Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009130.1 Corchorus olitorius cultivar O-4 contig09158, 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, 898

Length: 1497
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23


Found at i:289 original size:154 final size:154

Alignment explanation


    Indices: 6--1463  Score: 2050
    Period size: 154  Copynumber: 9.5  Consensus size: 154

          1 CCGAA

                 *                        *             *             *      
          6 AGGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAATGGACTAATCTCATCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                        *  *                                           *     
         71 GATTATAGTTAGTCCCTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTC
         66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                                     
        136 AAAACAG-AACTAATGGGCCTCGAT
        131 AAAAC-GTAACTAATGGGCCTCGAT

                                              *       *   *           *      
        160 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCTCATCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                   **              *  *   *    * *                           
        225 GATTATAACTAGGCCATAAACGACT-TAAAAAAAAACTTTGAGGTTTGCCAAATCGAAGACGATT
         66 GATTATAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT

                         *   *       
        289 CAAAACGT--C-ACT-GTCCTCGAT
        130 CAAAACGTAACTAATGGGCCTCGAT

             *    *                    *               *   *           *     
        310 AAGCCCCAAATAACAAGTGTTCCAAATTAGC-AAAGAACTTCATAGTAGACTAATCTCATCAAAA
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA-AACTTCACAGTGGACTAATCTCACCAAAA

                    **                 *        * *                          
        374 TGATTATAACTAGGCCATAAACAACT-TAAAGAAAAACTTTGAGGTTT-CCAAATCGAAGACGAT
         65 TGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                                 *    
        437 TCAAAACGTAACTAATGGGCCCCGAT
        129 TCAAAACGTAACTAATGGGCCTCGAT

                                                            *       *        
        463 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGTCTAATCTGACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                        *  *                                                 
        528 GATTATAGTTAGTCCGTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
         66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                  *   *         *  *
        593 AAAACGGAACAAATGGGCCTTGAA
        131 AAAACGTAACTAATGGGCCTCGAT

                 *                     *                                     
        617 AGGCCTAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                        *                                                    
        682 GATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
         66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                   * *          *   
        747 AAAACGTTAGTAATGGGCCTTGAT
        131 AAAACGTAACTAATGGGCCTCGAT

                                              *       *   *           *      
        771 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCTCATCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                   **              *  *        *                             
        836 GATTATAACTAGGCCATAAACGACT-TAAAGAAAAAC-TTCGAGGTTTGCCAAATCGAAGACGAT
         66 GATTATAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAGACGAT

                     *                
        899 TCAAAACGTCACTAATGGGCCTCGAT
        129 TCAAAACGTAACTAATGGGCCTCGAT

                  *                    *                            *        
        925 AGGCCCCAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                        *                                                    
        990 GATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
         66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                   *                 
       1055 AAAACGTCACATAATGGGCC-CGAT
        131 AAAACGTAAC-TAATGGGCCTCGAT

                                                                             
       1079 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                                *     *          *     *               *     
       1144 GATTATAGTTAGGCCATAAAAAACT-TAAAGAAAAGCTTTGAGCTTTGCCAAATCGAAGGCGATT
         66 GATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT

                    *                
       1208 CAAAACGTTACTAATGGG---C-AT
        130 CAAAACGTAACTAATGGGCCTCGAT

             *                                            *                  
       1229 ATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

            *  *                                                             
       1294 TATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
         66 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC

                   *           *    
       1359 AAAACGTCACTAATGGGCCCCGAT
        131 AAAACGTAACTAATGGGCCTCGAT

                *                      *                                     
       1383 AGGCACAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
          1 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT

                            
       1448 GATTATAGTTAGGCCA
         66 GATTATAGTTAGGCCA

       1464 CAAAAAAGCT


Statistics
Matches: 1171,  Mismatches: 111, Indels: 44
        0.88            0.08        0.03

Matches are distributed among these distances:
 149   29  0.02
 150  245  0.21
 151    4  0.00
 152    4  0.00
 153  110  0.09
 154  763  0.65
 155   16  0.01

ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23


Consensus pattern (154 bp):   
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
AAAACGTAACTAATGGGCCTCGAT

Done.