Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013001.1 Corchorus capsularis cultivar CVL-1 contig13022, 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: 2028
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34


Found at i:453 original size:35 final size:34

Alignment explanation


    Indices: 16--1251  Score: 1042
    Period size: 35  Copynumber: 35.4  Consensus size: 34

          6 TTACTAGAGG

                            *            *     *
         16 TCAGAGTTGATCTCATATCAAGAAGTTTTTAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                            *                  *
         51 TCAGAGTTGATCTCATATCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                                               *
         86 TCAGAGTTGATCTCATTTCTAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                         *                     *
        121 TCAGAGTTGATCTAATTTCATGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTCA-GAAGTTTTCA-ACGA

                             *                 *
        156 TCAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                             *                 *
        191 TCAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                                           *   *
        226 TCAGAGTTGATCTCATTTCAAGAAGTTTTCTGA-GT
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTC-AACGA

                             *                 *
        261 TCAGAGTTGATCTCATTCCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                                               *
        296 TCAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                             *       *         *
        331 TCAGAGTTGATCTCATTCCAAGAAGCTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

             *               *              * *
        366 TTAGAGTTGATCTCATTCCAAGAAGTTTTCAAAGG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCAACGA

                                               *
        401 TCAGAGTTGATCTCATTTCAAGAAGTTTTCAGA-GG
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCA-ACGA

                                  *             
        436 TCAGAGTTGATCTCATTTCCAGTA-TTTTCCAACGA
          1 TCAGAGTTGATCTCATTT-CAGAAGTTTT-CAACGA

                        *         * *   *      
        471 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         * *   *      
        506 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *      *               
        541 TCAGAGTTGATCACATGTTTAGAAGTTTTCAACGA
          1 TCAGAGTTGATCTCAT-TTCAGAAGTTTTCAACGA

                        *         *     *    * 
        576 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACTA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         * *   *      
        611 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *               *      
        646 TCAGAGTTGATCACATGTTCAGAAGTTTCCAACGA
          1 TCAGAGTTGATCTCAT-TTCAGAAGTTTTCAACGA

                        *         * *   *      
        681 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         * *   *      
        716 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *                      
        751 TCAGAGTTGATCACATGTTCAGAAGTTTTCAACGA
          1 TCAGAGTTGATCTCAT-TTCAGAAGTTTTCAACGA

                        *         *     *    * 
        786 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACTA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         * *   *      
        821 TCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *               *      
        856 TCAGAGTTGATCACATGTTCAGAAGTTTCCAACGA
          1 TCAGAGTTGATCTCAT-TTCAGAAGTTTTCAACGA

                        *         * *   *   *  
        891 TCAGAGTTGATCGCATTTTCAGTACTTTCCAATGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *               *      
        926 TCAGAGTTGATCACATGTTCAGAAGTTTCCAACGA
          1 TCAGAGTTGATCTCAT-TTCAGAAGTTTTCAACGA

                        *         *     *      
        961 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         *     *    * 
        996 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         *             
       1031 TCAGA-TTGATCGCATTTTCAGTA-TTTTGCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTT-CAACGA

                        *         *     *      
       1065 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         *     *      
       1100 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         *     *      
       1135 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                        *         *     * *  * 
       1170 TCAGAGTTGATCACATTTTCAGTAGTTTCCTACCA
          1 TCAGAGTTGATCTCA-TTTCAGAAGTTTTCAACGA

                  *                 *   * * *  
       1205 TCAGAGGTGATCTCATTTCAAGAAATTTCCGATGA
          1 TCAGAGTTGATCTCATTTC-AGAAGTTTTCAACGA

                        
       1240 TCAGAGTTGATC
          1 TCAGAGTTGATC

       1252 CAGAGGAGTT


Statistics
Matches: 1097,  Mismatches: 79, Indels: 50
        0.89            0.06        0.04

Matches are distributed among these distances:
  33    3  0.00
  34   44  0.04
  35  1033  0.94
  36   17  0.02

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Consensus pattern (34 bp):   
TCAGAGTTGATCTCATTTCAGAAGTTTTCAACGA

Found at i:477 original size:105 final size:105

Alignment explanation


    Indices: 16--1251  Score: 1148
    Period size: 105  Copynumber: 11.8  Consensus size: 105

          6 TTACTAGAGG

                        *   *             *     *            *    *     *    
         16 TCAGAGTTGATCTCATATCAAGAAGTTTT-TAGA-GGTCAGAGTTGATCTCA-TATCAAGAAGTT
          1 TCAGAGTTGATCACATTTC-AGAAGTTTTCCA-ACGATCAGAGTTGATCGCATTTTC-AGTAGTT

             *  *  *            *                *      *
         78 TTCAGAGGTCAGAGTTGATCTCA-TTTCTAGAAGTTTTCAGA-GG
         63 TCCAAAGATCAGAGTTGATCGCATTTTC-AGAAGTTTCCA-ACGA

                                                 *            *     *    *   
        121 TCAGAGTTGATCTA-ATTTCATGAAGTTTT-CAGA-GGTCAGAGTTGATCTCA-TTCCAAGAAGT
          1 TCAGAGTTGATC-ACATTTCA-GAAGTTTTCCA-ACGATCAGAGTTGATCGCATTTTC-AGTAGT

              *  *  *            *     *          *      *
        182 TTTCAGAGGTCAGAGTTGATCTCA-TTCCAAGAAGTTTTCAGA-GG
         62 TTCCAAAGATCAGAGTTGATCGCATTTTC-AGAAGTTTCCA-ACGA

                        *                 **   *            *     *    *     
        226 TCAGAGTTGATCTCATTTCAAGAAGTTTTCTGA-GTTCAGAGTTGATCTCA-TTCCAAGAAGTTT
          1 TCAGAGTTGATCACATTTC-AGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTAGTTT

            *  *  *            *                *      *
        289 TCAGAGGTCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GG
         64 CCAAAGATCAGAGTTGATCGCATTTTC-AGAAGTTTCCA-ACGA

                        *    *       *          * *          *     *    *    
        331 TCAGAGTTGATCTCATTCCAAGAAGCTTT-CAGA-GGTTAGAGTTGATCTCA-TTCCAAGAAGTT
          1 TCAGAGTTGATCACATTTC-AGAAGTTTTCCA-ACGATCAGAGTTGATCGCATTTTC-AGTAGTT

             *     *            *                *      *
        393 TTCAAAGGTCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GG
         63 TCCAAAGATCAGAGTTGATCGCATTTTC-AGAAGTTTCCA-ACGA

                        *         *                                     *    
        436 TCAGAGTTGATCTCATTTCCAGTA-TTTTCCAACGATCAGAGTTGATCGCATTTTCAGTACTTTC
          1 TCAGAGTTGATCACATTT-CAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               *                        * *          
        500 CAACGATCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                               *                                             
        541 TCAGAGTTGATCACATGTTTAGAAGTTTT-CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
          1 TCAGAGTTGATCACAT-TTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               **                       * *          
        605 CAACTATCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                                                                        *    
        646 TCAGAGTTGATCACATGTTCAGAAG-TTTCCAACGATCAGAGTTGATCGCATTTTCAGTACTTTC
          1 TCAGAGTTGATCACAT-TTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               *                        * *          
        710 CAACGATCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                                                                             
        751 TCAGAGTTGATCACATGTTCAGAAGTTTT-CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
          1 TCAGAGTTGATCACAT-TTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               **                       * *          
        815 CAACTATCAGAGTTGATCGCATTTTCAGTACTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                                                                        *    
        856 TCAGAGTTGATCACATGTTCAGAAG-TTTCCAACGATCAGAGTTGATCGCATTTTCAGTACTTTC
          1 TCAGAGTTGATCACAT-TTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               *              *   *                  
        920 CAATGATCAGAGTTGATCACATGTTCAGAAGTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                        *         *                                          
        961 TCAGAGTTGATCGCATTTTCAGTAG-TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
          1 TCAGAGTTGATCACA-TTTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

                                         * *   *      
       1025 CAACA-ATCAGA-TTGATCGCATTTTCAGTATTTTGCAACGA
         65 CAA-AGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                        *         *                         *                
       1065 TCAGAGTTGATCGCATTTTCAGTAG-TTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTC
          1 TCAGAGTTGATCACA-TTTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC

               *              *         *            
       1129 CAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
         65 CAAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA

                                  *        *  *       *     *          * *   
       1170 TCAGAGTTGATCACATTTTCAGTAG-TTTCCTACCATCAGAGGTGATCTCA-TTTCAAGAAATTT
          1 TCAGAGTTGATCACA-TTTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTAGTTT

              * *              
       1233 CCGATGATCAGAGTTGATC
         64 CCAAAGATCAGAGTTGATC

       1252 CAGAGGAGTT


Statistics
Matches: 1033,  Mismatches: 76, Indels: 44
        0.90            0.07        0.04

Matches are distributed among these distances:
 104  112  0.11
 105  902  0.87
 106   19  0.02

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Consensus pattern (105 bp):   
TCAGAGTTGATCACATTTCAGAAGTTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
AAAGATCAGAGTTGATCGCATTTTCAGAAGTTTCCAACGA
Done.