Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001959.1 Corchorus capsularis cultivar CVL-1 contig01961, 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, 907

Length: 1512
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35


Found at i:675 original size:324 final size:322

Alignment explanation


    Indices: 14--938  Score: 1203
    Period size: 323  Copynumber: 2.9  Consensus size: 322

          4 TTAGTGCATA

                                                                             
         14 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT
          1 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT

                                                  *                 *        
         79 ATATAATTCAACGCCAAAAATATTGACAGGCTTTTCACACTTCTAATATCGTTTTTTCATTTTTT
         66 ATATAATTCAACGCCAAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT

             * *                        *      *        ** *   *             
        144 TTCAAATTAATTTCTAATTAAATCGAAATAAGATTCAAATGCTCTTATAAACAAATCCTTATATC
        131 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAAATGCTCGAAAAAATAAATCCTTATATC

                      * *                                *                   
        209 CAATATGGCTAACATTTGGCTT-GATGAATATAGATATTTTCAAGAATTCTTTGTGCCAAAAATC
        196 CAATATGGCTGAGATTT-GCTTCGATGAATATAGATA-TTTCAAGGATTCTTTGTGCCAAAAATC

                         *                            *                   * 
        273 ATGCAAAATTGAGTAAGGGCTCCGGAACGCGTTTTTAGCCAAGAACCGTGATGGTTAGAACATG
        259 ATGCAAAATTGAGCAAGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGAACACG

                                                                   *         
        337 ATTTCGGCTAAAAACTGACCCGAATATTTTTTTTCTCAATTTTTTGCCACAATACACAGAAAAAA
          1 ATTTCGGCTAAAAACTGACCCGAA-ATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA

                 *      *                **                                  
        402 TATATTATTCAATGCCAAAAATATTGACAAACTTTTCACGCTTCTAATATCG-TTTTCCATTTTT
         65 TATATAATTCAACGCCAAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTT

                   *                *             *                          
        466 TTCCGAACTAATTTCTAATTAAATTGAAACAAGATTGACATGCTCGAAAAAAATAAATCCTTATA
        130 TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAAATGCTCG-AAAAAATAAATCCTTATA

                *   *                                *               *       
        531 TCCACTATTGCTGAGATTTGCTTCGATGAATATAGATATTTGAAGGATTCTTTGTGCAAAAAATC
        194 TCCAATATGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAGGATTCTTTGTGCCAAAAATC

                           *                                          *     
        596 ATGCAAAATTGAGCAGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACG
        259 ATGCAAAATTGAGCAAGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGAACACG

                *                *    ** *            *   **                 
        660 ATTTTGGCATAAAAACTGACCTGAAAAGTATTTTCTCAATTTATTGTTACAATACTCA-AAAAAA
          1 ATTTCGGC-TAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA

                                 *    ***                               **   
        724 TATATAATTCAACGCCAAAAAGATTGGTGGGCTTTTCACGCTTCTAATAT-GTTTTTTCTTTTTT
         65 TATATAATTCAACGCCAAAAATATTGACAGGCTTTTCACGCTTCTAATATCG-TTTTTC-CATTT

                                                    *       *                
        788 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCT-GGAAAAATCAAATCCTTA
        128 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAAATGCTCGAAAAAAT-AAATCCTTA

               **       *  *      *          *    *    *  *  *      *    *  *
        852 TATTTAATATGGTTGGGATTTGGTTCGATGAATGTAGAAATTTTAAAGAGTCTTTGCGCCATAAT
        192 TATCCAATATGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAGGATTCTTTGTGCCAAAAA

                    *             
        917 TCATGCAATATTGAGCAAGGGC
        257 TCATGCAAAATTGAGCAAGGGC

        939 CTAAAACTGA


Statistics
Matches: 523,  Mismatches: 71, Indels: 16
        0.86            0.12        0.03

Matches are distributed among these distances:
 321    1  0.00
 322   54  0.10
 323  277  0.53
 324  191  0.37

ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Consensus pattern (322 bp):   
ATTTCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAT
ATATAATTCAACGCCAAAAATATTGACAGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
TCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAAATGCTCGAAAAAATAAATCCTTATATC
CAATATGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAGGATTCTTTGTGCCAAAAATCAT
GCAAAATTGAGCAAGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGAACACG
Done.