Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011978.1 Corchorus capsularis cultivar CVL-1 contig11999, 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, 645

Length: 1075
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32


Found at i:673 original size:330 final size:330

Alignment explanation


    Indices: 1--994  Score: 1341
    Period size: 330  Copynumber: 3.0  Consensus size: 330

                         *      **                     *                     
          1 AAATCAAATCCTTTAATCCACCGTGGCTGAGATTTTGTTAGATAAATATAGATATTAT-AATGAG
          1 AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATT-TCAATGAG

                                *                   *                        
         65 ACTTGGCG-CAAAAATCAAGTAAAACAGAGCCGGTG-CCCTTGAACGCGTTTTTAGTCAAAAACC
         65 ACTTGGCGCCAAAAATCAAGCAAAACAGAGCCGGTGCCCCGT-AACGC--TTTTAGTCAAAAACC

                        *****       *                *              *       *
        128 GTGATGGTTAGTGTGTAATTTCGGGTAAAATTTTGCAAAAATTTGACCCGAAAATTGTCTCCTCT
        127 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATTGACCCGAAAATTTTCTCCT-A

             *          *       *                                      *     
        193 ATTTTTAGGCCAAAATACTGAAAAAAAATATATAACTCAACGCCAAAAAAATTGAAGGGTTTCTG
        191 AATTTTAGGCCACAATACT-CAAAAAAATATATAACTCAACGCCAAAAAAATTGAAGGGCTTCTG

                           *                                          *      
        258 ACATTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAAACGGATT
        255 ACATTTCTAATATC-ATTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCGGATT

              *         
        323 GAAATGCTTGTA
        319 GAGATGCTTGTA

                                                           *                 
        335 AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATGTAGATATTTCAATGAGA
          1 AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAATGAGA

                                                                             
        400 CTTGGCGCCAAAAATCAAGCAAAACAGAGCCGGTGCCCCGTAACGCTTTTAGTCAAAAACCGTGA
         66 CTTGGCGCCAAAAATCAAGCAAAACAGAGCCGGTGCCCCGTAACGCTTTTAGTCAAAAACCGTGA

                                    *       *           *                    
        465 TGGTTAGTACACGATTTCGGCTAACATTTTGAAAAAAAATTGACTCGAAAATTTTCTCCTAAATT
        131 TGGTTAGTACACGATTTCGGCTAAAATTTTG-CAAAAAATTGACCCGAAAATTTTCTCCTAAATT

              *                                           *  *               
        530 TTCGGCCACAATACTCAAAAAAATATATAACTCAACGCCAAAAAAACTGCA-GGCTTCTGACATT
        195 TTAGGCCACAATACTCAAAAAAATATATAACTCAACGCCAAAAAAATTGAAGGGCTTCTGACATT

                                                 * *                         
        594 TCTAATATCATTTTCCTATTTTTTTCCAAATTAATTTATGATTAAATCGAAACCGGATTGAGATG
        260 TCTAATATCATTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCGGATTGAGATG

                  
        659 CTTGTA
        325 CTTGTA

                            *  *      **                                     
        665 AAATCAAATCCTTAAAACCTATGTGGGAGAGATTTTGTTAGATGAATATAGATATTTCAATGAGA
          1 AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAATGAGA

             *                      *    *           *     *        *     *  
        730 CCTGGCGCCAAAAATCAAGCAAAATAGAGTCGGTGCCCCGGAACACGTTTTTAGT-TAAAACTGT
         66 CTTGGCGCCAAAAATCAAGCAAAACAGAGCCGGTGCCCC-GTA-ACGCTTTTAGTCAAAAACCGT

                *                 *                   *            *     *   
        794 GATGTTTAGTACACGATTTCGGTTAAAATTTTGCAAAAAATTAACCCGAAAATTTGCTCCTCAAT
        129 GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATTGACCCGAAAATTTTCTCCTAAAT

               *    *              **        * *                             
        859 TTTTGGCCTCAATACTCATTAAAGTATATATAAGTAAACGCCAAAAAAATTGAAGGGCTTCTGAC
        194 TTTAGGCCACAATACTCA--AAAAAATATATAACTCAACGCCAAAAAAATTGAAGGGCTTCTGAC

                                                                *            
        924 ATTTCTAATATCATTTTTCCTAGTTTTTTTCCAAATTAATTTCTAATTAAATTGAAACCGGATTG
        257 ATTTCTAATATCA-TTTTCCTA-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCGGATTG

                  
        989 AGATGC
        320 AGATGC

        995 CTCTGTTTTT


Statistics
Matches: 587,  Mismatches: 62, Indels: 21
        0.88            0.09        0.03

Matches are distributed among these distances:
 330  196  0.33
 331   60  0.10
 332   71  0.12
 333   83  0.14
 334   97  0.17
 335   76  0.13
 336    4  0.01

ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32


Consensus pattern (330 bp):   
AAATCAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAATGAGA
CTTGGCGCCAAAAATCAAGCAAAACAGAGCCGGTGCCCCGTAACGCTTTTAGTCAAAAACCGTGA
TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATTGACCCGAAAATTTTCTCCTAAATTT
TAGGCCACAATACTCAAAAAAATATATAACTCAACGCCAAAAAAATTGAAGGGCTTCTGACATTT
CTAATATCATTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGC
TTGTA
Done.