGATTACTTAAATGTCCTAAACTTT

        457 TAATTCTTGA


Statistics
Matches: 89,  Mismatches: 12, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
 112   41  0.46
 113   48  0.54

ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36


Consensus pattern (112 bp):   
GTGGAATTACTAAAAGATCCCTACCAAGGATTAATGATGAGTTAGAGAACTAATCTTTTTCGTCT
TTACCTACCTGGCAGATTACTTAAATGTCCTAAACTTTAATAGAGTA

Found at i:631 original size:166 final size:167

Alignment explanation


    Indices: 340--670  Score: 425
    Period size: 166  Copynumber: 2.0  Consensus size: 167

        330 AATGTCCTAA

                *                  *           *       *   * **     *    *   
        340 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAAC
          1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC

             * *             *                                               
        405 TTATTTTTCTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGA-GA
         66 TAAATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGACG-

                       *   *                      
        469 GGATTAAATAAGTAATCTTTTTGATCATTTCTCAATGG
        130 GGATTAAATAACTAAACTTTTTGATCATTTCTCAATGG

                                        *        *                           
        507 ACTTGAATAGAGTAGTGGAATTAATAAAGGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAAC
          1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC

                                                           ***    *          
        571 TAACATTTT-TCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTCTTTTTTTATTCTTGACG
         66 TAA-ATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGACG

                                   *      *     
        635 GGATTAAATAACTAAACTTTTTGGTCATTTTTCAAT
        130 GGATTAAATAACTAAACTTTTTGATCATTTCTCAAT

        671 TGACAAATGA


Statistics
Matches: 140,  Mismatches: 22, Indels: 5
        0.84            0.13        0.03

Matches are distributed among these distances:
 166   92  0.66
 167   48  0.34

ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39


Consensus pattern (167 bp):   
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGCTAGAGAAC
TAAATTTTCTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTAATTCTTGACGG
GATTAAATAACTAAACTTTTTGATCATTTCTCAATGG
Done.