Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014631.1 Corchorus capsularis cultivar CVL-1 contig14652, 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, 967

Length: 1613
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:1524 original size:328 final size:329

Alignment explanation


    Indices: 5--1611  Score: 1834
    Period size: 332  Copynumber: 4.9  Consensus size: 329

          1 ATCG

                             *               *                               
          5 GAAGCGTGAAAAGCCATCCAATCTTTTTTTGCAATGAATTTTATATTTTTTAAGAGTGTGGTGGC
          1 GAAGCGTGAAAAGCCATTCAATC-TTTTTTGCATTGAATTTTATATTTTTTAAGAGTGTGGTGGC

                             *     *       *                *                
         70 AAAAGAAATTGAGGAAAATTTTTAAGGTCTTTTTTTTGCAAAATTTTAACTC-AAATCGTGTATT
         65 -AAA-AAATTGAGGAAATTTTTTCAGGTC--ATTTTTGCAAAATTTTAGC-CGAAATCGTGTATT

                              *                  *     *           * *       
        134 AACCATCACAGTCTTTTGTTAAAAAAGCATTAT-GGATCCCCGACTCAGTT-TGCTTTATTTTTG
        125 AACCATCACAGTCTTTTGCTAAAAAAGCATT-TCGGAACCCCGGCTCAGTTCTGCATGATTTTTG

                       * *        *                         * *   **         
        197 GCGCCAAGACAGATTGAAATATTTATATCCATCTAACCAAATCTCAGCCAGATTGGATTTAAGGA
        189 GCGCCAAGACACACTGAAATATCTATATCCATCTAACCAAATCTCAGCTACATTAAATTTAAGGA

                     *         *                          * *                
        262 TTTGCTTTTACGAGCATCAGAATCATTTTTCGATTTTATTAGAAATCAATTCGAAAAAATAGGAA
        254 TTTGCTTTTTCGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTCGAAAAAATAGGAA

                 *   * 
        327 AAACGGTATTA
        319 AAACGATATCA

                       *   *                                       *         
        338 GAAGCGTGAAAGGCCTTTCAAT-TTTTTTGCATTGAATTTTATATTTTATTAAGAATGTGGTGGC
          1 GAAGCGTGAAAAGCCATTCAATCTTTTTTGCATTGAATTTTATATTTT-TTAAGAGTGTGGTGGC

                                    *                        **              
        402 AAAAGAAATTGAGGAAAATTTTTTAAGGTCATTTTTTGCAAAATTTTAGTTGAAATCGTGTATTA
         65 -AAA-AAATTGAGG-AAATTTTTTCAGGTCA-TTTTTGCAAAATTTTAGCCGAAATCGTGTATTA

                           * *              **                * * *          
        467 ACCATCACAGTCTTTCGTTAAAAAAGCA-TTCTAAGACCCCGGCTCAGTTTTACTTGATTTTTGG
        126 ACCATCACAGTCTTTTGCTAAAAAAGCATTTCGGA-ACCCCGGCTCAGTTCTGCATGATTTTTGG

             *          *               *       *             *    *         
        531 CACCAAGACACAATGAAATATCTATATCAATCTAA-AATAATCTCAGCTAGATTGGAA-TTAAGG
        190 CGCCAAGACACACTGAAATATCTATATCCATCTAACCA-AATCTCAGCTACATT-AAATTTAAGG

                         *                  * *                              
        594 ATTTGCTTTTAT-TAGCATCAAAATCATTTTTTGCTTTTATTAGAAATTATTTCAGAAAAAA-AG
        253 ATTTGCTTTT-TCGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTC-GAAAAAATAG

                          
        657 GAAAAACG-TATCA
        316 GAAAAACGATATCA

              * *       *               *   *                           *    
        670 GAGGAGTGAAAATCCATTCAATCTTTTTGGCAAT-ATATTTTATATTTTTTTAAGAGTGTTGTGG
          1 GAAGCGTGAAAAGCCATTCAATCTTTTTTGCATTGA-ATTTTATA-TTTTTTAAGAGTGTGGTGG

             *               *                      *                        
        734 CGAAAAATTGAGTAGAATTTTTTTCAGGTCAGTTTTTGCACAATTTTAGCCGAAATCGTGTATT-
         64 CAAAAAATTGAG--GAAATTTTTTCAGGTCA-TTTTTGCAAAATTTTAGCCGAAATCGTGTATTA

                     *                         *         *    *  *           
        798 ACTCATCACGGTCTTTTGCTAAAAAAGCATTTCGGGACCCCGGCTTAGTTTTGGATGATTTTTGG
        126 AC-CATCACAGTCTTTTGCTAAAAAAGCATTTCGGAACCCCGGCTCAGTTCTGCATGATTTTTGG

            *            *   *                  * *                *      *  
        863 TGCCAAGACACACCGAATTATCTATATCCATCTAACTAGATCTCAG-TCACATTAGATTTAAAGA
        190 CGCCAAGACACACTGAAATATCTATATCCATCTAACCAAATCTCAGCT-ACATTAAATTTAAGGA

               *         *     *                                             
        927 TTTACTTTTTCGAACATCAGAATCATTTTTCGATTTTATTAGAAATTATTTCGAAAAAATAGGAA
        254 TTTGCTTTTTCGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTCGAAAAAATAGGAA

                       
        992 AAACGATATCA
        319 AAACGATATCA

               *                              *  **                   *     *
       1003 GAATCGTGAAAAGCCATTCAATCTTTTTTGCATTTAAAATTATATTTTTTAAGAGTG-CGT---T
          1 GAAGCGTGAAAAGCCATTCAATCTTTTTTGCATTGAATTTTATATTTTTTAAGAGTGTGGTGGCA

                                   *                                        *
       1064 AAAAATTGAGGAAATTTTTTTCACGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACT
         66 AAAAATTGAGGAAA-TTTTTTCAGGTC-ATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACC

                                 *      *  *         *         *      * *    
       1129 ATCACAGTCTTTTGCTAAAAATGCATTTTGGGACCCCGGCTGAGTTCTGCAAGATTTTCGACGCC
        129 ATCACAGTCTTTTGCTAAAAAAGCATTTCGGAACCCCGGCTCAGTTCTGCATGATTTTTGGCGCC

                   *  *                          *                           
       1194 AAGACACGCTAAAATATCTATATCCATCTAACCAAATGTCAGCTACATTAAATTTAAGGATTTGC
        194 AAGACACACTGAAATATCTATATCCATCTAACCAAATCTCAGCTACATTAAATTTAAGGATTTGC

                 *                                               *           
       1259 TTTTTTGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTCGGAAAAGATAGGAAAAAC
        259 TTTTTCGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTC-GAAAAAATAGGAAAAAC

                   
       1324 GATATCA
        323 GATATCA

                         *                                            *  *   
       1331 GAAGCGTGAAAAGTCATTCAATCTTTTTTGCATTGAATTTTATATTTTTTAAGAGTGTTGTTGC-
          1 GAAGCGTGAAAAGCCATTCAATCTTTTTTGCATTGAATTTTATATTTTTTAAGAGTGTGGTGGCA

                   *       *          * *                                    
       1395 AAAAATTAAGGTAAACTTTTTCAGGTTAGTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCA
         66 AAAAATTGAGG-AAATTTTTTCAGGTCATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCA

                                      * *      *            *                
       1460 TCACAGTCTTTTGCT-AAAAA-CATTCCCGAACCCTGGCTCTA-TTCTACATGATTTTTGGCGCC
        130 TCACAGTCTTTTGCTAAAAAAGCATTTCGGAACCCCGGCTC-AGTTCTGCATGATTTTTGGCGCC

                  *                                  * *        *            
       1522 AAGACAAACTGAAATATCTATATCCATCTAACCAAATCTCAACGACATTAAACTTAAGGATTTGC
        194 AAGACACACTGAAATATCTATATCCATCTAACCAAATCTCAGCTACATTAAATTTAAGGATTTGC

                *           * *      
       1587 TTTTACGAGCATCAAAGTAATTTTT
        259 TTTTTCGAGCATCAAAATCATTTTT

       1612 GA


Statistics
Matches: 1089,  Mismatches: 149, Indels: 77
        0.83            0.11        0.06

Matches are distributed among these distances:
 326    3  0.00
 327  194  0.18
 328  198  0.18
 329    7  0.01
 330   52  0.05
 331   67  0.06
 332  329  0.30
 333  225  0.21
 334   14  0.01

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36


Consensus pattern (329 bp):   
GAAGCGTGAAAAGCCATTCAATCTTTTTTGCATTGAATTTTATATTTTTTAAGAGTGTGGTGGCA
AAAAATTGAGGAAATTTTTTCAGGTCATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCAT
CACAGTCTTTTGCTAAAAAAGCATTTCGGAACCCCGGCTCAGTTCTGCATGATTTTTGGCGCCAA
GACACACTGAAATATCTATATCCATCTAACCAAATCTCAGCTACATTAAATTTAAGGATTTGCTT
TTTCGAGCATCAAAATCATTTTTCGATTTTATTAGAAATTATTTCGAAAAAATAGGAAAAACGAT
ATCA
Done.