Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005736.1 Corchorus capsularis cultivar CVL-1 contig05754, 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, 899

Length: 1499
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1028 original size:321 final size:322

Alignment explanation


    Indices: 4--1498  Score: 1738
    Period size: 321  Copynumber: 4.6  Consensus size: 322

          1 AAT

                                                                         *   
          4 AAAAAAA-TCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATG
          1 AAAAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATG

                *   *    *  * *  *         *                          *      
         68 AATACAGATATTTCAATGCGGCTTT-TCGCAAAAAAATCATGCAAAACTGAGCC-GGTTCCCGAA
         66 AATATAGACATTTGAAGGAGGGTTTCT-GC-CAAAAATCATGCAAAACTGAGCCGGGTCCCCGAA

                        * *       *      *     *    *                        
        131 ACGCGTTTTTAGTCTAAAAACCATGATGGCTAGTACACGGTTTTCGGCTAAAAAGTGACCCGAAA
        129 ACGCGTTTTTAGCCCAAAAACCGTGA--GTTAGTATAC-GATTTCGGCTAAAAAGTGACCCGAAA

                                * *    *   * *                     *         
        196 TTTTTTTTTTC-GAAATTTTGGGCACATTACTCGGAAAAAATATATAATTCAATGCCAAAAAAAA
        191 TTTTTTTTTTCTGAAATTTTTGCCACAATACACAGAAAAAATATATAATTCAATGGCAAAAAAAA

                  *                          *          *            *       
        260 -TGAAGAGTTTTTCACGCTTACAATATCGTTTTGCCATTTTTTTTCGAATTTATTTCAAATTAAA
        256 TTGAAGGGTTTTTCACGCTTACAATATCGTTTTTCCA-TTTTTTCCGAATTTATTTCTAATTAAA

              *
        324 TCG
        320 TCA

                           *         *              *                        
        327 AAAAAAATTCAGATGGTCGTAAAAAAAAAT-CTTCAAATCAATTGTGGCTGAGATTTGGTTCTAT
          1 AAAAAAATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCATTGTGGCTGAGATTTGGTTCTAT

                                             *                               
        391 GAATATAGACATTTGAAGGAGGGTTTCTGCCAAGAATCATGCAAAACTGAGCCGGGTCCCCGAAA
         65 GAATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAA

                                                   *        *                
        456 CGCGTTTTTAGCCCAAAAACCGTGATGTGTTAGTATACGGTTTCGGCTGAAAAGTGACCCGAAAT
        130 CGCGTTTTTAGCCCAAAAACCGTGA---GTTAGTATACGATTTCGGCTAAAAAGTGACCCGAAAT

                 *      *      *              *          * *   *   *         
        521 TTATTCTTTTCTCAAATTTATGCCACAATA-ATCGGAAAAAA-ATCTCATTTAA-CGCAAAAAAA
        192 TT-TTTTTTTCTGAAATTTTTGCCACAATACA-CAGAAAAAATATATAATTCAATGGC-AAAAAA

                                           *                                 
        583 AATTTGAAGGGTTTTTCACGCTTACAATATCCTTTTTCCATTTTTTTCCGAATTTATTTCTAATT
        254 AA-TTGAAGGGTTTTTCACGCTTACAATATCGTTTTTCCA-TTTTTTCCGAATTTATTTCTAATT

               *  
        648 AAACCA
        317 AAATCA

                        *                       *         *           *      
        654 AAACAAAATTCATATGCTCGTAAAAACAAATCCTTAGATCCATTGTTGCTGAGATTTGATTCTAT
          1 AAA-AAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTAT

                             *   *                                    **     
        719 GAATATAGACATTTGAAAGAGAGTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGTCTTCGAAA
         65 GAATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAA

             *        **                *               *      *             
        784 CACGTTTTTTCCCCCAAAAACCGTGA-TAACGTATACGATTTCGACTAAAACGTGACCCG-AATT
        130 CGCG-TTTTTAGCCCAAAAACCGTGAGTTA-GTATACGATTTCGGCTAAAAAGTGACCCGAAATT

                          *                                *             *   
        847 CTTTTTTTTCTGAATTTTTTGCCACAATACACAGAAAAAATATATAAGTCAATGGC-AAAATAA-
        193 -TTTTTTTTCTGAAATTTTTGCCACAATACACAGAAAAAATATATAATTCAATGGCAAAAAAAAT

                 *   *         **           *                               *
        910 TGAAGTGTTCTTCACGCTTGGAATATCGTTTTCCCA-TTTTTCCGAATTTATTTCTAATTAAATT
        257 TGAAGGGTTTTTCACGCTTACAATATCGTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAATC

             
        974 A
        322 A

                             *     *            *                            
        975 AAACAAAATTCAGATGCCCGTAAGAACAAATCCTTAGATCCATTGTGGCTGAGATTTGGTTCTAT
          1 AAA-AAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTAT

                    *                    ***                   *             
       1040 GAATATAGGCATTTGAAGGAGGGTTTCTTTTAAAAAATCATGCAAAACTGAACCGGGTCCCCGAA
         65 GAATATAGACATTTGAAGGAGGGTTTC-TGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAA

                      *   *                    *       *        *     *      
       1105 ACGCGTTTTTTGCCTAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAACGTGACTCGAAA-
        129 ACGCGTTTTTAGCCCAAAAACCGTGA--GTTAGTATACGATTTCGGCTAAAAAGTGACCCGAAAT

             * *                *         *                                  
       1169 -ATCTTTTTCTGAAATTTTTACCACAATACCCAG-AAAAATATATAATTCAACT--CAAAAAAAA
        192 TTTTTTTTTCTGAAATTTTTGCCACAATACACAGAAAAAATATATAATTCAA-TGGCAAAAAAAA

                       **                                                    
       1230 TTGAAGGGTTTACCACGCTT-CTAATATCGTTTTTCCATTTTTTTCCCGAATTTATTTCTAATTA
        256 TTGAAGGGTTTTTCACGCTTAC-AATATCGTTTTTCCA-TTTTTT-CCGAATTTATTTCTAATTA

                 
       1294 AAT-A
        318 AATCA

                                           *                            *    
       1298 AAAAAAA-TCAGATGCTCGTAAAAACAAATCTTTAAATCCATTGTGGCTGAGATTTGGTTATATG
          1 AAAAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATG

                    *                *                        *   *          
       1362 AATATAGATATTTGAAGGAGGGTTTTTGCCAAAAATCATGCAAAACTGAGTCGGATCCCCGAAAC
         66 AATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAAC

                                                      *                      
       1427 GCGTTTTTAGCCCAAAAACCGTGATTGTTAGTATACGATTTCAGCTAAAAAAGTGACCCGAAATT
        131 GCGTTTTTAGCCCAAAAACCGTGA--GTTAGTATACGATTTCGGCT-AAAAAGTGACCCGAAATT

                   
       1492 TTTTTTT
        193 TTTTTTT

       1499 C


Statistics
Matches: 998,  Mismatches: 140, Indels: 68
        0.83            0.12        0.06

Matches are distributed among these distances:
 319    1  0.00
 320   95  0.10
 321  276  0.28
 322   39  0.04
 323  100  0.10
 324  156  0.16
 325   75  0.08
 326   56  0.06
 327   65  0.07
 328  113  0.11
 329   22  0.02

ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Consensus pattern (322 bp):   
AAAAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCTATG
AATATAGACATTTGAAGGAGGGTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAAC
GCGTTTTTAGCCCAAAAACCGTGAGTTAGTATACGATTTCGGCTAAAAAGTGACCCGAAATTTTT
TTTTTCTGAAATTTTTGCCACAATACACAGAAAAAATATATAATTCAATGGCAAAAAAAATTGAA
GGGTTTTTCACGCTTACAATATCGTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAATCA
Done.