Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006794.1 Corchorus capsularis cultivar CVL-1 contig06815, 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: 5993
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32


Found at i:333 original size:159 final size:159

Alignment explanation


    Indices: 5--3340  Score: 4453
    Period size: 159  Copynumber: 21.0  Consensus size: 159

          1 ACAT

                                                                             
          5 GCAATGTTGAGGACTTT--GCTTCAAGGAGAGCTTTG-TTTT-CACAGGGCTGTCCAACAAGCTC
          1 GCAATGTTGAGGA-TTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTC

                *     *   *              *                      *         *  
         66 ATCTGACTCCAACAAAAGACTTTTGAGCAATCGTTGCGC-AAAAATCGCTTCCGGAATGAGCATT
         65 ATCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGAATGAGCCTT

                       *                   
        130 TCGATAAGAACCATGTTTTGCACACAAACGC
        129 TCGATAAGAACGATGTTTTGCACACAAACGC

                                      *                      *            * *
        161 GCAATGTTGAGGATTTGGGCTTCAAGAAGAGCTTTGTTTTTGCACAGGGTTGTCCAACAAGCACT
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                       *    *                   *                            
        226 TCTCACTCCGATACAACACTTTTGAGCACTCGTTGCACAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                                       * 
        291 GATAAGAACGATGTTTTGCACACAAACTC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                   *                                                         
        320 GCAATGTAGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                    *       *                   *                            
        385 TCTCACTCTGACACAACACTTTTGAGCACTCGTTGCAC-AAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                         *               
        449 GATAAGAACGATGATTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  **                  *                                      
        478 GCAATGCAGAGGATTTGGGCTTCAAGAAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                    *        *                 *                             
        543 TCTCACTCTGACACAAGGCTTTTGAGCACTCGTTGTGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                     *  *                
        608 GATAAGAACAATTTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  *     *         *       **                   *   *         
        637 GCAATGCTGAGGGTTTGGGCTTGAAGGAGATTTTTGTTTTTGCACAGGGCTATCCTACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                                                                             
        702 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

             *                  * *    **
        767 GCTAAGAACGATGTTTTGCATAGAAACAT
        131 GATAAGAACGATGTTTTGCACACAAACGC

                *           *           * *                       *  *       
        796 GCAAAGTTGAGGATTTTGGCTTCAAGGATATCTTTGTTTTTGCACAGGGCTGTCAAATAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

               *     *   *   *   *  *                          *         *   
        861 TCTTACTCCAACAAAAGGCTTCTGTGCACTCGTTGCGC-AAAAATCGCTTCCGGAATGAGCATTT
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGAATGAGCCTTT

                      *              *    
        925 CGATAAGAACCATGTTTTGCACACAGACGC
        130 CGATAAGAACGATGTTTTGCACACAAACGC

                 *                                                           
        955 GCAATCTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                 ** *        *           *     *                             
       1020 TCTCAGGCTGACACAAGGCTTTTGAGCACGCGTTGTGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                     *  *                
       1085 GATAAGAACAATTTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  *               *       **                       *         
       1114 GCAATGCTGAGGATTTGGGCTTGAAGGAGATTTTTGTTTTTGCACAGGGCTGTCCTACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                                                                             
       1179 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

             *                  * *    **
       1244 GCTAAGAACGATGTTTTGCATAGAAACAT
        131 GATAAGAACGATGTTTTGCACACAAACGC

                *           **          * *               *       *  *       
       1273 GCAAAGTTGAGGATTTTCGCTTCAAGGATATCTTTGTTTTTGCACAAGGCTGTCAAATAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

               *     *   *   *   *                     *       *         *   
       1338 TCTTACTCCAACAAAAGGCTTCTGAGCACTCGTTGCGC-AAAACTCGCTTCCGGAATGAGCATTT
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGAATGAGCCTTT

                      *              *    
       1402 CGATAAGAACCATGTTTTGCACACAGACGC
        130 CGATAAGAACGATGTTTTGCACACAAACGC

                        *                                    *              *
       1432 GCAATGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGTTGTCCAACAAGCTCT
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                       *    *                   *                            
       1497 TCTCACTCCGATACAACACTTTTGAGCACTCGTTGCACAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                                         
       1562 GATAAGAACGATGTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  **                                                         
       1591 GCAATGCAGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                    *        *                 *                             
       1656 TCTCACTCTGACACAAGGCTTTTGAGCACTCGTTGTGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                     *          *        
       1721 GATAAGAACAATGTTTTGCAAACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  *     *         *                        **                
       1750 GCAATGCTGAGGCTTTGGGCTTGAAGGAGAGCTTTGTTTTTGCACAGTTCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                    *                         * **                           
       1815 TCTCACTCAGACACAAGACTTTTGAGCACTCGTTACAAAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

            **                  * *    **
       1880 TCTAAGAACGATGTTTTGCATAGAAACAT
        131 GATAAGAACGATGTTTTGCACACAAACGC

                 *          *                        *            *  *  *    
       1909 GCAATTTTGAGGATTTTGGCTTCAAGGAGAGCTTTGTTTTTCCACAGGGCTGTCAAATAATCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

               *     *   *   *   *                     *      *         *    
       1974 TCTTACTCCAACAAAAGGCTTCTGAGCACTCGTTGCGCAAAAATTGCTTCCGGAATGAGCATTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                     *                   
       2039 GATAAGAACCATGTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                        *                   *             *                 *
       2068 GCAATGTTGAGGCTTTGGGCTTCAAGGAGAGCATTGTTTTTGCACAAGGCTGTCCAACAAGCTCT
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                       *                       ***                           
       2133 TCTCACTCCGATACAAGACTTTTGAGCACTCGTTGAATAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                                         
       2198 GATAAGAACGATGTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

            *     **                                                         
       2227 ACAATGCAGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

            *    ** *        *           *     *                             
       2292 ACTCAGGCTGACACAAGGCTTTTGAGCACGCGTTGTGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                     *  *                
       2357 GATAAGAACAATTTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  *     *         *       **   *                   *         
       2386 GCAATGCTGAGGGTTTGGGCTTGAAGGAGATTTTTCTTTTTGCACAGGGCTGTCCTACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                                              *                              
       2451 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTTCGCAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

             *                  * *    **
       2516 GCTAAGAACGATGTTTTGCATAGAAACAT
        131 GATAAGAACGATGTTTTGCACACAAACGC

                *           **          * *                       *  *       
       2545 GCAAAGTTGAGGATTTTCGCTTCAAGGATATCTTTGTTTTTGCACAGGGCTGTCAAATAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

               *     *   *   *   *                     *       *         *   
       2610 TCTTACTCCAACAAAAGGCTTCTGAGCACTCGTTGCGC-AAAACTCGCTTCCGGAATGAGCATTT
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGAATGAGCCTTT

                      *              *    
       2674 CGATAAGAACCATGTTTTGCACACAGACGC
        130 CGATAAGAACGATGTTTTGCACACAAACGC

                        *                                    *              *
       2704 GCAATGTTGAGGCTTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGTTGTCCAACAAGCTCT
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                       *    *                   *                            
       2769 TCTCACTCCGATACAACACTTTTGAGCACTCGTTGCACAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                         *               
       2834 GATAAGAACGATGATTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

                  **              *                           *              
       2863 GCAATGCAGAGGATTTGGGCTTGAAGGAGAGCTTTGTTTTTGCACAGGGCAGTCCAACAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                      *  *             *         *                           
       2928 TCTCACTCCGTCATAAGACTTTTGAGCCCTCGTTGCGTAAAAAATGCTTCTGGAATGAGCCTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

             *                  * *    **
       2993 GCTAAGAACGATGTTTTGCATAGAAACAT
        131 GATAAGAACGATGTTTTGCACACAAACGC

                            *           *                      *  *  *       
       3022 GCAATGTTGAGGATTTTGGCTTCAAGGATAGCTTTGTTTTTGCACA-GGCTTTCTAATAAGCTCA
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

               *     *   *   *   *                             *      *  *   
       3086 TCTTACTCCAACAAAAGGCTTCTGAGCACTCGTTGCGC-AAAAATCGCTTCCGGAATGTGCATTT
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGAATGAGCCTTT

             *        *            *      
       3150 CAATAAGAACCATGTTTTGCACAAAAACGC
        130 CGATAAGAACGATGTTTTGCACACAAACGC

            *           *               *                 *                 *
       3180 ACAATGTTGAGGCTTTGGGCTTCAAGGAAAGCTTTGTTTTTGCACAAGGCTGTCCAACAAGCTCT
          1 GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA

                       *      *                 *      *               *     
       3245 TCTCACTCCGATACAAGAGTTTTGAGCACTCGTTGCTCAAAAATTGCTTCTGGAATGAGACTTTC
         66 TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC

                                         
       3310 GATAAGAACGATGTTTTGCACACAAACGC
        131 GATAAGAACGATGTTTTGCACACAAACGC

              
       3339 GC
          1 GC

       3341 GATGCAACTT


Statistics
Matches: 2747,  Mismatches: 418, Indels: 27
        0.86            0.13        0.01

Matches are distributed among these distances:
 155    3  0.00
 156   13  0.00
 157   23  0.01
 158  295  0.11
 159  2386  0.87
 160   27  0.01

ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28


Consensus pattern (159 bp):   
GCAATGTTGAGGATTTGGGCTTCAAGGAGAGCTTTGTTTTTGCACAGGGCTGTCCAACAAGCTCA
TCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAATGAGCCTTTC
GATAAGAACGATGTTTTGCACACAAACGC

Done.