Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011045.1 Corchorus capsularis cultivar CVL-1 contig11066, 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: 3089
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:1717 original size:480 final size:481

Alignment explanation


    Indices: 789--3086  Score: 3287
    Period size: 480  Copynumber: 4.8  Consensus size: 481

        779 CGTTTTAATT

                                *                            *     *         
        789 GGAAAAACAATATTAGAAGCCCTAAAGGCCCTTCAATCTTTTTGATGTCAAATTACATATTTTTT
          1 GGAAAAACAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT

               *  *           *                               *         *  * 
        854 ATGTGTTTTTTAGCCAAATATTGAGGAAAAATATTTC-GAGTCAATTTTTACAAAATTTTTGCAG
         66 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGA-TCAATTTTTGCAAAATTTTAGCCG

                *                                                            
        918 AAATTGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTG
        130 AAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTG

                         *                    *                          *   
        983 CATGAATTATATACATTTTCATTGGTATTTTCGCGAGAAATTGAGGAAATATCTTTCGAGTTAGT
        195 CATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGAGTCAGT

                 *                              *    *     *                 
       1048 TTTTGAAAAATTTTAGCCGAAATCGT-TAACTAACCGTCACGGTTTTGGGCT-AAAACGCTTTCC
        260 TTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCACAGTTTTCGGCTAAAAACGCTTTCC

               *                        *                                    
       1111 GGGCCCCGGCTCAGTTTTGCATAATTTTGGGTGCCAAGATTCCTTGAAATATCTATATACATCTA
        324 GGGGCCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTA

              *                         *     *                              
       1176 ACGAAATCTCAGCCACATTAGATTTAAGTATTTCGTTTTACGAGCATCTGAATCTTGTTTCGTTT
        389 ACCAAATCTCAGCCACATTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTT

                 *              *       
       1241 TAATTCGAAACTAATTCGGACAAAAAAA
        454 TAATTGGAAACTAATTCGGAAAAAAAAA

                  *                                                          
       1269 GGAAAATCAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATA-TTTTT
          1 GGAAAAACAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT

                    *                                *                       
       1333 -TGAGTATATTAGCCAAAAATTGAGGAAAAATATTTCGGATAAATTTTTGCAAAATTTTAGCCGA
         66 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGATCAATTTTTGCAAAATTTTAGCCGA

                                                                 **          
       1397 AATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAACTCTATTTTGC
        131 AATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTGC

                                                       *                     
       1462 ATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAAGAAATATCTTTCGAGTCAGTT
        196 ATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGAGTCAGTT

                *                                   *                        
       1527 TTTGAAAAATTTTAGCCGAAATCGTGTACTAACCCATCACGGTTTTCGGCTAAAAACGCTTTCCG
        261 TTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CCATCACAGTTTTCGGCTAAAAACGCTTTCCG

              *                                                              
       1592 GGACCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTAA
        325 GGGCCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTAA

                    *       * *                                              
       1657 CCAAATCTAAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTTT
        390 CCAAATCTCAGCCACATTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTTT

                  *                      
       1722 AATTGGGAACTAATTCGGGAAAAAAAGAA
        455 AATTGGAAACTAATTC-GGAAAAAAA-AA

                  *        *    *                                            
       1751 GGAAAACCAATATTATAAGCACTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT
          1 GGAAAAACAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT

                                                              **     *       
       1816 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCAGG-TCAATTTTTAAAAAATATTAGCCG
         66 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTC-GGATCAATTTTTGCAAAATTTTAGCCG

                       *            *                             **         
       1880 AAATCGTGTACAAACCATCACTGTATTTGGCTAAAAACGCATTCTTGGGCCACAACTCTATTTTG
        130 AAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTG

                            *               *                                
       1945 CATGAATTATATATATATTCATTGGTATTTTCACTAGAAATTGAGGAAATATCTTTCGAGTCAGT
        195 CATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGAGTCAGT

                             *                            *                  
       2010 TTTTGCAAAATTTTAGCAGAAATCGTGTACTAACCATCACAGTTTTGGGCT-AAAACGCTTTCCG
        260 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAACGCTTTCCG

                                                                             
       2074 GGGCCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTAA
        325 GGGCCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTAA

                                       *    *                                
       2139 CCAAATCTCAGCCACATTAGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTTTCGTTTT
        390 CCAAATCTCAGCCACATTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTTT

                *                      
       2204 AATTTGAAACTAATTCGGAAAAAAAAA
        455 AATTGGAAACTAATTCGGAAAAAAAAA

                                         *                   *            *  
       2231 GGAAAAACAATATTAGAAGCGCTAAAGGCTCTTCAATCTTTTTGATGTCAAATTATATATTTGTT
          1 GGAAAAACAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT

                 *        *       *                *                         
       2296 ATGAGAATTTTAGCGAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG-CGA
         66 ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGATCAATTTTTGCAAAATTTTAGCCGA

             *                  *                      *        *   * *      
       2360 AGTCGTGTA-T---CATCACGGTTTTTGGCTAAAAACGCATTCCTGGGCCACGGTTTTGTTTTGC
        131 AATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTGC

                                 *                        *           *      
       2421 ATGAATTATATATATTTTCATGGGTATTTTCGCGT-GAAATTGAGGTAATATCTTTCGGGTCAGT
        196 ATGAATTATATATATTTTCATTGGTATTTTCGC-TAGAAATTGAGGAAATATCTTTCGAGTCAGT

                            ***               *  *          *       *      * 
       2485 TTTTGCAAAATTTTAGTTAAAATCGTGTACTAACTATTACAGTTTTCGTCTAAAAAAGCTTTCTG
        260 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAACGCTTTCCG

                    *              *     *         *                         
       2550 GGGCCCGGTTCAGTTTTGCATGATTTTTTTGTGCCAAGACTCCTTGAAATATCTATATACATCTA
        325 GGGCCCGGCTCAGTTTTGCAT-AATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTA

              *                *      *                    *                 
       2615 ACGAAATCTCAGCCACATTGGATTTATGGATTTCTTTTTACGAGCATTTGAATCTTGTTTCGTTT
        389 ACCAAATCTCAGCCACATTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTT

                            *         * 
       2680 TAATTGGAAACTAATTTGG-AAAAAATA
        454 TAATTGGAAACTAATTCGGAAAAAAAAA

                             *                 *                             
       2707 GG-AAAACAATATTAGAGGACGCTAAAGGCCCTTCTATCTTTTTGATGTCGAATTATATATTTTT
          1 GGAAAAACAATATTAGAAG-CGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTT

                                                    *                        
       2771 TATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCG
         65 TATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGATCAATTTTTGCAAAATTTTAGCCG

                 *        **   * *                      **       *     *     
       2836 AAATCATGTACTAATAATCGCGGTTTTTGGCTAAAAACGCATTCCGGGGCCACGGTTCTGTTTTG
        130 AAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTG

                    * *    *     **                   *  *            *     *
       2901 CATGAATTTTTTATACTTTCACGGGTATTTTCGCTAGAAATTAAGCAAATATCTTTCGGGTCAGA
        195 CATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGAGTCAGT

                *           *                             *                 *
       2966 TTTTCCAAAATTTTAGTCGAAATCGTG---T---CAT---AGTTTTTGGCTAAAAACGCTTTCCA
        260 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAACGCTTTCCG

                   *                               *  *                      
       3022 GGGCCCGTCTCAGTTTTGCA-AGATTTTTGGTGCCAAGACTCGTTGAAATATCTATATACATCTA
        325 GGGCCCGGCTCAGTTTTGCATA-ATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTA

             
       3086 A
        389 A

       3087 ACA


Statistics
Matches: 1655,  Mismatches: 142, Indels: 51
        0.90            0.08        0.03

Matches are distributed among these distances:
 470    1  0.00
 471   40  0.02
 472   38  0.02
 475  161  0.10
 476  141  0.09
 477  126  0.08
 478  208  0.13
 479   37  0.02
 480  318  0.19
 481  142  0.09
 482  209  0.13
 483   21  0.01
 484  211  0.13
 485    2  0.00

ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Consensus pattern (481 bp):   
GGAAAAACAATATTAGAAGCGCTAAAGGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTT
ATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGATCAATTTTTGCAAAATTTTAGCCGA
AATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCATTCTTGGGCCACAGTTCTATTTTGC
ATGAATTATATATATTTTCATTGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGAGTCAGTT
TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTCGGCTAAAAACGCTTTCCGG
GGCCCGGCTCAGTTTTGCATAATTTTTGGTGCCAAGATTCCTTGAAATATCTATATACATCTAAC
CAAATCTCAGCCACATTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGTTTTA
ATTGGAAACTAATTCGGAAAAAAAAA
Done.