Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014305.1 Corchorus olitorius cultivar O-4 contig14338, 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: 3484
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:794 original size:333 final size:332

Alignment explanation


    Indices: 72--836  Score: 914
    Period size: 332  Copynumber: 2.3  Consensus size: 332

         62 GGGCATTGGC

                       *                                                     
         72 TAAATATCTATTTTCATCTGACCAAATCTCAG-ACACATTGGATTTAAGGATTTATTTTTACGAG
          1 TAAATATCTATATTCATCTGACCAAATCTCAGCA-ACATTGGATTTAA-GATTTATTTTTACGAG

                                    *                            *     *     
        136 CATCTGAATATTGTTTCGATTTAAGTAGAAATTAATTCAGAAAAAAATAAAAATAAAACGATAAT
         64 CATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAAAAAGAAAACAATAAT

                                          *        *                    *    
        201 AGAAGCGTCAAAAGCCCTCCAATCTTTTCGGCATTGAATTATATATTTCTTATGAGTATTTTGAC
        129 AGAAGCGTCAAAAGCCCTCCAATCTTTTCGACATTGAATCATATATTTCTTATGAGTATTGTGAC

                            *      *     *     **         *        *         
        266 TAAAAATTGAGGAAAATTATATCGGGTCAGTTTTTGTAAAATTTTATCCGAAATCGTGTAATATA
        194 TAAAAATTGAGGAAAAATATATCAGGTCAATTTTTACAAAATTTTAGCCGAAATCATGTAATATA

                * *            *       * *   *                **           * 
        331 CATCTCGGTTTTTGGCTAAGAACGAGTTCTTGGTCCCCGCTCAGTTTTGCTTGATTTTTGGCGTC
        259 CATCACAGTTTTTGGCTAAAAACGAGTGCCTGGGCCCCGCTCAGTTTTGCAAGATTTTTGGCGCC

                     
        396 AAGACTCCT
        324 AAGACTCCT

                                *             ***                        *   
        405 TAAAGTATCTATATTCATCTAACCAAATCTCAGCGTGATTGGATTTAATGATTTATTTTTATGAG
          1 TAAA-TATCTATATTCATCTGACCAAATCTCAGCAACATTGGATTTAA-GATTTATTTTTACGAG

                *    *                              *         *             *
        470 CATCAGAATGTTGTTTCGATTCT-ATTAGAAATTAATTC-TAAAAAAA-AGAAAGAAAACAATAC
         64 CATCTGAATATTGTTTCGATT-TAATTAGAAATTAATTCAGAAAAAAATAAAAAGAAAACAATAA

                     *    *    *         *   *  *                    *       
        532 TAGAAGCGTGAAAATCCCTTCAATCTTTTTGACGTTTAATCATATATTT-TCTATGATTATTGTG
        128 TAGAAGCGTCAAAAGCCCTCCAATCTTTTCGACATTGAATCATATATTTCT-TATGAGTATTGTG

            *                   * * *                                     *  
        596 GCTAAAAATTGAGGAAAAATCTTTTAGGTCAATTTTTACAAAATTTTAGCCGAAATCATGTACTA
        192 ACTAAAAATTGAGGAAAAATATATCAGGTCAATTTTTACAAAATTTTAGCCGAAATCATGTAATA

                *                                                           *
        661 -ATCCTCACAGTTTTTGGCTAAAAACGCA-TGCCTGGGCCCCGACTCAGTTTTGCAAGATTTTTT
        257 TA-CATCACAGTTTTTGGCTAAAAACG-AGTGCCTGGGCCCCG-CTCAGTTTTGCAAGATTTTTG

             *            
        724 GTGCCAAGACTCCT
        319 GCGCCAAGACTCCT

                                                    *                       *
        738 TGAAATATCTATATTCATCTGACCAAATCTCAGCAACATTTGATTTAAGAATTTATTTTTACGAA
          1 T-AAATATCTATATTCATCTGACCAAATCTCAGCAACATTGGATTTAAG-ATTTATTTTTACGAG

            *        *                        
        803 AATCTGAATCTTGTTTCGATTTAATTAGAAATTA
         64 CATCTGAATATTGTTTCGATTTAATTAGAAATTA

        837 TTAGAAGCGT


Statistics
Matches: 363,  Mismatches: 59, Indels: 20
        0.82            0.13        0.05

Matches are distributed among these distances:
 331    2  0.01
 332  149  0.41
 333  123  0.34
 334   88  0.24
 335    1  0.00

ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37


Consensus pattern (332 bp):   
TAAATATCTATATTCATCTGACCAAATCTCAGCAACATTGGATTTAAGATTTATTTTTACGAGCA
TCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAAAAAGAAAACAATAATAG
AAGCGTCAAAAGCCCTCCAATCTTTTCGACATTGAATCATATATTTCTTATGAGTATTGTGACTA
AAAATTGAGGAAAAATATATCAGGTCAATTTTTACAAAATTTTAGCCGAAATCATGTAATATACA
TCACAGTTTTTGGCTAAAAACGAGTGCCTGGGCCCCGCTCAGTTTTGCAAGATTTTTGGCGCCAA
GACTCCT
Done.